Compositions and methods for binding to covalent peptide conjugates containing divarasib
Patent Information
- Application Number
- PCT/US2025/031368
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2024-10-22
- Filing Date
- 2025-05-29
- Publication Date
- 2026-01-29
AI Technical Summary
There is an unmet need for agents that can effectively bind to covalently modified proteins or peptides, particularly to enhance targeted therapy and tumor immunogenicity against cancer driven by intracellular oncogenes and loss of tumor suppressor genes.
Development of polypeptides with antigen-binding domains that specifically bind to peptide-drug conjugates in the context of a human leukocyte antigen (HLA) complex, demonstrating high affinity and specificity for covalently modified peptides, including those with divarasib or sotorasib, with dissociation constants (KD) ranging from at most 250 nM to at least 1,000,000 nM.
The polypeptides enhance the efficacy of targeted and immune therapies by specifically binding to peptide-MHC complexes, improving therapeutic outcomes and tumor immunogenicity.
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Figure US2025031368_29012026_PF_FP_ABST
Abstract
Description
COMPOSITIONS AND METHODS FOR BINDING TO COVALENT PEPTIDECONJUGATES CONTAINING DIVARASIBCROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional Patent Application No. 63 / 653,420, filed on May 30, 2024, and U.S. Provisional Patent Application No. 63 / 710,218, filed on October 22, 2024, the entire content of each of which is entirely incorporated herein by reference.BACKGROUND
[0002] There is an ongoing and unmet need for agents that can bind to targets that include drugs that are covalently bound to proteins or peptides. In particular, there is a need to improve the efficacy of targeted therapy and also to increase tumor immunogenicity and the efficacy of immune therapy against cancer driven by intracellular oncogenes and loss of tumor suppressor genes. The disclosure is pertinent to these needs.BRIEF SUMMARY
[0003] Recognized herein are compositions and methods that include binding partners (e.g., polypeptides) that bind with specificity to target sites on proteins or peptides that comprise a covalently attached molecule. The disclosure illustrates this approach using binding partners in the form of numerous antibodies and antibody derivatives that specifically bind to proteins and peptides that have been covalently modified by attachment of a molecule, wherein the molecules are illustrated by a variety of drugs. Further, the disclosure demonstrates binding partners that bind with specificity to peptides that have been covalently modified by attachment of a small molecule drug are specific for the described covalently modified peptides when presented in the context of a human leukocyte antigen (HLA), wherein HLA is a representative example of a major histocompatibility complex (MHC). Thus, binding partners that are specific for peptide-drug conjugates in an HLA complex are demonstrated. The disclosure includes polynucleotides encoding the described binding partners and cells that are modified to express the binding partners. The disclosure includes diagnostic, prophylactic and therapeutic approaches using the binding partners.
[0004] In an aspect, the present disclosure provides a polypeptide comprising an antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalentinhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; and wherein the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant (KD) of at most 250 nM.
[0005] In some embodiments, the MHC of the peptide conjugate / MHC complex is encoded by an HLA allele selected from the group consisting of HLA-A*02, HLA-A*03, and HLA-A*11.
[0006] In some embodiments, the MHC is encoded by an HLA allele of HLA-A3 supertype. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A*03:01, HLA-A*l l:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A*03 :01, HLA-A* 11 :01, HLA- A*68:01, and HLA-A*34:02. In some embodiments, the MHC is encoded by an HLA allele of HLA-A2 super-type. In some embodiments, the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01. In some embodiments, the HLA allele of the HLA-A2 supertype is HLA- A*02:01.
[0007] In some aspects, the present disclosure provides a polypeptide comprising an antigenbinding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; wherein the polypeptide binds to each of (i) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele, (ii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele, and (iii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A* 11 allele with a dissociation constant (KD) of at most 250 nM.
[0008] In some aspects, the present disclosure provides a polypeptide comprising an antigenbinding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA allele selected from the group consisting of HLA-A*02, HLA-A*03, and HLA-A*11.
[0009] In some embodiments, the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant (KD) of at most 250 nM. In some embodiments, the KD is at most 200 nM, at most 150 nM, at most 100 nM, or at most 50 nM. In some embodiments, the polypeptide binds to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele with a KD of at least 2-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele. In some embodiments, the polypeptide binds to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*11 allele with a KD of at least 2-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele.
[0010] In some aspects, the present disclosure provides a polypeptide comprising an antigenbinding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; wherein the polypeptide binds to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof, the same peptide, and the same MHC with a dissociation constant (KD) that is at least 1,000 nM.
[0011] In some embodiments, the polypeptide binds to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof, the same peptide, and the same MHC with a KD that is at least 5,000 nM, at least 10,000 nM, at least 50,000 nM, at least 100,000 nM, at least 500,000 nM, or at least 1,000,000 nM. In some embodiments, the MHC of the peptide conjugate / MHC complex is encoded by an HLA allele selected from the group consisting of HLA- A*02, HLA-A*03, and HLA-A*11. In some embodiments, the polypeptide binds to each of (i) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele, (ii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele, and (iii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*11 allele with a dissociation constant (KD) of at most 250 nM.
[0012] In some embodiments, the KD is at most 200 nM, at most 150 nM, at most 100 nM, or at most 50 nM. In some embodiments, the polypeptide binds to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele with a KD of at least 2-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele. In some embodiments, the polypeptide binds to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A* 11 allele with a KD of at least 2-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele.
[0013] In some embodiments, the HLA-A*02 allele is an HLA-A*02:01 allele. In some embodiments, the HLA-A*03 allele is an HLA-A*03:01 allele. In some embodiments, the HLA- A*l l allele is an HLA-A* 11 :01 allele.
[0014] In some embodiments, the MHC is encoded by an HLA allele of HLA-A3 supertype. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A*03:01, HLA-A*l l:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A*03 :01, HLA-A* 11 :01, HLA- A*68:01, and HLA-A*34:02. In some embodiments, the MHC is encoded by an HLA allele of HLA-A2 super-type. In some embodiments, the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01. In some embodiments, the HLA allele of the HLA-A2 supertype is HLA- A*02:01.
[0015] In some embodiments, the peptide is a RAS peptide. In some embodiments, the RAS peptide comprises a mutation. In some embodiments, the mutation is G12C. In some embodiments, the RAS peptide comprises a sequence selected from the group consisting of VVVGACGVGK, VVGACGVGK, and KLVVVGACGV.
[0016] In some embodiments, an interface area of the polypeptide with the peptide conjugate / MHC complex is at least about 500A2, 600 A2, 700A2, 800A2, 900A2, l,000A2, l,200A2, l,500A2, or 2,000A2.
[0017] In some embodiments, the polypeptide binds an epitope of the MHC, and wherein the epitope comprises one or more amino acid residues conserved among HLA-A*03, HLA-A*02, and HLA-A* 11. In some embodiments, the polypeptide binds an epitope of the MHC, and wherein the epitope comprises one or more amino acid residues at positions 42-73 and 167 of HLA-A*03, HLA-A*02, or HLA-A* 11. In some embodiments, the polypeptide binds an epitope of the MHC, and wherein the epitope comprises one or more amino acid residues at positions 42-73 and 167 of SEQ ID NO: 80.
[0018] In some embodiments, the polypeptide binds an epitope of the MHC, and wherein the epitope comprises one or more amino acid residues selected from the group consisting of S42, Q43, R44, P57, E58, D61, Q62, T64, R65, K68, Q72, W167, and any combination thereof of the HLA-A*03, HLA-A*02, or HLA-A*11, or of SEQ ID NO: 80. In some embodiments, a VL domain of the antigen-binding domain binds to an epitope of the MHC, and wherein the epitopecomprises one or more residues selected from the group consisting of residues S42, Q43, D61, T64, R65, K68, and Q72 of HLA-A*03, HLA-A*02, or HLA-A*11, or of SEQ ID NO: 80. In some embodiments, a VH domain of the antigen-binding domain binds to an epitope of the MHC, and wherein the epitope comprises one or more residues selected from the group consisting of residues R44, P57, E58, D61, Q62, R65, and W167 of HLA-A*03, HLA-A*02, or HLA-A*11, or of SEQ ID NO: 80.
[0019] In some embodiments, the polypeptide interacts with one or more residues of the peptide conjugate in the peptide conjugate / MHC complex, and wherein the peptide comprises p? peptide of VVVGACGVGK, p5peptide of KLVVVGACGV, or p8peptide of VVGACGVGK.
[0020] In some embodiments, the one or more residues of the peptide conjugate in the peptide conjugate / MHC complex comprises one or more residues from the regions of p? peptide, ps peptide, or p8peptide comprising residues G10, Al l, C12, or any combination thereof of the peptide conjugate.
[0021] In some embodiments, one or more residues of a VH domain of the antigen-binding domain interact with the MHC, and wherein the one or more residues of the VH domain comprise amino acid residues selected from the group consisting of residues S31, Y32, S52, Y53, G100, N101, S102, and Y103 as set forth in SEQ ID NO: 9. In some embodiments, one or more residues of the VH domain of the antigen-binding domain interact with the targeted covalent inhibitor, and wherein the one or more residues of the VH domain comprise amino acid residues selected from the group consisting of residues G33, H35, W47, V50, S52, N57, Y59, Y60, A61, and D62 as set forth in SEQ ID NO: 9. In some embodiments, one or more residues of the VH domain of the antigen-binding domain interact with the peptide, and wherein the one or more residues of the VH domain comprise amino acid residues N57 or Y59 as set forth in SEQ ID NO: 9.
[0022] In some embodiments, one or more residues of a VL domain of the antigen-binding domain interact with the MHC, and wherein the one or more residues of the VL domain comprise amino acid residues selected from the group consisting of residues Q27, S28, L29, S30, S31, S32, F33, S92, E93, S94, A95, and L96 as set forth in SEQ ID NO: 10. In some embodiments, one or more residues of the VL domain of the antigen-binding domain interact with the targeted covalent inhibitor, and wherein the one or more residues of the VL domain comprise amino acid residues selected from the group consisting of residues DI, 12, S92, E93, S94, A95, L96, and T97 as set forth in SEQ ID NO: 10.
[0023] In some embodiments, the polypeptide comprises an antigen-binding domain that comprises a heavy chain variable region (VH), and wherein the VH comprises a heavy chaincomplementarity determining region 3 (CDR-H3) comprising the amino acid sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5). In some embodiments, the VH comprises a CDR- H2 comprising the amino acid sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4). In some embodiments, the VH comprises a CDR-H1 comprising the amino acid sequence of STNWWT (SEQ ID NO: 3).
[0024] In some embodiments, the antigen-binding domain further comprises a light chain variable region (VL), and wherein the VL comprises a light chain complementarity determining region 3 (CDR-L3) comprising the amino acid sequence of QAWDSNTVV (SEQ ID NO: 8). In some embodiments, the VL comprises a CDR-L2 comprising the amino acid sequence of GKNERPS (SEQ ID NO: 7). In some embodiments, the VL comprises a CDR-L1 comprising the amino acid sequence of RGDSFRVFSAS (SEQ ID NO: 6).
[0025] In some embodiments, the antigen-binding domain comprises: a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5), a CDR-H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4), a CDR-H1 sequence of STNWWT (SEQ ID NO: 3), a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8), a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7), and a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6).
[0026] In some embodiments, the VH comprises a sequence with at least 80% sequence identity to the sequenceQLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHTGNTD YNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIYFYYGLDVW GQGTTVTVSS (SEQ ID NO: 1). In some embodiments, the VL comprises a sequence with at least 80% sequence identity to the sequence SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERPSGIPD RFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
[0027] In some embodiments, the polypeptide comprises an antigen-binding domain that comprises a heavy chain variable region (VH), and wherein the VH comprises a heavy chain complementarity determining region 3 (CDR-H3) comprising the amino acid sequence of GGNSYGMDV (SEQ ID NO: 13). In some embodiments, the VH comprises a CDR-H2 comprising the amino acid sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12). In some embodiments, the VH comprises a CDR-H1 comprising the amino acid sequence of SYGMH (SEQ ID NO: 11).
[0028] In some embodiments, the antigen-binding domain further comprises a light chain variable region (VL), and wherein the VL comprises a light chain complementarity determining region 3(CDR-L3) comprising the amino acid sequence of QQSESALT (SEQ ID NO: 16). In some embodiments, the VL comprises a CDR-L2 comprising the amino acid sequence of GASSRAT (SEQ ID NO: 15). In some embodiments, the VL comprises a CDR-L1 comprising the amino acid sequence of RASQSLSSSFLA (SEQ ID NO: 14).
[0029] In some embodiments, the antigen-binding domain comprises: a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13), a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12), a CDR-H1 sequence of SYGMH (SEQ ID NO: 11), a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16), a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15), and a CDR-L1 sequence of RASQSLSSSFLA (SEQ ID NO: 14).
[0030] In some embodiments, the VH comprises a sequence with at least 80% sequence identity to the sequenceEVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISYDGSN KYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGMDVWGQGTM VTVSS (SEQ ID NO: 9). In some embodiments, the VL comprises a sequence with at least 80% sequence identity to the sequenceDIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSRATGIP DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
[0031] In some aspects, the present disclosure provides a polypeptide comprising an antigenbinding domain that comprises a heavy chain variable region (VH), wherein the VH comprises: a CDR-H3 sequence according to Kabat according to Table 1, or a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5) or GGNSYGMDV (SEQ ID NO: 13).
[0032] In some embodiments, the VH comprises a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5). In some embodiments, the VH further comprises a CDR-H1 sequence of STNWWT (SEQ ID NO: 3). In some embodiments, the VH further comprises a CDR-H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4). In some embodiments, the polypeptide further comprises a light chain variable region (VL), wherein the VL comprises a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8). In some embodiments, the VL further comprises a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6). In some embodiments, the VL further comprises a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7).
[0033] In some embodiments, the polypeptide comprises: a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5); a CDR-H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4); a CDR-H1 sequence of STNWWT (SEQ ID NO: 3); a CDR-L3 sequence ofQAWDSNTVV (SEQ ID NO: 8); a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7); and a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6).
[0034] In some embodiments, the VH comprises a sequence with at least 80% sequence identity to the sequenceQLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHTGNTD YNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIYFYYGLDVW GQGTTVTVSS (SEQ ID NO: 1). In some embodiments, the VL comprises a sequence with at least 80% sequence identity to the sequence SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERPSGIPD RFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
[0035] In some embodiments, the VH comprises the sequence QLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHTGNTD YNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIYFYYGLDVW GQGTTVTVSS (SEQ ID NO: 1). In some embodiments, the VL comprises the sequence SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERPSGIPD RFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
[0036] In some embodiments, the VH comprises a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13). In some embodiments, the VH further comprises a CDR-H1 sequence of SYGMH (SEQ ID NO: 11). In some embodiments, the VH further comprises a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12). In some embodiments, the polypeptide further comprises a light chain variable region (VL), wherein the VL comprises a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16). In some embodiments, the VL further comprises a CDR-L1 sequence of RASQSLSSSFLA (SEQ ID NO: 14). In some embodiments, the VL further comprises a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15).
[0037] In some embodiments, the polypeptide comprises: a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13); a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12); a CDR- H1 sequence of SYGMH (SEQ ID NO: 11); a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16); a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15); and a CDR-L1 sequence of RASQSLSSSFLA (SEQ ID NO: 14).
[0038] In some embodiments, the VH comprises a sequence with at least 80% sequence identity to the sequenceEVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGMDVWGQGTMVTVSS (SEQ ID NO: 9). In some embodiments, the VL comprises a sequence with at least 80% sequence identity to the sequenceDIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSRATGIP DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
[0039] In some embodiments, the VH comprises the sequence EVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISYDGSN KYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGMDVWGQGTM VTVSS (SEQ ID NO: 9). In some embodiments, the VL comprises the sequence DIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSRATGIP DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
[0040] In some aspects, the present disclosure provides a polypeptide comprising an antigenbinding domain that comprises a light chain variable region (VL), wherein the VL comprises: a CDR-L3 sequence according to Kabat according to Table 1, or a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8) or QQSESALT (SEQ ID NO: 16).
[0041] In some embodiments, the VL comprises a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8). In some embodiments, the VL comprises a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6). In some embodiments, the VL comprises a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7). In some embodiments, the polypeptide further comprises a heavy chain variable region (VH), wherein the VH comprises a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5). In some embodiments, the VH further comprises a CDR-H1 sequence of STNWWT (SEQ ID NO: 3). In some embodiments, the VH further comprises a CDR-H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4).
[0042] In some embodiments, the polypeptide comprises: a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5); a CDR-H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4); a CDR-H1 sequence of STNWWT (SEQ ID NO: 3); a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8); a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7); and a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6).
[0043] In some embodiments, the VH comprises a sequence with at least 80% sequence identity to the sequenceQLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHTGNTD YNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIYFYYGLDVW GQGTTVTVSS (SEQ ID NO: 1). In some embodiments, the VL comprises a sequence with at least 80% sequence identity to the sequenceSSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERPSGIPD RFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
[0044] In some embodiments, the VH comprises the sequence QLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHTGNTD YNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIYFYYGLDVW GQGTTVTVSS (SEQ ID NO: 1). In some embodiments, the VL comprises the sequence SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERPSGIPD RFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
[0045] In some embodiments, the VL comprises a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16). In some embodiments, the VL comprises a CDR-L1 sequence of RASQSLSSSFLA (SEQ ID NO: 14). In some embodiments, the VL further comprises a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15). In some embodiments, the polypeptide further comprises a heavy chain variable region (VH), wherein the VH comprises a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13). In some embodiments, the VH further comprises a CDR-H1 sequence of SYGMH (SEQ ID NO: 11). In some embodiments, the VH further comprises a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12).
[0046] In some embodiments, the polypeptide comprises: a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13); a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12); a CDR- H1 sequence of SYGMH (SEQ ID NO: 11); a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16); a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15); and a CDR-L1 sequence of RASQSLSSSFLA (SEQ ID NO: 14).
[0047] In some embodiments, the VH comprises a sequence with at least 80% sequence identity to the sequenceEVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISYDGSN KYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGMDVWGQGTM VTVSS (SEQ ID NO: 9). In some embodiments, the VL comprises a sequence with at least 80% sequence identity to the sequenceDIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSRATGIP DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
[0048] In some embodiments, the VH comprises the sequence EVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISYDGSN KYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGMDVWGQGTM VTVSS (SEQ ID NO: 9). In some embodiments, the VL comprises the sequenceDIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSRATGIP DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
[0049] In some embodiments, the polypeptide binds to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof the same peptide, and the same MHC with a KD that is at least 2-fold more than the KD of the polypeptide to the peptide conjugate / MHC complex comprising divarasib or the fragment thereof. In some embodiments, the polypeptide binds to free divarasib with a KD that is at least 2-fold more than the KD of the polypeptide to the peptide conjugate / MHC complex. In some embodiments, the MHC of the peptide conjugate / MHC complex is encoded by an HLA-A*02 allele. In some embodiments, the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant of at most 50 nM, at most 25 nM, or at most 10 nM. In some embodiments, the MHC of the peptide conjugate / MHC complex is encoded by an HLA-A*03 allele. In some embodiments, the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant of at most 50 nM, at most 25 nM, at most 20 nM, or at most 15 nM. In some embodiments, the MHC of the peptide conjugate / MHC complex is encoded by an HLA-A*11 allele. In some embodiments, the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant of at most 50 nM, at most 45 nM, or at most 40 nM.
[0050] In some embodiments, the MHC is encoded by an HLA allele of HLA-A3 supertype. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A*03:01, HLA-A*l l:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A*03 :01, HLA-A* 11 :01, HLA- A*68:01, and HLA-A*34:02. In some embodiments, the MHC is encoded by an HLA allele of HLA-A2 super-type. In some embodiments, the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A*02:01, HLA-A* 02: 02, HLA-A* 02: 03, HLA-A* 02: 04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01. In some embodiments, the HLA allele of the HLA-A2 supertype is HLA- A*02:01.
[0051] In some aspects, the present disclosure provides a multivalent polypeptide comprising: a first antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the first antigen-binding domain comprises a polypeptide described herein; a second antigen-binding domain that binds to a T cell surface protein; and an Fc region comprising a first Fc subunit and a second Fc subunit; and wherein the first antigen-binding domain, the second antigen-bindingdomain, the first Fc subunit, and the second Fc subunit are operably linked to form a single continuous polypeptide chain.
[0052] In some embodiments, the multivalent polypeptide comprises, from N-terminus to C- terminus, the first antigen-binding domain, the second antigen-binding domain, the first Fc subunit, and the second Fc subunit. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the first antigen-binding domain, a first linker, the second antigenbinding domain, a second linker, the first Fc subunit, a third linker, and the second Fc subunit. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the second antigen-binding domain, the first antigen -binding domain, the first Fc subunit, and the second Fc subunit. In some embodiments, the multivalent polypeptide comprises, from N- terminus to C-terminus, the second antigen-binding domain, a first linker, the first antigen-binding domain, a second linker, the first Fc subunit, a third linker, and the second Fc subunit.
[0053] In some embodiments, the Fc region comprises an amino acid sequence as set forth in SEQ ID NOs: 46 or 51, or an amino acid sequence with at least 90% sequence identity to SEQ ID NO: 46 or 51. In some embodiments, the first linker, the second linker, and / or the third linker comprises an amino acid sequence as set forth in SEQ ID NOs: 43, 44, 45, 57, and 63. In some embodiments, the first linker comprises an amino acid sequence as set forth in SEQ ID NO: 44. In some embodiments, the second linker comprises an amino acid sequence as set forth in SEQ ID NO: 45. In some embodiments, the third linker comprises an amino acid sequence as set forth in SEQ ID NO: 63 (GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS). In some embodiments, the first linker has a length of from 4-12, 4-10, 4-8, 4-6 or 6 amino acids. In some embodiments, the first linker comprises an amino acid sequence according to the formula SGxS or GxS, wherein X is 3 or 4. In some embodiments, the first linker comprises an amino acid sequence according to the formula SGxS, wherein X is 4. In some embodiments, the first linker comprises an amino acid sequence according to the formula SxG, wherein X is 3 or 4. In some embodiments, the second linker has a length of from 3-12, 3-10, 3-8, 3-6 or 4 amino acids. In some embodiments, the second linker comprises an amino acid sequence according to the formula Gx, wherein X is 3, 4, or 5. In some embodiments, X is 4. In some embodiments, the second linker comprises an amino acid sequence according to the formula SGx, wherein X is 3 or 4. In some embodiments, the third linker has a length of from 20-40, 20-35, 25-40, 25-35, 25-30, 30-35, 28-32 or 30 amino acids. In some embodiments, the third linker comprises an amino acid sequence according to the formula (GXS)N or GxS, wherein X is 3 or 4 and N is 3, 4, 5, 6, 7, 8, 9 or 10. In some embodiments, X is 4 and N is 5, 6 or 7. In some embodiments, X is 4 and N is 6.
[0054] In some embodiments, the Fc region comprises one or more amino acid substitutions relative to a wild-type Fc region selected from the group consisting of heavy chain constant regions of human IgE, IgM, IgGl, IgG2, IgG3, IgG4, IgAl, and IgA2. In some embodiments, the Fc region comprises an Fc-silencing mutation, which Fc-silencing mutation decreases an antibody-directed cytotoxicity effector function. In some embodiments, the Fc-silencing mutation comprises a AAA mutation or a CGC mutation, wherein the AAA mutation comprises L234A, L235A, G237A of a sequence of SEQ ID NO: 23, and wherein the CGC mutation comprises R292C, N297G, V302C of a sequence of SEQ ID NO: 23. In some embodiments, the multivalent polypeptide comprises an amino acid sequence with at least 80% sequence identity to an amino acid sequence as set forth in SEQ ID NOs: 42, 47-50, and 52-54. In some embodiments, the multivalent polypeptide comprises an amino acid sequence as set forth in SEQ ID NOs: 42, 47- 50, and 52-54.
[0055] In some embodiments, the first antigen-binding domain comprises a first single-chain variable fragment (scFv) comprising a heavy chain variable region (VH) and a light chain variable region (VL). In some embodiments, the second antigen-binding domain comprises a second single-chain variable fragment (scFv) comprising a heavy chain variable region (VH) and a light chain variable region (VL). In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the VH of the first scFv, the VL of the first scFv, the VH of the second scFv, and the VL of the second scFv. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the VH of the second scFv, the VL of the second scFv, the VH of the first scFv, and the VL of the first scFv. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the VL of the first scFv, the VH of the first scFv, the VL of the second scFv, and the VH of the second scFv. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the VL of the second scFv, the VH of the second scFv, the VL of the first scFv, and the VH of the first scFv. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the VH of the second scFv, the VL of the second scFv, the VL of the first scFv, and the VH of the first scFv. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the VH of the first scFv, the VL of the first scFv, the VL of the second scFv, and the VH of the second scFv. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the VL of the first scFv, the VH of the first scFv, the VH of the second scFv, and the VL of the second scFv. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the VL of the second scFv, the VH of the second scFv, the VH of the first scFv, and the VL of the first scFv.
[0056] In some aspects, the present disclosure provides a multivalent polypeptide comprising: a first antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the first antigen-binding domain comprises a polypeptide described herein; and a second antigen-binding domain that binds to a T cell surface protein; wherein the second antigen-binding domain comprises a second VH and a second VL, and wherein the second VL comprises: a CDR-L3 sequence of QQGNTLPWT (SEQ ID NO: 36), a CDR-L2 sequence of YTSRLES (SEQ ID NO: 37), and a CDR-L1 sequence of RASQDIRNYLN (SEQ ID NO: 38).
[0057] In some embodiments, the second antigen-binding domain comprises six complementarity determining regions (CDRs) from heavy chain variable region (VH) and light chain variable region (VL) of a UCHT1 antibody, comprising: a CDR-H3 sequence of SGYYGDSDWYFDV (SEQ ID NO: 33), a CDR-H2 sequence of LINPYKGVSTYNQKFKD (SEQ ID NO: 34), a CDR- H1 sequence of GYTMN (SEQ ID NO: 35), a CDR-L3 sequence of QQGNTLPWT (SEQ ID NO: 36), a CDR-L2 sequence of YTSRLES (SEQ ID NO: 37), and a CDR-L1 sequence of RASQDIRNYLN (SEQ ID NO: 38).
[0058] In some embodiments, the VH comprises a sequence with at least 90% sequence identity to the sequenceEVQLVESGGGLVQPGGSLRLSCAASGYSFTGYTMNWVRQAPGKGLEWVALINPYKGV STYNQKFKDRFTISVDKSKNTAYLQMNSLRAEDTAVYYCARSGYYGDSDWYFDVWG QGTLVTVSS (SEQ ID NO: 31). In some embodiments, the VH comprises a sequence of EVQLVESGGGLVQPGGSLRLSCAASGYSFTGYTMNWVRQAPGKGLEWVALINPYKGV STYNQKFKDRFTISVDKSKNTAYLQMNSLRAEDTAVYYCARSGYYGDSDWYFDVWG QGTLVTVSS (SEQ ID NO: 31).
[0059] In some embodiments, the VL comprises a sequence with at least 90% sequence identity to the sequenceDIQMTQSPSSLSASVGDRVTITCRASQDIRNYLNWYQQKPGKAPKLLIYYTSRLESGVPS RFSGSGSGTDYTLTISSLQPEDFATYYCQQGNTLPWTFGQGTKVEIK (SEQ ID NO: 32). In some embodiments, the VL comprises a sequence of DIQMTQSPSSLSASVGDRVTITCRASQDIRNYLNWYQQKPGKAPKLLIYYTSRLESGVPS RFSGSGSGTDYTLTISSLQPEDFATYYCQQGNTLPWTFGQGTKVEIK (SEQ ID NO: 32).
[0060] In some embodiments, the MHC is encoded by an HLA allele of HLA-A3 supertype. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the groupconsisting of HLA-A*03:01, HLA-A*l l:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A*03 :01, HLA-A* 11 :01, HLA- A*68:01, and HLA-A*34:02. In some embodiments, the MHC is encoded by an HLA allele of HLA-A2 super-type. In some embodiments, the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01. In some embodiments, the HLA allele of the HLA-A2 supertype is HLA- A*02:0L
[0061] In some aspects, the present disclosure provides a recombinant nucleic acid comprising a sequence encoding the polypeptide described herein or the multivalent polypeptide described herein.
[0062] In some aspects, the present disclosure provides a pharmaceutical composition comprising the polypeptide described herein or the multivalent polypeptide described herein, and a pharmaceutically acceptable carrier.
[0063] In some aspects, the present disclosure provides a method of treating a cancer in a subject in need thereof, the method comprising administering into the subject the polypeptide described herein or the multivalent polypeptide described herein, or the pharmaceutical composition described herein.
[0064] In some aspects, the present disclosure provides a method for stabilizing a peptide conjugate / MHC complex, the method comprising: contacting the peptide conjugate / MHC complex with a multivalent polypeptide, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC, and wherein the multivalent polypeptide comprises a first antigen-binding domain, a second antigen-binding domain that binds to a T cell surface protein, and an Fc region comprising a first Fc subunit and a second Fc subunit, wherein the first antigenbinding domain comprises a polypeptide described herein; and measuring the half-life of the bound peptide conjugate / MHC complex and multivalent polypeptide.
[0065] In some embodiments, the half-life of the peptide conjugate / MHC complex is between 0.1 and 30 hours. In some embodiments, the half-life of the peptide conjugate / MHC complex is between 10 and 26 hours. In some embodiments, the half-life of the peptide conjugate / MHC complex is at least 1 day. In some embodiments, the contacting occurs at 25 °C or 37 °C.
[0066] In some aspects, the present disclosure provides a method for activating an immune cell, the method comprising: contacting the immune cell with a multivalent polypeptide comprising a first antigen-binding domain, a second antigen-binding domain that binds to a T cell surface protein, and an Fc region comprising a first Fc subunit and a second Fc subunit, wherein the first antigen-binding domain comprises a polypeptide described herein; and wherein the immune cell expresses a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC.
[0067] In some embodiments, the immune cell is a T cell. In some embodiments, the contacting increases expression of at least one T cell activation marker. In some embodiments, the at least one T cell activation marker is CD26, CD27, CD28, CD30, CD154, CD40L, CD134. CD25, CD44, CD69, CD 137, PD-1, KLRG1, CCR7, CD45RA, HLA-DR, NKG2D, or any combination thereof. In some embodiments, the at least one T cell activation marker is CD25 and / or CD69.
[0068] In some embodiments, the contacting produces a greater number of CD25+CD69+T cells compared to a number of CD25+CD69+T cells produced from contacting the multivalent polypeptide with an otherwise identical peptide conjugate / MHC complex without the targeted covalent inhibitor. In some embodiments, the contacting increases expression of IFNy, TNFa, Granzyme A, Granzyme B, IL-6, perforin, IL-2, granulysin, or any combination thereof. In some embodiments, the contacting increases an expression level of cytokine molecules compared to an expression level of cytokine molecules produced from contacting the multivalent polypeptide with an otherwise identical peptide conjugate / MHC complex without the targeted covalent inhibitor.
[0069] In some aspects, the present disclosure provides a method for treating a cancer in a subject in need thereof, the method comprising administering to the subject (A) a polypeptide described herein, or (B) a multivalent polypeptide comprising (i) a first antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the first antigen-binding domain is a polypeptide described herein; (ii) a second antigen-binding domain that binds to a T cell surface protein; and (iii) an Fc region comprising a first Fc subunit and a second Fc subunit; wherein the first antigenbinding domain, the second antigen-binding domain, the first Fc subunit, and the second Fc subunit are operably linked to form a single continuous polypeptide chain.
[0070] In some embodiments, the cancer is renal cell carcinoma, breast cancer, prostate cancer, pancreatic cancer, lung cancer, liver cancer, ovarian cancer, cervical cancer, colon cancer, esophageal cancer, glioma, glioblastoma, brain cancer, stomach cancer, bladder cancer, testicular cancer, thyroid cancer, adrenal cancer, head and neck cancer, melanoma, skin cancer, sarcoma,fibrosarcoma, angiosarcoma, osteosarcoma, rhabdomyosarcoma, leukemia, lymphoma, myeloma, endometrial cancer, or a neuroendocrine tumor.
[0071] In some embodiments, the peptide is a RAS peptide. In some embodiments, the RAS peptide comprises a mutation. In some embodiments, the mutation is G12C. In some embodiments, the RAS peptide comprises a sequence selected from the group consisting of VVVGACGVGK, VVGACGVGK, and KLVVVGACGV. In some embodiments, the MHC is selected from the group consisting of HLA-A*03:01, HLA-A* 11 :01, HLA-A*02:01, HLA- A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*33:03, HLA-A*33:01, HLA-A*74:01, HLA- A*34:02, HLA-A*66:01, HLA-A*68:02, HLA-A*02:05, HLA-A*02:02, HLA-A*02:06. In some embodiments, the MHC is encoded by an HLA allele of HLA-A3 supertype. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A*03:01, HLA-A*l l:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A* 03:01, HLA-A* 11 :01, HLA-A*68:01, and HLA-A*34:02. In some embodiments, the MHC is encoded by an HLA allele of HLA-A2 super-type. In some embodiments, the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA- A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02:14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01. In some embodiments, the HLA allele of the HLA-A2 supertype is HLA-A*02:01. In some embodiments, the targeted covalent inhibitor or fragment thereof comprises divarasib.
[0072] In some aspects, the present disclosure provides a method for stabilizing a peptide conjugate / MHC complex in a subject, the method comprising: administering (A) a polypeptide described herein, or (B) a multivalent polypeptide to the subject, wherein the multivalent polypeptide comprises a first antigen-binding domain comprising a polypeptide described herein, a second antigen-binding domain that binds to a T cell surface protein, and wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC.
[0073] In some embodiments, the method further comprises, prior to administering the polypeptide or the multivalent polypeptide to the subject, administering the targeted covalent inhibitor.
[0074] In some embodiments, the subject has a cancer. In some embodiments, the cancer is refractory or relapsed.
[0075] In some embodiments, the subject expresses at least one MHC encoded by an HLA, wherein the HLA is HLA-A*03:01, HLA-A* 11 :01, HLA-A*02:01, HLA-A*68:01, HLA- A*31:01, HLA-A*30:01, HLA-A*33:03, HLA-A*33:01, HLA-A*74:01, HLA-A*34:02, HLA- A*66:01, HLA-A*68:02, HLA-A*02:05, HLA-A*02:02, HLA-A*02:06, or any combination thereof. In some embodiments, the method further comprises, prior to administering the polypeptide or the multivalent polypeptide to the subject, determining an HLA allele expression of the subject. In some embodiments, the subject expresses an MHC encoded by the HLA wherein the HLA is HLA-A*03:01, HLA-A* 11:01, HLA-A*02:01, HLA-A*68:01, HLA-A*31:01, HLA- A*30:01, HLA-A*33:03, HLA-A*33:01, HLA-A*74:01, HLA-A*34:02, HLA-A*66:01, HLA- A*68:02, HLA-A*02:05, HLA-A*02:02, HLA-A*02:06, or any combination thereof. In some embodiments, the MHC is encoded by an HLA allele of HLA-A3 supertype. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A*03:01, HLA-A*l l:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01. In some embodiments, the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A* 03:01, HLA-A* 11 :01, HLA-A*68:01, and HLA-A*34:02. In some embodiments, the MHC is encoded by an HLA allele of HLA-A2 super-type. In some embodiments, the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA- A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02:14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01. In some embodiments, the HLA allele of the HLA-A2 supertype is HLA-A*02:01.
[0076] In some embodiments, the multivalent polypeptide comprises an Fc region comprising a first Fc subunit and a second Fc subunit. In some embodiments, the Fc region comprises one or more amino acid substitutions relative to a wild-type Fc region selected from the group consisting of heavy chain constant regions of human IgE, IgM, IgGl, IgG2, IgG3, IgG4, IgAl, and IgA2. In some embodiments, the Fc region comprises an Fc-silencing mutation, which Fc-silencing mutation decreases an antibody-directed cytotoxicity effector function. In some embodiments, administering the polypeptide or the multivalent polypeptide to the subject increases a half-life of the peptide conjugate / MHC complex compared to a half-life of the peptide conjugate / MHC complex following administration of the targeted covalent inhibitor alone.
[0077] In some aspects, the present disclosure provides a method of killing a target cell expressing a peptide conjugate / MHC complex, the method comprising: contacting the multivalent polypeptide described herein with the target cell expressing the peptide conjugate / MHC complex,wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC.
[0078] In some embodiments, the targeted covalent inhibitor or fragment thereof comprises divarasib.
[0079] In some embodiments, the peptide is a RAS peptide. In some embodiments, the RAS peptide comprises a mutation. In some embodiments, the mutation is G12C. In some embodiments, the RAS peptide comprises a sequence of VVVGACGVGK, VVGACGVGK, or KLVVVGACGV.
[0080] In some embodiments, a greater level of T cell cytotoxicity mediated by the multivalent polypeptide is observed in the presence of cells expressing the peptide conjugate / MHC complex comprising the RAS peptide compared to a level of cytotoxicity observed in cells expressing a peptide conjugate / MHC complex comprising a wild-type RAS peptide. In some embodiments, the wild-type RAS peptide comprises a sequence of KLVVVGAGGV, VVGAGGVGK, or VVVGAGGVGK.
[0081] In some embodiments, an EC50 of a T cell cytotoxicity mediated by the multivalent polypeptide is at most about 150 nM, at most about 100 nM, at most about 50 nM, at most about 20 nM, at most about 10 nM, at most about 1 nM, at most about 0.1 nM, at most about 0.01 nM, or less.
[0082] In some embodiments, the MHC is HLA-A*03:01, HLA-A* 11 :01, HLA-A*02:01, or HLA-A*68:01.INCORPORATION BY REFERENCE
[0083] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and / or take precedence over any such contradictory material.BRIEF DESCRIPTION OF THE DRAWINGS
[0084] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and the disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles ofthe invention are utilized, and the accompanying drawings (also “Figure” and “FIG.” herein), of which:
[0085] FIGs. 1A-1B show binding efficacy for binder R301. FIG. 1A shows binding affinities to divarasib-modified KRASG12Cpeptide-MHC complexes. Binding was evaluated by mean fluorescence intensity (MFI), with binder R301 displayed in scFv format on yeast showing the strongest binding for divarasib-modified KRASG12Cpeptide ps displayed by HLA-A*02. FIG. IB shows free drug inhibition of R301 with increasing concentrations of divarasib. Binder R301 showed high free drug inhibition.
[0086] FIGs. 2A-2B show binding efficacy for binder R302. FIG. 2A shows binding affinities to divarasib-modified KRASG12Cpeptide-MHC complexes. Binding was evaluated by mean fluorescence intensity (MFI), with binder R302 displayed in scFv format on yeast showing the strongest binding for divarasib-modified KRASG12Cpeptide ps displayed by HLA-A*02. FIG. 2B shows free drug inhibition of R302 with increasing concentrations of divarasib. Binder R302 showed extremely low free-drug inhibition.
[0087] FIG. 3 shows results of an experiment to evaluate binding of R302 displayed in scFv format on yeast to sotorasib-modified peptide-MHC complexes. R302 showed no cross-reactivity to sotorasib-based peptide-MHC complexes. Binder R302 showed similarly low levels of binding to unmodified peptide-MHC complexes (e.g., ps / 7WT / A02 / A03 / Al 1).
[0088] FIG. 4 shows mirror plot visualizations of representative MS2 spectrum of light, endogenous divarasib (diva)-modified KRASG12CMHC-I peptide (diva-p?, top) and an embedded stable isotope labeled (SIL) synthetic peptide standard of the diva-p? peptide (bottom) in cells treated with DMSO (left, no identification) and divarasib (right, diva-p? identification). The left plot denotes treatment with DMSO and the right plot denotes treatment with divarasib. The peptide is annotated where C* indicates divarasib modification on cysteine, and X+yindicates the mass addition of the SIL amino acid. Identified a, b, and y, fragment ions are annotated. Annotated ions with an * (e.g., ys*) indicate a fragment where divarasib has lost a pyrrolidine group (-97.09).
[0089] FIG. 5 shows a cryo-electron microscopy (CryoEM) structure of binder R302 in complex with divarasib-modified KRASG12Cpeptide p? displayed by HLA-A*03. The labels denote the individual components of the complex, including the VH binder of R302 (R302 VH), VL binder of R302 (R302 VL), peptide p?, divarasib, and the HLA-A*03.
[0090] FIG. 6 shows details of the interaction between R302 and diva-p? / HLA. Binder R302’s target recognition uses three layers of specificity, including HLA residues, hapten, and peptideresidues. The approximate areas of recognition are shown in the schematic representation of the diva-p? / HLA complex.
[0091] FIG. 7 shows pan-HLA recognition of R302 with conserved residues in HLA-A*03, A*02, and A*l l. Binder R302 recognizes an HLA epitope almost completely conserved among HLA-A*03, A*02, and A*l l. In the HLA residues in the epitope, the residue glutamine 62 (Gln62) is conserved between HLA-A*03 and A*11, and is a glycine (Gly62) in HLA-A*02.
[0092] FIG. 8 shows the structure of the R302 binder and diva-p? / A03 complex. The figure shows a cartoon representation of the structure of R302 binding to diva-p? / A03. The left schematic shows the “front view” and the right schematic shows the “lateral view”. Individual parts of the R302 binder and diva-p? / A03 complex are labeled.
[0093] FIG. 9 shows the structure of the R302 binder and diva-p? / A03 complex. The figure shows a cartoon representation of the structure of R302 binding to diva-p? / A03. The top schematic shows the “front view” and the bottom schematic shows the “top view”. Individual parts of the R302 binder and diva-p? / A03 complex are labeled.
[0094] FIGs. 10A-10B show the R302 epitope. FIG. 10A depicts a cartoon representation of the p*MHC diva-p? / A03 (top view). Residues involved in contacts with R302 binder or divarasib are represented as sticks. HLA-A*03, peptide p?, and divarasib are individually labeled. FIG. 10B depicts the surface of the p*MHC diva-p? / A03 buried upon the binding of R302 binder. The HLA and peptide are represented as surfaces and divarasib is represented as sticks. The epitopes are shaded along a gray gradient according to which chain of the R302 binder is burying that area (VH: gray; VL: light gray; VH and VL shared epitope: darkest gray).
[0095] FIGs. 11A-11B show the R302 paratope. FIG. HA shows a cartoon representation of the R302 binder (paratope view). Residues involved in contacts with diva-p7 / A03 are represented as sticks. The R302 VL is represented in light gray, and the R302 VH is represented in dark gray. Divarasib is shown in sticks and labeled for clarity. FIG. 11B shows the surface of the R302 binder buried upon the binding to diva-p? / A03. Divarasib is represented as gray sticks while the R302 VH (dark gray) and VL (white) are represented as surfaces. Areas on the surface are labeled according to which moiety of the diva-p? / A03 complex is burying that area.
[0096] FIG. 12 shows residues involved in binder R302 - diva-p? / A03 interaction. Buried surface areas of interface residues of binder R302 and diva-p? / A03, as calculated by PDBePISA. The shades of gray indicate different percentages of the solvent-accessible residue surfaces buried upon the interaction between the indicated molecules, as shown on the legend on the right.
[0097] FIGs. 13A-13E show AETX-F1-R302 expression, Protein A capture, and size exclusion chromatography polishing. FIGs. 13A-13C show reduced SDS-PAGE of AETX-F1-R302 in the Expi293F cell culture harvested supernatant (Sup) (FIG. 13A), protein A chromatography flow- through (FT) and elution (E1-E3) fractions (FIG. 13B), and size exclusion chromatography elution (E1-E3) fractions (FIG. 13C). FIG. 13D shows the Protein A chromatogram and FIG. 13E shows the size exclusion purification chromatogram.
[0098] FIGs. 14A-14F show results from a cytotoxicity assay with an A375 isogenic cell line series. FIGs. 14A-14D show A375 isogenic cell lines pulsed with a dose response of wild type (WT) or divarasib-labeled p?-peptide, followed by treatment with a constant (10 nM) concentration of AETX-F1-RSV or AETX-F1-R302 (G3-18c-AAA-R302) T cell engagers (TCEs). The AETX-F1-RSV construct had the same backbone as the AETX-F1-R302, with the R302 VH and R302 VL replaced with the RSV VH and RSV VL, respectively. FIG. 14A shows A375 WT, FIG. 14B shows A375 with HLA-A*03, FIG. 14C shows A375 with HLA-A*11, and FIG. 14D shows A375 with HLA-A*68. FIGs. 14E-14F show A375 isogenic cell lines pulsed with a dose response of wild type (WT) or divarasib-labeled ps-peptide, followed by treatment with a constant (10 nM) concentration of AETX-F1-RSV or AETX-F1-R302 T cell engagers (TCEs). FIG. 14E shows A375 WT and FIG. 14F shows A375 with HLA-A*02. T cell cytotoxicity was assessed by IncuCyte analysis 48 hours after plating T cells and TCEs.
[0099] FIGs. 15A-15F show results from a cytotoxicity assay with an NCI-H2122 isogenic cell line series. FIGs. 15A-15E show NCI-H2122 isogenic cell lines pulsed with wild type (WT) or divarasib-labeled p?-peptide, followed by treatment with a dose response of AETX-F1-RSV or AETX-F1-R302 T cell engagers (TCEs). FIG. 15A shows cytotoxicity measurement using H2122 wild type (WT), FIG. 15B shows cytotoxicity measurement using H2122 knockout (KO), FIG. 15C shows cytotoxicity measurement using H2122 KO expressing HLA-A*03, FIG. 15D shows cytotoxicity measurement using H2122 KO expressing HLA-A*11, and FIG. 15E shows cytotoxicity measurement using H2122 KO expressing HLA-A*68. FIG. 15F shows an NCI- 142122 isogenic cell line expressing HLA-A*02 pulsed with divarasib-labeled ps-peptide, followed by treatment with a dose response of AETX-F1-RSV or AETX-F1-R302 T cell engagers (TCEs).
[0100] FIGs. 16A-16C show the workflow for the immunopeptidomics analysis. FIG. 16A shows sequences of KRASG12Cepitopes. The p?WTsequence is set forth as VVVGAGGVGK (SEQ ID NO: 157), the psWTsequence is set forth as VVGAGGVGK (SEQ ID NO: 158), the p? sequence is set forth as VVVGACGVGK (SEQ ID NO: 160), and the ps sequence is set forth asVVGACGVGK (SEQ ID NO: 161). The p? and ps epitopes are conjugated to the drug. FIG. 16B shows the targeted MS workflow for identifying and quantifying haptenated MHC-I peptides. FIG. 16C shows a schematic of SureQuant targeted data acquisition and analysis.
[0101] FIGs. 17A-17B show spectral validation for KRASG12Cp*MHC peptides presented on HLA-A* 11 :01. FIG. 17A shows a schematic of cell line engineering for generating HLA / KRASG12Coverexpression A375-derived cell lines. FIG. 17B shows mirror plots depicting the mass spectra for the double heavy -labeled synthetic (bottom) and endogenous (top) peptides. Mass spectra show ps (left) and p? (right) peptides presented on A375-A11KCcells. C: carb ami dom ethyl ati on .
[0102] FIGs. 18A-18C show spectral validation of additional KRASG12Chapten peptides presented on HLA-A* 11 :01. The figures show mirror plots depicting the mass spectra for the double heavy-labeled synthetic (bottom) and endogenous (top) peptides presented on A375- A11KCcells. FIG. 18A shows cells treated with DMSO (left) or 1 pM divarasib (right) for 48 hours. FIG. 18B shows cells treated with DMSO (left) or 1 pM adagrasib (right) for 48 hours. Annotated ions depict identified b, y, a, or precursor ion fragment. *Denotes ions with a loss of 97.09 Da from the drug modification, as depicted in FIG. 18C, for divarasib (left) or adagrasib (right). Underlined amino acids are heavy-isotope labeled (V, K) or drug-modified (C).
[0103] FIG. 19 shows a table of netMHCpan-4.1 peptide prediction scores (% rank) for p? or OW to model a bulky modified residue (e.g., haptenated peptide) on selected A3 supertype alleles. % Rank < 0.5 is a predicted strong binder, < 2% a predicted weak binder.
[0104] FIG. 20 shows sequence logos generated from eluted ligands (mass spectrometry data, netMHCpan-4.1) of A3 supertype alleles with a lysine present in the c-terminal position.
[0105] FIGs. 21A-21C show spectral validation of KRASG12CpMHC presentation. Each figures shows mirror plots depicting mass spectra for the double heavy-labeled synthetic (bottom) and endogenous (top) KRASG12Cp? or ps peptides. Underlined amino acids are heavy-isotope labeled (V, K) or carbamidomethylated (C).
[0106] FIGs. 22A-22B show binding curves for the R302 binder. FIG. 22 A shows binding titrations of R302 scFv displayed on the yeast cell surface to the indicated p / p*MHCs. Each graph shows the sequences of the peptides used in the binding experiment. C* indicates cysteine residues conjugated to divarasib. FIG. 22B shows inhibition by free divarasib of the interaction between scFv R302 displayed on the yeast cell surface and 10 nM of the indicated diva-p / MHC. The binding signal intensity was normalized to the values in the absence of free divarasib (100%) and in the absence of antigen (0%). ICso values are reported for each antigen.
[0107] FIGs. 23A-23D show additional characterization of R302 binding. FIG. 23A shows SPR sensorgrams of the interaction between AETX-F1-R302 and the indicated divarasib p*MHC antigens. Biotinylated divarasib p*MHCs were immobilized, and binding of soluble AETX-F1- R302 was measured using single cycle kinetic experiments. Kinetic values of fitted data are shown in the table. FIGs. 23B-23C show SPR sensorgrams of the interaction between AETX-F1-R302 and the indicated p / p*MHC antigens. Biotinylated antigens were immobilized, and binding of soluble AETX-F1-R302 samples was measured. For each sensorgram, next to the sample name is indicated if the antibody is binding to the target (check mark) or not (X). FIG. 23D shows a schematic depicting A375eGFPcell line engineered to express HLA allele of interest (where “X” is A02, A03, or Al l).
[0108] FIG. 24 shows results of an Incucyte-based cytotoxicity analysis. A375eGFPisogenic cell lines were pulsed with diva-ps, diva-p?, psWT, or p?WTpeptides for four hours prior to adding activated human T cells (10: 1 E:T ratio) and AETX-F1-R302 for 48 hours. The plots show 3 technical replicates per condition; error bars indicate standard deviation. Table shows ECso values for fitted curves (n.d. = not determined).
[0109] FIG. 25 shows flow charts of Cryo-EM data processing. The flow chart for R302_diva- p5 / A*02 is shown on the left, and the flow chart for R302_diva-p7 / A*03 is shown on the right. All map figures were prepared with ChimeraX.
[0110] FIGs. 26A-26C show Cryo-EM data processing. FIG. 26A shows statistics for the final maps of R302_diva-p5 / A*02 (left) and R302_diva-p? / A*03 (right). Gold Standard Fourier Shell Correlation (GSFSC) (top) and angular distribution of the particles used for the final reconstruction (middle) as calculated by CryoSPARC are shown. Fourier Shell Correlation (FSC) plot was calculated based on the fitted structure models and cryo-EM maps (bottom). FIG. 26B shows local resolution calculated for the final maps of complexes R302_diva-ps / A*02 (left) and R302_diva-p? / A*03 (right). FIG. 26C shows cryo-EM maps and corresponding models of diva- p conjugates, HLAs (residues 60-70), and R302 heavy chains (residues 91-98) for the complexes R302_diva-ps / A*02 (left) and R302_diva-p? / A*03 (right), demonstrating appropriate features for each reported resolution.
[0111] FIGs. 27A-27B show representations to characterize the geometrical analysis of R302. FIG. 27A shows a cartoon representation of the structures of Fab R302 (R302 in Fab format; only the variable chains are shown) in complex with diva-ps / A*02 (left representation) and diva- p? / A*03 (right representation). HLAs are depicted below the R302 binder in each figure. For the left representation with diva-ps / A*02, the HLA-A*02 is depicted in dark gray. For the rightrepresentation with diva-p? / A*03, the HLA-A*03 is depicted in white. P2m is shown in gray. The VH of R302 is shown in dark gray, and the VL of R302 is shown in light gray. Conjugated peptides for each cartoon representation are labeled in the center (diva-ps for the left, and diva-p? for the right). FIG. 27B shows a geometrical analysis of antibody-p*MHCs complexes. Schematic representation of the docking angles of antibody-p / p*MHC complexes is shown in the top-left of the figure. The antibody is represented in dark gray (heavy chain) and light gray (light chain) between the y-axis and z-axis, and the p / p*MHC in light gray (HLA), dark gray (P2m), and black (peptide). Analysis of TCR-pMHCs vs. antibody-p*MHC docking angles using the TCR CoM (center of mass) method is shown in the top-right of the figure. Black dots: CoM of the MHC peptide binding domain; gray dots: CoM of TCR / Fab variable chains. 9 is the angle between the x-axis and the projection of the TCR / Fab CoM-MHC CoM vector onto the XY plane, cp is the angle between the z axis and the TCR CoM-MHC CoM vector. The bottom of FIG. 20B shows cartoon representations of the different antibodies binding to p*MHCs sharing the same peptide to demonstrate comparison of the aligned structures. The peptide was p7 and HLA was HLA- A*03. The relative regions of R302_diva-p7 / A*03, PlB7_soto-p7 / A*03, and R023_soto- p7 / A*03 are labeled and marked with shades of gray.
[0112] FIG. 28 shows interface areas (A2) and their A‘G (kcal / M), for the R302_diva-p5 / A*02 (left) and R302_diva-p7 / A*03 (right) complexes. Interface areas (A2) and their A‘G (kcal / M) were calculated with PDBePISA. A‘G indicates the solvation free energy gain upon formation of the complex, calculated as the difference in total solvation energies of isolated and interfacing structures. Negative A‘G corresponds to hydrophobic interfaces (positive protein affinity). It does not include the effect of satisfied hydrogen bonds and salt bridges across the interface; NSB and NSB, respectively, indicate the number of potential salt bridges and hydrogen bonds across the considered interface. Underneath each table is depicted the corresponding structure (peptide molecules represented as ribbons and divarasib represented in sticks) with the chain identifications (divarasib is indicated with its PDB five letter code “Al AWR”).
[0113] FIG. 29 shows surfaces (light gray) of diva-ps / A*02 (left) and diva-p? / A*03 (right) buried upon the binding of Fab R302. The hapten is represented as sticks. On the bottom of the panel is the sequence alignment of HLA-A*02, HLA-A*03 and HLA-A*11 (residues 1 - 180), performed with BLASTp. The only non-conserved residue among the alleles located in R302 epitope (#62, on HLA-A*03 only) is indicated both on the aligned sequences (black triangle) and on the structures.
[0114] FIGs. 30A-30B show interfacing residues of Fab R302 and divarasib p*MHCs. FIG. 30A shows residues for R302 with diva-p5 / A*02 and FIG. 30B shows residues for R302 with diva- p7 / A*03.
[0115] FIG. 31 shows surface and cartoon representation of the divarasib -binding pocket in the R302_diva-ps / A*02 and R302_diva-p? / A*03 complexes. Divarasib is shown in sticks.
[0116] FIG. 32 shows details of R302 residues contacting diva-p / MHCs in the structures of the R302_diva-ps / A*02 (left) and R302_diva-p? / A*03 (right) complexes. The peptide backbones are shown as transparent ribbons, while the side chains (orbackbone, if involved) of residues included in the antibody-antigen interface are shown as sticks. H-bonds and salt-bridges are represented as black dashed lines.
[0117] FIG. 33 shows alignment of R302_diva-ps / A*02 and R302_diva-p? / A*03 structures. On the right, the cartoon representation of the aligned HLAs (residues 1 - 180), the hapten-peptide conjugates (divarasib is represented as sticks), and R302 variable chains. On the left, the hapten- peptide conjugates only represented as sticks. Anchoring residues of the two peptides are indicated with a *. Residues V8 and V9 in diva-p5, and G10 and Al 1 in diva-p7, are all included in R302 binding interface, and they share similar chemical properties (small aliphatic sidechains), and the same conformation.
[0118] FIG. 34 shows details of R302 CDR-H3. On the left is reported the sequence of R302 CDR-H3. Underneath it is presented the sequence logo indicating the residue frequency for each indicated position, reported for human IgGs8 . For clarity, in the following panels is used the CDR-H3 residue # (1 to 11). The central panel shows the CDR-H3 (11 residues long) of aligned human antibodies presenting the highly conserved sequence “ARXXXXXX[FMLI]DX” (PDBIDs: 2QR0, 4DKF, 4G5Z, 4HWB, 4XGZ, 5BVJ, 6NV0 and 8VRA). They all present the large hydrophobic residue at position 9 (F, M, L or I) buried next to the alanine in position 1, and the arginine at position 2 forming a salt-bridge with the aspartic acid at position 10. The right panel shows the distinct conformation of R302 CDR-H3, with the side chain of M9 being solvent- exposed instead of buried. Unlike the common Al, LI would sterically clash with a buried M9, and unlike the common R2, Y2 does not form a salt bridge with D10. Thus, the unique “LY” sequence of R302 is a determinant of its’ paratope and p*MHC binding characteristics. CDRs-H3 are depicted with partially transparent cartoons (dark gray in the central panel, and light gray for R302 in the right panel), and side chains of residues at position 1, 2, 9 and 10 are shown as sticks. Grey dashed lines represent H-bonds and salt bridges formed between residues 2 and 9.DETAILED DESCRIPTION
[0119] While various embodiments of the invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions can occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein can be employed.
[0120] Unless the context requires otherwise, throughout the specification and claims which follow, the word “comprise” and variations thereof, such as, “comprises” and “comprising” are to be construed in an open, inclusive sense, that is, as “including, but not limited to.” Further, headings provided herein are for convenience only and do not interpret the scope or meaning of the claimed disclosure.
[0121] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.
[0122] Every numerical range given throughout this specification includes its upper and lower values, as well as every narrower numerical range that falls within it, as if such narrower numerical ranges were all expressly written herein.
[0123] As used in the specification and the appended claims, the singular forms “a” “and” and “the” include plural referents unless the context clearly dictates otherwise. Ranges may be expressed herein as from “about” one particular value, and / or to “about” another particular value. When such a range is expressed, another embodiment includes from the one particular value and / or to the other particular value. Similarly, when values are expressed as approximations, by the use of the antecedent “about” it will be understood that the particular value forms another embodiment. The term “about” in relation to a numerical value encompasses variations of + / - 10%, + / - 5%, or + / - 1%.
[0124] This disclosure includes every amino acid sequence described herein and all nucleotide sequences encoding the amino acid sequences. Every antibody sequence and antigen-binding fragments of them are included. Polynucleotide and amino acid sequences having from 80-99% similarity, inclusive, and including all numbers and ranges of numbers there between, with the sequences provided herein, are included in the invention. The polynucleotides provided herein can be modified polynucleotides. All of the amino acid sequences described herein can include amino acid substitutions, such as conservative substitutions, that do not adversely affect the function of the protein that comprises the amino acid sequences. In this regard, the disclosure providesalternative residues for certain positions in described binding partners as described below. In certain examples, the alternative residues were identified by deep mutational scanning, which demonstrates binding functionality for each binding partner that contains the described amino acid change(s). The disclosure includes each binding partner with each alternative residue substituted for the original residue alone and in any combination with the described alternative residues. Thus, any binding partner described herein may have any single described residue change or a combination of described changes. Representative changes for particular antibodies are described in the Tables. The changes may be in CDR1, CDR2, CDR3, and combinations thereof. The changes can also include amino acid insertions. The disclosure includes each amino acid sequence that is encompassed by the description of alternative amino acids by reference to a specific sequence identifier and those described in the aforementioned Tables.
[0125] As described above, the present disclosure provides antibodies and antigen-binding domains or fragments thereof (collectively “binding partners” and each individually a “binding partner”). The term “antibody” includes each binding partner format herein. The antibody can comprise a polypeptide with an antigen-binding domain or fragment thereof. The binding partners bind with specificity to a protein or fragment thereof, or a peptide provided in peptide form, that comprises a covalently attached molecule. The covalently attached molecule forms a peptide conjugate. A “peptide conjugate” as used herein means any protein or peptide that has been modified so that it is covalently conjugated to another molecule. The peptide conjugate is considered to be a novel antigen, i.e., a neoantigen. The other molecule that is covalently conjugated to the protein or peptide to form the peptide conjugate is not particularly limited, with the proviso that the other molecule is not an additional amino acid that is added to the described peptide conjugates. In embodiments, the molecule that is covalently conjugated to the protein or peptide could have or could have had biological activity before conjugation, or it may be biologically inert before conjugation. In embodiments, the molecule is a drug, including but not necessarily limited to small molecule drugs. As used herein, the molecule that is covalently attached to a peptide to form peptide conjugate is referred to as a “targeted covalent inhibitor (TCI)” or as a “covalent drug.” Representative and non-limiting examples of drugs that covalently attach to a peptide or protein to form a peptide conjugate are described below. Peptide conjugates include but are not limited to covalently modified full length proteins and fragments thereof. Peptide conjugates include fragments of full length proteins that include a covalent modification and are produced, for example, by intracellular processing. In certain embodiments, a full length protein may be covalently modified within a cell and subsequently processed such that a peptideconjugate that is a fragment of the full length protein is produced. In an embodiment, the peptide conjugate comprises a fragment of a full-length protein. As described further below, the produced peptide conjugate may be displayed on a cell surface. The cell surface display of the peptide conjugate may be any form of cell surface display, including but not limited to by way of any receptor having an extracellular segment, or it may be displayed by way of any type of major histocompatibility complex (MHC) or human leukocyte antigen (HLA). Non-limiting examples of HLA types that display peptide conjugates, and to which the described binding partners bind with specificity, are described further below.
[0126] As used herein, the term “peptide conjugate / MHC complex” refers to a peptide conjugate comprising: a peptide and a chemical fragment of a targeted covalent inhibitor, presented by a major histocompatibility complex (MHC). For example, the peptide conjugate can be formed by the covalent reaction of a targeted covalent inhibitor with a residue (e.g., a cysteine residue) in a peptide. In some embodiments, the peptide conjugate is formed by the covalent reaction of divarasib with a KRASG12Cpeptide. In some embodiments, the peptide is externally introduced as a vaccine. In some embodiments, the peptide comprises a nucleophilic or an electrophilic residue. In some embodiments, the residue comprises cysteine, aspartic acid, arginine, serine, or tyrosine. In an embodiment, the MHC is a human leukocyte antigen (HLA). In an embodiment, the HLA i s HL A- A* 02 : 01 , HL A- A* 03 : 01 , or HL A- A* 11 :01.
[0127] As used herein, the term “CDR” or “complementarity determining region” means the noncontiguous antigen combining sites found within the variable regions of heavy and light chain polypeptides. These particular regions have been described by, for example, Kabat et al., J. Biol. Chem. 252, 6609-6616 (1977) and Kabat et al., Sequences of protein of immunological interest (1991), by Chothia et al., J. Mol. Biol. 196:901-917 (1987), and by MacCallum et al., J. Mol. Biol. 262:732-745 (1996), all of which are herein incorporated by reference in their entireties, where the definitions include overlapping or subsets of amino acid residues when compared against each other. In certain embodiments, the term “CDR” is a CDR as defined by MacCallum et al., J. Mol. Biol. 262:732-745 (1996) and Martin A. “Protein Sequence and Structure Analysis of Antibody Variable Domains,” in Antibody Engineering, Kontermann and Diibel, eds., Chapter 31, pp. 422-439, Springer-Verlag, Berlin (2001). In certain embodiments, the term “CDR” is a CDR as defined by Kabat et al., J. Biol. Chem. 252, 6609-6616 (1977) and Kabat etal., Sequences of protein of immunological interest (1991). In certain embodiments, heavy chain CDRs and light chain CDRs of an antibody are defined using different conventions. In certain embodiments, heavy chain CDRs and / or light chain CDRs are defined by performing structural analysis of anantibody and identifying residues in the variable region(s) predicted to make contact with an epitope region of a target molecule (e.g., a peptide conjugate). HC CDR1, HC CDR2, and HC CDR3 denote the heavy chain CDRs, and LC CDR1, LC CDR2 and LC CDR3 denote the light chain CDRs. The CDRs for any binders (e.g., binding partners, antigen binding domains, or T cell engagers) described herein can be designated by Kabat numbering scheme. In some cases, the light chain (LC) CDRs can be designated by Kabat numbering scheme. In some cases, the LC CDRs can be designated by Kabat numbering scheme with modifications. In some cases, the heavy chain (HC) CDRs can be designated by Kabat numbering scheme. In some cases, the HC CDRs can be designated by Kabat numbering scheme with modifications.
[0128] The determination of “percent identity” between two sequences (e.g., amino acid sequences or nucleic acid sequences) can be accomplished using a mathematical algorithm. A specific, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin S & Altschul SF (1990) PNAS 87: 2264-2268, modified as in Karlin S & Altschul SF (1993) PNAS 90: 5873-5877, each of which is herein incorporated by reference in its entirety. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul SF et al., (1990) J Mol Biol 215: 403, which is herein incorporated by reference in its entirety. BLAST nucleotide searches can be performed with the NBLAST nucleotide program parameters set, e.g., for score=100, word length=12 to obtain nucleotide sequences homologous to a nucleic acid molecule described herein. BLAST protein searches can be performed with the XBLAST program parameters set, e.g., to score 50, word length=3 to obtain amino acid sequences homologous to a protein molecule described herein. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul SF et al., (1997) Nuc Acids Res 25: 3389-3402, which is herein incorporated by reference in its entirety. Alternatively, PSI BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.). When utilizing BLAST, Gapped BLAST, and PSI Blast programs, the default parameters of the respective programs (e.g., of XBLAST and NBLAST) can be used (see, e.g., National Center for Biotechnology Information (NCBI) on the worldwide web, ncbi.nlm.nih.gov). Another specific, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4: 11-17, which is herein incorporated by reference in its entirety. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. The percent identitybetween two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.
[0129] As used herein, the terms “free targeted covalent inhibitor” or “free drug” refer to a targeted covalent inhibitor that is not covalently linked to a protein or peptide. Once the targeted covalent inhibitor is covalently linked to a protein or peptide, the targeted covalent inhibitor can be referred as a portion or fragment of the free target covalent inhibitor or drug. For example, the protein or fragment thereof can be the chemical fragment that is bonded to the cysteine residue of the peptide upon covalent reaction of the free drug with the cysteine residue of the peptide. As used herein the term “KRASG12C” refers to the KRAS protein (UniProt Accession No. P01116) with a G12C mutation, i.e., a cysteine at amino acid position 12. As used herein the term “KRASG12D” refers to the KRAS protein (UniProt Accession No. P01116) with a G12D mutation, i.e., an aspartic acid at amino acid position 12. As used herein the term “KRASG12R” refers to the KRAS protein (UniProt Accession No. P01116) with a G12R mutation, i.e., an arginine at amino acid position 12. As used herein the term “KRASG12S” refers to the KRAS protein (UniProt Accession No. P01116) with a G12S mutation, i.e., a serine at amino acid position 12.
[0130] In embodiments, the binding partners bind to the protein or peptide or a complex comprising the protein or peptide when covalently bound to the peptide conjugate, relative to the same protein or peptide that is not bound to the drug. Accordingly, binding partners described herein either may not detectably bind, or bind with a lower affinity, to the same protein or fragment thereof in the absence of the covalently attached molecule. In embodiments, the binding partners bind to the protein or peptide comprising the covalently attached drug with an affinity that is 10- 10,000 fold, including all numbers and ranges of numbers from 10-10,000, greater than the affinity for the protein or peptide that does not comprise the covalently bound molecule. In this regard, and without intending to be bound by any particular theory, it is considered that the presence of the covalently bound molecule contributes to the epitope to which the binding partners bind with specificity. Likewise, binding partners of this disclosure preferentially bind to the peptide conjugate relative to binding to the free drug. In embodiments, the binding partners bind to the peptide comprising the covalently attached drug (e.g., the peptide-conjugate / MHC complex) with an affinity that is 10-10,000 fold, including all numbers and ranges of numbers from 10-10,000, greater than the affinity for the free drug. In some embodiments, the interaction between the binding partner and the peptide-conjugate / MHC complex is not inhibited by the free drug. For example, the interaction between the binding partner and the peptide-conjugate / MHC complex is not inhibited by a lOOx, l,000x, 10,000x, 100,000x or more excess of the free drug.
[0131] In embodiments, the molecule that is covalently bound to form the peptide conjugate is a drug and may be any targeted covalent inhibitor (TCI), but the covalent drug need not necessarily inhibit the target peptide. In embodiments, the molecule reacts with a specific residue within the target protein. In embodiments, the molecule reacts at least in part with a segment of the protein or peptide that comprises a nucleophilic, or an electrophilic, residue. In embodiments, the segment of the protein or peptide to which the molecule reacts comprises any of Cys, Lys, Tyr, His, Ser, Thr, Tyr, or Arg, the latter being described in Ziyang Zhang, Johannes Morstein, Andrew K. Ecker, Keelan Z. Guiley, and Kevan M. Shokat Journal of the American Chemical Society Article ASAP, DOI: 10.1021 / jacs.2c05377, from which the disclosure is incorporated herein by reference. In embodiments, the protein or peptide comprises a selenocysteine. In embodiments, the targeted covalent inhibitor reacts with selenocysteine. In embodiments, the molecule reacts at least in part with a segment of the protein or peptide that comprises a wild type Cys, or a mutation of a residue to a Cys, and thus may be covalently attached by a so-called sulfur tether. In embodiments, the drug is any drug described in Ghosh AK, Samanta I, Mondal A, Liu WR. Covalent Inhibition in Drug Discovery. ChemMedChem. 2019;14(9):889-906. Doi: 10.1002 / cmdc.201900107, or in De Cesco, et al., European Journal of Medicinal Chemistry 138 (2017) 96el 14, or in Bauer, RA, Drug Discovery Today, Volume 20, Number 9, September 2015, from which the disclosures of compounds that covalently modify protein targets is incorporated herein by reference.
[0132] In non-limiting embodiments, any of said Asp, Cys, and Arg amino acids are present in the protein or peptide to which the molecule binds because the gene encoding the wild type protein has been mutated to encode a protein that includes one or a combination of the described residues. In non-limiting embodiments, the molecule binds to a protein or peptide that is correlated with a disease or condition, such as a cancer, an autoimmune disease, or other disease or disorder that is treated with a targeted covalent inhibitor. In embodiments, the target (e.g., the protein or peptide to which the molecule covalently binds) is a receptor, including but not necessarily limited to any receptor having a catalytically active segment. In embodiments, the drug binds to an enzyme that is not necessarily a receptor, including but not limited to any kinase. In embodiments, a protein target comprises a receptor with one or more activating mutations, which promote ligandindependent enzyme activity.
[0133] In embodiments, the molecule targets and thus covalently binds to an amino acid sequence present within any of the following proteins and / or variants thereof, which may or may not comprise a mutation, such as a mutation that is related to a particular condition, including but not limited to any type of cancer. In embodiments, the protein is any protein described in Visscher M,et al., Covalent targeting of acquired cysteines in cancer. Curr Opin Chem Biol. 2016;30:61-67. Doi: 10.1016 / j.cbpa.2015.11.004, from which the description is incorporated herein by reference. Visscher et al. also teaches methods for identifying disease-associated mutated genes that introduces a Cys residue suitable for covalent modification. In embodiments, the protein is KRAS, Bruton's tyrosine kinase (BTK), any member of the epidermal growth factor receptor (EGFR) family, also referred to as the ERBB family, including but not limited to EGFR (ERBB1), HER2 / NEU (ERBB2), HER3 (ERBB3), and HER4 (ERBB4); a fibroblast growth factor receptor (FGFR); the receptor kinase known in the art as MET, BRAF, a cyclin-dependent kinase (CDK); Acetyl Choline Esterase (ACHE); TP53, IDH1, GNAS, FBXW7, CTNNB1, DNMT3A, any cathepsin, including cathepsin B, C, F, H, K, L, O, S, V, W and X; any caspase; any protein involved in obesity, such as Pancreatic lipase and METAP2, or any Cancer Testis Antigen. In embodiments, the drug targets and therefore covalently binds to any viral protein, including but not limited to a polymerase, including any viral DNA polymerase, RNA polymerase, reverse transcriptase, or RNA-dependent RNA polymerase, or a viral protein that is required, for example, viral cell entry, or a protein encoded by any a transposable element. In embodiments, the drug targets EGFR and may be selected from PD168393, PF00299804 (dacomitinib), EKB569 (pelitinib), afatinib, WZ4002, osimertinib (formerly known as AZD9291), PF-06459988, nazartinib, naquotinib, olmutinib, avitinib, and rociletinib, neratinib, pyrotinib, poziotinib, and derivatives thereof. In embodiments, the drug targets Bruton’s tyrosine kinase (BTK), and may be selected from ibrutinib, acalabrutinib, zanubrutinib, CHMFL-BTK-11, ONO / GS-405, PRN1008, and CC-292. In embodiments, the drug targets any p90 ribosomal S6 kinase (RSK), and may be selected from fluoromethylketone (FMK) and dimethyl fumarate. In embodiments, the drug targets any FGFR, and may be selected from FIIN-1, FIIN-2, FIIN-3, BGJ398, AZD4547, PRN1371, FGF401. In an embodiment, the targeted covalent inhibitor targets an E3 ligase, such as RNF4, HOIP, RSP5, SMURF 1, E6AP, HUWE1, and NEDD4-1. In an embodiment, the targeted covalent inhibitor targets a DDB 1 - and CUL4- associated factor (DCAF), such as DC AF 1 or DCAF15. In an embodiment, the targeted covalent inhibitor targets any cancer testis antigen, any endogenous retroviral protein, a long interspersed element- 1 (LINE-1), or a short interspersed element (SINE). In an embodiment, the targeted covalent inhibitor targets a short interspersed element that is optionally Alu. In an embodiment, the targeted covalent inhibitor is iniparib, abiraterone, carfilzomib, afatinib, or neratinib.
[0134] The “antigen-binding site,” or “binding portion” of an antibody molecule refers to the part of an antibody molecule, e.g., an immunoglobulin (Ig) molecule, that participates in antigenbinding. In embodiments, the antigen binding site is formed by amino acid residues of the variable (V) regions of the heavy (H) and light (L) chains. Three highly divergent stretches within the variable regions of the heavy and light chains, referred to as hypervariable regions, are disposed between more conserved flanking stretches called “framework regions,” (FRs). FRs are amino acid sequences that are naturally found between, and adjacent to, hypervariable regions in immunoglobulins. In embodiments, in an antibody molecule, the three hypervariable regions of a light chain and the three hypervariable regions of a heavy chain are disposed relative to each other in three dimensional space to form an antigen-binding surface, which is complementary to the three-dimensional surface of a bound antigen. The three hypervariable regions of each of the heavy and light chains are referred to as “complementarity-determining regions,” or “CDRs.” The framework region and CDRs have been defined and described, e.g, in Kabat, E.A., et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242, and Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917. Each variable region (e.g, variable heavy chain and variable light chain region) is typically made up of three CDRs and four FRs, arranged from amino-terminus to carboxyterminus in the amino acid order: FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4.
[0135] As used herein, an “immune cell” refers to any of various cells that function in the immune system, e.g., to protect against agents of infection and foreign matter. In embodiments, this term includes leukocytes, e.g., neutrophils, eosinophils, basophils, lymphocytes, and monocytes. Innate leukocytes include phagocytes (e.g., macrophages, neutrophils, and dendritic cells), mast cells, eosinophils, basophils, and natural killer cells. Innate leukocytes identify and eliminate pathogens, either by attacking larger pathogens through contact or by engulfing and then killing microorganisms, and are mediators in the activation of an adaptive immune response. The cells of the adaptive immune system are special types of leukocytes, called lymphocytes. B cells and T cells are important types of lymphocytes and are derived from hematopoietic stem cells in the bone marrow. B cells are involved in the humoral immune response, whereas T cells are involved in cell-mediated immune response. The term “immune cell” includes immune effector cells.
[0136] “Immune effector cell,” as that term is used herein, refers to a cell that is involved in an immune response, e.g., in the promotion of an immune effector response. Examples of immune effector cells include, but are not limited to, T cells, e.g., alpha / beta T cells and gamma / delta T cells, B cells, natural killer (NK) cells, natural killer T (NK T) cells, macrophages, neutrophils, and mast cells.
[0137] The term “effector function” or “effector response” refers to a specialized function of a cell. Effector function of a T cell, for example, may be cytolytic activity or helper activity including the secretion of cytokines.
[0138] The terms “polypeptide”, “peptide” and “protein” (if single chain) are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. The polypeptide can be isolated from natural sources, can be a produced by recombinant techniques from a eukaryotic or prokaryotic host, or can be a product of synthetic procedures.
[0139] The compositions and methods of the present invention encompass polypeptides and nucleic acids having the sequences specified, or sequences substantially identical or similar thereto, e.g. , sequences at least 80%, 85%, 90%, 95% identical or higher to the sequence specified. In the context of an amino acid sequence, the term “substantially identical” is used herein to refer to a first amino acid that contains a sufficient or minimum number of amino acid residues that are i) identical to, or ii) conservative substitutions of aligned amino acid residues in a second amino acid sequence such that the first and second amino acid sequences can have a common structural domain and / or common functional activity. For example, amino acid sequences that contain a common structural domain having at least about 80%, 85%, 90%. 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% 99%, 99.5%, 99.9%, or 100% sequence identity to a reference sequence, e.g., a sequence provided herein. In the context of nucleotide sequence, the term “substantially identical” is used herein to refer to a first nucleic acid sequence that contains a sufficient or minimum number of nucleotides that are identical to aligned nucleotides in a second nucleic acid sequence such that the first and second nucleotide sequences encode a polypeptide having common functional activity, or encode a common structural polypeptide domain or a common functional polypeptide activity. For example, nucleotide sequences having at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% 99%, 99.5%, 99.9%, or 100% sequence identity to a reference sequence, e.g., a sequence provided herein.
[0140] The term “variant” refers to a polypeptide that has a substantially identical amino acid sequence to a reference amino acid sequence, or is encoded by a substantially identical nucleotide sequence. In some embodiments, the variant is a functional variant. In some embodiments, a TCRPV variant can bind to TCRa and form a TCR a:P complex.
[0141] The term “functional variant” refers to a polypeptide that has a substantially identical amino acid sequence to a reference amino acid sequence, or is encoded by a substantially identical nucleotide sequence, and is capable of having one or more activities of the reference amino acid sequence.
[0142] Calculations of homology or sequence identity between sequences (the terms are used interchange-ably herein) are performed as follows. To determine the percent identity of two amino acid sequences, or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). In a preferred embodiment, the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, 60%, and even more preferably at least 70%, 80%, 90%, 100% of the length of the reference sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”).
[0143] The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. In a preferred embodiment, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch ((1970) J. Mol. Biol. 48:444-453 ) algorithm which has been incorporated into the GAP program in the GCG software package (available at http: / / www.gcg.com), using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In yet another preferred embodiment, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available at http: / / www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. A particularly preferred set of parameters (and the one that should be used unless otherwise specified) are a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
[0144] The percent identity between two amino acid or nucleotide sequences can be determined using the algorithm of E. Meyers and W. Miller ((1989) CABIOS, 4: 11-17) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. The nucleic acid and protein sequences described herein can be used as a “query sequence” to perform a search against public databases to, for example, identify other family members or related sequences. Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10. BLAST nucleotide searches can be performed with the NBLAST program, score = 100, wordlength = 12 to obtain nucleotide sequences homologous to a nucleic acid molecule of the invention. BLAST protein searches can be performed with the XBLAST program, score = 50, wordlength = 3 to obtain amino acid sequences homologous to protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., (1997) Nucleic Acids Res. 25:3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used.
[0145] It is understood that the molecules of the present invention may have additional conservative or non-essential amino acid substitutions, which do not have a substantial effect on their functions.
[0146] The term “amino acid” is intended to embrace all molecules, whether natural or synthetic, which include both an amino functionality and an acid functionality and capable of being included in a polymer of naturally-occurring amino acids. Exemplary amino acids include naturally- occurring amino acids; analogs, derivatives and congeners thereof; amino acid analogs having variant side chains; and all stereoisomers of any of the foregoing. As used herein the term “amino acid” includes both the D- or L- optical isomers and peptidomimetics.
[0147] A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyro-sine, phenylalanine, tryptophan, histidine).
[0148] As used herein, the term “molecule” as used in, e.g., antibody molecule, cytokine molecule, receptor molecule, includes full-length, naturally-occurring molecules, as well as variants, e.g., functional variants (e.g., truncations, fragments, mutated (e.g., substantially similar sequences) or derivatized form thereof), so long as at least one function and / or activity of the unmodified (e.g., naturally-occurring) molecule remains.
[0149] As used herein, the term “mutation” refers to an alteration in the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA. In some embodiments, the mutation may be a large-scale mutation, such as amplifications (or gene duplications) or repetitions of a chromosomal segment, deletions of large chromosomal regions, chromosomal rearrangements (e.g., chromosomal translocations, chromosomal inversions, non-homologous chromosomal crossover, and interstitial deletions), and loss of heterozygosity. In some embodiments, the mutation may be a small-scale mutation, such as insertions, deletions, and substitution mutations. As used herein, the term “substitution mutation” refers to the transition that exchange a single nucleotide for another.Overview
[0150] Covalent inhibitors of the oncoprotein KRAS have significant initial efficacy, but responses lack durability. Covalent inhibitor-modified oncoproteins can be presented as MHC- restricted hapten-peptides (p*MHC) on the cancer cell surface, creating an opportunity to combine targeted therapy with immunotherapy to overcome drug resistance. Tumor antigen-targeting immunotherapies in principle can have superior safety and efficacy compared to systemic immunotherapy by immune checkpoint inhibitors, but identifying tumor-specific antigens remains a significant challenge. Unlike patient-specific neoantigens, which may utilize individualized immunotherapeutic development, commonly mutated oncoprotein-derived epitopes presented on major histocompatibility complex (MHC) molecules (e.g., class I MHCs) can provide an opportunity to target cancer-specific antigens shared across patient populations. However, their development has been limited by human leukocyte antigen (HLA) restriction and low pMHC presentation levels, resulting in a limited repertoire of well -validated neoantigen peptide-MHC (pMHC) targets. Additionally, generating high-affinity, highly specific binders to pMHC targets using traditional TCR or TCR-mimicking (TCRm) antibodies can remain challenging due to the subtle differences between many mutant and wild-type antigens.
[0151] Mutated KRASG12Xproteins can be examples of tumor-specific, shared pMHC targets due to their high prevalence and well -characterized epitope landscape across high-frequency HLAalleles. Despite their low surface density (~1O or fewer copies-per-cell), promising immunotherapies, for example on KRASG12Dand KRASG12V, can be pursued. Although KRASG12Cmutations may occur relatively frequently (9% in non-small cell lung cancer, 3% in colorectal cancer, and 1% in pancreatic cancer), the development of KRASG12C-pMHC immunotherapies remains limited. A key challenge can arise from the cysteine residue, which is prone to heterogeneous post-translational modifications of the thiol group that result in multiple unknown isoforms, effectively diluting an already low-density target. Mass spectrometry techniques to identify KRASG12Cepitopes cleave thiol modifications to enable detection, preventing precise characterization of the cysteine’s modification state or states. Thus, innovative strategies are being sought to fully exploit the therapeutic potential of KRASG12Cneoepitopes.
[0152] Synthetic neoantigens formed by proteasome-resistant modification of KRASG12Cpeptides with covalent inhibitors can be loaded onto HLAs as so-called “haptenated peptides” or p* (e.g., peptides still carrying the covalent inhibitor) and presented as p*MHCs on the cancer cell surface as homogeneously modified epitopes. These p*MHCs can be referred to as peptide conjugate / MHC complexes. The distinct nature of these cancer-specific targets can facilitate their high-specificity targeting by engineered antibodies and enables tumor-specific killing in vitro when antibodies are converted to T cell engagers (TCEs).
[0153] The present disclosure provides compositions and methods that include binding partners that bind with specificity to target sites on proteins or peptides that comprise a covalently attached molecule. The strategies presented in the present disclosure may have the potential to counteract disease progression driven by inherent or acquired resistance to covalent KRASG12Cinhibitors, remaining effective in recurrent settings because the G12C mutation may be retained in resistant cells. Additionally, the strategies provided herein can leverage the immunomodulatory effects of covalent inhibitors such as increased HLA expression and T cell infiltration to enhance therapeutic impact.Polypeptides
[0154] In some aspects, the present disclosure provides a polypeptide comprising an antigenbinding domain that binds to a peptide-conjugate / MHC complex described herein. The peptide conjugate / MHC complex can comprise a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof, with a peptide. The peptide conjugate may then be expressed by an MHC to form a peptide conjugate / MHC complex. In some embodiments, the targeted covalent inhibitor may be divarasib, AMG-510 (e.g., sotorasib), MRTX849 (e.g.,adagrasib), opnurasib, garsorasib, l-[4-[6-chloro-8-fluoro-7-(2-fluoro-6- hydroxyphenyl)quinazolin-4-yl]piperazin- 1 -yl]prop-2-en- 1 -one, 1 -(3 -(4-((4-chloro-2-hydroxy-5- ( 1 -methylcyclopropyl)phenyl)glycyl)piperazin- 1 -yl)azetidin- 1 -yl)prop-2-en- 1 -one, 1 -(4-(7-(2-Amino-7-fluoro- 1 ,3 -benzothiazol-4-yl)-6-chloro-8-fluoro-quinazolin-4-yl)piperazin- 1 -yljprop- 2-en-l-one, 2-Amino-4-[(4aS)-8-chloro-10-fluoro-2,3,4,4a,5,6-hexahydro-12-oxo-3-(l-oxo-2- propen-l-yl)-lH,12H-pyrazino[2,l-d][l,5]benzoxazocin-9-yl]-7-fluorobenzo[b]thiophene-3- carbonitrile, 2-[(2S)-4-[7-(8-methylnaphthalen-l-yl)-2-[[(2S)-l-methylpyrrolidin-2- yl]methoxy]-6,8-dihydro-5H-pyrido[3,4-d]pyrimidin-4-yl]-l-prop-2-enoylpiperazin-2- yl]acetonitrile, 4-(4-(3,8-Diazabicyclo[3.2.1]octan-3-yl)-8-fluoro-2-(((2R,7aS)-2- fluorohexahydro-lH-pyrrolizin-7a-yl)methoxy)pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6- fluoronaphthalen-2-ol, l-[4-(dimethylamino)-4-methylpent-2-ynoyl]-N-[(2S)-l-[[(6S,8S,14S)- 22-ethyl-21-[2-[(lS)-l-methoxyethyl]pyridin-3-yl]-18,18-dimethyl-9,15-dioxo-5,16-dioxa- 2,10,22,28-tetrazapentacyclo[18.5.2.12,6.110,14.023,27]nonacosa-l(26),20,23(27),24-tetraen-8- yl]amino]-3-methyl-l-oxobutan-2-yl]-4-fluoro-N-methylpiperidine-4-carboxamide, or[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-lH-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy- hydroxyphosphoryl] 2-[(2-chloroacetyl)amino]ethyl hydrogen phosphate]. The targeted covalent inhibitor may be divarasib. In some embodiments, the MHC of the peptide conjugate / MHC complex may be encoded by an HLA allele selected from the group consisting of HLA-A*02, HLA-A*03, and HLA-A* 11.
[0155] As an example, the polypeptide can comprise an antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; and wherein the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant (KD) of at most 250 nM.
[0156] As another example, the polypeptide can comprise an antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; and wherein the polypeptide binds to each of (i) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele, (ii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele, and (iii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A* 11 allele with a dissociation constant (KD) of at most 250 nM.
[0157] As another example, the polypeptide can comprise an antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; and wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA allele selected from the group consisting of HL A- A* 02, HL A- A* 03, and HLA-A*11.
[0158] In some embodiments, a sequence of an alpha chain wild-type HLA-A*03:01 is: GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY WDQETRNVKAQSQTDRVDLGTLRGYYNQSEAGSHTIQIMYGCDVGSDGRFLRGYRQD AYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHEAEQLRAYLDGTCVEWLRRYL ENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTEL VETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAG LVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSLTACKV (SEQ ID NO: 80). As described herein, in the Cryo-EM structure, the residue positions of the buried area of the alpha wild-type HLA-A*03:01 are numbered according to the positions shown in SEQ ID NO: 80.
[0159] In some embodiments, the polypeptide may bind to the peptide conjugate / MHC complex with a dissociation constant (KD) of at most about 500 nM, at most about 400 nM, at most about 300 nM, at most about 250 nM, at most about 200 nM, at most about 150 nM, at most about 100 nM, at most about 90 nM, at most about 80 nM, at most about 70 nM, at most about 60 nM, at most about 50 nM, at most about 40 nM, at most about 30 nM, at most about 20 nM, at most about 10 nM, at most about 5 nM, at most about 1 nM, at most about 0.5 nM, at most about 0.1 nM, or less than about 0.1 nM. In some embodiments, the polypeptide may bind to the peptide conjugate / MHC complex with a dissociation constant (KD) from about 0.1 nM to about 200 nM. In some embodiments, the polypeptide may bind to the peptide conjugate / MHC complex with a dissociation constant (KD) from about 0.1 nM to about 1 nM, about 0.1 nM to about 5 nM, about 0.1 nM to about 10 nM, about 0.1 nM to about 20 nM, about 0.1 nM to about 30 nM, about 0.1 nM to about 40 nM, about 0.1 nM to about 50 nM, about 0.1 nM to about 75 nM, about 0.1 nM to about 100 nM, about 0.1 nM to about 150 nM, about 0.1 nM to about 200 nM, about 1 nM to about 5 nM, about 1 nM to about 10 nM, about 1 nM to about 20 nM, about 1 nM to about 30 nM, about 1 nM to about 40 nM, about 1 nM to about 50 nM, about 1 nM to about 75 nM, about 1 nM to about 100 nM, about 1 nM to about 150 nM, about 1 nM to about 200 nM, about 5 nM to about 10 nM, about 5 nM to about 20 nM, about 5 nM to about 30 nM, about 5 nM to about 40 nM,about 5 nM to about 50 nM, about 5 nM to about 75 nM, about 5 nM to about 100 nM, about 5 nM to about 150 nM, about 5 nM to about 200 nM, about 10 nM to about 20 nM, about 10 nM to about 30 nM, about 10 nM to about 40 nM, about 10 nM to about 50 nM, about 10 nM to about 75 nM, about 10 nM to about 100 nM, about 10 nM to about 150 nM, about 10 nM to about 200 nM, about 20 nM to about 30 nM, about 20 nM to about 40 nM, about 20 nM to about 50 nM, about 20 nM to about 75 nM, about 20 nM to about 100 nM, about 20 nM to about 150 nM, about 20 nM to about 200 nM, about 30 nM to about 40 nM, about 30 nM to about 50 nM, about 30 nM to about 75 nM, about 30 nM to about 100 nM, about 30 nM to about 150 nM, about 30 nM to about 200 nM, about 40 nM to about 50 nM, about 40 nM to about 75 nM, about 40 nM to about 100 nM, about 40 nM to about 150 nM, about 40 nM to about 200 nM, about 50 nM to about 75 nM, about 50 nM to about 100 nM, about 50 nM to about 150 nM, about 50 nM to about 200 nM, about 75 nM to about 100 nM, about 75 nM to about 150 nM, about 75 nM to about 200 nM, about 100 nM to about 150 nM, about 100 nM to about 200 nM, or about 150 nM to about 200 nM.
[0160] In some embodiments, a polypeptide described herein may bind to a peptide conjugate / MHC complex encoded by one HLA allele with a greater affinity than another peptide conjugate / MHC complex encoded by a different HLA allele. In some embodiments, a polypeptide may bind to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele with a KD of at least about 1.5 fold, at least about 2-fold, at least about 2.5-fold, at least about 3- fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, or at least about 10-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele. In some embodiments, a polypeptide may bind to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele with a KD of at most about 10-fold, at most about 9-fold, at most about 8-fold, at most about 7-fold, at most about 6-fold, at most about 5-fold, at most about 4- fold, at most about 3-fold, at most about 2.5-fold, at most about 2-fold, or at most about 1.5-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele.
[0161] In some embodiments, a polypeptide may bind to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*11 allele with a KD of at least about 1.5 fold, at least about 2- fold, at least about 2.5-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, or at least about 10-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHCencoded by an HLA-A*03 allele. In some embodiments, a polypeptide may bind to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*11 allele with a KD of at most about 10-fold, at most about 9-fold, at most about 8-fold, at most about 7-fold, at most about 6- fold, at most about 5-fold, at most about 4-fold, at most about 3-fold, at most about 2.5-fold, at most about 2-fold, or at most about 1.5-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele. In some embodiments, a polypeptide may bind to a peptide conjugate / MHC complex with an MHC encoded by an HLA- A*11 allele with a KD of at least about 1.5 fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, or at least about 10-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele. In some embodiments, a polypeptide may bind to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*11 allele with a KD of at most about 10-fold, at most about 9-fold, at most about 8-fold, at most about 7-fold, at most about 6-fold, at most about 5-fold, at most about 4-fold, at most about 3-fold, at most about 2.5-fold, at most about 2-fold, or at most about 1.5-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele.
[0162] In some embodiments, a polypeptide described herein may bind to a peptide conjugate / MHC complex comprising sotorasib with a reduced binding affinity compared to an affinity of the polypeptide binding to a peptide conjugate / MHC complex comprising divarasib. In some embodiments, a polypeptide described herein does not bind to a peptide conjugate / MHC complex comprising sotorasib or derivative thereof.
[0163] For example, a polypeptide can comprise an antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; wherein the polypeptide binds to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof, the same peptide, and the same MHC with a dissociation constant (KD) that is at least 1,000 nM. In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof with a KD that is at least about 800 nM, at least about 900 nM, at least about 1,000 nM, at least about 2,000 nM, at least about 3,000 nM, at least about 4,000 nM, at least about 5,000 nM, at least about 7,500 nM, at least about 10,000 nM, at least about 25,000 nM, at least about 50,000 nM, at least about 75,000 nM, at least about 100,000 nM,at least about 250,000 nM, at least about 500,000 nM, at least about 1,000,000 nM, at least about 2,500 pM, at least about 5,000 pM, or greater than about 5,000 pM.
[0164] In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof with a KD that is from about 1,000 nM to about 1,000,000 nM. In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof with a KD that is from about 1,000 nM to about 2,000 nM, about 1,000 nM to about 3,000 nM, about 1,000 nM to about 4,000 nM, about 1,000 nM to about 5,000 nM, about 1,000 nM to about 10,000 nM, about 1,000 nM to about 25,000 nM, about 1,000 nM to about 50,000 nM, about 1,000 nM to about 75,000 nM, about 1,000 nM to about 100,000 nM, about 1,000 nM to about 500,000 nM, about 1,000 nM to about 1,000,000 nM, about 2,000 nM to about 3,000 nM, about 2,000 nM to about 4,000 nM, about 2,000 nM to about 5,000 nM, about 2,000 nM to about 10,000 nM, about 2,000 nM to about 25,000 nM, about 2,000 nM to about 50,000 nM, about 2,000 nM to about 75,000 nM, about 2,000 nM to about 100,000 nM, about 2,000 nM to about 500,000 nM, about 2,000 nM to about 1,000,000 nM, about 3,000 nM to about 4,000 nM, about 3,000 nM to about 5,000 nM, about 3,000 nM to about 10,000 nM, about 3,000 nM to about 25,000 nM, about 3,000 nM to about 50,000 nM, about 3,000 nM to about 75,000 nM, about 3,000 nM to about 100,000 nM, about 3,000 nM to about 500,000 nM, about 3,000 nM to about 1,000,000 nM, about 4,000 nM to about 5,000 nM, about 4,000 nM to about 10,000 nM, about 4,000 nM to about 25,000 nM, about 4,000 nM to about 50,000 nM, about 4,000 nM to about 75,000 nM, about 4,000 nM to about 100,000 nM, about 4,000 nM to about 500,000 nM, about 4,000 nM to about 1,000,000 nM, about 5,000 nM to about 10,000 nM, about 5,000 nM to about 25,000 nM, about 5,000 nM to about 50,000 nM, about 5,000 nM to about 75,000 nM, about 5,000 nM to about 100,000 nM, about 5,000 nM to about 500,000 nM, about 5,000 nM to about 1,000,000 nM, about 10,000 nM to about 25,000 nM, about 10,000 nM to about 50,000 nM, about 10,000 nM to about 75,000 nM, about 10,000 nM to about 100,000 nM, about 10,000 nM to about 500,000 nM, about 10,000 nM to about 1,000,000 nM, about 25,000 nM to about 50,000 nM, about 25,000 nM to about 75,000 nM, about 25,000 nM to about 100,000 nM, about 25,000 nM to about 500,000 nM, about 25,000 nM to about 1,000,000 nM, about 50,000 nM to about 75,000 nM, about 50,000 nM to about 100,000 nM, about 50,000 nM to about 500,000 nM, about 50,000 nM to about 1,000,000 nM, about 75,000 nM to about 100,000 nM, about 75,000 nM to about 500,000 nM, about 75,000 nM to about 1,000,000 nM, about 100,000 nM to about 500,000 nM, about 100,000 nM to about 1,000,000 nM, or about 500,000 nM to about 1,000,000 nM.
[0165] In some embodiments, the polypeptide described herein may comprise a VH comprising a CDR-H1 having the amino acid sequence as set forth in SEQ ID NO: 3 or 11, or a variant thereof with 1, 2, 3, or more amino acid modifications. In some embodiments, the polypeptide described herein may comprise a VH comprising a CDR-H2 having the amino acid sequence as set forth in SEQ ID NO: 4 or 12, or a variant thereof with 1, 2, 3, 4, 5, or more amino acid modifications. In some embodiments, the polypeptide described herein may comprise a VH comprising a CDR-H3 having the amino acid sequence as set forth in SEQ ID NO: 5 or 13, or a variant thereof with 1, 2, 3, or more amino acid modifications. In some embodiments, the VH of the polypeptide comprises about one (e.g., 0, 1) amino acid substitution in an amino acid sequence of one or more CDR regions as set forth in SEQ ID NOs: 1 or 9.
[0166] In some embodiments, the polypeptide described herein may comprise a VL comprising a CDR-L1 having the amino acid sequence as set forth in SEQ ID NO: 6 or 14, or a variant thereof with 1, 2, 3, 4, 5, or more amino acid modifications. In some embodiments, the polypeptide described herein may comprise a VL comprising a CDR-L2 having the amino acid sequence as set forth in SEQ ID NO: 7 or 15, or a variant thereof with 1, 2, 3, 4, 5, or more amino acid modifications. In some embodiments, the polypeptide described herein may comprise a VL comprising a CDR-L3 having the amino acid sequence as set forth in SEQ ID NO: 8 or 16, or a variant thereof with 1, 2, 3, 4, 5, or more amino acid modifications. In some embodiments, the VL of the polypeptide comprises about one (e.g., 0, 1) amino acid substitution in an amino acid sequence of one or more CDR regions as set forth in SEQ ID NOs: 2 or 10.
[0167] In some embodiments, the polypeptide comprises an antigen-binding domain. In some embodiments, an antigen-binding domain (e.g., a first antigen-binding domain) may comprise a heavy chain variable region (VH), and the VH may comprise a heavy chain complementarity determining region 3 (CDR-H3) comprising the amino acid sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5). In some embodiments, the VH may further comprise a CDR-H2 comprising the amino acid sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4). In some embodiments, the VH may further comprise a CDR-H1 comprising the amino acid sequence of STNWWT (SEQ ID NO: 3). In some embodiments, the antigen-binding domain (e.g., a first antigen-binding domain) may comprise a light chain variable region (VL), and the VL may comprise a light chain complementarity determining region 3 (CDR-L3) comprising the amino acid sequence of QAWDSNTVV (SEQ ID NO: 8). In some embodiments, the VL may further comprise a CDR-L2 comprising the amino acid sequence of GKNERPS (SEQ ID NO: 7). In some embodiments, the VL may further comprise a CDR-L1 comprising the amino acidsequence of RGDSFRVFSAS (SEQ ID NO: 6). In some embodiments, the polypeptide can comprise an antigen-binding domain comprising: (i) a CDR-H3 sequence ofGRFGSSWNYIYFYYGLDV (SEQ ID NO: 5), (ii) a CDR-H2 sequence ofEIYHTGNTDYNPSLES (SEQ ID NO: 4), (iii) a CDR-H1 sequence of STNWWT (SEQ ID NO: 3), (iv) a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8), (v) a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7), and (vi) a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6). In some embodiments, a VH of a multivalent polypeptide described herein may comprise an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to the amino acid sequence as set forth:QLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHTGNTD YNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIYFYYGLDVW GQGTTVTVSS (SEQ ID NO: 1). In some embodiments, a VH of a multivalent polypeptide described herein may comprise an amino acid sequence as set forth in SEQ ID NO: 1. In some embodiments, a VL of a multivalent polypeptide described herein may comprise an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to the amino acid sequence as set forth:SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERPSGIPD RFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2). In some embodiments, a VL of a multivalent polypeptide described herein may comprise an amino acid sequence as set forth in SEQ ID NO: 2.
[0168] In some embodiments, an antigen-binding domain (e.g., a first antigen-binding domain) may comprise a heavy chain variable region (VH), and the VH may comprise a heavy chain complementarity determining region 3 (CDR-H3) comprising the amino acid sequence of GGNSYGMDV (SEQ ID NO: 13). In some embodiments, the VH may further comprise a CDR- H2 comprising the amino acid sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12). Insome embodiments, the VH may further comprise a CDR-H1 comprising the amino acid sequence of SYGMH (SEQ ID NO: 11). In some embodiments, the antigen-binding domain (e.g., a first antigen-binding domain) may comprise a light chain variable region (VL), and the VL may comprise a light chain complementarity determining region 3 (CDR-L3) comprising the amino acid sequence of QQSESALT (SEQ ID NO: 16). In some embodiments, the VL may further comprise a CDR-L2 comprising the amino acid sequence of GASSRAT (SEQ ID NO: 15). In some embodiments, the VL may further comprise a CDR-L1 comprising the amino acid sequence of RASQSLSSSFLA (SEQ ID NO: 14). In some embodiments, the polypeptide can comprise an antigen-binding domain comprising: (i) a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13), (ii) a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12), (iii) a CDR-H1 sequence of SYGMH (SEQ ID NO: 11), (iv) a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16), (v) a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15), and (vi) a CDR-L1 sequence of RASQSLSSSFLA (SEQ ID NO: 14). In some embodiments, a VH of a multivalent polypeptide described herein may comprise an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to the amino acid sequence as set forth: EVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISYDGSN KYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGMDVWGQGTM VTVSS (SEQ ID NO: 9). In some embodiments, a VH of a multivalent polypeptide described herein may comprise an amino acid sequence as set forth in SEQ ID NO: 1. In some embodiments, a VL of a multivalent polypeptide described herein may comprise an amino acid sequence with at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to the amino acid sequence as set forth: DIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSRATGIP DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10). In some embodiments, a VL of a multivalent polypeptide described herein may comprise an amino acid sequence as set forth in SEQ ID NO: 10.
[0169] In some embodiments, a first antigen-binding domain of a multivalent polypeptide as described herein may comprise a VH and / or VL as set forth in Table 1. In some embodiments, a first antigen-binding domain of a multivalent polypeptide as described herein can comprise a HC CDR1, HC CDR2, HC CDR3, LC CDR1, LC CDR2, LC CDR3, or any combination thereof, as set forth in Table 1.
[0170] In some aspects, the present disclosure provides a polypeptide comprising an antigenbinding domain that comprises a heavy chain variable region (VH), wherein the VH comprises: a CDR-H3 sequence according to Kabat according to Table 1, or a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5) or GGNSYGMDV (SEQ ID NO: 13).
[0171] In some aspects, the present disclosure provides a polypeptide comprising an antigenbinding domain that comprises a light chain variable region (VL), wherein the VL comprises: a CDR-L3 sequence according to Kabat according to Table 1, or a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8) or QQSESALT (SEQ ID NO: 16).Table 1. Exemplary amino acid sequences of antibodies that bind to divarasib-KRASG12Cpeptides presented by HLA molecules.
[0172] In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof, the same peptide, and the same MHC with a KD that is at least about 1.5-fold, at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 25-fold, at least about 50-fold, at least about 100-fold, at least about 250-fold, at least about 500-fold, at least about 750-fold, at least about 1,000-fold, at least about 5,000-fold, at least about10,000-fold, at least about 25,000-fold, at least about 50,000-fold, or at least about 100,000-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof. In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof, the same peptide, and the same MHC with a KD that is from about 2-fold to about 50,000-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof. In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof, the same peptide, and the same MHC with a KD that is from about 2-fold to about 3-fold, about 2-fold to about 4-fold, about 2-fold to about 5-fold, about 2- fold to about 10-fold, about 2-fold to about 50-fold, about 2-fold to about 100-fold, about 2-fold to about 500-fold, about 2-fold to about 1,000-fold, about 2-fold to about 5,000-fold, about 2-fold to about 10,000-fold, about 2-fold to about 50,000-fold, about 3-fold to about 4-fold, about 3-fold to about 5-fold, about 3-fold to about 10-fold, about 3-fold to about 50-fold, about 3-fold to about 100-fold, about 3-fold to about 500-fold, about 3-fold to about 1,000-fold, about 3-fold to about 5,000-fold, about 3-fold to about 10,000-fold, about 3-fold to about 50,000-fold, about 4-fold to about 5-fold, about 4-fold to about 10-fold, about 4-fold to about 50-fold, about 4-fold to about 100-fold, about 4-fold to about 500-fold, about 4-fold to about 1,000-fold, about 4-fold to about 5,000-fold, about 4-fold to about 10,000-fold, about 4-fold to about 50,000-fold, about 5-fold to about 10-fold, about 5-fold to about 50-fold, about 5-fold to about 100-fold, about 5-fold to about 500-fold, about 5-fold to about 1,000-fold, about 5-fold to about 5,000-fold, about 5-fold to about 10,000-fold, about 5-fold to about 50,000-fold, about 10-fold to about 50-fold, about 10-fold to about 100-fold, about 10-fold to about 500-fold, about 10-fold to about 1,000-fold, about 10-fold to about 5,000-fold, about 10-fold to about 10,000-fold, about 10-fold to about 50,000-fold, about 50-fold to about 100-fold, about 50-fold to about 500-fold, about 50-fold to about 1,000-fold, about 50-fold to about 5,000-fold, about 50-fold to about 10,000-fold, about 50-fold to about 50,000-fold, about 100-fold to about 500-fold, about 100-fold to about 1,000-fold, about 100-fold to about 5,000-fold, about 100-fold to about 10,000-fold, about 100-fold to about 50,000-fold, about 500-fold to about 1,000-fold, about 500-fold to about 5,000-fold, about 500-fold to about 10,000-fold, about 500-fold to about 50,000-fold, about 1,000-fold to about 5,000-fold, about 1,000-fold to about 10,000-fold, about 1,000-fold to about 50,000-fold, about 5,000-fold to about 10,000-fold, about 5,000-fold to about 50,000-fold, or about 10,000-fold to about 50,000-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof.
[0173] In some embodiments, the polypeptide can bind to a free targeted covalent inhibitor (e.g., free divarasib) with a KD that is at least about 1.5-fold, at least about 2-fold, at least about 5-fold, at least about 10-fold, at least about 25-fold, at least about 50-fold, at least about 100-fold, at least about 250-fold, at least about 500-fold, at least about 750-fold, at least about 1,000-fold, at least about 5,000-fold, at least about 10,000-fold, at least about 25,000-fold, at least about 50,000-fold, or at least about 100,000-fold more than the KD of the polypeptide bound to the peptide conjugate / MHC complex. In some embodiments, the polypeptide can bind to a free targeted covalent inhibitor (e.g., free divarasib) with a KD that is from about 2-fold to about 50,000-fold more than the KD of the polypeptide bound to the peptide conjugate / MHC complex. In some embodiments, the polypeptide can bind to a free targeted covalent inhibitor (e.g., free divarasib) with a KD that is from about 2-fold to about 3-fold, about 2-fold to about 4-fold, about 2-fold to about 5-fold, about 2-fold to about 10-fold, about 2-fold to about 50-fold, about 2-fold to about 100-fold, about 2-fold to about 500-fold, about 2-fold to about 1,000-fold, about 2-fold to about 5,000-fold, about 2-fold to about 10,000-fold, about 2-fold to about 50,000-fold, about 3-fold to about 4-fold, about 3-fold to about 5-fold, about 3-fold to about 10-fold, about 3-fold to about 50- fold, about 3-fold to about 100-fold, about 3-fold to about 500-fold, about 3-fold to about 1,000- fold, about 3-fold to about 5,000-fold, about 3-fold to about 10,000-fold, about 3-fold to about 50,000-fold, about 4-fold to about 5-fold, about 4-fold to about 10-fold, about 4-fold to about 50- fold, about 4-fold to about 100-fold, about 4-fold to about 500-fold, about 4-fold to about 1,000- fold, about 4-fold to about 5,000-fold, about 4-fold to about 10,000-fold, about 4-fold to about 50,000-fold, about 5-fold to about 10-fold, about 5-fold to about 50-fold, about 5-fold to about 100-fold, about 5-fold to about 500-fold, about 5-fold to about 1,000-fold, about 5-fold to about 5,000-fold, about 5-fold to about 10,000-fold, about 5-fold to about 50,000-fold, about 10-fold to about 50-fold, about 10-fold to about 100-fold, about 10-fold to about 500-fold, about 10-fold to about 1,000-fold, about 10-fold to about 5,000-fold, about 10-fold to about 10,000-fold, about 10- fold to about 50,000-fold, about 50-fold to about 100-fold, about 50-fold to about 500-fold, about 50-fold to about 1,000-fold, about 50-fold to about 5,000-fold, about 50-fold to about 10,000-fold, about 50-fold to about 50,000-fold, about 100-fold to about 500-fold, about 100-fold to about 1,000-fold, about 100-fold to about 5,000-fold, about 100-fold to about 10,000-fold, about 100- fold to about 50,000-fold, about 500-fold to about 1,000-fold, about 500-fold to about 5,000-fold, about 500-fold to about 10,000-fold, about 500-fold to about 50,000-fold, about 1,000-fold to about 5,000-fold, about 1,000-fold to about 10,000-fold, about 1,000-fold to about 50,000-fold, about 5,000-fold to about 10,000-fold, about 5,000-fold to about 50,000-fold, or about 10,000-fold to about 50,000-fold more than the KD of the polypeptide bound to the peptide conjugate / MHC complex.
[0174] In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof and an MHC encoded by an HLA-A*02 allele with a KD of at most about 75 nM, at most about 50 nM, at most about 25 nM, at most about 10 nM, at most about 9 nM, at most about 8 nM, at most about 7 nM, at most about 6 nM, at most about 5 nM, at most about 4 nM, at most about 3 nM, at most about 2 nM, at most about 1 nM, or less than about 1 nM. In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof and an MHC encoded by an HLA-A*02 allele with a KD from about 1 nM to about 50 nM. In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof and an MHC encoded by an HLA-A*02 allele with a KD from about 1 nM to about 2 nM, about 1 nM to about3 nM, about 1 nM to about 4 nM, about 1 nM to about 5 nM, about 1 nM to about 6 nM, about 1 nM to about 7 nM, about 1 nM to about 8 nM, about 1 nM to about 9 nM, about 1 nM to about 10 nM, about 1 nM to about 25 nM, about 1 nM to about 50 nM, about 2 nM to about 3 nM, about 2 nM to about 4 nM, about 2 nM to about 5 nM, about 2 nM to about 6 nM, about 2 nM to about 7 nM, about 2 nM to about 8 nM, about 2 nM to about 9 nM, about 2 nM to about 10 nM, about 2 nM to about 25 nM, about 2 nM to about 50 nM, about 3 nM to about 4 nM, about 3 nM to about 5 nM, about 3 nM to about 6 nM, about 3 nM to about 7 nM, about 3 nM to about 8 nM, about 3 nM to about 9 nM, about 3 nM to about 10 nM, about 3 nM to about 25 nM, about 3 nM to about 50 nM, about 4 nM to about 5 nM, about 4 nM to about 6 nM, about 4 nM to about 7 nM, about4 nM to about 8 nM, about 4 nM to about 9 nM, about 4 nM to about 10 nM, about 4 nM to about 25 nM, about 4 nM to about 50 nM, about 5 nM to about 6 nM, about 5 nM to about 7 nM, about5 nM to about 8 nM, about 5 nM to about 9 nM, about 5 nM to about 10 nM, about 5 nM to about 25 nM, about 5 nM to about 50 nM, about 6 nM to about 7 nM, about 6 nM to about 8 nM, about6 nM to about 9 nM, about 6 nM to about 10 nM, about 6 nM to about 25 nM, about 6 nM to about 50 nM, about 7 nM to about 8 nM, about 7 nM to about 9 nM, about 7 nM to about 10 nM, about7 nM to about 25 nM, about 7 nM to about 50 nM, about 8 nM to about 9 nM, about 8 nM to about 10 nM, about 8 nM to about 25 nM, about 8 nM to about 50 nM, about 9 nM to about 10 nM, about 9 nM to about 25 nM, about 9 nM to about 50 nM, about 10 nM to about 25 nM, about 10 nM to about 50 nM, or about 25 nM to about 50 nM.
[0175] In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof and an MHC encoded by an HLA-A*03 allele witha KD of at most about 75 nM, at most about 50 nM, at most about 25 nM, at most about 10 nM, at most about 9 nM, at most about 8 nM, at most about 7 nM, at most about 6 nM, at most about 5 nM, at most about 4 nM, at most about 3 nM, at most about 2 nM, at most about 1 nM, or less than about 1 nM. In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof and an MHC encoded by an HLA-A*03 allele with a KD from about 1 nM to about 50 nM. In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof and an MHC encoded by an HLA-A*03 allele with a KD from about 1 nM to about 2 nM, about 1 nM to about3 nM, about 1 nM to about 4 nM, about 1 nM to about 5 nM, about 1 nM to about 6 nM, about 1 nM to about 7 nM, about 1 nM to about 8 nM, about 1 nM to about 9 nM, about 1 nM to about 10 nM, about 1 nM to about 25 nM, about 1 nM to about 50 nM, about 2 nM to about 3 nM, about 2 nM to about 4 nM, about 2 nM to about 5 nM, about 2 nM to about 6 nM, about 2 nM to about 7 nM, about 2 nM to about 8 nM, about 2 nM to about 9 nM, about 2 nM to about 10 nM, about 2 nM to about 25 nM, about 2 nM to about 50 nM, about 3 nM to about 4 nM, about 3 nM to about 5 nM, about 3 nM to about 6 nM, about 3 nM to about 7 nM, about 3 nM to about 8 nM, about 3 nM to about 9 nM, about 3 nM to about 10 nM, about 3 nM to about 25 nM, about 3 nM to about 50 nM, about 4 nM to about 5 nM, about 4 nM to about 6 nM, about 4 nM to about 7 nM, about4 nM to about 8 nM, about 4 nM to about 9 nM, about 4 nM to about 10 nM, about 4 nM to about 25 nM, about 4 nM to about 50 nM, about 5 nM to about 6 nM, about 5 nM to about 7 nM, about5 nM to about 8 nM, about 5 nM to about 9 nM, about 5 nM to about 10 nM, about 5 nM to about 25 nM, about 5 nM to about 50 nM, about 6 nM to about 7 nM, about 6 nM to about 8 nM, about6 nM to about 9 nM, about 6 nM to about 10 nM, about 6 nM to about 25 nM, about 6 nM to about 50 nM, about 7 nM to about 8 nM, about 7 nM to about 9 nM, about 7 nM to about 10 nM, about7 nM to about 25 nM, about 7 nM to about 50 nM, about 8 nM to about 9 nM, about 8 nM to about 10 nM, about 8 nM to about 25 nM, about 8 nM to about 50 nM, about 9 nM to about 10 nM, about 9 nM to about 25 nM, about 9 nM to about 50 nM, about 10 nM to about 25 nM, about 10 nM to about 50 nM, or about 25 nM to about 50 nM.
[0176] In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof and an MHC encoded by an HLA-A* 11 allele with a KD of at most about 75 nM, at most about 50 nM, at most about 25 nM, at most about 10 nM, at most about 9 nM, at most about 8 nM, at most about 7 nM, at most about 6 nM, at most about 5 nM, at most about 4 nM, at most about 3 nM, at most about 2 nM, at most about 1 nM, or less than about 1 nM. In some embodiments, the polypeptide can bind to a peptide conjugate / MHCcomplex comprising divarasib or the fragment thereof and an MHC encoded by an HLA-A*11 allele with a KD from about 1 nM to about 50 nM. In some embodiments, the polypeptide can bind to a peptide conjugate / MHC complex comprising divarasib or the fragment thereof and an MHC encoded by an HLA-A* 11 allele with a KD from about 1 nM to about 2 nM, about 1 nM to about3 nM, about 1 nM to about 4 nM, about 1 nM to about 5 nM, about 1 nM to about 6 nM, about 1 nM to about 7 nM, about 1 nM to about 8 nM, about 1 nM to about 9 nM, about 1 nM to about 10 nM, about 1 nM to about 25 nM, about 1 nM to about 50 nM, about 2 nM to about 3 nM, about 2 nM to about 4 nM, about 2 nM to about 5 nM, about 2 nM to about 6 nM, about 2 nM to about 7 nM, about 2 nM to about 8 nM, about 2 nM to about 9 nM, about 2 nM to about 10 nM, about 2 nM to about 25 nM, about 2 nM to about 50 nM, about 3 nM to about 4 nM, about 3 nM to about 5 nM, about 3 nM to about 6 nM, about 3 nM to about 7 nM, about 3 nM to about 8 nM, about 3 nM to about 9 nM, about 3 nM to about 10 nM, about 3 nM to about 25 nM, about 3 nM to about 50 nM, about 4 nM to about 5 nM, about 4 nM to about 6 nM, about 4 nM to about 7 nM, about4 nM to about 8 nM, about 4 nM to about 9 nM, about 4 nM to about 10 nM, about 4 nM to about 25 nM, about 4 nM to about 50 nM, about 5 nM to about 6 nM, about 5 nM to about 7 nM, about5 nM to about 8 nM, about 5 nM to about 9 nM, about 5 nM to about 10 nM, about 5 nM to about 25 nM, about 5 nM to about 50 nM, about 6 nM to about 7 nM, about 6 nM to about 8 nM, about6 nM to about 9 nM, about 6 nM to about 10 nM, about 6 nM to about 25 nM, about 6 nM to about 50 nM, about 7 nM to about 8 nM, about 7 nM to about 9 nM, about 7 nM to about 10 nM, about7 nM to about 25 nM, about 7 nM to about 50 nM, about 8 nM to about 9 nM, about 8 nM to about 10 nM, about 8 nM to about 25 nM, about 8 nM to about 50 nM, about 9 nM to about 10 nM, about 9 nM to about 25 nM, about 9 nM to about 50 nM, about 10 nM to about 25 nM, about 10 nM to about 50 nM, or about 25 nM to about 50 nM.
[0177] In some embodiments, an interface area of the polypeptide described herein with the peptide conjugate / MHC complex can be at least about 100A2, at least about 200A2, at least about 300A2, at least about 400A2, at least about 500A2, at least about 600A2, at least about 700A2, at least about 800 A2, at least about 900 A2, at least about 1,000 A2, at least about 1,200 A2, at least about l,500A2, at least about 2,000A2, at least about 2,500A2, at least about 3,000A2, at least about 4,000A2, at least about 5,000A2, or greater than about 5,000A2. In some embodiments, an interface area of the polypeptide described herein with the peptide conjugate / MHC complex can be at most about 5,000A2, at most about 4,000A2, at most about 3,000A2, at most about 2,500A2, at most about 2,000A2, at most about l,500A2, at most about l,200A2, at most about l,000A2, at most about 900A2, at most about 800A2, at most about 700A2, at most about 600A2, at most about500A2, at most about 400A2, at most about 300A2, at most about 200A2, at most about 100A2, or less than about at most about 100A2.
[0178] In some embodiments, an interface area of the polypeptide described herein with the peptide conjugate / MHC complex can be from about 100 A2to about 2,000 A2. In some embodiments, an interface area of the polypeptide described herein with the peptide conjugate / MHC complex can be from about 100 A2to about 200 A2, about 100 A2to about 300 A2, about 100 A2to about 400 A2, about 100 A2to about 500 A2, about 100 A2to about 750 A2, about 100 A2to about 1,000 A2, about 100 A2to about 1,250 A2, about 100 A2to about 1,500 A2, about 100 A2to about 2,000 A2, about 200 A2to about 300 A2, about 200 A2to about 400 A2, about 200 A2to about 500 A2, about 200 A2to about 750 A2, about 200 A2to about 1,000 A2, about 200 A2to about 1,250 A2, about 200 A2to about 1,500 A2, about 200 A2to about 2,000 A2, about 300 A2to about 400 A2, about 300 A2to about 500 A2, about 300 A2to about 750 A2, about 300 A2to about 1,000 A2, about 300 A2to about 1,250 A2, about 300 A2to about 1,500 A2, about 300 A2to about 2,000 A2, about 400 A2to about 500 A2, about 400 A2to about 750 A2, about 400 A2to about 1,000 A2, about 400 A2to about 1,250 A2, about 400 A2to about 1,500 A2, about 400 A2to about 2,000 A2, about 500 A2to about 750 A2, about 500 A2to about 1,000 A2, about 500 A2to about 1,250 A2, about 500 A2to about 1,500 A2, about 500 A2to about 2,000 A2, about 750 A2to about 1,000 A2, about 750 A2to about 1,250 A2, about 750 A2to about 1,500 A2, about 750 A2to about 2,000 A2, about 1,000 A2to about 1,250 A2, about 1,000 A2to about 1,500 A2, about 1,000 A2to about 2,000 A2, about 1,250 A2to about 1,500 A2, about 1,250 A2to about 2,000 A2, or about 1,500 A2to about 2,000 A2.
[0179] The polypeptide described herein may bind to an epitope of the peptide conjugate / MHC complex. In some embodiments, the epitope can comprise one or more amino acid residues of the MHC molecule (encoded by an HLA allele), the hapten (e.g., the targeted covalent inhibitor), the peptide, or any combination thereof. The binding to the epitope can provide greater specificity for the polypeptide to the peptide conjugate / MHC complex. In some embodiments, the epitope comprises one or more amino acid residues of the MHC and the targeted covalent inhibitor. In some embodiments, the epitope comprises one or more amino acid residues of the MHC and the peptide. In some embodiments, the epitope comprises one or more amino acid residues of the targeted covalent inhibitor and the peptide. In some embodiments, the epitope comprises one or more amino acid residues of the MHC, the targeted covalent inhibitor, and the peptide.
[0180] In some examples, the peptide conjugate / MHC complex comprises an HLA molecule encoded by an HLA allele belonging to the HLA- A3 supertype. In some examples, the HLA alleleof the HLA-A3 supertype can be HLA-A*03:01, HLA-A* 11 :01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, HLA-A*66:01, HLA-A*03:02, HLA-A*03:04, HLA-A*03:05, HLA-A*03:06, HLA-A*03:07, HLA-A*03:08, HLA-A*03: 10, HLA-A*03: 12, HLA-A*03: 13, HLA-A*03: 14, HLA-A*03: 16, HLA-A*03: 17, HLA-A* 11 :02, HLA-A* 11 :03, HLA-A* 11 :04, HLA-A* 11 :05, HLA-A* 11 :07, HLA-A* 11 :08, HLA-A* 11 :09, HLA-A*l l : 10, HLA-A*11 : 12, HLA-A*11 : 13, HLA-A*11 : 14, HLA-A*11:15, HLA-A*11 : 16, HLA-A*l l :20, HLA-A* 11 :21, HLA-A* 11 :23, HLA-A*31 :03, HLA-A*31 :04, HLA-A*31:05, HLA-A*31 :06, HLA-A*31 :09, HLA-A*31 : 11, HLA-A*33:04, HLA-A*33:05, HLA-A*33:06, HLA-A*33:07, HLA-A*34:02, HLA-A*34:03, HLA-A*34:04, HLA-A*34:06, HLA-A*66:02, HLA-A*66:03, HLA-A*66:04, HLA-A*68:03, HLA-A*68:04, HLA-A*68:08, HLA-A*68:09, HLA-A*68: 10, HLA-A*68: 12, HLA-A*68: 13, HLA-A*68: 14, HLA-A*68: 16, HLA-A*68: 19, HLA-A*68:21, HLA-A*68:22, HLA-A*68:24, HLA-A*68:25, HLA-A*68:26, HLA-A*74:02, HLA-A*74:03, HLA-A*74:04, HLA-A*74:05, HLA-A*74:07, HLA-A*74:08, HLA-A*74:09, HLA-A*74: 11, or any combination thereof. In some examples, the HLA allele of the HLA-A3 supertype can be HLA-A*03:01, HLA-A*l l :01, HLA-A*68:01, HLA-A*31 :01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, HLA-A*66:01, or any combination thereof.
[0181] In some examples, the peptide conjugate / MHC complex comprises an HLA molecule encoded by an HLA allele belonging to the HLA-A2 supertype. In some examples, the HLA allele of the HLA-A2 supertype can be HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, HLA-A*69:01, HLA-A*02:09, HLA-A*02: l l, HLA-A*02: 12, HLA-A*02: 13, HLA-A*02: 15, HLA-A*02: 16, HLA-A*02: 18, HLA-A*02: 19, HLA-A*02:20, HLA-A*02:21, HLA-A*02:22, HLA-A*02:24, HLA-A*02:25, HLA-A*02:26, HLA-A*02:27, HLA-A*02:28, HLA-A*02:30, HLA-A*02:31, HLA-A*02:36, HLA-A*02:37, HLA-A*02:38, HLA-A*02:39, HLA-A*02:40, HLA-A*02:43, HLA-A*02:44, HLA-A*02:45, HLA-A*02:46, HLA-A*02:47, HLA-A*02:48, HLA-A*02:49, HLA-A*02:51, HLA-A*02:54, HLA-A*02:56, HLA-A*02:57, HLA-A*02:58, HLA-A*02:59, HLA-A*02:61, HLA-A*02:62, HLA-A*02:63, HLA-A*02:66, HLA-A*02:67, HLA-A*02:68, HLA-A*02:69, HLA-A*02:70, HLA-A*02:71, HLA-A*02:72, HLA-A*02:74, HLA-A*02:75, HLA-A*02:77, HLA-A*02:78, HLA-A*02:79, HLA-A*02:82, HLA-A*02:83, HLA-A*02:85, HLA-A*02:86, HLA-A*68:27, HLA-A*68:28, or any combination thereof. In some examples, the HLA allele of the HLA-A2 supertype can be HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, HLA-A*69:01, or any combination thereof.
[0182] In some embodiments, the one or more amino acid residues of the MHC may be conserved across MHC encoded by different HLA alleles. For example, the polypeptide can bind an epitope of the MHC, and the epitope may comprise one or more amino acid residues conserved among HLA-A*03, HLA-A*02, HLA-A*11, or any combination thereof. The one or more amino acid residues can comprise any number of residues as set forth in the amino acid sequence of SEQ ID NO: 80. The polypeptide may bind an epitope of the MHC, and the epitope may comprise one or more amino acid residues at positions 42-73 and 167 of HLA-A*03, HLA-A*02, or HLA-A*11. For example, the conserved residues may comprise residues at positions 42-167 of the HLA as set forth in SEQ ID NO: 80. As another example, the conserved residues may comprise residues at positions 42-73 of the HLA as set forth in SEQ ID NO: 80. The polypeptide may bind an epitope of the MHC, and the epitope may comprise one or more amino acid residues selected from the group consisting of S42, Q43, R44, P57, E58, D61, Q62, T64, R65, K68, Q72, W167, ofthe HLA- A*03, HLA-A*02, or HLA-A*11. The polypeptide may bind an epitope of the MHC, and the epitope may comprise one or more amino acid residues selected from the group consisting of S42, Q43, R44, P57, E58, D61, Q62, T64, R65, K68, Q72, W167, or any combination thereof of SEQ ID NO: 80.
[0183] In some embodiments, the VH domain and / or the VL domain of the antigen-binding domain of the polypeptide may bind to amino acid residues of the MHC. For example, the VL domain of the antigen-binding domain can bind to an epitope of the MHC, and the epitope may comprise one or more residues comprising residues S42, Q43, D61, T64, R65, K68, and Q72 of HLA-A*03, HLA-A*02, or HLA-A*11. The VL domain of the antigen-binding domain can bind to an epitope of the MHC, and the epitope may comprise one or more residues comprising residues S42, Q43, D61, T64, R65, K68, and Q72 of SEQ ID NO: 80. In some embodiments, the VH domain of the antigen-binding domain can bind to an epitope of the MHC, and the epitope may comprise one or more residues comprising residues R44, P57, E58, D61, Q62, R65, and W167 of HL A- A* 03, HL A- A* 02, or HLA-A*11. The VH domain of the antigen-binding domain can bind to an epitope of the MHC, and the epitope may comprise one or more residues comprising residues R44, P57, E58, D61, Q62, R65, and W167 of SEQ ID NO: 80.
[0184] The VH domain and / or the VL domain of the antigen-binding domain of the polypeptide may bind to one or more residues of the peptide of the peptide conjugate. The peptide conjugate can comprise a peptide comprising the p? peptide of VVVGACGVGK, the ps peptide of KLVVVGACGV, or the ps peptide of VVGACGVGK. In some embodiments, the polypeptide can contact one or more residues from the regions comprising residues G10, Al l, C12, or anycombination thereof of the peptide conjugate (e.g., the peptide of the peptide conjugate). Binding of the polypeptide to the peptide conjugate / MHC complex may comprise one or more amino acid residues of the VH and / or VL domain of the polypeptide contacting the MHC, the targeted covalent inhibitor, the polypeptide, and / or the peptide conjugate. In some embodiments, one or more residues of the VH domain of the antigen-binding domain can interact with an epitope of the MHC, and the one or more residues of the VH domain may comprise amino acid residues S31, Y32, S52, Y53, G100, N101, S102, and Y103 as set forth in SEQ ID NO: 9. In some embodiments, one or more residues of the VH domain of the antigen-binding domain can interact with the targeted covalent inhibitor, and the one or more residues of the VH domain may comprise amino acid residues G33, H35, W47, V50, S52, N57, Y59, Y60, A61, and D62 as set forth in SEQ ID NO: 9. In some embodiments, one or more residues of the VH domain of the antigen-binding domain can interact with the peptide, and the one or more residues of the VH domain may comprise amino acid residues N57 or Y59 as set forth in SEQ ID NO: 9. In some embodiments, one or more residues of a VL domain of the antigen-binding domain can bind to an epitope of the MHC, and the one or more residues of the VL domain may comprise amino acid residues Q27, S28, L29, S30, S31, S32, F33, S92, E93, S94, A95, and L96 as set forth in SEQ ID NO: 10. In some embodiments, one or more residues of the VL domain of the antigen-binding domain may interact with the targeted covalent inhibitor, and the one or more residues of the VL domain can comprise amino acid residues DI, 12, S92, E93, S94, A95, L96, and T97 as set forth in SEQ ID NO: 10.Multivalent Polypeptides
[0185] In some aspects, provided herein are compositions and methods comprising multivalent polypeptides. The multivalent polypeptide can comprise a first antigen-binding domain. In some embodiments, the multivalent polypeptide can comprise at least a first antigen-binding domain. The multivalent polypeptide may comprise a second antigen-binding domain.
[0186] In some embodiments, the polypeptides (e.g., binding partners) preferentially bind to (e.g., specifically bind to) the protein or peptide or a complex comprising the protein or peptide when covalently bound to the peptide conjugate, relative to the same protein or peptide that is not bound to the drug. Accordingly, binding partners described herein either do not detectably bind, or bind with a lower affinity, to the same protein or fragment thereof in the absence of the covalently attached molecule. The term “specifically binds” can refer to a molecule (e.g., an antibody or an antigen-binding portion thereof) that binds to an epitope or target or peptide-MHC complex withgreater affinity, greater avidity, and / or greater duration to that epitope or target or peptide-MHC complex in a sample than it binds to another epitope or non-target compound or non-target or peptide-MHC complex (e.g., a structurally different antigen, a peptide-MHC complex with a different MHC and different peptide, a peptide-MHC complex with a different MHC and the same peptide or a peptide-MHC complex with the same MHC and different peptide). For example, a molecule (e.g., an antibody or an antigen-binding portion thereof) that specifically binds to an epitope or target or peptide-MHC complex can be an molecule (e.g., an antibody or an antigenbinding portion thereof) that binds this epitope or target or peptide-MHC complex with greater affinity, avidity, more readily, and / or with greater duration than it binds to other epitopes or targets or peptide-MHC complexes. In some embodiments, a molecule (e.g., an antibody or an antigenbinding portion thereof) that specifically binds to an epitope or target or peptide-MHC complex is a molecule (e.g., an antibody or an antigen-binding portion thereof) that binds to the epitope or target or peptide-MHC complex with at least 5-fold greater affinity than other epitopes or non- target compounds or non-target peptide-MHC complex, e.g., at least 5-fold, 10-fold, 100-fold, 1,000-fold, 10,000-fold, or greater affinity. A molecule (e.g., an antibody or an antigen-binding portion thereof) that specifically binds to a particular epitope or target or peptide-MHC complex can be exhibited, for example, by a molecule having an equilibrium dissociation constant KD for the epitope or target or peptide-MHC complex to which it binds of, e.g., 104M or smaller, e.g., I O5M, 106M, 107M, 108M, 109M, 1010M, 10 " M, or 1012M, such as determined by, e.g., immunoassays, surface plasma resonance (e.g., Biacore™ assay), biolayer interferometry, or other assays known in the art. It will be recognized by one of skill that an antibody that specifically binds to a target from one species may also specifically bind to orthologs of that target. In some embodiments, the extent of binding of a molecule (e.g., an antibody or an antigen-binding portion thereof) to an unrelated epitope or unrelated target or unrelated peptide-MHC complex is less than about 0.0001%, 0.001%, 0.01%, 0.1%, 1%, 10% or 20% of the binding of the antibody to the epitope or target or peptide-MHC complex as measured, e.g., by an immunoassays, surface plasma resonance (e.g., Biacore™ assay), biolayer interferometry, or other assay known in the art. For example, a multivalent polypeptide may specifically bind to an epitope sequence in complex with an MHC with a binding affinity of at least about 2-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1,000-fold, 5,000-fold, or 10,000-fold greater than a binding affinity of the multivalent polypeptide binding to a different epitope sequence in complex with the same MHC. As another example, a multivalent polypeptide may bind to a peptide-conjugate in complex with an MHC encoded by a specific HLA allele, with a binding affinity of at least about 2-fold, 5-fold,10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1,000-fold, 5,000-fold, or 10,000-fold greater than a binding affinity of the multivalent polypeptide binding to the peptide-conjugate in complex with an MHC encoded by a different HLA allele. As another example, a multivalent polypeptide may bind to a peptide-conjugate in complex with an MHC with a binding affinity of at least about 2-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1,000-fold, 5,000-fold, or 10,000-fold greater than a binding affinity of the multivalent polypeptide binding to the peptide-conjugate alone. As another example, a multivalent polypeptide may bind to a peptide-conjugate in complex with an MHC with a binding affinity of at least about 2-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1,000-fold, 5,000-fold, or 10,000-fold greater than a binding affinity of the multivalent polypeptide binding to the peptide alone (e.g., without the targeted covalent inhibitor). As another example, a multivalent polypeptide may bind to a peptide-conjugate in complex with an MHC with a binding affinity of at least about 2-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 500-fold, 1,000-fold, 5,000-fold, or 10,000- fold greater than a binding affinity of the multivalent polypeptide binding to the free targeted covalent inhibitor (e.g., the targeted covalent inhibitor not covalently linked to a peptide).
[0187] In some embodiments, the binding partners bind to the protein or peptide comprising the covalently attached drug with an affinity that is 10-10,000 fold, including all numbers and ranges of numbers from 10-10,000, greater than the affinity for the protein or peptide that does not comprise the covalently bound molecule. In this regard, and without intending to be bound by any particular theory, it is considered that the presence of the covalently bound molecule contributes to the epitope to which the binding partners bind with specificity. Likewise, binding partners of this disclosure preferentially bind to the peptide conjugate relative to binding to the free drug. In some embodiments, the binding partners bind to the peptide comprising the covalently attached drug (e.g., the peptide-conjugate / MHC complex) with an affinity that is 10-10,000 fold, including all numbers and ranges of numbers from 10-10,000, greater than the affinity for the free drug. In some embodiments, the interaction between the binding partner and the peptide-conjugate / MHC complex is not inhibited by the free drug. For example, the interaction between the binding partner and the peptide-conjugate / MHC complex is not inhibited by a lOOx, l,000x, 10,000x, 100,000x or more excess of the free drug.
[0188] In some embodiments, the molecule that is covalently bound to form the peptide conjugate is a drug and may be any targeted covalent inhibitor (TCI), but the covalent drug need not necessarily inhibit the target peptide. In some embodiments, the molecule reacts with a specific residue within the target protein. In some embodiments, the molecule reacts at least in part with asegment of the protein or peptide that comprises a nucleophilic, or an electrophilic, residue. In some embodiments, the segment of the protein or peptide to which the molecule reacts comprises any of Cys, Lys, Tyr, His, Ser, Thr, or Arg, the latter being described in Ziyang Zhang, Johannes Morstein, Andrew K. Ecker, Keelan Z. Guiley, and Kevan M. Shokat Journal of the American Chemical Society Article ASAP, DOI: 10.1021 / jacs.2c05377, from which the disclosure is incorporated herein by reference. In some embodiments, the protein or peptide comprises a selenocysteine. In some embodiments, the targeted covalent inhibitor reacts with selenocysteine. In some embodiments, the molecule reacts at least in part with a segment of the protein or peptide that comprises a wild type Cys, or a mutation of a residue to a Cys, and thus may be covalently attached by a so-called sulfur tether. In some embodiments, the drug is any drug described in Ghosh AK, Samanta I, Mondal A, Liu WR. Covalent Inhibition in Drug Discovery. ChemMedChem. 2019;14(9):889-906. doi: 10.1002 / cmdc.201900107, or in De Cesco, et al., European Journal of Medicinal Chemistry 138 (2017) 96el l4, or in Bauer, RA, Drug Discovery Today, Volume 20, Number 9, September 2015, from which the disclosures of compounds that covalently modify protein targets is incorporated herein by reference.
[0189] In non-limiting embodiments, any of said Asp, Cys, and / or Arg amino acids are present in the protein or peptide to which the molecule binds because the gene encoding the wild type protein has been mutated to encode a protein that includes one or a combination of the described residues. In non-limiting embodiments, the molecule binds to a protein or peptide that is correlated with a disease or condition, such as a cancer, an autoimmune disease, or other disease or disorder that is treated with a targeted covalent inhibitor. In some embodiments, the target (e.g., the protein or peptide to which the molecule covalently binds) is a receptor, including but not necessarily limited to any receptor having a catalytically active segment. In some embodiments, the drug binds to an enzyme that is not necessarily a receptor, including but not limited to any kinase. In some embodiments, a protein target comprises a receptor with one or more activating mutations, which promote ligand-independent enzyme activity.
[0190] In some embodiments, the molecule that becomes covalently bound to form the peptide conjugate targets any RAS oncogene protein product, including but not necessarily limited to HRAS, NRAS, KRAS4A, and KRAS4B. The amino acid sequences of RAS proteins are known in the art, and residue numbering is identical for the relevant part of all RAS isotypes that are discussed in this disclosure for which the amino acid sequence is available from, for example, UniProt P01116, from which the amino acid sequence is incorporated herein as of the effective filing date of this application or patent. The G12 position is numbered according to the knownamino acid sequence, regardless of whether or not the G12 is the twelfth amino acid in an express RAS peptide sequence of this disclosure. The G13 position is numbered according to the known amino acid sequence, regardless of whether or not the G13 is the twelfth amino acid in an express RAS peptide sequence of this disclosure.
[0191] In some embodiments, the molecule covalently binds to a KRAS protein or peptide that comprises a mutation. In some embodiments, the mutation is at least one of KRAS residues 12, 13, or 61. Reference to any drug herein includes its name in capitalized and un-capitalized form.
[0192] In some embodiments, the drug targets a KRAS protein comprising a KRAS G12C mutation. In some embodiments, the drug targets a KRAS protein comprising a KRAS G12D mutation. In some embodiments, the drug targets a KRAS protein comprising a KRAS G12R mutation. In some embodiments, the drug targets a KRAS protein comprises a KRAS G13C mutation. In some embodiments, the drug targets a KRAS protein comprising a KRAS G12S mutation. In non-limiting embodiments, the drug that targets a KRAS protein is selected from 2E07, 6H05, SML-8-73-1, MRTX849, JNJ74699157, LY3499446, ARS-853, ARS-1620, ARS- 3284, GDC-6036, D-1553, JDQ443, RMC-6291, RMC-6236, RMC-9805, BI 1823911, MRTX1257, AMG-510, G12Si-l, G12Si-2, G12Si-3, G12Si-4, G12Si-5, divarasib, or derivatives thereof. Examples of additional compounds that can covalently target a KRAS peptide containing a G12C mutation can be found in Internal Application No. PCT / IB2019 / 050993, Internal Application No. PCT / EP2018 / 083853, and U.S. Application No. US16 / 917,128, each of which is incorporated herein by reference in its entirety. In some embodiments, the drug comprises a proteolysis targeting chimera (PROTAC) derivative of a covalent drug. In some embodiments, the PROTAC is LC-1 or LC-2.
[0193] The peptide conjugate described herein can be formed by the covalent reaction of a targeted covalent inhibitor with a KRAS peptide. The peptide conjugate can be formed by the covalent reaction of a targeted covalent inhibitor with a KRASG12Cpeptide, a KRASG12Dpeptide, a KRASG13Cpeptide, a KRASG12Rpeptide, or a KRASG12Speptide. The targeted covalent inhibitor can be any free targeted covalent inhibitor described herein. For example, the targeted covalent inhibitor can be divarasib, AMG-510 (e.g., sotorasib), MRTX849 (e.g., adagrasib), opnurasib, garsorasib, l-[4-[6-chloro-8-fluoro-7-(2-fluoro-6-hydroxyphenyl)quinazolin-4-yl]piperazin-l- yl]prop-2-en- 1 -one, 1 -(3 -(4-((4-chloro-2-hydroxy-5-(l - methylcyclopropyl)phenyl)glycyl)piperazin- 1 -yljazetidin- 1 -yl)prop-2-en- 1 -one, 1 -(4-(7-(2-Amino-7-fluoro- 1 ,3 -benzothiazol-4-yl)-6-chloro-8-fluoro-quinazolin-4-yl)piperazin- 1 -yljprop- 2-en-l-one, 2-Amino-4-[(4aS)-8-chloro-10-fluoro-2,3,4,4a,5,6-hexahydro-12-oxo-3-(l-oxo-2-propen-l-yl)-lH,12H-pyrazino[2,l-d][l,5]benzoxazocin-9-yl]-7-fluorobenzo[b]thiophene-3- carbonitrile, 2-[(2S)-4-[7-(8-methylnaphthalen-l-yl)-2-[[(2S)-l-methylpyrrolidin-2- yl]methoxy]-6,8-dihydro-5H-pyrido[3,4-d]pyrimidin-4-yl]-l-prop-2-enoylpiperazin-2- yl]acetonitrile, 4-(4-(3,8-Diazabicyclo[3.2.1]octan-3-yl)-8-fhroro-2-(((2R,7aS)-2- fluorohexahydro-lH-pyrrolizin-7a-yl)methoxy)pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6- fluoronaphthalen-2-ol, l-[4-(dimethylamino)-4-methylpent-2-ynoyl]-N-[(2S)-l-[[(6S,8S,14S)- 22-ethyl-21-[2-[(lS)-l-methoxyethyl]pyridin-3-yl]-18,18-dimethyl-9,15-dioxo-5,16-dioxa- 2,10,22,28-tetrazapentacyclo[18.5.2.12,6.110,14.023,27]nonacosa-l(26),20,23(27),24-tetraen-8- yl]amino]-3-methyl-l-oxobutan-2-yl]-4-fluoro-N-methylpiperidine-4-carboxamide, or[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-lH-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy- hydroxyphosphoryl] 2-[(2-chloroacetyl)amino]ethyl hydrogen phosphate]. In some embodiments, the targeted covalent inhibitor can comprise GDC6036, MK-1084, l-((3R,14aS)-l l-Chloro-9- fluoro- 10-(2-fluoro-6-hy droxyphenyl)-3 -methyl- 1 ,3,4,13,14,14a-hexahydro-2H- pyrazino[l',2':5,6][l,5]oxazocino[4,3,2-de]quinazolin-2-yl)prop-2-en-l-one (e.g., AZD4625), or N-(5 -(3 , 5 -dimethoxyphenethyl)- 1 H-pyrazol-3 -yl)-4-((3 S, 5R)-3 , 5 -dimethylpiperazin- 1 - yl)benzamide (e.g., AZD4747). In some embodiments, the targeted covalent inhibitor can be a beta-lactone (e.g., G12Si-l, G12Si-2, G12Si-3, G12Si-4, or G12Si-5).
[0194] In some embodiments, the targeted covalent inhibitor is (i) a tri-complex KRASG12Cinhibitor or a KRASG12Cdegrader, (ii) a tri-complex KRASG12Dinhibitor or a KRASG12Ddegrader, (iii) a tri-complex KRASG12Rinhibitor or a KRASG12Rdegrader, (iv) a tri-complex KRASG13Cinhibitor or a KRASG13Cdegrader, (v) a tri-complex KRASG12Sinhibitor or a KRASG12Sdegrader, or any combination thereof.
[0195] In some cases, the peptide conjugate can be formed by the covalent reaction of divarasib with a KRASG12Cpeptide. The peptide can comprise or consist of the amino acid sequence of VVVGACGVGK, VVGACGVGK, or KLVVVGACGV. In some embodiments, the peptide can comprise a KRASG12Cmutation, and the targeted covalent inhibitor is a KRASG12Cinhibitor, (ii) the peptide can comprise a KRASG12Dmutation, and the targeted covalent inhibitor is a KRASG12Dinhibitor, (iii) the peptide can comprise a KRASG12Rmutation, and the targeted covalent inhibitor is a KRASG12Rinhibitor, (iv) the peptide can comprise a KRASG12Cmutation, and the targeted covalent inhibitor is a KRASG12Cinhibitor, or (v) the peptide can comprise a KRASG12Smutation, and the targeted covalent inhibitor is a KRASG12Sinhibitor.
[0196] In some embodiments, the peptide comprises the amino acid sequence of VVVGACGVGK and the MHC is HLA-A* 11 :01, HLA-A*03 :01, or any combination thereof. Insome embodiments, the peptide comprises the amino acid sequence of VVGACGVGK and the MHC is HLA-A* 11 :01, HLA-A*03:01, or any combination thereof. In some embodiments, the peptide comprises the amino acid sequence of KLVVVGACGV and the MHC is HLA-A*02:01.
[0197] The antigen-binding domain of the polypeptide described herein or the binding partner described herein can bind to a peptide conjugate complexed with different HLAs. In some embodiments, the peptide conjugate / MHC complex comprises an HLA molecule is selected from the group consisting of HLA-A*03:01, HLA-A*l l:01, HLA-A*02:01, HLA-A*68:01, HLA- A*31:01, HLA-A*30:01, HLA-A*33:03, HLA-A*33:01, HLA-A*74:01, HLA-A*34:02, HLA- A*66:01, HLA-A*68:02, HLA-A*02:05, HLA-A*02:02, and HLA-A*02:06. For example, in certain some embodiments, the antigen-binding domain can have specificity to: (i) a peptide conjugate / MHC complex comprising VVGACGVGK conjugated to a targeted covalent inhibitor or fragment thereof presented by HLA-A*03:01, (ii) a peptide conjugate / MHC complex comprising VVVGACGVGK conjugated to a targeted covalent inhibitor or fragment thereof presented by HLA-A*03:01, or (iii) both. In certain other embodiments, the antigen-binding domain can have specificity to: (i) a peptide conjugate / MHC complex comprising VVVGACGVGK conjugated to a targeted covalent inhibitor or fragment thereof presented by HLA-A*03:01, (ii) a peptide conjugate / MHC complex comprising VVVGACGVGK conjugated to a targeted covalent inhibitor or fragment thereof presented by HLA-A* 11 :01, or (iii) both. In other embodiments, the antigen-binding domain can have specificity to: (i) a peptide conjugate / MHC complex comprising VVGACGVGK conjugated to a targeted covalent inhibitor or fragment thereof presented by HLA-A*03:01, (ii) a peptide conjugate / MHC complex comprising VVVGACGVGK conjugated to a targeted covalent inhibitor or fragment thereof presented by HLA-A*03:01, (iii) a peptide conjugate / MHC complex comprising VVVGACGVGK conjugated to a targeted covalent inhibitor or fragment thereof presented by HLA-A* 11 :01, (iv) a peptide conjugate / MHC complex comprising KLVVVGACGV conjugated to a targeted covalent inhibitor or fragment thereof presented by HLA-A*02:01, or (v) any combination of (i) - (iv) (e.g., (i) and (ii); or (i), (ii), and (iv)), or (vi) all of (i)-(iv). In certain specific embodiments, the polypeptide binds to: (i) a peptide conjugate / HLA-A*03:01 MHC complex containing a peptide consisting of the amino acid sequence VVGACGVGK, (ii) a peptide conjugate / HLA-A*03:01 MHC complex containing a peptide consisting of the amino acid sequence VVVGACGVGK, (iii) a peptide conjugate / HLA-A* 11 :01 MHC complex containing a peptide consisting of the amino acid sequence VVVGACGVGK, and / or (iv) a peptide conjugate / HLA-A*02:01 MHC complex containing a peptide consisting of the amino acid sequenceKLVVVGACGV. In still other embodiments, the polypeptide binds to: (i) a peptide conjugate / HLA-A*03:01 MHC complex containing a peptide consisting of the amino acid sequence VVGACGVGK and a peptide conjugate / HLA-A*03:01 MHC complex containing a peptide consisting of the amino acid sequence VVVGACGVGK; (ii) a peptide conjugate / HLA-A*03:01 MHC complex containing a peptide consisting of the amino acid sequence VVVGACGVGK and a peptide conjugate / HLA-A* 11:01 MHC complex containing a peptide consisting of the amino acid sequence VVVGACGVGK; (iii) a peptide conjugate / HLA-A*02:01 MHC complex containing a peptide consisting of the amino acid sequence KLVVVGACGV; or any combination of (i)-(iii) (e.g., (i) and (ii); or (i) and (iii)); or all of (i) - (iii).
[0198] The targeted covalent inhibitor that targets the peptide conjugate / MHC complex can have a chemical structure comprising C-Rl, where C is a chemical fragment linked to R1 of any Compound 1 illustrated below:
[0199] R1 group of the C-Rl chemical structure of the covalent inhibitor can be any of the structures illustrated below.
[0200] The targeted covalent inhibitor with the structure comprising C-Rl can form a covalent bond to several different amino acid residues on the peptide. For example, the targeted covalentinhibitor can form a covalent bond to the cysteine residue in a peptide comprising the amino acid sequence of VVVGACGVGK, VVGACGVGK, or KLVVVGACGV. In other embodiments, the targeted covalent inhibitor can form a covalent bond to the aspartic acid residue, the serine residue, or the arginine residue in a peptide comprising the amino acid sequence of VVVGADGVGK, VVGADGVGK, or KLVVVGADGV. In some embodiments, the antigen-binding domain of the polypeptide recognizes the C portion of the targeted covalent inhibitor with the structure comprising C-Rl of the peptide conjugate / MHC complex. In certain other embodiments, the antigen-binding domain of the polypeptide recognizes C portion but not R1 portion of the targeted covalent inhibitor of the peptide conjugate / MHC complex.
[0201] Small molecules (e.g., targeted covalent inhibitors) having an electrophilic warhead group can undergo covalent reaction with a cysteine residue of a peptide to form a peptide-small molecule conjugate. This type of reaction is illustrated in the following scheme for divarasib.(1) (2J
[0202] In some embodiments, the multivalent polypeptide described herein binds with specificity to a site comprising a neoantigen that includes a covalently linked small molecule drug or other covalently linked molecule as a component of an antigen in a specific MHC context.
[0203] In some embodiments, the peptide comprises an amino acid sequence as set forth in Table 2.Table 2. Exemplary peptide sequences.
[0204] In an aspect, provided herein is a multivalent polypeptide comprising a first-antigen binding domain and a second antigen-binding domain. The first antigen-binding domain can bind to a peptide conjugate / MHC complex, wherein the peptide conjugate is formed by the covalent reaction of a targeted covalent inhibitor with a peptide. In some embodiments, the binding partner binds to the peptide conjugate / MHC complex with a greater affinity than to the peptide or free targeted covalent inhibitor. In some embodiments, the second antigen-binding domain can bind to a T cell surface protein. In some embodiments, the multivalent polypeptide comprises an Fc region, wherein the Fc region comprises a first Fc subunit and a second Fc subunit. In some embodiments, the multivalent polypeptide comprises a single continuous polypeptide chain. The single polypeptide chain can be formed by operably linking a first-antigen binding domain, a second antigen-binding domain, a first Fc subunit, and a second Fc subunit of a multivalent polypeptide described herein.
[0205] For example, a multivalent polypeptide can comprise a first antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the first antigen-binding domain comprises a polypeptide described herein; a second antigen-binding domain that binds to a T cell surface protein; and an Fc region comprising a first Fc subunit and a second Fc subunit; and wherein the first antigen-binding domain, the second antigen-binding domain, the first Fc subunit, and the second Fc subunit are operably linked to form a single continuous polypeptide chain.
[0206] In some embodiments, the binding partner is an intact antibody, a bispecific antibody, a multispecific antibody, an antigen-binding (Fab) fragment, an Fab’ fragment, an (Fab’)2 fragment, an Fd, an Fv, a dAb, a single domain fragment or single monomeric variable antibody domain, a single-chain Diabody (scDb), a diabody (Db), a dual-affinity retargeting (DART) molecule, a single-chain variable fragment (scFv), a camelid antibody, a bi-specific T cell engager (BiTE), bispecific killer cell engager (BiKE), CrossMab, a tri-specific binding partner, a chimeric antigen receptor (CAR), a monobody (aka Adnectin), a DARPin, an anticalin, an affibody, or an affimer. In some embodiments, the binding partner is bispecific. The binding partners of this disclosure can be a Bi-specific T-cell engager (BiTE). BiTE therapies can be used to connect a subject’s endogenous T cells to cancerous cells. A BiTE molecule can comprise two Fv fragments from monoclonal antibodies, joined by a peptide linker. A BiTE molecule can comprise a first antigen-binding domain and a second antigen-binding domain. The first antigen-binding domain can be specific for and bind to a T cell antigen. The second antigen-binding domain can bind to a tumor antigen (e.g., a tumor-associated antigen) expressed on the surface of cancerous cells. In some embodiments, the BiTE molecule can specifically bind to a peptide conjugate / MHC complex and a T cell surface antigen. In some embodiments, the T cell surface antigen is CD3 (e.g., CD3 epsilon, CD3 delta, or CD3 gamma), a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, ICOS, CD28, CD27, HVEM, LIGHT, CD40, 4-1BB (CD137), 0X40, DR3, GITR, CD30, TIM1, SLAM (e.g., a SLAM family member), CD2, CD4, CD8, or CD226. In some embodiments, the binding partner specifically binds to the peptide conjugate / MHC complex and a T cell antigen. In some embodiments, the binding partner specifically binds to the peptide conjugate / MHC complex and human CD3. In some embodiments, the polypeptide may be a BiKE or a CAR-NK. The polypeptide may be a BiKE or a CAR-NK comprising a blockade of a killer cell immunoglobulin-like receptor (KIR), NKG2A, immunoglobulin-like transcript (ILT), or any combination thereof. The polypeptide may be a tri-specific antibody.
[0207] In some embodiments, the binding partner can comprise a cytokine or fragment thereof. In some embodiments, the binding partner can comprise IL-2, IL-7, IL-15, IL-12, IL-18, or IL- 21, or an interferon (IFN). In some embodiments, the cytokine can be selected from the group consisting of TFNy, IL-2, IL-4, IL-6, IL-7, IL-10, IL-12, IL-13, IL-15, IL-18, IL-23, IL-24, IL-27, IL-28a, IL-28b, IL-29, KGF, IFN a (e.g., INF a 2b), IFN 0, IFN , and GM-CSF. The cytokine may be a modified cytokine. In some embodiments, the cytokine may be a modified (or mutated) cytokine (e.g., IL-2, IL-7, IL-8, IL-15, IL-17, IL-18, IL-21, or any combination thereof). In some embodiments, the polypeptide can comprise an agonist (e.g., an agonist to CD28 or 4-1BB).
[0208] In embodiments, the binding partners described herein can be used to carry drugs or toxins. The binding partner may be provided as an immunotoxin or in the form of antibody-drug conjugates (ADCs). In some embodiments, the binding partner described herein may be linked to an enzyme. In some embodiments, the binding partner described herein may be linked to sialidase. Conjugation of sialidase to the binding partner may inactivate one or more inhibitory receptors (e.g., 1, 2, 3, 4, 5, or more inhibitory receptors) at once.
[0209] In some embodiments, the multivalent polypeptide may be specific for a peptide- conjugate / MHC complex comprising a specific MHC. In some cases, the MHC can be HLA-A*02:01. In some cases, the MHC can be HLA-A*03:01. In some cases, the MHC can be HLA-A* 11 :01. In some cases, the MHC can be HLA-A*68:01. In some cases, the MHC can be HLA-A*31:01. In some cases, the MHC can be HLA-A*30:01. In some cases, the MHC can be HLA-A*33:03. In some cases, the MHC can be HLA-A*33:01. In some cases, the MHC can be HLA-A*74:01. In some cases, the MHC can be HLA-A*34:02. In some cases, the MHC can be HLA-A*66:01. In some cases, the MHC can be HLA-A*68:02. In some cases, the MHC can be HLA-A*02:05. In some cases, the MHC can be HLA-A*02:02. In some cases, the MHC can be HLA-A*02:06.
[0210] In some embodiments, the multivalent polypeptide comprises a configuration from N- terminus to C-terminus. In some embodiments, the multivalent polypeptide comprises, from N- terminus to C-terminus, the first antigen-binding domain, the second antigen-binding domain, the first Fc subunit, and the second Fc subunit. In some embodiments, the multivalent polypeptide comprises, from N-terminus to C-terminus, the first antigen-binding domain, a first linker, the second antigen-binding domain, a second linker, the first Fc subunit, a third linker, and the second Fc subunit. The multivalent polypeptide may comprise a linker. The multivalent polypeptide may not comprise a linker.
[0211] In some embodiments, the multivalent polypeptide comprises from N-terminus to C- terminus, the second antigen-binding domain, the first antigen -binding domain, the first Fc subunit, and the second Fc subunit. In some embodiments, the multivalent polypeptide comprises from N-terminus to C-terminus, the second antigen-binding domain, a first linker, the first antigenbinding domain, a second linker, the first Fc subunit, a third linker, and the second Fc subunit. In some embodiments, the Fc region may comprise an amino acid sequence as set forth in any one of SEQ ID NOs: 46 or 51. In some embodiments, the Fc region may comprise an amino acid sequence comprising at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 46 or 51.
[0212] In some embodiments, a linker (e.g., a first linker, a second linker, a third linker, a fourth linker, a fifth linker, or a sixth linker) of a multivalent polypeptide may comprise an amino acid sequence as set forth in any one of SEQ ID NOs: 43, 44, 45, 57, and 63. The multivalent polypeptide may comprise at least one linker (e.g., two linkers, three linkers, four linkers, five linkers, or more). In some embodiments, a first linker can comprise an amino acid sequence as set forth in SEQ ID NO: 44. In some embodiments, a second linker can comprise an amino acid sequence as set forth in SEQ ID NO: 45. In some embodiments, a third linker can comprise anamino acid sequence as set forth in SEQ ID NO: 63. In some embodiments, SEQ ID NO: 63 can comprise GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS .
[0213] A linker can be any length. In some embodiments, a linker (e.g., a first linker, a second linker, a third linker, a fourth linker, a fifth linker, or a sixth linker) can be at least about 2 amino acid residues, at least about 3 amino acid residues, at least about 4 amino acid residues, at least about 5 amino acid residues, at least about 6 amino acid residues, at least about 7 amino acid residues, at least about 8 amino acid residues, at least about 9 amino acid residues, at least about 10 amino acid residues, at least about 11 amino acid residues, at least about 12 amino acid residues, at least about 13 amino acid residues, at least about 14 amino acid residues, at least about 15 amino acid residues, at least about 20 amino acid residues, at least about 25 amino acid residues, at least about 30 amino acid residues, or greater than 30 amino acid residues. In some embodiments, a linker (e.g., a first linker, a second linker, a third linker, a fourth linker, a fifth linker, or a sixth linker) can be at most about 30 amino acid residues, at most about 25 amino acid residues, at most about 20 amino acid residues, at most about 15 amino acid residues, at most about 14 amino acid residues, at most about 13 amino acid residues, at most about 12 amino acid residues, at most about 11 amino acid residues, at most about 10 amino acid residues, at most about 10 amino acid residues, at most about 9 amino acid residues, at most about 8 amino acid residues, at most about 7 amino acid residues, at most about 6 amino acid residues, at most about 5 amino acid residues, at most about 4 amino acid residues, at most about 3 amino acid residues, at most about 2 amino acid residues, or less than about 2 amino acid residues.
[0214] In some embodiments, a linker (e.g., a first linker, a second linker, a third linker, a fourth linker, a fifth linker, or a sixth linker) can be from about 3 amino acid residues to about 40 amino acid residues. In some embodiments, a linker (e.g., a first linker, a second linker, a third linker, a fourth linker, a fifth linker, or a sixth linker) can be from about 3 amino acid residues to about 4 amino acid residues, about 3 amino acid residues to about 5 amino acid residues, about 3 amino acid residues to about 6 amino acid residues, about 3 amino acid residues to about 7 amino acid residues, about 3 amino acid residues to about 8 amino acid residues, about 3 amino acid residues to about 9 amino acid residues, about 3 amino acid residues to about 10 amino acid residues, about 3 amino acid residues to about 15 amino acid residues, about 3 amino acid residues to about 20 amino acid residues, about 3 amino acid residues to about 30 amino acid residues, about 3 amino acid residues to about 40 amino acid residues, about 4 amino acid residues to about 5 amino acid residues, about 4 amino acid residues to about 6 amino acid residues, about 4 amino acid residues to about 7 amino acid residues, about 4 amino acid residues to about 8 amino acid residues, about4 amino acid residues to about 9 amino acid residues, about 4 amino acid residues to about 10 amino acid residues, about 4 amino acid residues to about 15 amino acid residues, about 4 amino acid residues to about 20 amino acid residues, about 4 amino acid residues to about 30 amino acid residues, about 4 amino acid residues to about 40 amino acid residues, about 5 amino acid residues to about 6 amino acid residues, about 5 amino acid residues to about 7 amino acid residues, about5 amino acid residues to about 8 amino acid residues, about 5 amino acid residues to about 9 amino acid residues, about 5 amino acid residues to about 10 amino acid residues, about 5 amino acid residues to about 15 amino acid residues, about 5 amino acid residues to about 20 amino acid residues, about 5 amino acid residues to about 30 amino acid residues, about 5 amino acid residues to about 40 amino acid residues, about 6 amino acid residues to about 7 amino acid residues, about6 amino acid residues to about 8 amino acid residues, about 6 amino acid residues to about 9 amino acid residues, about 6 amino acid residues to about 10 amino acid residues, about 6 amino acid residues to about 15 amino acid residues, about 6 amino acid residues to about 20 amino acid residues, about 6 amino acid residues to about 30 amino acid residues, about 6 amino acid residues to about 40 amino acid residues, about 7 amino acid residues to about 8 amino acid residues, about7 amino acid residues to about 9 amino acid residues, about 7 amino acid residues to about 10 amino acid residues, about 7 amino acid residues to about 15 amino acid residues, about 7 amino acid residues to about 20 amino acid residues, about 7 amino acid residues to about 30 amino acid residues, about 7 amino acid residues to about 40 amino acid residues, about 8 amino acid residues to about 9 amino acid residues, about 8 amino acid residues to about 10 amino acid residues, about8 amino acid residues to about 15 amino acid residues, about 8 amino acid residues to about 20 amino acid residues, about 8 amino acid residues to about 30 amino acid residues, about 8 amino acid residues to about 40 amino acid residues, about 9 amino acid residues to about 10 amino acid residues, about 9 amino acid residues to about 15 amino acid residues, about 9 amino acid residues to about 20 amino acid residues, about 9 amino acid residues to about 30 amino acid residues, about 9 amino acid residues to about 40 amino acid residues, about 10 amino acid residues to about 15 amino acid residues, about 10 amino acid residues to about 20 amino acid residues, about 10 amino acid residues to about 30 amino acid residues, about 10 amino acid residues to about 40 amino acid residues, about 15 amino acid residues to about 20 amino acid residues, about 15 amino acid residues to about 30 amino acid residues, about 15 amino acid residues to about 40 amino acid residues, about 20 amino acid residues to about 30 amino acid residues, about 20 amino acid residues to about 40 amino acid residues, or about 30 amino acid residues to about 40 amino acid residues.
[0215] In some embodiments, the linker may be an amino acid sequence according to the formula SGxS or GxS, and X can be 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, X can be 3 or 4. In some embodiments, the linker may be an amino acid sequence according to the formula Gx, and X can be 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, X can be 3 or 4. In some embodiments, the linker may be an amino acid sequence according to the formula (GXS)N or GxS, and X can be 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 and N can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15. In some embodiments, X can be 4 and N can be 4, 5, or 6. In some embodiments, the linker can be an amino acid sequence according to the formula SxG, and X can be 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, X may be 3 or 4. In some embodiments, the linker can be an amino acid sequence according to the formula SGx, and X can be 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, X may be 3 or 4.
[0216] In some embodiments, an Fc region of a multivalent polypeptide described herein may comprise one or more amino acid substitutions relative to a wild-type Fc region. The wild-type Fc region can comprise an Fc region of a heavy chain constant region. In some embodiments, the heavy chain constant region can be a wild-type IgE, IgM, IgGl, IgG2, IgG3, IgG4, IgAl, or IgA2. In some embodiments, the Fc region comprises at least one amino acid substitution relative to a wild-type heavy chain constant region as set forth in any one of SEQ ID NOs: 23-30. In some embodiments, the Fc region comprises a Fc region with at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in any one of SEQ ID NOs: 23-30. In some embodiments, the Fc region comprises an amino acid sequence as set forth in any one of SEQ ID NOs: 23-30. In some embodiments, the Fc region comprises a Fc region with at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in Table 3. In some embodiments, the Fc region comprises an amino acid sequence as set forth in Table 3Table 3. Immunoglobulin Fc Region Sequences.
[0217] In some embodiments, the Fc region (e.g., a subunit of the Fc region) can comprise a mutation. The mutation may be an Fc-silencing mutation. In some embodiments, the Fc mutation decreases an effector function. The Fc-silencing mutation may decrease an antibody dependent cell mediated cytotoxicity (ADCC) effector function, an antibody dependent cell mediated phagocytosis (ADCP), a complement-dependent cytotoxicity (CDC), or any combination thereof. The Fc mutation (e.g., Fc-silencing mutation) can comprise an AAA mutation, a CGC mutation, or any combination thereof. An AAA mutation may comprise a mutation at any amino acid residue position of an amino acid sequence of SEQ ID NO: 23. A CGC mutation may comprise a mutation at any amino acid residue position of an amino acid sequence of SEQ ID NO: 23. Amino acid positions can be referenced according to the positions of wild-type heavy chain using EU indexing. In some embodiments, the Fc mutation (e.g., Fc-silencing mutation) can comprise a mutation at a leucine of position 234 (e.g., L234), a leucine of position 235 (e.g., L235), a glycine of position 237 (e.g., G237), or any combination thereof, at residue position(s) of an amino acid sequence set forth in SEQ ID NO: 23. In some embodiments, the Fc mutation (e.g., Fc-silencing mutation) comprises at least one AAA mutation comprising L234A, L235A, G237A, or any combination thereof, of a sequence as set forth in SEQ ID NO: 23. In some embodiments, the Fc mutation (e.g., Fc-silencing mutation) can comprise a mutation at an arginine of position 292 (e.g., R292), an asparagine of position 297 (e.g., N297), a valine of position 302 (e.g., V302), or any combination thereof, at residue position(s) of an amino acid sequence set forth in SEQ ID NO: 23. In some embodiments, the Fc mutation (e.g., Fc-silencing mutation) comprises at least one CGC mutation comprising R292C, N297G, V302C, or any combination thereof, of a sequence as set forth in SEQ ID NO: 23.
[0218] The multivalent polypeptide described herein may comprise an amino acid sequence as set forth in any one of SEQ ID NOs: 42, 47-50, or 52-54. In some embodiments, the multivalent polypeptide described herein may comprise a sequence comprising at least about 75%, at leastabout 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in any one of SEQ ID NOs: 42, 47-50, or 52-54. In some embodiments, the multivalent polypeptide described herein may comprise a sequence comprising at most about 100%, at most about 99.9%, at most about 99.5%, at most about 99%, at most about 98.5%, at most about 98%, at most about 97%, at most about 96%, at most about 95%, at most about 94%, at most about 93%, at most about 92%, at most about 91%, at most about 90%, at most about 85%, at most about 80%, at most about 75%, or less than about 75% sequence identity to an amino acid sequence as set forth in any one of SEQ ID NOs: 42, 47-50, or 52-54.
[0219] In some embodiments, a first antigen-binding domain and a second antigen-binding domain of the multivalent polypeptide are the same binder. In some embodiments, a first antigenbinding domain and a second antigen-binding domain of the multivalent polypeptide are different binders. In some embodiments, at least one antigen-binding domain of the multivalent polypeptide comprises a single-chain variable fragment (scFv). In some embodiments, the first antigenbinding domain of the multivalent polypeptide comprises a first scFv. In some embodiments, the second antigen-binding domain of the multivalent polypeptide comprises a second scFv.
[0220] In some embodiments, the configuration of the antigen-binding domains of the multivalent polypeptide may provide an advantage in binding the target peptide-conjugate / MHC complex. In some embodiments, a multivalent polypeptide can comprise, from N-terminus to C-terminus, a configuration comprising: the VH of the first scFv (VH1), the VL of the first scFv (VL1), the VH of the second scFv (VH2), and the VL of the second scFv (VL2). In some embodiments, a multivalent polypeptide can comprise, from N-terminus to C-terminus, a configuration comprising: VH2-VL2-VH1-VL1, VL1-VH1-VL2-VH2, VL2-VH2-VL1-VH1, VH2-VL2-VL1- VH1, VH1-VL1-VL2-VH2, VL1-VH1-VH2-VL2, or VL2-VH2-VH I -VL I . In some embodiments, a linker may be inserted between the VH of the first scFv (VH1) and the VL of the first scFv (VL1), the VH of the first scFv (VH1) and the VL of the second scFv (VL2), the VH of the first scFv (VH1) and the VH of the second scFv (VH2), the VL of the first scFv (VL1) and the VL of the second scFv (VL2), the VL of the first scFv (VL1) and the VH of the second scFv (VH2), the VL of the second scFv (VL2) and the VH of the second scFv (VH2), or any combination thereof.
[0221] The multivalent polypeptides (e.g., T cell engagers) described herein may be designated “G3-18c-AAA”, “G3-18a-AAA”, “G3-18c-CGC”, or “G3-18a-CGC” followed by a binder from Table 1 (e.g., G3-18C-AAA-R301). The T cell engager can comprise an antibody (e.g., R301 or R302) linked to an antibody that binds to CD3s (e.g., UCHT1 antibody) and linked to Fc subunits in a continuous polypeptide chain. In some embodiments, the multivalent polypeptide described herein can comprise one or more amino acid sequences as set forth in Table 4.Table 4. Exemplary construct sequences (scFv)i-scFc format.
[0222] In an aspect, the present disclosure provides a multivalent polypeptide that specifically binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises: (a) a peptide conjugate formed by the covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide; and (b) an MHC.
[0223] In some embodiments, the multivalent polypeptide (e.g., T cell engager) described herein comprises a first antigen-binding domain comprising a heavy chain variable region (VH) comprising a sequence that may be at least about 80%, least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9%, or 100% sequence identity to any one amino acid sequence as set forth in SEQ ID NOs: 1 or 9. In some embodiments, the multivalent polypeptide (e.g., binding partner or T cell engager) described herein comprises a first antigen-binding domain comprising a heavy chain variable region (VH) comprising a sequence that may be at most about 99.9%, at most about 99.5%, at most about 99%, at most about 98.5%, at most about 98%, at most about 97%, at most about 96%, at most about 95%, at most about 94%, at most about 93%, at most about 92%, at most about 91%, at most about 90%, at most about 85%, at most about 80%, or less than about 80% sequence identity to any one amino acid sequence as set forth in SEQ ID NOs: 1 or 9. In some cases, the first antigen-binding domain of the multivalent polypeptide described herein comprises a VH comprising a sequence as set forth in any one of SEQ ID NOs: 1 or 9.
[0224] In some embodiments, the multivalent polypeptide (e.g., T cell engager) described herein comprises a first antigen-binding domain comprising a light chain variable region (VL) comprising a sequence that may be at least about 80%, least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to any one amino acid sequence as set forth in SEQ ID NOs: 2 or 10. In some embodiments, the multivalent polypeptide (e.g., binding partner or T cell engager) described herein comprises a first antigen-binding domain comprising a light chain variable region (VL) comprising a sequence that may be at most about 99.9%, at most about 99.5%, at most about 99%, at most about 98.5%, at most about 98%, at most about 97%, at most about 96%, at most about 95%, at most about 94%, at most about 93%, at most about 92%, at most about 91%, at most about 90%, at most about 85%, at most about 80%, or less than about 80% sequence identity to any one amino acid sequence as set forth in SEQ ID NOs: 2 or 10. In some cases, the first antigen-binding domain of the multivalent polypeptide described herein comprises VL comprising a sequence as set forth in any one of SEQ ID NOs: 2 or 10.
[0225] In another aspect, the present disclosure provides a multivalent polypeptide that binds to a peptide conjugate / MHC complex and may not comprise a single continuous polypeptide chain. In some embodiments, the multivalent polypeptide can comprise a first antigen-binding domain and a second antigen-binding domain. In some embodiments, the first antigen-binding domain comprises a first heavy chain variable region (VH) and a first light chain variable region (VL) and the second antigen-binding domain comprises a second VH and a second VL. In some embodiments, the first antigen binding domain can bind to the peptide conjugate / MHC complex and the second antigen-binding domain can bind to a T cell surface protein. The T cell surface protein can be a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, CD3s, CD35, CD3y, ICOS, CD28, CD27, HVEM, LIGHT, CD40, 4-1BB (CD137), 0X40, DR3, GITR, CD30, TIM1, SLAM (e.g., a SLAM family member), CD2, CD4, CD8, or CD226. In some embodiments, the T cell surface protein comprises CD3s, CD35, CD3y, TCRa, TCRP, TCR5, TCRy, or CD3(^. In some embodiments, the T cell surface protein is CD3 (e.g., CD3s).
[0226] In some embodiments, the second antigen-binding domain comprises complementarity determining regions (CDRs) from a heavy chain variable region (VH) and a light chain variable region (VL) of a UCHT1 antibody. In some embodiments, an amino acid sequence of a CDR of the second antigen-binding domain may comprise a sequence as set forth in Table 5. In some embodiments, an amino acid sequence of a HC CDR3, HC CDR2, and HC CDR1 may comprise an amino acid sequence as set forth in SEQ ID NOs: 33, 34, and 35, respectively. In some embodiments, an amino acid sequence of a HC CDR3, HC CDR2, and HC CDR1 may comprise at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in SEQ ID NOs: 33, 34, and 35, respectively. In some embodiments, an amino acid sequence of a HC CDR3, HC CDR2, and HC CDR1 may comprise at most about 99.9%, at most about 99.5%, at most about 99%, at most about 98.5%, at most about 98%, at most about 97%, at most about 96%, at most about 95%, at most about 94%, at most about 93%, at most about 92%, at most about 91%, at most about 90%, or less than about 90% sequence identity to an amino acid sequence as set forth in SEQ ID NOs: 33, 34, and 35, respectively. In some embodiments, an amino acid sequence of a LC CDR3, LC CDR2, and LC CDR1 may comprise an amino acid sequence as set forth in SEQ ID NOs: 36, 37, and 38, respectively. In some embodiments, an amino acid sequence of a LC CDR3, LC CDR2, and LC CDR1 may comprise at least about 90%, at least about 91%, at least about 92%, at least about93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in SEQ ID NOs: 36, 37, and 38, respectively. In some embodiments, an amino acid sequence of a LC CDR3, LC CDR2, and LC CDR1 may comprise at most about 99.9%, at most about 99.5%, at most about 99%, at most about 98.5%, at most about 98%, at most about 97%, at most about 96%, at most about 95%, at most about 94%, at most about 93%, at most about 92%, at most about 91%, at most about 90%, or less than about 90% sequence identity to an amino acid sequence as set forth in SEQ ID NOs: 36, 37, and 38, respectively.
[0227] In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a VL comprising a sequence that may be at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 32. In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a VL comprising a sequence that may be at most about 99.9%, at most about 99.5%, at most about 99%, at most about 98.5%, at most about 98%, at most about 97%, at most about 96%, at most about 95%, at most about 94%, at most about 93%, at most about 92%, at most about 91%, at most about 90%, at most about 85%, or less than about 85% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 32. In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a VL comprising a sequence as set forth in SEQ ID NO: 32.
[0228] In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a VH comprising a sequence that may be at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 31. In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a VH comprising a sequence that may be at most about 99.9%, at most about 99.5%, at most about 99%, at most about 98.5%, at most about 98%, at most about 97%, at most about 96%, at most about 95%, at most about 94%, at most about 93%, at most about 92%, at most about 91%, atmost about 90%, at most about 85%, or less than about 85% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 31. In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a VH comprising a sequence as set forth in SEQ ID NO: 31.
[0229] The UCHT1 antibody or fragment thereof described herein (e.g., second antigen-binding domain) can comprise a VH having at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 39. The UCHT1 antibody or fragment thereof described herein (e.g., second antigen-binding domain) can comprise a VH having at most about 99.9%, at most about 99.5%, at most about 99%, at most about 98.5%, at most about 98%, at most about 97%, at most about 96%, at most about 95%, at most about 94%, at most about 93%, at most about 92%, at most about 91%, at most about 90%, at most about 85%, or less than about 85% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 39. In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a VH comprising a sequence as set forth in SEQ ID NO: 39.
[0230] The UCHT1 antibody or fragment thereof described herein (e.g., second antigen-binding domain) can comprise a VL having at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 40. The UCHT1 antibody or fragment thereof described herein (e.g., second antigen-binding domain) can comprise a VL having at most about 99.9%, at most about 99.5%, at most about 99%, at most about 98.5%, at most about 98%, at most about 97%, at most about 96%, at most about 95%, at most about 94%, at most about 93%, at most about 92%, at most about 91%, at most about 90%, at most about 85%, or less than about 85% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 40. In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a VH comprising a sequence as set forth in SEQ ID NO: 40.
[0231] Any UCHT1 in a T cell engager (TCE) construct described herein may comprise the UCHT1 antibody or fragment thereof comprising a VH having at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 39, and / or a VL having at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than about 99.9% sequence identity to an amino acid sequence as set forth in SEQ ID NO: 40.
[0232] In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a VH and / or VL as set forth in Table 5. In some embodiments, the second antigen-binding domain of a multivalent polypeptide as described herein can comprise a HC CDR1, HC CDR2, HC CDR3, LC CDR1, LC CDR2, LC CDR3, or any combination thereof, as set forth in Table 5.Table 5. UCHT1 Sequences
[0233] In some embodiments, the first antigen-binding domain and the second antigen-binding domain comprise a diabody. In some embodiments, the multivalent polypeptide comprises anamino acid sequence having at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 98.5%, at least about 99%, at least about 99.5%, at least about 99.9%, or greater than 99.9% sequence identity to any one of the amino acid sequences as set forth in SEQ ID NOs: 93 or 98- 110. In some embodiments, the multivalent polypeptide comprises an amino acid sequence as set forth in SEQ ID NOs: 93 or 98-110.
[0234] The multivalent polypeptide may comprise a fusion tag. The fusion tag can comprise a protein or peptide fused to the multivalent polypeptide. The fusion tag may assist in detection of the polypeptide or an area of the polypeptide. The fusion tag may be an epitope tag, an affinity tag, a fluorescent tag, or any combination thereof. In some embodiments, the fusion tag may be an AviTag™. In some embodiments, the fusion tag may be a histidine tag (His-tag). The fusion tag may comprise a tag selected from the group consisting of CBP, GST, strep-tag, c-myc, hemagglutinin (HA), DDDK tag, T7 tag, V5 tag, GFP, ALFA tag, and mCherry. In some embodiments, the fusion tag comprises an amino acid sequence as set forth in SEQ ID NO: 58. In some embodiments, the fusion tag comprises an amino acid sequence as set forth in SEQ ID NO: 59. The fusion tag may be fused to the N-terminal of the multivalent polypeptide or the C-terminal of the multivalent polypeptide. The multivalent polypeptide may comprise at least 1, at least 2, at least 3, at least 4, at least 5, or greater than 5 fusion tags. In some embodiments, the multivalent polypeptide comprises no fusion tag.
[0235] In some embodiments, the multivalent polypeptide described herein can comprise one or more amino acid sequences as set forth in Table 6.Table 6. Exemplary construct sequences (scDb).
[0236] As another example, a multivalent polypeptide can comprise a first antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the first antigen-binding domain comprises a polypeptide described herein; and a second antigen-binding domain that binds to a Tcell surface protein; wherein the second antigen-binding domain comprises a second VH and a second VL, and wherein the second VL comprises: a CDR-L3 sequence of QQGNTLPWT (SEQ ID NO: 36), a CDR-L2 sequence of YTSRLES (SEQ ID NO: 37), and a CDR-L1 sequence of RASQDIRNYLN (SEQ ID NO: 38). The second antigen-binding domain of a multivalent polypeptide described herein can comprise six complementarity determining regions (CDRs) from heavy chain variable region (VH) and light chain variable region (VL) of a UCHT1 antibody. The six CDRs may comprise: (i) a CDR-H3 sequence of SGYYGDSDWYFDV (SEQ ID NO: 33), (ii) a CDR-H2 sequence of LINPYKGVSTYNQKFKD (SEQ ID NO: 34), (iii) a CDR-H1 sequence of GYTMN (SEQ ID NO: 35), (iv) a CDR-L3 sequence of QQGNTLPWT (SEQ ID NO: 36), (v) a CDR-L2 sequence of YTSRLES (SEQ ID NO: 37), and (vi) a CDR-L1 sequence of RASQDIRNYLN (SEQ ID NO: 38).
[0237] In an embodiment, the affinity of the multivalent polypeptide for the peptide conjugate / MHC complex is 100-10,000 times greater than the affinity of the multivalent polypeptide for the peptide or free targeted covalent inhibitor. In an embodiment, the affinity of the multivalent polypeptide for the peptide conjugate / MHC complex is at least 100 times, at least 200 times, at least 300 times, at least 400 times, at least 500 times, at least 600 times, at least 700 times, at least 800 times, at least 900 times, at least 1,000 times, at least 2,500 times, at least 5,000 times, at least 10,000 times, at least 20,000 times, at least 30,000 times, at least 40,000 times, at least 50,000 times, or at least 100,000 times greater than the affinity of the multivalent polypeptide to the free targeted covalent inhibitor or the free peptide conjugate. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as ICso. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an ICso of more than 1 pM. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an ICso of more than 5 pM. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an ICso of more than 10 pM. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an ICso of more than 15 pM. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an ICso of more than 20 pM. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an ICso of more than 30 pM. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an ICso of more than 40 pM. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an ICso of more than 50 pM. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an ICso of more than 75 pM. In some embodiments, the affinity of themultivalent polypeptide to the free drug is reported as an IC50 of more than 100 pM. In some embodiments, the affinity of the multivalent polypeptide to the free drug is reported as an IC50 of more than 200 pM.
[0238] In some embodiments, the first antigen-binding domain does not detectably bind to the free targeted covalent inhibitor. In some embodiments, the first antigen-binding domain binds to the free targeted covalent inhibitor with an IC50 of at least about 50 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 5 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 25 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 40 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 60 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 75 nM. The first antigenbinding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 100 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 250 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 500 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 750 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 1000 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 2 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 5 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 10 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 15 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 20 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 25 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of at least about 50 pM.
[0239] In some embodiments, the first antigen-binding domain binds to the free targeted covalent inhibitor with an IC50 of less than about 50 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 5 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 25 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 40 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitorwith an IC50 of less than about 60 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 75 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 100 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 250 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 500 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 750 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 1000 nM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 2 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 5 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 10 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 15 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 20 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 25 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with an IC50 of less than about 50 pM.
[0240] The multivalent polypeptide described herein may not bind to the peptide / MHC complex without the conjugate (e.g., the targeted covalent inhibitor). In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) from 10 pM to 50 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) from 1 pM to 10 pM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) from 0.01 pM to 10 pM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) from 0.1 nM to 1 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) from 1 nM to 2 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) from 2 nM to 5 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) of equal to less than about 5 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) of equal to less than about 4 nM. In some cases, the affinity of themultivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) of equal to less than about 3 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) of equal to less than about 2 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) of equal to less than about 1 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) of equal to less than about 0.1 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) of about equal to less than 0.01 nM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) of equal to less than about 1 pM. In some cases, the affinity of the multivalent polypeptide to the peptide conjugate / MHC complex is reported as a dissociation constant (KD) of equal to less than about 0.1 pM.
[0241] In some embodiments, the multivalent polypeptide does not detectably bind to a complex of a peptide with an MHC molecule, wherein the peptide is not covalently bound to a non-peptide molecule. In some embodiments, the multivalent polypeptide binds at less than lOx affinity to a complex of a peptide with an MHC molecule, wherein the peptide is not covalently bound to a non-peptide molecule. In some embodiments, the multivalent polypeptide binds at less than lOOx affinity to a complex of a peptide with an MHC molecule, wherein the peptide is not covalently bound to a non-peptide molecule. In some embodiments, the multivalent polypeptide binds at less than l,000x affinity to a complex of a peptide with an MHC molecule, wherein the peptide is not covalently bound to a non-peptide molecule.
[0242] The first antigen-binding domain can bind to the free targeted covalent inhibitor with a dissociation constant KD that is higher than the KD of the antibody or the antigen-binding fragment to the peptide conjugate / MHC complex. In some cases, the first antigen-binding domain can bind to the free targeted covalent inhibitor with a dissociation constant (KD) of at least about 100 nM, at least about 200 nM, at least about 300 nM, at least about 400 nM, at least about 500 nM, at least about 1 pM, at least about 10 pM, at least about 20 pM, at least about 30 pM, at least about 40 pM, at least about 50 pM, or at least 100 pM. The first antigen-binding domain can bind to the free targeted covalent inhibitor with a dissociation constant (KD) of at least about 2, 3, 4, 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000 times more than the KD of the first antigen-binding domain binding to the peptide conjugate / MHC complex. The first antigen-binding domain can bind to the free peptide conjugate with a dissociation constant(KD) that is higher than a Ko of the first antigen-binding domain binding to the peptide conjugate / MHC complex. The first antigen-binding domain can bind to the free peptide conjugate with a dissociation constant (KD) of more than about 100 nM, more than about 200 nM, more than about 300 nM, more than about 400 nM, more than about 500 nM, more than 1 pM, more than 10 pM, more than 20 pM, more than 30 pM, more than 40 pM, more than 50 pM, or more than 100 pM. The first antigen-binding domain can bind to the free peptide conjugate with a dissociation constant (KD) at least about 10, 100, 10,000, or 100,000 times more than the KD of the first antigenbinding domain binding to the peptide conjugate / MHC complex. The first antigen-binding domain can bind to the free peptide conjugate with a dissociation constant (KD) that is at least 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, or 10 times more than the KD of the antibody or the antigen-binding fragment to the peptide conjugate / MHC complex. In some embodiments, the first antigen-binding domain binds to the free peptide conjugate with a dissociation constant KD that is at least 2.5 times more than the Ko of the antibody or the antigen-binding fragment to the peptide conjugate / MHC complex. The first antigen-binding domain can bind to the peptide conjugate / MHC complex with an affinity that is at least 100 times, at least 200 times, at least 300 times, at least 400 times, at least 500 times, at least 600 times, at least 700 times, at least 800 times, at least 900 times, at least 1,000 times, at least 2,500 times, at least 5,000 times, or at least 10,000 times greater than the affinity of first antigen-binding domain to the free targeted covalent inhibitor or the free peptide conjugate.
[0243] Binding of the first antigen-binding domain to a peptide conjugate / MHC complex may be characterized by a dissociation rate constant (koir). In some embodiments, the first antigen-binding domain binds to the peptide conjugate / MHC complex with a dissociation rate constant (koir) of at least about 0.001 hr1, at least about 0.005 hr’1, at least about 0.01 hr’1, at least about 0.02 hr’1, at least about 0.03 hr’1, at least about 0.04 hr’1, at least about 0.05 hr’1, at least about 0.06 hr’1, at least about 0.07 hr’1, at least about 0.08 hr’1, at least about 0.09 hr’1, at least about 0.1 hr’1, at least about 0.2 hr’1, at least about 0.3 hr’1, at least about 0.4 hr’1, at least about 0.5 hr’1, at least about 1.0 hr’1, at least about 2.0 hr’1, at least about 3.0 hr’1, at least about 4.0 hr’1, at least about 5.0 hr’1, at least about 10.0 hr’1, at least about 15.0 hr’1, at least about 20.0 hr’1, at least about 25.0 hr’1, or greater than about 50.0 hr’1. In some embodiments, the first antigen-binding domain binds to the peptide conjugate / MHC complex with a dissociation rate constant (koir) of at most about 50.0 hr’1, at mostabout 25.0 hr’1, at most about 20.0 hr’1, at most about 15.0 hr’1, at most about 10.0 hr’1, at most about 5.0 hr’1, at most about 4.0 hr’1, at most about 3.0 hr’1, at most about 2.0 hr’1, at most about 1.0 hr’1, at most about 0.5 hr’1, at most about 0.4 hr’1, at most about 0.3 hr’1, at most about 0.2 hr’ at most about 0.1 hr’1, at most about 0.09 hr’1, at most about 0.08 hr’1, at most about 0.07 hr’1, at most about 0.06 hr’1, at most about 0.05 hr’1, at most about 0.04 hr’1, at most about 0.03 hr’1, at most about 0.02 hr’1, at most about 0.01 hr’1, at most about 0.005 hr’1, at most about 0.001 hr’1, or less than about 0.001 hr’1.
[0244] In some embodiments, the first antigen-binding domain binds to the peptide conjugate / MHC complex with a dissociation rate constant (koff) from about 0.001 hr’1to about 25 hr’1. In some embodiments, the first antigen-binding domain binds to the peptide conjugate / MHC complex with a dissociation rate constant (koff) from about 0.001 hr’1to about 0.005 hr’1, about 0.001 hr’1to about 0.01 hr’1, about 0.001 hr’1to about 0.05 hr’1, about 0.001 hr’1to about 0.1 hr’1, about 0.001 hr’1to about 0.5 hr’1, about 0.001 hr’1to about 1 hr’1, about 0.001 hr’1to about 5 hr’1, about 0.001 hr’1to about 10 hr’1, about 0.001 hr’1to about 15 hr’1, about 0.001 hr’1to about 20 hr’ about 0.001 hr’1to about 25 hr’1, about 0.005 hr’1to about 0.01 hr’1, about 0.005 hr’1to about 0.05 hr’1, about 0.005 hr’1to about 0.1 hr’1, about 0.005 hr’1to about 0.5 hr’1, about 0.005 hr’1to about 1 hr’1, about 0.005 hr’1to about 5 hr’1, about 0.005 hr’1to about 10 hr’1, about 0.005 hr’1to about 15 hr’1, about 0.005 hr’1to about 20 hr’1, about 0.005 hr’1to about 25 hr’1, about 0.01 hr’1to about 0.05 hr’1, about 0.01 hr’1to about 0.1 hr’1, about 0.01 hr’1to about 0.5 hr’1, about 0.01 hr’1to about 1 hr’1, about 0.01 hr’1to about 5 hr’1, about 0.01 hr’1to about 10 hr’1, about 0.01 hr’1to about 15 hr’1, about 0.01 hr’1to about 20 hr’1, about 0.01 hr’1to about 25 hr’1, about 0.05 hr’1to about 0.1 hr’1, about 0.05 hr’1to about 0.5 hr’1, about 0.05 hr’1to about 1 hr’1, about 0.05 hr’1to about 5 hr’1, about 0.05 hr’1to about 10 hr’1, about 0.05 hr’1to about 15 hr’1, about 0.05 hr’1to about 20 hr’1, about 0.05 hr’1to about 25 hr’1, about 0.1 hr’1to about 0.5 hr’1, about 0.1 hr’1to about 1 hr’1, about 0.1 hr’1to about 5 hr’1, about 0.1 hr’1to about 10 hr’1, about 0.1 hr’1to about 15 hr’1, about 0.1 hr’1to about 20 hr’1, about 0.1 hr’1to about 25 hr’1, about 0.5 hr’1to about 1 hr’1, about 0.5 hr’1to about 5 hr’1, about 0.5 hr’1to about 10 hr’1, about 0.5 hr’1to about 15 hr’1, about 0.5 hr’1to about 20 hr’1, about 0.5 hr’1to about 25 hr’1, about 1 hr’1to about 5 hr’1, about 1 hr’1to about 10 hr’1, about 1 hr’1to about 15 hr’1, about 1 hr’1to about 20 hr’1, about 1 hr’1to about 25 hr’1, about 5 hr’1to about 10 hr’1, about 5 hr’1to about 15 hr’1, about 5 hr’1to about 20 hr’1, about 5 hr’1to about 25 hr’1, about 10 hr’1to about 15 hr’1, about 10 hr’1to about 20 hr’1, about 10 hr’1to about 25 hr’1, about 15 hr’1to about 20 hr’1, about 15 hr’1to about 25 hr’1, or about 20 hr’1to about 25 hr’1.
[0245] In some embodiments, a first-antigen binding domain of a multivalent polypeptide (e.g., binding partner) described herein comprises R301 or R302. In some embodiments, the multivalent polypeptide comprises a first antigen-binding domain comprising a VH, VL, HC CDR1, HC CDR2, HC CDR3, LC CDR1, LC CDR2, LC CDR3, or any combination thereof, as set forth in Table 1
[0246] The CDRs for any binder described herein can be designated by Kabat numbering scheme. In some cases, the light chain (LC) CDRs can be designated by Kabat numbering scheme. In some cases, the LC CDRs can be designated by Kabat numbering scheme with modifications. In some cases, the heavy chain (HC) CDRs can be designated by Kabat numbering scheme. In some cases, the HC CDRs can be designated by Kabat numbering scheme with at least one modification. The CDRs for any binder described herein can be designated by Chothia numbering scheme. In some cases, the light chain (LC) CDRs can be designated by Chothia numbering scheme. In some cases, the LC CDRs can be designated by Chothia numbering scheme with modifications. In some cases, the heavy chain (HC) CDRs can be designated by Chothia numbering scheme. In some cases, the HC CDRs can be designated by Chothia numbering scheme with at least one modification. The modification to the Kabat or Chothia numbering scheme may comprise amino acids flanking the sequence identified by the Kabat or Chothia numbering scheme.Polynucleotides
[0247] In another aspect, the present disclosure provides a polynucleotide encoding the polypeptide or the multivalent polypeptide of disclosed herein. In another aspect, the present disclosure provides a polynucleotide encoding a heavy chain variable region and / or a light chain variable region of the polypeptide or the multivalent polypeptide disclosed herein. The polynucleotide may comprise at least one sequence encoding a VH region and / or a VL region as set forth in Table 1. The polynucleotide may comprise at least one sequence encoding a VH region of a first antigen-binding domain as set forth in any one of SEQ ID NOs: 1 or 9. The polynucleotide may comprise at least one sequence encoding a VL region of a first antigen-binding domain as set forth in any one of SEQ ID NOs: 2 or 10. In some embodiments, the polynucleotide can comprise at least one sequence encoding a VH of a second antigen-binding domain as set forth in SEQ ID NO: 31. In some embodiments, the polynucleotide can comprise at least one sequence encoding a VL of a second antigen-binding domain as set forth in SEQ ID NO: 32. In some embodiments, the polynucleotide can comprise at least one sequence encoding a VH of a second antigen-bindingdomain as set forth in SEQ ID NO: 39. In some embodiments, the polynucleotide can comprise at least one sequence encoding a VL of a second anti gen -binding domain as set forth in SEQ ID NO: 40. In some embodiments, the polynucleotide may comprise at least a portion of a sequence encoding a component of a polypeptide or a multivalent polypeptide as set forth in any one of Tables 4 or 6.
[0248] In some embodiments, a polynucleotide encoding the polypeptide described herein may comprise a sequence as set forth in Table 7. In some embodiments, the polynucleotide may comprise a sequence with at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 98.5%, 99%, 99.5%, 99.9%, or 100% sequence identity to a polynucleotide sequence as set forth in SEQ ID NOs: 64-79.Table 7. Exemplary polynucleotide sequences of antibodies that bind to divarasib-KRASG12Cpeptides presented by HLA molecules.Vectors
[0249] In another aspect, the present disclosure provides a vector comprising a polynucleotide disclosed herein. In some embodiments, the vector is a viral vector. In some embodiments, the viral vector is an adenoviral vector, lentiviral vector, retroviral vector, or adeno-associated viral vector.
[0250] Methods of delivering polynucleotides encoding proteins can be adapted to deliver the multivalent polypeptides (e.g., binding partners), given the benefit of the present disclosure. In some embodiments, one or more expression vectors may be used and comprise viral vectors. Thus, in some embodiments, a viral expression vector can be used. Viral expression vectors may be used as naked polynucleotides, or may comprise any of viral particles, including but not limited to, defective interfering particles or other replication defective viral constructs, and virus-like particles. In some embodiments, the expression vector comprises a modified viral polynucleotide, such as from an adenovirus, a herpesvirus, or a retrovirus. In some embodiments, a retroviral vector adapted from a murine Moloney leukemia virus (MLV) or a lentiviral vector may be used, such as a lentiviral vector adapted from human immunodeficiency virus type 1 (HIV-1). In some embodiments, the polynucleotides encoding the binding partners may be delivered as nanoparticles. In some embodiments, the RNAs (or mRNAs) encoding the binding partners may be delivered as nanoparticles. In some embodiments, the RNAs (or mRNAs) encoding the binding partners may be delivered as lipid nanoparticles. In some embodiments, the RNA encoding the binding partner can be a modified RNA. The modifications can include Nl-methyl-pseudouri dine ( I m ) nucleotide substitutions and / or 5-methylcytidine (m5C) substitutions.
[0251] In some embodiment, an oncolytic viral vector can be used. Oncolytic viruses (OVs), for example vaccinia (OVV), can mediate anticancer effects by both direct oncolysis andstimulation of innate immune responses through production of damage-associated molecular patterns (DAMPs) and the presence of virus-derived pathogen-associated molecular patterns (PAMPs), leading to increased type I interferon production. Additionally, OVV-mediated oncolysis may facilitate the direct acquisition of tumor-derived antigens by host antigen- presenting cells within the tumor microenvironment, thereby leading to improved T cell priming as well as coordination of the effector phase of antitumor immune responses. In some embodiments, a recombinant adeno-associated virus (AAV) vector may be used. In some embodiments, the expression vector can be a self-complementary adeno-associated virus (sc AAV).Cells
[0252] In another aspect, the present disclosure provides a cell (e.g., a recombinant host cell) comprising (a) a polynucleotide disclosed herein; (b) a vector disclosed herein; (c) a first polynucleotide encoding a VH or a heavy chain of the multivalent polypeptide disclosed herein, and a second polynucleotide encoding a VL or a light chain of the multivalent polypeptide disclosed herein; or (d) a first vector comprising a first polynucleotide encoding a VH or a heavy chain of the multivalent polypeptide disclosed herein, and a second vector comprising a second polynucleotide encoding a VL or a light chain of the multivalent polypeptide disclosed herein. A cell may comprise a polypeptide described herein.
[0253] Polynucleotides includes, for example, genomic DNA, cDNA, RNA, e.g., mRNA, and DNA-RNA hybrid molecules. Polynucleotides can be naturally occurring, recombinant, or synthetic. In addition, polynucleotides can be single-stranded, double-stranded or triple-stranded. In certain embodiments, polynucleotides can be modified. In the case of a double-stranded polymer, “nucleic acid” can refer to either or both strands of the molecule. In some embodiments, the polynucleotide is provided as DNA. In some embodiments, the polynucleotide is provided as RNA, e.g., an mRNA. In some embodiments, a polynucleotide described herein can be expressed in a host cell and the multivalent polypeptide may be produced. In some embodiments, the cell can be a eukaryotic cell comprising the polynucleotide or vector described herein. In some embodiments, the cell is optionally a totipotent, multipotent, or pluripotent stem cell. In some embodiments, the stem cell has an induced stem cell phenotype, or wherein the cell is optionally a leukocyte, optionally a CD4+ T cell, optionally a CD8+ T cell, optionally a y5 T cell, optionally a natural killer cell or a macrophage.
[0254] In another aspect, the present disclosure provides a method of producing a polypeptide, the method comprising culturing the host cell disclosed herein under suitable conditions so that the polynucleotide is expressed and the polypeptide (e.g., binding partner) is produced.
[0255] In some embodiments, the multivalent polypeptide can be expressed by a T cell, killer macrophage, neutrophil, or natural killer cell. In some embodiments, binding of the multivalent polypeptide to the peptide conjugate / MHC complex is not inhibited by free targeted covalent inhibitor.
[0256] In another aspect, the present disclosure provides for a composition for use in the manufacture of a medicament for treating a subject in need thereof. The composition may comprise the multivalent polypeptide described herein, the polypeptide described herein, the polynucleotide described herein, the vector described herein, or the cell described herein. In some cases, the subject has a cancer. In some cases, the subject is refractory from a cancer treatment. In some cases, the subject is a relapsed cancer patient.Pharmaceutical Compositions
[0257] In another aspect, the present disclosure provides a pharmaceutical composition. In some embodiments, the pharmaceutical composition may comprise a multivalent polypeptide as described herein, the polypeptide described herein, the polynucleotide disclosed herein, the vector disclosed herein, or the host cell disclosed herein and a pharmaceutically acceptable carrier or excipient. The pharmaceutical composition may comprise at least one multivalent polypeptide described herein (e.g., the pharmaceutical composition may comprise 1, 2, 3, 4, 5, or more multivalent polypeptides). The pharmaceutical composition can be in the form of a liquid, e.g., a solution, emulsion, or suspension. The liquid compositions of the disclosure, whether they are solutions, suspensions or other like form, can also include one or more of the following: sterile diluents such as water, saline solution, preferably physiological saline, Ringer's solution, isotonic sodium chloride, fixed oils such as synthetic mono or diglycerides, polyethylene glycols, glycerin, or other solvents; antibacterial agents such as benzyl alcohol or methyl paraben; and agents for the adjustment of tonicity such as sodium chloride or dextrose. The pharmaceutical composition can be enclosed in an ampoule, a disposable syringe or a multiple-dose vial made of glass, plastic or other material.
[0258] In some embodiments, the pharmaceutical composition comprises additional agents, e.g., for specific delivery, increasing half-life, or other therapeutic compounds. In some embodiments,the pharmaceutical composition may comprise one or more of dimethylsulfoxide (DMSO), dextrose, water, succinate, poly I: poly C, poly-L-lysine, carboxymethylcellulose, and / or chloride.
[0259] In some embodiments, a pharmaceutically acceptable carrier comprises any vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the compound from one site (e.g., the delivery site) of the body, to another site (e.g., organ, tissue or portion of the body). A pharmaceutically acceptable carrier is “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the tissue of the subject (e.g., physiologically compatible, sterile, physiologic pH, etc.).Methods of Activating an Immune Cell
[0260] In some aspects, the present disclosure provides methods of activating an immune cell. In some embodiments, the method comprises contacting the immune cell with the multivalent polypeptide described herein. In some embodiments, the immune cell can be a T cell. The T cell can be a CD8+T cell or a CD4+T cell. T cell activation may be measured at least about 1 hour, at least about 2 hours, at least about 3 hours, at least about 4 hours, at least about 5 hours, at least about 6 hours, at least about 12 hours, at least about 24 hours, at least about 36 hours, at least about 48 hours, at least about 72 hours, or greater than 72 hours post contacting of the multivalent polypeptide. In some embodiments, contacting the immune cell (e.g., T cell) with the multivalent polypeptide described herein may increase expression of at least one T cell activation marker. The T cell activation marker may comprise CD26, CD27, CD28, CD30, CD154, CD40L, CD134. CD25, CD44, CD69, CD137, PD-1, KLRG1, or any combination thereof. In some embodiments, measuring of T cell activation can comprise measuring a level of CD25-positive (e.g., CD25+) and CD69-positive (e.g., CD69+) T cells. In some embodiments, contacting the cell (e.g., T cell) with the multivalent polypeptide increases expression of PD-1. In some embodiments, a targeted covalent inhibitor has been administered. In some moments, the targeted covalent inhibitor can be administered prior to the multivalent polypeptide, subsequent to the multivalent polypeptide, or simultaneously with the multivalent polypeptide. In some embodiments, a greater T cell activation may occur in the presence of a targeted covalent inhibitor described herein (e.g., divarasib).
[0261] For example, the method for activating an immune cell can comprise: contacting the immune cell with a multivalent polypeptide comprising a first antigen-binding domain, a second antigen-binding domain that binds to a T cell surface protein, and an Fc region comprising a first Fc subunit and a second Fc subunit, wherein the first antigen-binding domain comprises apolypeptide described herein; and wherein the immune cell expresses a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC.
[0262] In some embodiments, the contacting can produce a greater number of CD25+CD69+ T cells compared with a number of CD25+CD69+ T cells produced from contacting the multivalent polypeptide with an otherwise identical peptide conjugate / MHC complex without the targeted covalent inhibitor. In some embodiments, contacting the multivalent polypeptide to the immune cell may result in an increase in level of CD25+CD69+ T cells prior to contacting of at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 11%, at least about 12%, at least about 13%, at least about 14%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 80%, at least about 90%, or greater than 90% CD25+CD69+ T cells. In some embodiments, contacting the multivalent polypeptide to the immune cell may result in an increase in level of CD25+CD69+ T cells prior to contacting of at most about 90%, at most about 80%, at most about 70%, at most about 60%, at most about 50%, at most about 40%, at most about 30%, at most about 25%, at most about 20%, at most about 15%, at most about 14%, at most about 13%, at most about 12%, at most about 11%, at most about 10%, at most about 9%, at most about 8%, at most about 7%, at most about 6%, at most about 5%, at most about 4%, at most about 3%, at most about 2%, at most about 1%, or less than about 1% CD25+CD69+ T cells.
[0263] In some embodiments, contacting the multivalent polypeptide to the immune cell may result in an increase in level of CD25+CD69+ T cells prior to contacting from about 1% to about 100%. In some embodiments, contacting the multivalent polypeptide to the immune cell may result in an increase in level of CD25+CD69+ T cells prior to contacting from about 1% to about 2%, about 1% to about 3%, about 1% to about 4%, about 1% to about 5%, about 1% to about 10%, about 1% to about 15%, about 1% to about 20%, about 1% to about 25%, about 1% to about 50%, about 1% to about 75%, about 1% to about 100%, about 2% to about 3%, about 2% to about 4%, about 2% to about 5%, about 2% to about 10%, about 2% to about 15%, about 2% to about 20%, about 2% to about 25%, about 2% to about 50%, about 2% to about 75%, about 2% to about 100%, about 3% to about 4%, about 3% to about 5%, about 3% to about 10%, about 3% to about 15%, about 3% to about 20%, about 3% to about 25%, about 3% to about 50%, about 3% to about 75%, about 3% to about 100%, about 4% to about 5%, about 4% to about 10%, about 4% to about 15%, about 4% to about 20%, about 4% to about 25%, about 4% to about 50%, about 4% to about75%, about 4% to about 100%, about 5% to about 10%, about 5% to about 15%, about 5% to about 20%, about 5% to about 25%, about 5% to about 50%, about 5% to about 75%, about 5% to about 100%, about 10% to about 15%, about 10% to about 20%, about 10% to about 25%, about 10% to about 50%, about 10% to about 75%, about 10% to about 100%, about 15% to about 20%, about 15% to about 25%, about 15% to about 50%, about 15% to about 75%, about 15% to about 100%, about 20% to about 25%, about 20% to about 50%, about 20% to about 75%, about 20% to about 100%, about 25% to about 50%, about 25% to about 75%, about 25% to about 100%, about 50% to about 75%, about 50% to about 100%, or about 75% to about 100%.
[0264] In some embodiments, contacting the multivalent polypeptide to the immune cell may result in an increased expression of PD-1. The percentage of PD-1 positive cells (e.g., PD-1+ cells) following contacting of an immune cell with a multivalent polypeptide described herein may be at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 11%, at least about 12%, at least about 13%, at least about 14%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 80%, or greater than 80%. The percentage of PD-1 positive cells (e.g., PD-1+ cells) following contacting of an immune cell with a multivalent polypeptide described herein may be at most about 80%, at most about 70%, at most about 60%, at most about 50%, at most about 40%, at most about 30%, at most about 25%, at most about 20%, at most about 15%, at most about 14%, at most about 13%, at most about 12%, at most about 11%, at most about 10%, at most about 9%, at most about 8%, at most about 7%, at most about 6%, at most about 5%, at most about 4%, at most about 3%, at most about 2%, at most about 1%, or less than about 1%.
[0265] T cell activation may also be measured by a level of inducible costimulator (ICOS). An increase in ICOS signaling can indicate T cell activation. ICOS can be measured by a mean fluorescence intensity (MFI). In some cases, contacting an immune cell with the multivalent polypeptide may result in an ICOS MFI of at least about, at most about, or about 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, 10000, or a range between any of these two values.
[0266] In some embodiments, contacting a T cell with a multivalent polypeptide described herein may increase expression of at least one cytokine. In some embodiments, contacting a T cell with a multivalent polypeptide described herein may increase expression of IFNy, TNFa, Granzyme A, Granzyme B, IL-6, perforin, IL-2, granulysin, or any combination thereof. In some embodiments, the contacting may increase an expression level of at least one cytokine moleculecompared to an expression level of the at least one cytokine molecule produced from contacting the multivalent polypeptide with an otherwise identical peptide conjugate / MHC complex without the targeted covalent inhibitor.
[0267] In some embodiments, a T cell contacted by a multivalent polypeptide described herein may express a concentration of IFNy of at least about, at most about, or about 1000 pg / mL, 1500 pg / mL, 2000 pg / mL, 3000 pg / mL, 4000 pg / mL, 5000 pg / mL, 10,000 pg / mL, 20,000 pg / mL, 25,000 pg / mL, 50,000 pg / mL, 100,000 pg / mL, 200,000 pg / mL, or a range between any of these two values. In some embodiments, a T cell contacted by a multivalent polypeptide described herein may express a concentration of granzyme B of at least about, at most about, or about 1000 pg / mL, 1500 pg / mL, 2000 pg / mL, 3000 pg / mL, 4000 pg / mL, 5000 pg / mL, 10,000 pg / mL, 20,000 pg / mL, 25,000 pg / mL, 50,000 pg / mL, 100,000 pg / mL, 200,000 pg / mL, or a range between any of these two values. In some embodiments, a T cell contacted by a multivalent polypeptide described herein may express a concentration of granzyme A of at least about, at most about, or about 1000 pg / mL, 1500 pg / mL, 2000 pg / mL, 3000 pg / mL, 4000 pg / mL, 5000 pg / mL, 10,000 pg / mL, 20,000 pg / mL, 25,000 pg / mL, 50,000 pg / mL, 100,000 pg / mL, 200,000 pg / mL, or a range between any of these two values. In some embodiments, a T cell contacted by a multivalent polypeptide described herein may express a concentration of TNFa of at least about, at most about, or about 1 pg / mL, 5 pg / mL, 10 pg / mL, 50 pg / mL, 100 pg / mL, 250 pg / mL, 500 pg / mL, 1,000 pg / mL, 2,000 pg / mL, 2,500 pg / mL, 3,000 pg / mL, 5,000 pg / mL, or a range between any of these two values. In some embodiments, a T cell contacted by a multivalent polypeptide described herein may express a concentration of IL-6 of at least about, at most about, or about 1000 pg / mL, 1500 pg / mL, 2000 pg / mL, 3000 pg / mL, 4000 pg / mL, 5000 pg / mL, 10,000 pg / mL, 20,000 pg / mL, 25,000 pg / mL, 50,000 pg / mL, 100,000 pg / mL, 200,000 pg / mL, or a range between any of these two values. In some embodiments, a T cell contacted by a multivalent polypeptide described herein may express a concentration of granulysin of at least about, at most about, or about 1000 pg / mL, 1500 pg / mL, 2000 pg / mL, 3000 pg / mL, 4000 pg / mL, 5000 pg / mL, 6,000 pg / mL, 8,000 pg / mL, 10,000 pg / mL, 15,000 pg / mL, 20,000 pg / mL, or a range between any of these two values. In some embodiments, a T cell contacted by a multivalent polypeptide described herein may express a concentration of perforin of at least about, at most about, or about 1000 pg / mL, 1500 pg / mL, 2000 pg / mL, 3000 pg / mL, 4000 pg / mL, 5000 pg / mL, 6,000 pg / mL, 8,000 pg / mL, 10,000 pg / mL, 15,000 pg / mL, 20,000 pg / mL, or a range between any of these two values. In some embodiments, a T cell contacted by a multivalent polypeptide described herein may express a concentration of IL-2 of at least about, at most about, or about 1 pg / mL, 5 pg / mL, 10 pg / mL, 50pg / mL, 100 pg / mL, 250 pg / mL, 500 pg / mL, 1,000 pg / mL, 2,000 pg / mL, 2,500 pg / mL, 3,000 pg / mL, 5,000 pg / mL, or a range between any of these two values.Methods of Targeting and / or Killing a Cell
[0268] In an aspect, provided herein are methods of killing a cancer cell in a subject in need thereof. In some embodiments, the method comprises administering a targeted covalent inhibitor (e.g., divarasib) to the subject. The method can comprise administering the multivalent polypeptide described herein, the polynucleotide described herein, the vector described herein, the cell described herein, or the pharmaceutical composition described herein.
[0269] The targeted covalent inhibitor and multivalent polypeptide may be administered concurrently. In some cases, the targeted covalent inhibitor can be administered prior to the multivalent polypeptide.
[0270] In some embodiments, a potency of a multivalent polypeptide may be determined by a half maximal effective concentration value (ECso value). In some embodiments, multivalent polypeptides may have similar potencies across different HL A alleles from subjects. In some embodiments, multivalent polypeptides may have different potencies across different HLA alleles from subjects. In some embodiments, a multivalent polypeptide may comprise an ECso value of at least about 0.001 nM, at least about 0.01 nM, at least about 0.1 nM, at least about 0.15 nM, at least about 0.2 nM, at least about 0.25 nM, at least about 0.3 nM, at least about 0.35 nM, at least about 0.4 nM, at least about 0.45 nM, at least about 0.5 nM, at least about 0.55 nM, at least about 0.6 nM, at least about 0.65 nM, at least about 0.7 nM, at least about 0.75 nM, at least about 0.8 nM, at least about 0.9 nM, at least about 1 nM, at least about 1.5 nM, at least about 2 nM, at least about 2.5 nM, at least about 3 nM, at least about 4 nM, at least about 5 nM, at least about 6 nM, at least about 7 nM, at least about 8 nM, at least about 9 nM, at least about 10 nM, or greater than about 10 nM. In some embodiments, a multivalent polypeptide may comprise an ECso value of at most about 10 nM, at most about 9 nM, at most about 8 nM, at most about 7 nM, at most about 6 nM, at most about 5 nM, at most about 4 nM, at most about 3 nM, at most about 2.5 nM, at most about 2 nM, at most about 1.5 nM, at most about 1 nM, at most about 0.9 nM, at most about 0.8 nM, at most about 0.75 nM, at most about 0.7 nM, at most about 0.65 nM, at most about 0.6 nM, at most about 0.55 nM, at most about 0.5 nM, at most about 0.45 nM, at most about 0.4 nM, at most about 0.35 nM, at most about 0.3 nM, at most about 0.25 nM, at most about 0.2 nM, at most about 0.15 nM, at most about 0.1 nM, at most about 0.01 nM, at most about 0.001 nM, or less than about 0.001 nM.
[0271] In some embodiments, a multivalent polypeptide may comprise an ECso value from about 0.1 nM to about 5 nM. In some embodiments, a multivalent polypeptide may comprise an ECso value from about 0.1 nM to about 0.2 nM, about 0.1 nM to about 0.3 nM, about 0.1 nM to about 0.4 nM, about 0.1 nM to about 0.5 nM, about 0.1 nM to about 0.6 nM, about 0.1 nM to about 0.7 nM, about 0.1 nM to about 0.8 nM, about 0.1 nM to about 1 nM, about 0.1 nM to about 2 nM, about 0.1 nM to about 3 nM, about 0.1 nM to about 5 nM, about 0.2 nM to about 0.3 nM, about 0.2 nM to about 0.4 nM, about 0.2 nM to about 0.5 nM, about 0.2 nM to about 0.6 nM, about 0.2 nM to about 0.7 nM, about 0.2 nM to about 0.8 nM, about 0.2 nM to about 1 nM, about 0.2 nM to about 2 nM, about 0.2 nM to about 3 nM, about 0.2 nM to about 5 nM, about 0.3 nM to about 0.4 nM, about 0.3 nM to about 0.5 nM, about 0.3 nM to about 0.6 nM, about 0.3 nM to about 0.7 nM, about 0.3 nM to about 0.8 nM, about 0.3 nM to about 1 nM, about 0.3 nM to about 2 nM, about 0.3 nM to about 3 nM, about 0.3 nM to about 5 nM, about 0.4 nM to about 0.5 nM, about 0.4 nM to about 0.6 nM, about 0.4 nM to about 0.7 nM, about 0.4 nM to about 0.8 nM, about 0.4 nM to about 1 nM, about 0.4 nM to about 2 nM, about 0.4 nM to about 3 nM, about 0.4 nM to about 5 nM, about 0.5 nM to about 0.6 nM, about 0.5 nM to about 0.7 nM, about 0.5 nM to about 0.8 nM, about 0.5 nM to about 1 nM, about 0.5 nM to about 2 nM, about 0.5 nM to about 3 nM, about 0.5 nM to about 5 nM, about 0.6 nM to about 0.7 nM, about 0.6 nM to about 0.8 nM, about 0.6 nM to about 1 nM, about 0.6 nM to about 2 nM, about 0.6 nM to about 3 nM, about 0.6 nM to about 5 nM, about 0.7 nM to about 0.8 nM, about 0.7 nM to about 1 nM, about 0.7 nM to about 2 nM, about 0.7 nM to about 3 nM, about 0.7 nM to about 5 nM, about 0.8 nM to about 1 nM, about 0.8 nM to about 2 nM, about 0.8 nM to about 3 nM, about 0.8 nM to about 5 nM, about 1 nM to about 2 nM, about 1 nM to about 3 nM, about 1 nM to about 5 nM, about 2 nM to about 3 nM, about 2 nM to about 5 nM, or about 3 nM to about 5 nM.
[0272] In another aspect, the present disclosure provides a method of targeting a cell that expresses KRAS in a subject in need thereof. In some embodiments, the KRAS comprises a G12C mutation (e.g., KRASG12C). In some embodiments, the KRAS comprises a G13C mutation (e.g., KRASG13C). In some embodiments, the KRAS comprises a G12D mutation (e.g., KRASG12D). In some embodiments, the KRAS comprises a G12R mutation (e.g., KRASG12R). In some embodiments, the KRAS comprises a G12R mutation (e.g., KRASG12S). In some cases, the subject is administered the multivalent polypeptide described herein, the polynucleotide described herein, the vector described herein, the cell described herein, or the pharmaceutical composition described herein. In some embodiments, the subject has previously been administered a targeted covalent inhibitor. In some embodiments, the targeted covalent inhibitor can be a KRASG12Ctargetedcovalent inhibitor. In some embodiments, the targeted covalent inhibitor can be a KRASG13Ctargeted covalent inhibitor. In some embodiments, the targeted covalent inhibitor can be a KRASG12Dtargeted covalent inhibitor. In some embodiments, the targeted covalent inhibitor can be a KRASG12Rtargeted covalent inhibitor. In some embodiments, the targeted covalent inhibitor can be a KRASG12Stargeted covalent inhibitor. In some embodiments, the targeted covalent inhibitor can be a pan-KRAS inhibitor. The KRASG12Ctargeted covalent inhibitor may be divarasib.
[0273] In some embodiments, the subject has a cancer. In some embodiments, the subject is a refractory subject from a treatment with at least one targeted covalent inhibitor (e.g., a KRASG12Ctargeted covalent inhibitor, a KRASG13Ctargeted covalent inhibitor, a KRASG12Dtargeted covalent inhibitor, a KRASG12Rtargeted covalent inhibitor, a KRASG12Stargeted covalent inhibitor, a pan- KRAS inhibitor, or any combination thereof). In some embodiments, the subject has relapsed following treatment with at least one targeted covalent inhibitor (e.g., a KRASG12Ctargeted covalent inhibitor, a KRASG13Ctargeted covalent inhibitor, a KRASG12Dtargeted covalent inhibitor, a KRASG12Rtargeted covalent inhibitor, a KRASG12Stargeted covalent inhibitor, a pan- KRAS inhibitor, or any combination thereof).
[0274] As another example, provided herein are methods of killing a target cell expressing a peptide conjugate / MHC complex, the method comprising: contacting the multivalent polypeptide described herein with the target cell expressing a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC. The contacting may be in vitro or ex vivo. The level of killing may be measured by IncuCyte analysis and assessed as T cell cytotoxicity. In some embodiments, a multivalent polypeptide may demonstrate a higher level of cytotoxicity in the presence of a peptide conjugate / MHC complex described herein, compared to a level of cytotoxicity observed in the presence of a peptide alone or a peptide conjugate / MHC complex comprising a wild-type peptide (e.g., a RAS peptide with no mutation).
[0275] For example, a multivalent polypeptide may demonstrate cytotoxicity to cells expressing the peptide conjugate / MHC complex described herein of at least about 5%, at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or greater than about 80% higher than that of cytotoxicity to cells expressing the peptide alone or a peptide conjugate / MHC complex comprising a wild-type peptide (e.g., a RAS peptide with no mutation). A multivalent polypeptide may demonstrate cytotoxicity to cells expressing the peptide conjugate / MHC complex described herein of at mostabout 80%, at most about 70%, at most about 60%, at most about 50%, at most about 40%, at most about 30%, at most about 20%, at most about 10%, at most about 5%, or less than about 5% higher than that of cytotoxicity to cells expressing the peptide alone or a peptide conjugate / MHC complex comprising a wild-type peptide (e.g., a RAS peptide with no mutation).
[0276] The EC50 for T cell cytotoxicity can be measured by the percentage of living cells after exposure to the multivalent polypeptide described herein. The ECso of a T cell cytotoxicity mediated by the multivalent polypeptide, in the presence of the peptide conjugate / MHC complex comprising the mutant peptide (e.g., the RAS mutant peptide) described herein can be at most about 10 nM, at most about 9 nM, at most about 8 nM, at most about 7 nM, at most about 6 nM, at most about 5 nM, at most about 4 nM, at most about 3 nM, at most about 2.5 nM, at most about 2 nM, at most about 1.5 nM, at most about 1 nM, at most about 0.9 nM, at most about 0.8 nM, at most about 0.75 nM, at most about 0.7 nM, at most about 0.65 nM, at most about 0.6 nM, at most about 0.55 nM, at most about 0.5 nM, at most about 0.45 nM, at most about 0.4 nM, at most about 0.35 nM, at most about 0.3 nM, at most about 0.25 nM, at most about 0.2 nM, at most about 0.15 nM, at most about 0.1 nM, at most about 0.01 nM, at most about 0.001 nM, or less than about 0.001 nM.
[0277] In some cases, the subject expresses an MHC encoded by an HLA allele belonging to the HLA-A3 supertype. In some cases, the HLA allele of the HLA-A3 supertype can be HLA- A*03:01, HLA-A*l l:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA- A*34:02, HLA-A*66:01, HLA-A*03:02, HLA-A*03:04, HLA-A*03:05, HLA-A*03:06, HLA- A*03:07, HLA-A*03:08, HLA-A*03: 10, HLA-A*03: 12, HLA-A*03: 13, HLA-A*03: 14, HLA- A*03: 16, HLA-A*03: 17, HLA-A* 11 :02, HLA-A* 11 :03, HLA-A* 11 :04, HLA-A* 11 :05, HLA- A*l l:07, HLA-A*l l:08, HLA-A*l l:09, HLA-A*l l:10, HLA-A*11:12, HLA-A*11:13, HLA- A*l l:14, HLA-A*11:15, HLA-A*11:16, HLA-A*l l:20, HLA-A*11:21, HLA-A*11:23, HLA- A*31:03, HLA-A*31:04, HLA-A*31:05, HLA-A*31:06, HLA-A*31:09, HLA-A*31:11, HLA- A*33:04, HLA-A*33:05, HLA-A*33:06, HLA-A*33:07, HLA-A*34:02, HLA-A*34:03, HLA- A*34:04, HLA-A*34:06, HLA-A*66:02, HLA-A*66:03, HLA-A*66:04, HLA-A*68:03, HLA- A*68:04, HLA-A*68:08, HLA-A*68:09, HLA-A*68: 10, HLA-A*68: 12, HLA-A*68: 13, HLA- A*68: 14, HLA-A*68: 16, HLA-A*68: 19, HLA-A*68:21, HLA-A*68:22, HLA-A*68:24, HLA- A*68:25, HLA-A*68:26, HLA-A*74:02, HLA-A*74:03, HLA-A*74:04, HLA-A*74:05, HLA- A*74:07, HLA-A*74:08, HLA-A*74:09, HLA-A*74: 11, or any combination thereof. In some cases, the HLA allele of the HLA-A3 supertype can be HLA-A*03:01, HLA-A* 11 :01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, HLA-A*66:01, or any combination thereof.
[0278] In some cases, the subject expresses an MHC encoded by an HLA allele belonging to the HLA-A2 supertype. In some examples, the HLA allele of the HLA-A2 supertype can be HLA- A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA- A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, HLA-A*69:01, HLA-A*02:09, HLA- A*02:l l, HLA-A*02: 12, HLA-A*02: 13, HLA-A*02: 15, HLA-A*02: 16, HLA-A*02: 18, HLA- A*02: 19, HLA-A*02:20, HLA-A*02:21, HLA-A*02:22, HLA-A*02:24, HLA-A*02:25, HLA- A*02:26, HLA-A*02:27, HLA-A*02:28, HLA-A*02:30, HLA-A*02:31, HLA-A*02:36, HLA- A*02:37, HLA-A*02:38, HLA-A*02:39, HLA-A*02:40, HLA-A*02:43, HLA-A*02:44, HLA- A*02:45, HLA-A*02:46, HLA-A*02:47, HLA-A*02:48, HLA-A*02:49, HLA-A*02:51, HLA- A*02:54, HLA-A*02:56, HLA-A*02:57, HLA-A*02:58, HLA-A*02:59, HLA-A*02:61, HLA- A*02:62, HLA-A*02:63, HLA-A*02:66, HLA-A*02:67, HLA-A*02:68, HLA-A*02:69, HLA- A*02:70, HLA-A*02:71, HLA-A*02:72, HLA-A*02:74, HLA-A*02:75, HLA-A*02:77, HLA- A*02:78, HLA-A*02:79, HLA-A*02:82, HLA-A*02:83, HLA-A*02:85, HLA-A*02:86, HLA- A*68:27, HLA-A*68:28, or any combination thereof. In some cases, the HLA allele of the HLA- A2 supertype can be HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA- A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, HLA- A*69:01, or any combination thereof.Methods of Increasing a Half-Life of a Peptide-Conjugate / MHC Complex or Stabilizing a Peptide-Conjugate / MHC Complex
[0279] In some aspects, provided herein are methods for stabilizing a complex (such as a peptide- conjugate / MHC complex) and / or increasing a half-life of a complex (such as a peptide- conjugate / MHC complex). The method can comprise contacting the peptide conjugate / MHC complex with a multivalent polypeptide described herein. The peptide conjugate can form by the covalent reaction of a targeted covalent inhibitor (e.g., divarasib) and a peptide. The peptide conjugate / MHC complex can comprise the peptide conjugate presented by the MHC. The method can comprise measuring the half-life of the bound peptide conjugate / MHC complex and multivalent polypeptide. The contacting of the multivalent polypeptide to the peptide conjugate / MHC complex can occur at a temperature of at least about, at most about, or about 15 °C, 20 °C, 25 °C, 30 °C, 35 °C, 40 °C, 45 °C, 50 °C, or a range between any of these two values.
[0280] In some embodiments, a half-life of the peptide-conjugate / MHC complex may be at least about 5 minutes, at least about 10 minutes, at least about 15 minutes, at least about 30 minutes, at least about 45 minutes, at least about 60 minutes, at least about 2 hours, at least about 3 hours, at least about 4 hours, at least about 5 hours, at least about 6 hours, at least about 12 hours, at least about 18 hours, at least about 24 hours, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 7 days, at least about 2 weeks, at least about 3 weeks, at least about 4 weeks, or greater than 4 weeks. In some embodiments, a halflife of the peptide-conjugate / MHC complex may be at most about 4 weeks, at most about 3 weeks, at most about 2 weeks, at most about 7 days, at most about 6 days, at most about 5 days, at most about 4 days, at most about 3 days, at most about 2 days, at most about 24 hours, at most about 18 hours, at most about 12 hours, at most about 6 hours, at most about 5 hours, at most about 4 hours, at most about 3 hours, at most about 2 hours, at most about 60 minutes, at most about 45 minutes, at most about 30 minutes, at most about 15 minutes, at most about 10 minutes, at most about 5 minutes, or less than about 5 minutes.
[0281] In some cases, a half-life of the peptide-conjugate / MHC complex may be from about 0.1 hours to about 30 hours. In some cases, a half-life of the peptide-conjugate / MHC complex may be from about 0.1 hours to about 0.2 hours, about 0.1 hours to about 0.3 hours, about 0.1 hours to about 0.4 hours, about 0.1 hours to about 0.5 hours, about 0.1 hours to about 1 hour, about 0.1 hours to about 5 hours, about 0.1 hours to about 10 hours, about 0.1 hours to about 15 hours, about 0.1 hours to about 20 hours, about 0.1 hours to about 25 hours, about 0.1 hours to about 30 hours, about 0.2 hours to about 0.3 hours, about 0.2 hours to about 0.4 hours, about 0.2 hours to about 0.5 hours, about 0.2 hours to about 1 hour, about 0.2 hours to about 5 hours, about 0.2 hours to about 10 hours, about 0.2 hours to about 15 hours, about 0.2 hours to about 20 hours, about 0.2 hours to about 25 hours, about 0.2 hours to about 30 hours, about 0.3 hours to about 0.4 hours, about 0.3 hours to about 0.5 hours, about 0.3 hours to about 1 hour, about 0.3 hours to about 5 hours, about 0.3 hours to about 10 hours, about 0.3 hours to about 15 hours, about 0.3 hours to about 20 hours, about 0.3 hours to about 25 hours, about 0.3 hours to about 30 hours, about 0.4 hours to about 0.5 hours, about 0.4 hours to about 1 hour, about 0.4 hours to about 5 hours, about 0.4 hours to about 10 hours, about 0.4 hours to about 15 hours, about 0.4 hours to about 20 hours, about 0.4 hours to about 25 hours, about 0.4 hours to about 30 hours, about 0.5 hours to about 1 hour, about 0.5 hours to about 5 hours, about 0.5 hours to about 10 hours, about 0.5 hours to about 15 hours, about 0.5 hours to about 20 hours, about 0.5 hours to about 25 hours, about 0.5 hours to about 30 hours, about 1 hour to about 5 hours, about 1 hour to about 10 hours, about 1 hour toabout 15 hours, about 1 hour to about 20 hours, about 1 hour to about 25 hours, about 1 hour to about 30 hours, about 5 hours to about 10 hours, about 5 hours to about 15 hours, about 5 hours to about 20 hours, about 5 hours to about 25 hours, about 5 hours to about 30 hours, about 10 hours to about 15 hours, about 10 hours to about 20 hours, about 10 hours to about 25 hours, about 10 hours to about 30 hours, about 15 hours to about 20 hours, about 15 hours to about 25 hours, about 15 hours to about 30 hours, about 20 hours to about 25 hours, about 20 hours to about 30 hours, or about 25 hours to about 30 hours.
[0282] Stabilizing a peptide conjugate / MHC complex and / or increasing a half-life of a peptide conjugate / MHC complex described herein may comprise binding of a multivalent polypeptide to affect (e.g., increase) epitope density. Epitope density can refer to the amount of epitope bound to a mature protein (e.g., an MHC). A peptide conjugate / MHC complex may be stabilized or the half-life of a peptide conjugate / MHC complex may be increased in a subject administered a multivalent polypeptide described herein. Binding of a multivalent polypeptide may stabilize the presentation of a peptide conjugate on an MHC. Binding of a multivalent polypeptide may increase the half-life of a peptide conjugate / MHC complex compared with the half-life of a peptide conjugate / MHC complex not bound to the multivalent polypeptide. In some embodiments, administration of the multivalent polypeptide described herein may stabilize the peptide conjugate / MHC complex or increase the half-life of a peptide conjugate / MHC complex compared with the half-life of a peptide conjugate / MHC complex in a subject not administered the multivalent polypeptide. The stabilization or increase in half-life may occur in vitro or in vivo. The stability of the peptide conjugate / MHC complex may be increased compared with the stability of the peptide conjugate / MHC complex following administration of a targeted covalent inhibitor alone. The half-life of the peptide conjugate / MHC complex may be increased compared with halflife of the peptide conjugate / MHC complex following administration of a targeted covalent inhibitor alone. The half-life or stability of the peptide conjugate / MHC complex may be increased compared with a half-life or a level of stability in the absence of a multivalent polypeptide described herein.
[0283] Without wishing to be bound by theory, increasing the half-life or stabilizing the peptide conjugate / MHC complex on the surface of a cell using the multivalent polypeptide described herein can allow more time for an immune effector cell to kill the target cell expressing the peptide conjugate / MHC complex. An advantage of the present disclosure can be higher affinity multivalent polypeptides that increase the half-life or stabilize peptide conjugate / MHC complexes on the surface of target cells, providing for enhanced cell-killing effects. Addition of themultivalent polypeptide may increase the amount (e.g., increase a density) of peptide conjugate / MHC complex present on the surface of the cell.
[0284] In some embodiments, administering the multivalent polypeptide described herein can increase the density of a peptide conjugate / MHC complex on the surface of cells in the subject by at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or greater than about 90% compared with the density of a peptide conjugate / MHC complex on the surface of cells in a subject not administered the multivalent polypeptide. In some embodiments, administering the multivalent polypeptide described herein can increase the density of a peptide conjugate / MHC complex on the surface of cells in the subject by at most about 90%, at most about 80%, at most about 70%, at most about 60%, at most about 50%, at most about 45%, at most about 40%, at most about 35%, at most about 30%, at most about 25%, at most about 20%, at most about 15%, at most about 10%, at most about 5%, at most about 4%, at most about 3%, at most about 2%, at most about 1%, or less than about 1% compared with the density of a peptide conjugate / MHC complex on the surface of cells in a subject not administered the multivalent polypeptide.
[0285] In some embodiments, administering the multivalent polypeptide described herein can increase the density of a peptide conjugate / MHC complex on the surface of cells in the subject from about 5% to about 90% compared with the density of a peptide conjugate / MHC complex on the surface of cells in a subject not administered the multivalent polypeptide. In some embodiments, administering the multivalent polypeptide described herein can increase a density of a peptide conjugate / MHC complex on the surface of cells in the subject from about 5% to about 10%, about 5% to about 15%, about 5% to about 20%, about 5% to about 25%, about 5% to about 30%, about 5% to about 40%, about 5% to about 50%, about 5% to about 60%, about 5% to about 70%, about 5% to about 80%, about 5% to about 90%, about 10% to about 15%, about 10% to about 20%, about 10% to about 25%, about 10% to about 30%, about 10% to about 40%, about 10% to about 50%, about 10% to about 60%, about 10% to about 70%, about 10% to about 80%, about 10% to about 90%, about 15% to about 20%, about 15% to about 25%, about 15% to about 30%, about 15% to about 40%, about 15% to about 50%, about 15% to about 60%, about 15% to about 70%, about 15% to about 80%, about 15% to about 90%, about 20% to about 25%, about 20% to about 30%, about 20% to about 40%, about 20% to about 50%, about 20% to about 60%, about 20% to about 70%, about 20% to about 80%, about 20% to about 90%, about 25% to about30%, about 25% to about 40%, about 25% to about 50%, about 25% to about 60%, about 25% to about 70%, about 25% to about 80%, about 25% to about 90%, about 30% to about 40%, about 30% to about 50%, about 30% to about 60%, about 30% to about 70%, about 30% to about 80%, about 30% to about 90%, about 40% to about 50%, about 40% to about 60%, about 40% to about 70%, about 40% to about 80%, about 40% to about 90%, about 50% to about 60%, about 50% to about 70%, about 50% to about 80%, about 50% to about 90%, about 60% to about 70%, about 60% to about 80%, about 60% to about 90%, about 70% to about 80%, about 70% to about 90%, or about 80% to about 90% compared with the density of a peptide conjugate / MHC complex on the surface of cells in a subject not administered the multivalent polypeptide.Methods of Treatment
[0286] In some aspects, the present disclosure provides for methods of treating a subject in need thereof. In some embodiments, the method comprises administering to the subject a multivalent polypeptide described herein. In some embodiments, the method comprises administering to the subject a pharmaceutical composition described herein. In some embodiments, the subject has a cancer. The cancer can be renal cell carcinoma, breast cancer, prostate cancer, pancreatic cancer, lung cancer, liver cancer, ovarian cancer, cervical cancer, colon cancer, esophageal cancer, glioma, glioblastoma, brain cancer, stomach cancer, bladder cancer, testicular cancer, thyroid cancer, adrenal cancer, head and neck cancer, melanoma, skin cancer, sarcoma, fibrosarcoma, angiosarcoma, osteosarcoma, rhabdomyosarcoma, leukemia, lymphoma, myeloma, endometrial cancer, or a neuroendocrine tumor. In some embodiments, the cancer comprises a mutated KRAS gene (e.g., a KRAS-driven cancer or a KRAS-driven tumor).
[0287] For example, a method for treating a cancer in a subject in need thereof can comprise: administering to the subject (A) a polypeptide described herein, or (B) a multivalent polypeptide comprising (i) a first antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the first antigen-binding domain is a polypeptide described herein; (ii) a second antigenbinding domain that binds to a T cell surface protein; and (iii) an Fc region comprising a first Fc subunit and a second Fc subunit; wherein the first antigen-binding domain, the second antigenbinding domain, the first Fc subunit, and the second Fc subunit are operably linked to form a single continuous polypeptide chain.
[0288] In some embodiments, the subject can express an MHC selected from the group consisting ofHLA-A*03:01, HLA-A*l l:01, HLA-A*02:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*33:03, HLA-A*33:01, HLA-A*74:01, HLA-A*34:02, HLA-A*66:01, HLA-A*68:02,HLA-A*02:05, HLA-A*02:02, and HLA-A*02:06. In some cases, the methods can comprise identifying an HL A allele expressed by the subject. In some cases, serotyping may be performed to identity the HLA allele of the subject. The HLA allele may be identified prior to administering the multivalent polypeptide or pharmaceutical composition. In some embodiments, the subject can be heterozygous for HLA haplotype. In some embodiments, the subject can be homozygous for HLA haplotype. In some embodiments, a subject expresses an MHC encoded by an HLA allele comprising HLA-A*03 :01, HLA-A* 11 :01, HLA-A*02:01, HLA-A*68:01, HLA-A*31 :01, HLA- A*30:01, HLA-A*33:03, HLA-A*33:01, HLA-A*74:01, HLA-A*34:02, HLA-A*66:01, HLA- A*68:02, HLA-A*02:05, HLA-A*02:02, HLA-A*02:06, or any combination thereof.
[0289] In some embodiments, the subject expresses an MHC encoded by an HLA allele belonging to the HLA-A3 supertype. In some embodiments, the HLA allele of the HLA-A3 supertype can be HLA-A*03:01, HLA-A*l l:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA- A*74:01, HLA-A*34:02, HLA-A*66:01, HLA-A*03:02, HLA-A*03:04, HLA-A*03:05, HLA- A*03:06, HLA-A*03:07, HLA-A*03:08, HLA-A*03: 10, HLA-A*03: 12, HLA-A*03: 13, HLA- A*03: 14, HLA-A*03: 16, HLA-A*03: 17, HLA-A* 11 :02, HLA-A* 11 :03, HLA-A* 11 :04, HLA- A* 11 :05, HLA-A* 11 :07, HLA-A* 11 :08, HLA-A* 11 :09, HLA-A*l l : 10, HLA-A*11 : 12, HLA- A*l l : 13, HLA-A*11 : 14, HLA-A*11:15, HLA-A*11 : 16, HLA-A*l l :20, HLA-A*11 :21, HLA- A* 11 :23, HLA-A*31 :03, HLA-A*31 :04, HLA-A*31:05, HLA-A*31 :06, HLA-A*31 :09, HLA- A*31 : l l, HLA-A*33:04, HLA-A*33:05, HLA-A*33:06, HLA-A*33:07, HLA-A*34:02, HLA- A*34:03, HLA-A*34:04, HLA-A*34:06, HLA-A*66:02, HLA-A*66:03, HLA-A*66:04, HLA- A*68:03, HLA-A*68:04, HLA-A*68:08, HLA-A*68:09, HLA-A*68: 10, HLA-A*68: 12, HLA- A*68: 13, HLA-A*68: 14, HLA-A*68: 16, HLA-A*68: 19, HLA-A*68:21, HLA-A*68:22, HLA- A*68:24, HLA-A*68:25, HLA-A*68:26, HLA-A*74:02, HLA-A*74:03, HLA-A*74:04, HLA- A*74:05, HLA-A*74:07, HLA-A*74:08, HLA-A*74:09, HLA-A*74: 11, or any combination thereof. In some embodiments, the HLA allele of the HLA-A3 supertype can be HLA-A*03:01, HLA-A* 11 :01, HLA-A*68:01, HLA-A*31 :01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, HLA-A*66:01, or any combination thereof.
[0290] In some embodiments, the subject expresses an MHC encoded by an HLA allele belonging to the HLA-A2 supertype. In some embodiments, the HLA allele of the HLA-A2 supertype can be HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA- A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, HLA-A*69:01, HLA- A*02:09, HLA-A*02: l l, HLA-A*02: 12, HLA-A*02: 13, HLA-A*02: 15, HLA-A*02: 16, HLA- A*02: 18, HLA-A*02: 19, HLA-A*02:20, HLA-A*02:21, HLA-A*02:22, HLA-A*02:24, HLA-A*02:25, HLA-A*02:26, HLA-A*02:27, HLA-A*02:28, HLA-A*02:30, HLA-A*02:31, HLA- A*02:36, HLA-A*02:37, HLA-A*02:38, HLA-A*02:39, HLA-A*02:40, HLA-A*02:43, HLA- A*02:44, HLA-A*02:45, HLA-A*02:46, HLA-A*02:47, HLA-A*02:48, HLA-A*02:49, HLA- A*02:51, HLA-A*02:54, HLA-A*02:56, HLA-A*02:57, HLA-A*02:58, HLA-A*02:59, HLA- A*02:61, HLA-A*02:62, HLA-A*02:63, HLA-A*02:66, HLA-A*02:67, HLA-A*02:68, HLA- A*02:69, HLA-A*02:70, HLA-A*02:71, HLA-A*02:72, HLA-A*02:74, HLA-A*02:75, HLA- A*02:77, HLA-A*02:78, HLA-A*02:79, HLA-A*02:82, HLA-A*02:83, HLA-A*02:85, HLA- A*02:86, HLA-A*68:27, HLA-A*68:28, or any combination thereof. In some embodiments, the HLA allele of the HLA-A2 supertype can be HLA-A*02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, HLA-A*69:01, or any combination thereof.
[0291] In some embodiments, administration of the multivalent polypeptide is the first line of treatment. In some embodiments, the subject has previously been administered a targeted covalent inhibitor described herein. In some embodiments, the subject has previous been administered divarasib, AMG-510 (e.g., sotorasib), MRTX849 (e.g., adagrasib), opnurasib, garsorasib, l-[4- [6-chloro-8-fluoro-7-(2-fluoro-6-hydroxyphenyl)quinazolin-4-yl]piperazin- 1 -yl]prop-2-en- 1 - one, l-(3-(4-((4-chloro-2-hydroxy-5-(l-methylcyclopropyl)phenyl)glycyl)piperazin-l- yl)azetidin-l-yl)prop-2-en-l-one, l-(4-(7-(2-Amino-7-fluoro-l,3-benzothiazol-4-yl)-6-chloro-8- fluoro-quinazolin-4-yl)piperazin- 1 -yl)prop-2-en- 1 -one, 2- Amino-4-[(4aS)-8-chloro- 10-fluoro-2,3,4,4a, 5 ,6-hexahy dro- 12-oxo-3 -( 1 -oxo-2-propen- 1 -y 1 ) - 1 H, 12H-pyrazino[2, 1 - d][l,5]benzoxazocin-9-yl]-7-fluorobenzo[b]thiophene-3-carbonitrile, 2-[(2S)-4-[7-(8- methylnaphthalen-l-yl)-2-[[(2S)-l-methylpyrrolidin-2-yl]methoxy]-6,8-dihydro-5H-pyrido[3,4- d]pyrimidin-4-yl]-l-prop-2-enoylpiperazin-2-yl]acetonitrile, 4-(4-(3,8-Diazabicyclo[3.2.1]octan- 3-yl)-8-fluoro-2-(((2R,7aS)-2-fluorohexahydro-lH-pyrrolizin-7a-yl)methoxy)pyrido[4,3- d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol, l-[4-(dimethylamino)-4-methylpent-2- ynoyl]-N-[(2S)-l-[[(6S,8S,14S)-22-ethyl-21-[2-[(lS)-l-methoxyethyl]pyridin-3-yl]-18,18- dimethyl-9, 15-dioxo-5, 16-dioxa-2, 10,22,28- tetrazapentacyclo[18.5.2.12,6.110,14.023,27]nonacosa-l(26),20,23(27),24-tetraen-8-yl]amino]- 3-methyl-l-oxobutan-2-yl]-4-fluoro-N-methylpiperidine-4-carboxamide, or [[(2R,3S,4R,5R)-5- (2-amino-6-oxo-lH-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] 2-[(2- chloroacetyl)amino]ethyl hydrogen phosphate]. In some embodiments, the targeted covalent inhibitor can comprise GDC6036, MK-1084, l-((3R,14aS)-l l-Chloro-9-fluoro-10-(2-fluoro-6- hy droxyphenyl)-3 -methyl- 1,3,4,13,14,14a-hexahy dro-2H-pyrazino[l',2':5,6][l,5]oxazocino[4,3,2-de]quinazolin-2-yl)prop-2-en-l-one (e.g., AZD4625), or N-(5 -(3 , 5 -dimethoxyphenethyl)- 1 H-pyrazol-3 -yl)-4-((3 S, 5R)-3 , 5 -dimethylpiperazin- 1 - yl)benzamide (e.g., AZD4747).
[0292] In some embodiments, the subject is a refractory subject from a treatment with at least one targeted covalent inhibitor (e.g., a KRASG12Ctargeted covalent inhibitor, a KRASG13Ctargeted covalent inhibitor, a KRASG12Dtargeted covalent inhibitor, a KRASG12Rtargeted covalent inhibitor, a KRASG12Stargeted covalent inhibitor, a pan-KRAS inhibitor, or any combination thereof). In some embodiments, the subject has relapsed following treatment with at least one targeted covalent inhibitor (e.g., a KRASG12Ctargeted covalent inhibitor, a KRASG13Ctargeted covalent inhibitor, a KRASG12Dtargeted covalent inhibitor, a KRASG12Rtargeted covalent inhibitor, a KRASG12Stargeted covalent inhibitor, a pan-KRAS inhibitor, or any combination thereof).
[0293] In some cases, the peptide of the peptide-conjugate / MHC complex (e.g., VVVGACGVGK, VVGACGVGK, KLVVVGACGV, VVVGAGCVGK, VVGAGCVGK, or KLVVVGAGCV) can comprise a G12C or G13C mutation.
[0294] In some embodiments, a subject expresses an MHC encoded by HLA-A*03:01, in complex with a peptide conjugate comprising divarasib covalently bound to VVVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A* 11 :01, in complex with a peptide conjugate comprising divarasib covalently bound to VVVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*02:01, in complex with a peptide conjugate comprising divarasib covalently bound to VVVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*68:01, in complex with a peptide conjugate comprising divarasib covalently bound to VVVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*31 :01, in complex with a peptide conjugate comprising divarasib covalently bound to VVVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*30:01, in complex with a peptide conjugate comprising divarasib covalently bound to VVVGACGVGK, and isadministered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*33:03, in complex with a peptide conjugate comprising divarasib covalently bound to VVVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*68:02, in complex with a peptide conjugate comprising divarasib covalently bound to VVVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein.
[0295] In some embodiments, a subject expresses an MHC encoded by HLA-A*03:01, in complex with a peptide conjugate comprising divarasib covalently bound to VVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A* 11 :01, in complex with a peptide conjugate comprising divarasib covalently bound to VVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*02:01, in complex with a peptide conjugate comprising divarasib covalently bound to VVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*68:01, in complex with a peptide conjugate comprising divarasib covalently bound to VVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*31:01, in complex with a peptide conjugate comprising divarasib covalently bound to VVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*30:01, in complex with a peptide conjugate comprising divarasib covalently bound to VVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*33:03, in complex with a peptide conjugate comprising divarasib covalently bound to VVGACGVGK, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*68:02, in complex with a peptide conjugate comprising divarasib covalently bound to VVGACGVGK, and isadministered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein.
[0296] In some embodiments, a subject expresses an MHC encoded by HLA-A*03:01, in complex with a peptide conjugate comprising divarasib covalently bound to KLVVVGACGV, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A* 11 :01, in complex with a peptide conjugate comprising divarasib covalently bound to KLVVVGACGV, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*02:01, in complex with a peptide conjugate comprising divarasib covalently bound to KLVVVGACGV, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*68:01, in complex with a peptide conjugate comprising divarasib covalently bound to KLVVVGACGV, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*31 :01, in complex with a peptide conjugate comprising divarasib covalently bound to KLVVVGACGV, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*30:01, in complex with a peptide conjugate comprising divarasib covalently bound to KLVVVGACGV, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*33:03, in complex with a peptide conjugate comprising divarasib covalently bound to KLVVVGACGV, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein. In some embodiments, a subject expresses an MHC encoded by HLA-A*68:02, in complex with a peptide conjugate comprising divarasib covalently bound to KLVVVGACGV, and is administered (i) the multivalent polypeptide described herein, or (ii) the pharmaceutical composition described herein.
[0297] Suitable routes of administrating the multivalent polypeptides or pharmaceutical compositions described herein can include, but are not limited to, topical, subcutaneous, transdermal, intradermal, intralesional, intraarticular, intraperitoneal, intravesical, transmucosal, gingival, intradental, intracochlear, transtympanic, intraorgan, epidural, intrathecal, intramuscular, intravenous, intravascular, intraosseus, periocular, intratumoral, intracerebral, andintracerebroventricular administration. In some embodiments, the multivalent polypeptides or pharmaceutical compositions described herein can be administered locally to a diseased site (e.g., tumor site). In some embodiments, the multivalent polypeptides or pharmaceutical compositions described herein can be administered to a subject by injection, by means of a catheter, or by means of a suppository. In some embodiments, the multivalent polypeptides or pharmaceutical compositions described herein can be delivered in a controlled release system.
[0298] In some cases, provided herein is a method of preventing a disease or condition in a subject that will receive a drug to treat the disease or condition, the method comprising administering the peptide-drug conjugate prophylactically to a subject as a vaccine to a disease or condition treated with a drug, wherein the subject does not have the disease or condition at the time of administration, and wherein the subject will receive the drug if the subject develops the disease or condition.
[0299] In some embodiments, the method further comprises administering an additional therapeutic agent. In some embodiments, the additional therapeutic agent can be a conventional chemotherapeutic agent, a modulator of T-cell costimulatory molecules, an immune checkpoint inhibitor, or any combination thereof. In some embodiments, the additional therapeutic agent can be a chemotherapeutic or an immunomodulator. In some embodiments, the immunomodulator can be a checkpoint targeting agent.
[0300] In some embodiments, the additional therapeutic agent can be a checkpoint targeting agent selected from the group consisting of an antagonist anti-PD-1 antibody, an antagonist anti-PD-Ll antibody, an antagonist anti-PD-L2 antibody, an antagonist anti-CTLA-4 antibody, an antagonist anti-BTLA antibody, an antagonist anti-TREMR antibody, an antagonist anti-TIGIT antibody, an antagonist anti-VISTA antibody, an antagonist anti-TIM-3 antibody, an antagonist anti-LAG-3 antibody, an antagonist anti-CEACAMl antibody, an agonist anti-GITR antibody, an agonist anti- 0X40 antibody, and an agonist anti-CD137 antibody, an agonist anti-DR3 antibody, an agonist anti-TNFSF14 antibody, an agonist anti-CD27 antibody, an agonist anti-ICOS antibody, an agonist anti-CD28 antibody. In some embodiments, the additional therapeutic agent can be radiotherapy. In some embodiments, the anti-PD-1 a...
Claims
CLAIMSWHAT IS CLAIMED IS:
1. A polypeptide comprising an antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; and wherein the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant (KD) of at most 250 nanometers (nM).
2. The polypeptide of claim 1, wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA allele selected from the group consisting of HLA-A*02, HLA- A*03, and HLA-A*l l.
3. The polypeptide of claim 1, wherein the MHC is encoded by an HLA allele of HLA- A3 supertype.
4. The polypeptide of claim 3, wherein the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A* 03:01, HLA-A* 11 :01, HLA-A*68:01, HLA- A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01.
5. The polypeptide of claim 3, wherein the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A* 03:01, HLA-A* 11 :01, HLA-A*68:01, and HLA- A*34:02.
6. The polypeptide of claim 1, wherein the MHC is encoded by an HLA allele of HLA-A2 supertype.
7. The polypeptide of claim 6, wherein the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A* 02:01, HLA-A* 02: 02, HLA-A* 02: 03, HLA- A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01.
8. The polypeptide of claim 6, wherein the HLA allele of the HLA-A2 supertype is HLA- A*02:01.
9. A polypeptide comprising an antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib;wherein the polypeptide binds to each of (i) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele, (ii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele, and (iii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*11 allele with a dissociation constant (KD) of at most 250 nM.
10. A polypeptide comprising an antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA allele selected from the group consisting of HLA-A*02, HLA-A*03, and HLA-A*11.
11. The polypeptide of claim 10, wherein the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant (KD) of at most 250 nM.
12. The polypeptide of any one of claims 1-11, wherein the KD is at most 200 nM, at most 150 nM, at most 100 nM, or at most 50 nM.
13. The polypeptide of any one of claims 1-12, wherein the polypeptide binds to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele with a KD of at least 2-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele.
14. The polypeptide of any one of claims 1-13, wherein the polypeptide binds to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*11 allele with a KD of at least 2-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele.
15. A polypeptide comprising an antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC; wherein the targeted covalent inhibitor is divarasib; wherein the polypeptide binds to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof, the same peptide, and the same MHC with a dissociation constant (KD) that is at least 1,000 nM.
16. The polypeptide of claim 15, wherein the polypeptide binds to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof, the same peptide, and the same MHC with a Kothat is at least 5,000 nM, at least 10,000 nM, at least 50,000 nM, at least 100,000 nM, at least 500,000 nM, or at least 1,000,000 nM.
17. The polypeptide of claim 15 or 16, wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA allele selected from the group consisting of HLA-A*02, HLA-A*03, and HLA-A* 11.
18. The polypeptide of any one of claims 15-17, wherein the polypeptide binds to each of (i) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele, (ii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele, and (iii) a peptide conjugate / MHC complex with an MHC encoded by an HLA-A* 11 allele with a dissociation constant (KD) of at most 250 nM.
19. The polypeptide of claim 18, wherein the KD is at most 200 nM, at most 150 nM, at most 100 nM, or at most 50 nM.
20. The polypeptide of any one of claims 15-19, wherein the polypeptide binds to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele with a KD of at least 2-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*02 allele.
21. The polypeptide of any one of claims 15-20, wherein the polypeptide binds to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A* 11 allele with a KD of at least 2-fold more than the KD of the polypeptide to a peptide conjugate / MHC complex with an MHC encoded by an HLA-A*03 allele.
22. The polypeptide of any one of claims 17-19, wherein the HLA-A*02 allele is a HLA- A*02:01 allele.
23. The polypeptide of any one of claims 17-19, wherein the HLA-A*03 allele is an HLA- A*03:01 allele.
24. The polypeptide of any one of claims 17-19, wherein the HLA-A* 11 allele is an HLA- A* 11 :01 allele.
25. The polypeptide of claim 15 or 16, wherein the MHC is encoded by an HLA allele of HLA-A3 supertype.
26. The polypeptide of claim 25, wherein the HLA allele of the HLA-A3 supertype is selected from the group consisting of HL A-A* 03:01, HLA-A* 11 :01, HLA-A*68:01, HLA-A*31 :01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01.
27. The polypeptide of claim 25, wherein the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA- A* 03:01, HLA-A* 11 :01, HLA-A*68:01, and HLA-A*34:02.
28. The polypeptide of claim 15 or 16, wherein the MHC is encoded by an HLA allele of HLA-A2 supertype.
29. The polypeptide of claim 28, wherein the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A* 02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA- A*02: 17, HLA-A*68:02, and HLA-A* 69:01.
30. The polypeptide of claim 28, wherein the HLA allele of the HLA-A2 supertype is HLA- A*02:01.
31. The polypeptide of any one of claims 1-30, wherein the peptide is a RAS peptide.
32. The polypeptide of claim 31, wherein the RAS peptide comprises a mutation.
33. The polypeptide of claim 32, wherein the mutation is G12C.
34. The polypeptide of any one of claims 31-33, wherein the RAS peptide comprises a sequence selected from the group consisting of VVVGACGVGK, VVGACGVGK, and KLVVVGACGV.
35. The polypeptide of any one of claims 1-34, wherein an interface area of the polypeptide with the peptide conjugate / MHC complex is at least about 500A2, 600A2, 700A2, 800A2, 900A2, l,000A2, l,200A2, l,500A2, or 2,000A2.
36. The polypeptide of any one of claims 1-35, wherein the polypeptide binds an epitope of the MHC, and wherein the epitope comprises one or more amino acid residues conserved among HLA-A* 03, HLA-A* 02, and HLA-A* 11.
37. The polypeptide of any one of claims 1-36, wherein the polypeptide binds an epitope of the MHC, and wherein the epitope comprises one or more amino acid residues at positions 42-73 and 167 of HLA-A*03, HLA-A*02, or HLA-A*11.
38. The polypeptide of any one of claims 1-35, wherein the polypeptide binds an epitope of the MHC, and wherein the epitope comprises one or more amino acid residues at positions 42-73 and 167 of SEQ ID NO: 80.
39. The polypeptide of any one of claims 1-35, wherein the polypeptide binds an epitope of the MHC, and wherein the epitope comprises one or more amino acid residues selected from the group consisting of S42, Q43, R44, P57, E58, D61, Q62, T64, R65, K68, Q72,W167, and any combination thereof of the HLA-A*03, HLA-A*02, or HLA-A*11, or of SEQ ID NO: 80.
40. The polypeptide of any one of claims 1-35, wherein a VL domain of the antigen-binding domain binds to an epitope of the MHC, and wherein the epitope comprises one or more residues selected from the group consisting of residues S42, Q43, D61, T64, R65, K68, and Q72 of HLA-A*03, HLA-A*02, or HLA-A*11, or of SEQ ID NO: 80.
41. The polypeptide of any one of claims 1-35, wherein a VH domain of the antigen-binding domain binds to an epitope of the MHC, and wherein the epitope comprises one or more residues selected from the group consisting of residues R44, P57, E58, D61, Q62, R65, and W167 of HLA-A*03, HLA-A*02, or HLA-A*11, or of SEQ ID NO: 80.
42. The polypeptide of any one of claims 1-41, wherein the polypeptide interacts with one or more residues of the peptide conjugate in the peptide conjugate / MHC complex, and wherein the peptide comprises p? peptide of VVVGACGVGK, ps peptide of KLVVVGACGV, or p8peptide of VVGACGVGK.
43. The polypeptide of claim 42, wherein the one or more residues of the peptide conjugate in the peptide conjugate / MHC complex comprises one or more residues from the regions of p? peptide, ps peptide, or p8peptide comprising residues GIO, Al l, C12, or any combination thereof of the peptide conjugate.
44. The polypeptide of any one of claims 1-35, wherein one or more residues of a VH domain of the antigen-binding domain interact with the MHC, and wherein the one or more residues of the VH domain comprise amino acid residues selected from the group consisting of residues S31, Y32, S52, Y53, G100, N101, S102, and Y103 as set forth in SEQ ID NO: 9.
45. The polypeptide of claim 44, wherein one or more residues of the VH domain of the antigen-binding domain interact with the targeted covalent inhibitor, and wherein the one or more residues of the VH domain comprise amino acid residues selected from the group consisting of residues G33, H35, W47, V50, S52, N57, Y59, Y60, A61, and D62 as set forth in SEQ ID NO: 9.
46. The polypeptide of claim 44 or 45, wherein one or more residues of the VH domain of the antigen-binding domain interact with the peptide, and wherein the one or more residues of the VH domain comprise amino acid residues N57 or Y59 as set forth in SEQ ID NO: 9.
47. The polypeptide of any one of claims 1-35, wherein one or more residues of a VL domain of the antigen-binding domain interact with the MHC, and wherein the one or more residues of the VL domain comprise amino acid residues selected from the group consisting of residues Q27, S28, L29, S30, S31, S32, F33, S92, E93, S94, A95, and L96 as set forth in SEQ ID NO: 10.
48. The polypeptide of claim 47, wherein one or more residues of the VL domain of the antigen-binding domain interact with the targeted covalent inhibitor, and wherein the one or more residues of the VL domain comprise amino acid residues selected from the group consisting of residues DI, 12, S92, E93, S94, A95, L96, and T97 as set forth in SEQ ID NO: 10.
49. The polypeptide of any one of claims 1-48, wherein the polypeptide comprises an antigen-binding domain that comprises a heavy chain variable region (VH), and wherein the VH comprises a heavy chain complementarity determining region 3 (CDR-H3) comprising the amino acid sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5).
50. The polypeptide of claim 49, wherein the VH comprises a CDR-H2 comprising the amino acid sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4).
51. The polypeptide of claim 49 or 50, wherein the VH comprises a CDR-H1 comprising the amino acid sequence of STNWWT (SEQ ID NO: 3).
52. The polypeptide of any one of claims 49-51, wherein the antigen-binding domain further comprises a light chain variable region (VL), and wherein the VL comprises a light chain complementarity determining region 3 (CDR-L3) comprising the amino acid sequence of QAWDSNTVV (SEQ ID NO: 8).
53. The polypeptide of claim 52, wherein the VL comprises a CDR-L2 comprising the amino acid sequence of GKNERPS (SEQ ID NO: 7).
54. The polypeptide of claim 52 or 53, wherein the VL comprises a CDR-L1 comprising the amino acid sequence of RGDSFRVFSAS (SEQ ID NO: 6).
55. The polypeptide of any one of claims 49-54, wherein the antigen-binding domain comprises: a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5), a CDR-H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4), a CDR-H1 sequence of STNWWT (SEQ ID NO: 3), a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8), a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7), anda CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6).
56. The polypeptide of any one of claims 49-55, wherein the VH comprises a sequence with at least 80% sequence identity to the sequence QLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHT GNTDYNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIY FYYGLDVWGQGTTVTVSS (SEQ ID NO: 1).
57. The polypeptide of any one of claims 52-56, wherein the VL comprises a sequence with at least 80% sequence identity to the sequence SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERP SGIPDRFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
58. The polypeptide of any one of claims 1-43, wherein the polypeptide comprises an antigen-binding domain that comprises a heavy chain variable region (VH), and wherein the VH comprises a heavy chain complementarity determining region 3 (CDR-H3) comprising the amino acid sequence of GGNSYGMDV (SEQ ID NO: 13).
59. The polypeptide of claim 58, wherein the VH comprises a CDR-H2 comprising the amino acid sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12).
60. The polypeptide of claim 58 or 59, wherein the VH comprises a CDR-H1 comprising the amino acid sequence of SYGMH (SEQ ID NO: 11).
61. The polypeptide of any one of claims 58-60, wherein the antigen-binding domain further comprises a light chain variable region (VL), and wherein the VL comprises a light chain complementarity determining region 3 (CDR-L3) comprising the amino acid sequence of QQSESALT (SEQ ID NO: 16).
62. The polypeptide of claim 61, wherein the VL comprises a CDR-L2 comprising the amino acid sequence of GASSRAT (SEQ ID NO: 15).
63. The polypeptide of claim 61 or 62, wherein the VL comprises a CDR-L1 comprising the amino acid sequence of RASQSLSSSFLA (SEQ ID NO: 14).
64. The polypeptide of any one of claims 58-63, wherein the antigen-binding domain comprises: a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13), a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12), a CDR-H1 sequence of SYGMH (SEQ ID NO: 11), a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16),a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15), and a CDR-Ll sequence of RASQSLSSSFLA (SEQ ID NO: 14).
65. The polypeptide of any one of claims 58-64, wherein the VH comprises a sequence with at least 80% sequence identity to the sequence EVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISY DGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGM DVWGQGTMVTVSS (SEQ ID NO: 9).
66. The polypeptide of any one of claims 61-65, wherein the VL comprises a sequence with at least 80% sequence identity to the sequence DIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSR ATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
67. A polypeptide comprising an antigen-binding domain that comprises a heavy chain variable region (VH), wherein the VH comprises: a CDR-H3 sequence according to Kabat according to Table 1, or a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5) or GGNSYGMDV (SEQ ID NO: 13).
68. The polypeptide of claim 67, wherein the VH comprises a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5).
69. The polypeptide of claim 67 or 68, wherein the VH further comprises a CDR-H1 sequence of STNWWT (SEQ ID NO: 3).
70. The polypeptide of any one of claims 67-69, wherein the VH further comprises a CDR- H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4).
71. The polypeptide of any one of claims 67-70, wherein the polypeptide further comprises a light chain variable region (VL), wherein the VL comprises a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8).
72. The polypeptide of claim 71, wherein the VL further comprises a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6).
73. The polypeptide of claim 71 or 72, wherein the VL further comprises a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7).
74. The polypeptide of any one of claims 67-73, wherein the polypeptide comprises: a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5); a CDR-H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4); a CDR-H1 sequence of STNWWT (SEQ ID NO: 3);a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8); a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7); and a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6).
75. The polypeptide of any one of claims 67-74, wherein the VH comprises a sequence with at least 80% sequence identity to the sequence QLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHT GNTDYNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIY FYYGLDVWGQGTTVTVSS (SEQ ID NO: 1).
76. The polypeptide of any one of claims 71-75, wherein the VL comprises a sequence with at least 80% sequence identity to the sequence SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERP SGIPDRFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
77. The polypeptide of any one of claims 67-76, wherein the VH comprises the sequence QLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHT GNTDYNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIY FYYGLDVWGQGTTVTVSS (SEQ ID NO: 1).
78. The polypeptide of any one of claims 71-77, wherein the VL comprises the sequence SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERP SGIPDRFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
79. The polypeptide of claim 67, wherein the VH comprises a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13).
80. The polypeptide of claim 67 or 79, wherein the VH further comprises a CDR-H1 sequence of SYGMH (SEQ ID NO: 11).
81. The polypeptide of any one of claims 67, 79, and 80, wherein the VH further comprises a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12).
82. The polypeptide of any one of claims 67 and 79-81, wherein the polypeptide further comprises a light chain variable region (VL), wherein the VL comprises a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16).
83. The polypeptide of claim 82, wherein the VL further comprises a CDR-L1 sequence of RASQSLSSSFLA (SEQ ID NO: 14).
84. The polypeptide of claim 82 or 83, wherein the VL further comprises a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15).
85. The polypeptide of any one of claims 67 and 79-84, wherein the polypeptide comprises: a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13); a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12); a CDR-H1 sequence of SYGMH (SEQ ID NO: 11); a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16); a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15); and a CDR-Ll sequence of RASQSLSSSFLA (SEQ ID NO: 14).
86. The polypeptide of any one of claims 67 and 79-85, wherein the VH comprises a sequence with at least 80% sequence identity to the sequence EVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISY DGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGM DVWGQGTMVTVSS (SEQ ID NO: 9).
87. The polypeptide of any one of claims 82-86, wherein the VL comprises a sequence with at least 80% sequence identity to the sequence DIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSR ATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
88. The polypeptide of any one of claims 67 and 79-87, wherein the VH comprises the sequence EVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISY DGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGM DVWGQGTMVTVSS (SEQ ID NO: 9).
89. The polypeptide of any one of claims 82-88, wherein the VL comprises the sequence DIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSR ATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
90. A polypeptide comprising an antigen-binding domain that comprises a light chain variable region (VL), wherein the VL comprises: a CDR-L3 sequence according to Kabat according to Table 1, or a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8) or QQSESALT (SEQ ID NO: 16).
91. The polypeptide of claim 90, wherein the VL comprises a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8).
92. The polypeptide of claim 90 or 91, wherein the VL comprises a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6).
93. The polypeptide of any one of claims 90-92, wherein the VL comprises a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7).
94. The polypeptide of any one of claims 90-93, wherein the polypeptide further comprises a heavy chain variable region (VH), wherein the VH comprises a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5).
95. The polypeptide of claim 94, wherein the VH further comprises a CDR-H1 sequence of STNWWT (SEQ ID NO: 3).
96. The polypeptide of claim 94 or 95, wherein the VH further comprises a CDR-H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4).
97. The polypeptide of any one of claims 90-96, wherein the polypeptide comprises: a CDR-H3 sequence of GRFGSSWNYIYFYYGLDV (SEQ ID NO: 5); a CDR-H2 sequence of EIYHTGNTDYNPSLES (SEQ ID NO: 4); a CDR-H1 sequence of STNWWT (SEQ ID NO: 3); a CDR-L3 sequence of QAWDSNTVV (SEQ ID NO: 8); a CDR-L2 sequence of GKNERPS (SEQ ID NO: 7); and a CDR-L1 sequence of RGDSFRVFSAS (SEQ ID NO: 6).
98. The polypeptide of any one of claims 94-97, wherein the VH comprises a sequence with at least 80% sequence identity to the sequence QLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHT GNTDYNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIY FYYGLDVWGQGTTVTVSS (SEQ ID NO: 1).
99. The polypeptide of any one of claims 90-98, wherein the VL comprises a sequence with at least 80% sequence identity to the sequence SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERP SGIPDRFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
100. The polypeptide of any one of claims 94-99, wherein the VH comprises the sequence QLQLQESGPGLVKPSETLSLTCTVSGGSITSTNWWTWVRQSPGKGLEWIGEIYHTGNTDYNPSLESRVTISVDKSKNQFSLNLRSVTAADTAVYYCARGRFGSSWNYIY FYYGLDVWGQGTTVTVSS (SEQ ID NO: 1).
101. The polypeptide of any one of claims 90-100, wherein the VL comprises the sequence SSELTQDPDVSVALGQTVRISCRGDSFRVFSASWYQQKPGQVPVLVSYGKNERP SGIPDRFSGSTSGNIASLTITGAQAEDEADYYCQAWDSNTVVFGGGTKLTVL (SEQ ID NO: 2).
102. The polypeptide of claim 90, wherein the VL comprises a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16).
103. The polypeptide of claim 90 or 102, wherein the VL comprises a CDR-L1 sequence of RASQSLSSSFLA (SEQ ID NO: 14).
104. The polypeptide of any one of claims 90, 102, and 103, wherein the VL further comprises a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15).
105. The polypeptide of any one of claims 90 and 102-104, wherein the polypeptide further comprises a heavy chain variable region (VH), wherein the VH comprises a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13).
106. The polypeptide of claim 105, wherein the VH further comprises a CDR-H1 sequence of SYGMH (SEQ ID NO: 11).
107. The polypeptide of claim 105 or 106, wherein the VH further comprises a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12).
108. The polypeptide of any one of claims 90 and 102-107, wherein the polypeptide comprises: a CDR-H3 sequence of GGNSYGMDV (SEQ ID NO: 13); a CDR-H2 sequence of VISYDGSNKYYADSVKG (SEQ ID NO: 12); a CDR-H1 sequence of SYGMH (SEQ ID NO: 11); a CDR-L3 sequence of QQSESALT (SEQ ID NO: 16); a CDR-L2 sequence of GASSRAT (SEQ ID NO: 15); and a CDR-Ll sequence of RASQSLSSSFLA (SEQ ID NO: 14).
109. The polypeptide of any one of claims 105-108, wherein the VH comprises a sequence with at least 80% sequence identity to the sequence EVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISY DGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGM DVWGQGTMVTVSS (SEQ ID NO: 9).
110. The polypeptide of any one of claims 90 and 102-109, wherein the VL comprises a sequence with at least 80% sequence identity to the sequence DIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSR ATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
111. The polypeptide of any one of claims 105-110, wherein the VH comprises the sequence EVQLLESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISY DGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCLYGGNSYGM DVWGQGTMVTVSS (SEQ ID NO: 9).
112. The polypeptide of any one of claims 90 and 102-111, wherein the VL comprises the sequence DIVMTQSPATLSLSPGERATLSCRASQSLSSSFLAWYQQKPGQAPRLLIYGASSR ATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQSESALTFGGGTKVEIK (SEQ ID NO: 10).
113. The polypeptide of any one of claims 1-112, wherein the polypeptide binds to a peptide conjugate / MHC complex comprising sotorasib or the fragment thereof the same peptide, and the same MHC with a KD that is at least 2-fold more than the KD of the polypeptide to the peptide conjugate / MHC complex comprising divarasib or the fragment thereof.
114. The polypeptide of any one of claims 1-113, wherein the polypeptide binds to free divarasib with a KD that is at least 2-fold more than the KD of the polypeptide to the peptide conjugate / MHC complex.
115. The polypeptide of any one of claims 67-114, wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA-A*02 allele.
116. The polypeptide of any one of claims 67-115, wherein the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant of at most 50 nM, at most 25 nM, or at most 10 nM.
117. The polypeptide of any one of claims 67-114, wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA-A*03 allele.
118. The polypeptide of any one of claims 67-114 and 117, wherein the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant of at most 50 nM, at most 25 nM, at most 20 nM, or at most 15 nM.
119. The polypeptide of any one of claims 67-114, wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA-A*11 allele.
120. The polypeptide of any one of claims 67-114 and 119, wherein the polypeptide binds to the peptide conjugate / MHC complex with a dissociation constant of at most 50 nM, at most 45 nM, or at most 40 nM.
121. The polypeptide of any one of claims 67-114, wherein the MHC is encoded by an HLA allele of HLA- A3 supertype.
122. The polypeptide of claim 121, wherein the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA- A* 03:01, HLA-A* 11 :01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A* 66:01.
123. The polypeptide of claim 121, wherein the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA- A* 03:01, HLA-A* 11 :01, HLA-A*68:01, and HLA-A*34:02.
124. The polypeptide of any one of claims 67-114, wherein the MHC is encoded by an HLA allele of HLA-A2 supertype.
125. The polypeptide of claim 124, wherein the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A* 02:01, HLA-A*02:02, HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA- A*02: 17, HLA-A*68:02, and HLA-A* 69:01.
126. The polypeptide of claim 124, wherein the HLA allele of the HLA-A2 supertype is HLA-A*02:01.
127. A multivalent polypeptide comprising: a first antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the first antigen-binding domain comprises a polypeptide of any one of claims 1-126; a second antigen-binding domain that binds to a T cell surface protein; and an Fc region comprising a first Fc subunit and a second Fc subunit; and wherein the first antigen-binding domain, the second antigen-binding domain, the first Fc subunit, and the second Fc subunit are operably linked to form a single continuous polypeptide chain.
128. The multivalent polypeptide of claim 127, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the first antigen-binding domain, the second antigen-binding domain, the first Fc subunit, and the second Fc subunit.
129. The multivalent polypeptide of claim 127, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the first antigen-binding domain, a firstlinker, the second antigen-binding domain, a second linker, the first Fc subunit, a third linker, and the second Fc subunit.
130. The multivalent polypeptide of claim 127, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the second antigen-binding domain, the first antigen-binding domain, the first Fc subunit, and the second Fc subunit.
131. The multivalent polypeptide of claim 127, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the second antigen-binding domain, a first linker, the first antigen-binding domain, a second linker, the first Fc subunit, a third linker, and the second Fc subunit.
132. The multivalent polypeptide of any one of claims 127-131, wherein the Fc region comprises an amino acid sequence as set forth in SEQ ID NOs: 46 or 51, or an amino acid sequence with at least 90% sequence identity to SEQ ID NO: 46 or 51.
133. The multivalent polypeptide of claim 129 or 131, wherein the first linker, the second linker, and / or the third linker comprises an amino acid sequence as set forth in SEQ ID NOs: 43, 44, 45, 57, and 63.
134. The multivalent polypeptide of claim 133, wherein the first linker comprises an amino acid sequence as set forth in SEQ ID NO: 44.
135. The multivalent polypeptide of claim 133, wherein the second linker comprises an amino acid sequence as set forth in SEQ ID NO: 45.
136. The multivalent polypeptide of claim 133, wherein the third linker comprises an amino acid sequence as set forth in SEQ ID NO: 63 (GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS).
137. The multivalent polypeptide of any one of claims 129 and 131-136, wherein the first linker has a length of from 4-12, 4-10, 4-8, 4-6 or 6 amino acids.
138. The multivalent polypeptide of claim 137, wherein the first linker comprises an amino acid sequence according to the formula SGxS or GxS, wherein X is 3 or 4.
139. The multivalent polypeptide of claim 137 or 138, wherein the first linker comprises an amino acid sequence according to the formula SGxS, wherein X is 4.
140. The multivalent polypeptide of claim 137, wherein the first linker comprises an amino acid sequence according to the formula SxG, wherein X is 3 or 4.
141. The multivalent polypeptide of any one of claims 129 and 131-136, wherein the second linker has a length of from 3-12, 3-10, 3-8, 3-6 or 4 amino acids.
142. The multivalent polypeptide of claim 141, wherein the second linker comprises an amino acid sequence according to the formula Gx, wherein X is 3, 4, or 5.
143. The multivalent polypeptide of claim 142, wherein X is 4.
144. The multivalent polypeptide of claim 141, wherein the second linker comprises an amino acid sequence according to the formula SGx, wherein X is 3 or 4.
145. The multivalent polypeptide of any one of claims 129 and 131-144, wherein the third linker has a length of from 20-40, 20-35, 25-40, 25-35, 25-30, 30-35, 28-32 or 30 amino acids.
146. The multivalent polypeptide of claim 145, wherein the third linker comprises an amino acid sequence according to the formula (GXS)N or GxS, wherein X is 3 or 4 and N is 3, 4, 5, 6, 7, 8, 9 or 10.
147. The multivalent polypeptide of claim 146, wherein X is 4 and N is 5, 6 or 7.
148. The multivalent polypeptide of claim 146, wherein X is 4 and N is 6.
149. The multivalent polypeptide of any one of claims 127-148, wherein the Fc region comprises one or more amino acid substitutions relative to a wild-type Fc region selected from the group consisting of heavy chain constant regions of human IgE, IgM, IgGl, IgG2, IgG3, IgG4, IgAl, and IgA2.
150. The multivalent polypeptide of any one of claims 127-149, wherein the Fc region comprises an Fc-silencing mutation, which Fc-silencing mutation decreases an antibody- directed cytotoxicity effector function.
151. The multivalent polypeptide of claim 150, wherein the Fc-silencing mutation comprises a AAA mutation or a CGC mutation, wherein the AAA mutation comprises L234A, L235A, G237A of a sequence of SEQ ID NO: 23, and wherein the CGC mutation comprises R292C, N297G, V302C of a sequence of SEQ ID NO: 23.
152. The multivalent polypeptide of any one of claims 127-151, wherein the multivalent polypeptide comprises an amino acid sequence with at least 80% sequence identity to an amino acid sequence as set forth in SEQ ID NOs: 42, 47-50, and 52-54.
153. The multivalent polypeptide of any one of claims 127-152, wherein the multivalent polypeptide comprises an amino acid sequence as set forth in SEQ ID NOs: 42, 47-50, and 52-54.
154. The multivalent polypeptide of any one of claims 127-153, wherein the first antigenbinding domain comprises a first single-chain variable fragment (scFv) comprising a heavy chain variable region (VH) and a light chain variable region (VL).
155. The multivalent polypeptide of claim 154, wherein the second antigen-binding domain comprises a second single-chain variable fragment (scFv) comprising a heavy chain variable region (VH) and a light chain variable region (VL).
156. The multivalent polypeptide of claim 155, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the VH of the first scFv, the VL of the first scFv, the VH of the second scFv, and the VL of the second scFv.
157. The multivalent polypeptide of claim 155, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the VH of the second scFv, the VL of the second scFv, the VH of the first scFv, and the VL of the first scFv.
158. The multivalent polypeptide of claim 155, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the VL of the first scFv, the VH of the first scFv, the VL of the second scFv, and the VH of the second scFv.
159. The multivalent polypeptide of claim 155, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the VL of the second scFv, the VH of the second scFv, the VL of the first scFv, and the VH of the first scFv.
160. The multivalent polypeptide of claim 155, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the VH of the second scFv, the VL of the second scFv, the VL of the first scFv, and the VH of the first scFv.
161. The multivalent polypeptide of claim 155, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the VH of the first scFv, the VL of the first scFv, the VL of the second scFv, and the VH of the second scFv.
162. The multivalent polypeptide of claim 155, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the VL of the first scFv, the VH of the first scFv, the VH of the second scFv, and the VL of the second scFv.
163. The multivalent polypeptide of claim 155, wherein the multivalent polypeptide comprises, from N-terminus to C-terminus, the VL of the second scFv, the VH of the second scFv, the VH of the first scFv, and the VL of the first scFv.
164. A multivalent polypeptide comprising: a first antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the first antigen-binding domain comprises a polypeptide of any one of claims 1-126; and a second antigen-binding domain that binds to a T cell surface protein;wherein the second antigen-binding domain comprises a second VH and a second VL, and wherein the second VL comprises: a CDR-L3 sequence of QQGNTLPWT (SEQ ID NO: 36), a CDR-L2 sequence of YTSRLES (SEQ ID NO: 37), and a CDR-L1 sequence of RASQDIRNYLN (SEQ ID NO: 38).
165. The multivalent polypeptide of any one of claims 127-164, wherein the second antigenbinding domain comprises six complementarity determining regions (CDRs) from heavy chain variable region (VH) and light chain variable region (VL) of a UCHT1 antibody, comprising: a CDR-H3 sequence of SGYYGDSDWYFDV (SEQ ID NO: 33), a CDR-H2 sequence of LINPYKGVSTYNQKFKD (SEQ ID NO: 34), a CDR-H1 sequence of GYTMN (SEQ ID NO: 35), a CDR-L3 sequence of QQGNTLPWT (SEQ ID NO: 36), a CDR-L2 sequence of YTSRLES (SEQ ID NO: 37), and a CDR-L1 sequence of RASQDIRNYLN (SEQ ID NO: 38).
166. The multivalent polypeptide of claim 165, wherein the VH comprises a sequence with at least 90% sequence identity to the sequence EVQLVESGGGLVQPGGSLRLSCAASGYSFTGYTMNWVRQAPGKGLEWVALINP YKGVSTYNQKFKDRFTISVDKSKNTAYLQMNSLRAEDTAVYYCARSGYYGDSD WYFDVWGQGTLVTVSS (SEQ ID NO: 31).
167. The multivalent polypeptide of claim 165 or 166, wherein the VH comprises a sequence of EVQLVESGGGLVQPGGSLRLSCAASGYSFTGYTMNWVRQAPGKGLEWVALINP YKGVSTYNQKFKDRFTISVDKSKNTAYLQMNSLRAEDTAVYYCARSGYYGDSD WYFDVWGQGTLVTVSS (SEQ ID NO: 31).
168. The multivalent polypeptide of any one of claims 165-167, wherein the VL comprises a sequence with at least 90% sequence identity to the sequence DIQMTQSPSSLSASVGDRVTITCRASQDIRNYLNWYQQKPGKAPKLLIYYTSRLE SGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCQQGNTLPWTFGQGTKVEIK (SEQ ID NO: 32).
169. The multivalent polypeptide of any one of claims 165-168, wherein the VL comprises a sequence ofDIQMTQSPSSLSASVGDRVTITCRASQDIRNYLNWYQQKPGKAPKLLIYYTSRLE SGVPSRFSGSGSGTDYTLTISSLQPEDFATYYCQQGNTLPWTFGQGTKVEIK (SEQ ID NO: 32).
170. The multivalent polypeptide of any one of claims 127-169, wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA allele of HLA-A3 supertype.
171. The multivalent polypeptide of claim 170, wherein the HLA allele of the HLA- A3 supertype is selected from the group consisting of HLA-A*03:01, HLA-A* 11 :01, HLA- A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA- A*66:01.
172. The multivalent polypeptide of claim 170, wherein the HLA allele of the HLA- A3 supertype is selected from the group consisting of HLA-A* 03:01, HLA-A* 11 :01, HLA- A*68:01, and HLA-A*34:02.
173. The multivalent polypeptide of any one of claims 127-169, wherein the MHC of the peptide conjugate / MHC complex is encoded by an HLA allele of HLA-A2 supertype.
174. The multivalent polypeptide of claim 173, wherein the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA- A* 02:01, HLA-A*02:02, HLA- A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01.
175. The multivalent polypeptide of claim 173, wherein the HLA allele of the HLA-A2 supertype is HLA-A*02:01.
176. A recombinant nucleic acid comprising a sequence encoding the polypeptide of any one of claims 1-126 or the multivalent polypeptide of any one of claims 127-175.
177. A pharmaceutical composition comprising the polypeptide of any one of claims 1-126 or the multivalent polypeptide of any one of claims 127-175, and a pharmaceutically acceptable carrier.
178. A method of treating a cancer in a subject in need thereof, the method comprising administering into the subject the polypeptide of any one of claims 1-126 or the multivalent polypeptide of any one of claims 127-175, or the pharmaceutical composition of claim 177.
179. A method for stabilizing a peptide conjugate / MHC complex, the method comprising: (a) contacting the peptide conjugate / MHC complex with a multivalent polypeptide, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide andan MHC, and wherein the multivalent polypeptide comprises a first antigen-binding domain, a second antigen-binding domain that binds to a T cell surface protein, and an Fc region comprising a first Fc subunit and a second Fc subunit, wherein the first antigen-binding domain comprises a polypeptide of any one of claims 1-126; and (b) measuring the half-life of the bound peptide conjugate / MHC complex and multivalent polypeptide.
180. The method of claim 179, wherein the half-life of the peptide conjugate / MHC complex is between 0.1 and 30 hours.
181. The method of claim 179, wherein the half-life of the peptide conjugate / MHC complex is between 10 and 26 hours.
182. The method of claim 179, wherein the half-life of the peptide conjugate / MHC complex is at least 1 day.
183. The method of any one of claims 179-182, wherein the contacting occurs at 25 °C or 37 °C.
184. A method for activating an immune cell, the method comprising: contacting the immune cell with a multivalent polypeptide comprising a first antigen-binding domain, a second antigen-binding domain that binds to a T cell surface protein, and an Fc region comprising a first Fc subunit and a second Fc subunit, wherein the first antigen-binding domain comprises a polypeptide of any one of claims 1-126; and wherein the immune cell expresses a peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC.
185. The method of claim 184, wherein the immune cell is a T cell.
186. The method of claim 184 or 185, wherein the contacting increases expression of at least one T cell activation marker.
187. The method of claim 186, wherein the at least one T cell activation marker is CD26, CD27, CD28, CD30, CD154, CD40L, CD134. CD25, CD44, CD69, CD137, PD-1, KLRG1, CCR7, CD45RA, HLA-DR, NKG2D, or any combination thereof.
188. The method of claim 186 or 187, wherein the at least one T cell activation marker is CD25 and / or CD69.
189. The method of any one of claims 184-188, wherein the contacting produces a greater number of CD25+CD69+T cells compared to a number of CD25+CD69+T cellsproduced from contacting the multivalent polypeptide with an otherwise identical peptide conjugate / MHC complex without the targeted covalent inhibitor.
190. The method of any one of claims 184-189, wherein the contacting increases expression of IFNy, TNFa, Granzyme A, Granzyme B, IL-6, perforin, IL-2, granulysin, or any combination thereof.
191. The method of any one of claims 184-190, wherein the contacting increases an expression level of cytokine molecules compared to an expression level of cytokine molecules produced from contacting the multivalent polypeptide with an otherwise identical peptide conjugate / MHC complex without the targeted covalent inhibitor.
192. A method for treating a cancer in a subject in need thereof, the method comprising administering to the subject (A) a polypeptide of any one of claims 1-126, or (B) a multivalent polypeptide comprising (i) a first antigen-binding domain that binds to a peptide conjugate / MHC complex, wherein the first antigen-binding domain is a polypeptide of any one of claims 1-126; (ii) a second antigen-binding domain that binds to a T cell surface protein; and (iii) an Fc region comprising a first Fc subunit and a second Fc subunit; wherein the first antigen-binding domain, the second antigen-binding domain, the first Fc subunit, and the second Fc subunit are operably linked to form a single continuous polypeptide chain.
193. The method of claim 192, wherein the cancer is renal cell carcinoma, breast cancer, prostate cancer, pancreatic cancer, lung cancer, liver cancer, ovarian cancer, cervical cancer, colon cancer, esophageal cancer, glioma, glioblastoma, brain cancer, stomach cancer, bladder cancer, testicular cancer, thyroid cancer, adrenal cancer, head and neck cancer, melanoma, skin cancer, sarcoma, fibrosarcoma, angiosarcoma, osteosarcoma, rhabdomyosarcoma, leukemia, lymphoma, myeloma, endometrial cancer, or a neuroendocrine tumor.
194. The method of any one of claims 179-193, wherein the peptide is a RAS peptide.
195. The method of claim 194, wherein the RAS peptide comprises a mutation.
196. The method of claim 195, wherein the mutation is G12C.
197. The method of any one of claims 194-196, wherein the RAS peptide comprises a sequence selected from the group consisting of VVVGACGVGK, VVGACGVGK, and KLVVVGACGV.
198. The method of any one of claims 179-197, wherein the MHC is selected from the group consisting of HLA-A*03:01, HLA-A* 11 :01, HLA-A*02:01, HLA-A*68:01, HLA- A*31:01, HLA-A*30:01, HLA-A*33:03, HLA-A*33:01, HLA-A*74:01, HLA-A*34:02, HLA-A*66:01, HLA-A*68:02, HLA-A*02:05, HLA-A*02:02, or HLA-A* 02: 06.
199. The method of any one of claims 179-197, wherein the MHC is encoded by an HLA allele of HLA- A3 supertype.
200. The method of claim 199, wherein the HLA allele of the HLA- A3 supertype is selected from the group consisting of HLA-A* 03:01, HLA-A* 11 :01, HLA-A*68:01, HLA- A*31 :01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01.
201. The method of claim 199, wherein the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A* 03:01, HLA-A* 11 :01, HLA-A*68:01, and HLA- A*34:02.
202. The method of any one of claims 179-197, wherein the MHC is encoded by an HLA allele of HLA-A2 supertype.
203. The method of claim 202, wherein the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A* 02:01, HLA-A* 02: 02, HLA-A* 02: 03, HLA- A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01.
204. The method of claim 202, wherein the HLA allele of the HLA-A2 supertype is HLA- A*02:01.
205. The method of any one of claims 179-204, wherein the targeted covalent inhibitor or fragment thereof comprises divarasib.
206. A method for stabilizing a peptide conjugate / MHC complex in a subject, the method comprising: administering (A) a polypeptide of any one of claims 1-126, or (B) a multivalent polypeptide to the subject, wherein the multivalent polypeptide comprises a first antigenbinding domain comprising a polypeptide of any one of claims 1-126, a second antigenbinding domain that binds to a T cell surface protein, and wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC.
207. The method of claim 206, further comprising, prior to administering the polypeptide or the multivalent polypeptide to the subject, administering the targeted covalent inhibitor.
208. The method of claim 206 or 207, wherein the subject has a cancer.
209. The method of any one of claims 206-208, wherein the cancer is refractory or relapsed.
210. The method of any one of claims 206-209, wherein the subject expresses at least one MHC encoded by an HL A, wherein the HL A i s HL A- A* 03 : 01 , HL A- A* 11 :01, HL A- A*02:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*33:03, HLA-A*33:01, HLA-A*74:01, HLA-A*34:02, HLA-A*66:01, HLA-A*68:02, HLA-A*02:05, HLA- A*02:02, HLA-A*02:06, or any combination thereof.
211. The method of any one of claims 206-210, further comprising, prior to administering the polypeptide or the multivalent polypeptide to the subject, determining an HL A allele expression of the subject.
212. The method of claim 211, wherein the subject expresses an MHC encoded by the HLA wherein the HLA is HLA-A*03:01, HLA-A* 11 :01, HLA-A*02:01, HLA-A*68:01, HLA-A*31:01, HLA-A*30:01, HLA-A*33:03, HLA-A*33:01, HLA-A*74:01, HLA- A*34:02, HLA-A*66:01, HLA-A*68:02, HLA-A*02:05, HLA-A*02:02, HLA-A*02:06, or any combination thereof.
213. The method of any one of claims 206-209, wherein the MHC is encoded by an HLA allele of HLA- A3 supertype.
214. The method of claim 213, wherein the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A* 03:01, HLA-A* 11 :01, HLA-A*68:01, HLA- A*31 :01, HLA-A*30:01, HLA-A*74:01, HLA-A*34:02, and HLA-A*66:01.
215. The method of claim 213, wherein the HLA allele of the HLA-A3 supertype is selected from the group consisting of HLA-A* 03:01, HLA-A* 11 :01, HLA-A*68:01, and HLA- A*34:02.
216. The method of any one of claims 206-209, wherein the MHC is encoded by an HLA allele of HLA-A2 supertype.
217. The method of claim 216, wherein the HLA allele of the HLA-A2 supertype is selected from the group consisting of HLA-A* 02:01, HLA-A* 02: 02, HLA-A* 02: 03, HLA- A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*02: 14, HLA-A*02: 17, HLA-A*68:02, and HLA-A*69:01.
218. The method of claim 216, wherein the HLA allele of the HLA-A2 supertype is HLA- A*02:01.
219. The method of any one of claims 206-218, wherein the multivalent polypeptide comprises an Fc region comprising a first Fc subunit and a second Fc subunit.
220. The method of claim 219, wherein the Fc region comprises one or more amino acid substitutions relative to a wild-type Fc region selected from the group consisting of heavy chain constant regions of human IgE, IgM, IgGl, IgG2, IgG3, IgG4, IgAl, and IgA2.
221. The method of claim 219 or 220, wherein the Fc region comprises an Fc-silencing mutation, which Fc-silencing mutation decreases an antibody-directed cytotoxicity effector function.
222. The method of any one of claims 206-221, wherein administering the polypeptide or the multivalent polypeptide to the subject increases a half-life of the peptide conjugate / MHC complex compared to a half-life of the peptide conjugate / MHC complex following administration of the targeted covalent inhibitor alone.
223. A method of killing a target cell expressing a peptide conjugate / MHC complex, the method comprising: contacting the multivalent polypeptide of any one of claims 127-175 with the target cell expressing the peptide conjugate / MHC complex, wherein the peptide conjugate / MHC complex comprises a peptide conjugate formed by a covalent reaction of a targeted covalent inhibitor or fragment thereof with a peptide and an MHC.
224. The method of claims 223, wherein the targeted covalent inhibitor or fragment thereof comprises divarasib.
225. The method of claim 223 or 224, wherein the peptide is a RAS peptide.
226. The method of claim 225, wherein the RAS peptide comprises a mutation.
227. The method of claim 226, wherein the mutation is G12C.
228. The method of any one of claims 225-227, wherein the RAS peptide comprises a sequence of VVVGACGVGK, VVGACGVGK, or KLVVVGACGV.
229. The method of claim 228, wherein a greater level of T cell cytotoxicity mediated by the multivalent polypeptide is observed in the presence of cells expressing the peptide conjugate / MHC complex comprising the RAS peptide compared to a level of cytotoxicity observed in cells expressing a peptide conjugate / MHC complex comprising a wild-type RAS peptide.
230. The method of claim 229, wherein the wild-type RAS peptide comprises a sequence of KLVVVGAGGV, VVGAGGVGK, or VVVGAGGVGK.
231. The method of claim 229 or 230, wherein an ECso of a T cell cytotoxicity mediated by the multivalent polypeptide is at most about 150 nM, at most about 100 nM, at most about 50 nM, at most about 20 nM, at most about 10 nM, at most about 1 nM, at most about 0.1 nM, at most about 0.01 nM, or less.
232. The method of any one of claims 223-231, wherein the MHC is HLA-A*03:01, HLA- A*l l:01, HLA-A*02:01, or HLA-A*68:01.
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