Drug conjugates of cmet monoclonal binding agents, and uses thereof
Binder-drug conjugates targeting cMET with pyrrolobenzodiazepine toxins address the limitations of current cancer treatments by inducing receptor internalization and degradation, effectively inhibiting tumor growth and metastasis in cancers with aberrant cMET activity.
Patent Information
- Application Number
- JP2025131538
- Authority / Receiving Office
- JP · JP
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2018-03-28
- Filing Date
- 2025-08-06
- Publication Date
- 2025-11-18
AI Technical Summary
Current treatments for neoplastic disorders and cancers associated with aberrant cMET expression and activity, such as renal, liver, stomach, breast, and brain cancers, are inadequate in effectively inhibiting tumor growth, angiogenesis, and metastasis.
Development of binder-drug conjugates comprising monoclonal antibodies or their antigen-binding portions conjugated to pyrrolobenzodiazepine toxins, which specifically bind to the extracellular domain of cMET, inducing internalization and degradation of the receptor, thereby inhibiting its signaling and promoting cancer cell death.
The conjugates effectively inhibit cancer growth, viability, and metastasis by specifically targeting cMET, inducing receptor internalization and degradation, and demonstrating therapeutic efficacy in various cancer types, including gastric and lung cancers.
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Figure 2025170277000079 
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Abstract
Description
[Technical Field]
[0001] SUMMARY OF THE INVENTION Embodiments of the present invention relate to cMET binding agents conjugated to pyrrolobenzodiazepine toxins, compositions comprising the conjugates, and uses of the conjugates. [Background technology]
[0002] The protein cMET, sometimes called MET or hepatocyte growth factor receptor (HGFR), is encoded by the MET gene (MET proto-oncogene, receptor tyrosine kinase) in humans. cMET is a single-pass cell surface receptor with tyrosine kinase activity. The primary single-chain precursor protein of MET translation is posttranslationally cleaved to produce α and β subunits, which are disulfide-linked to form the mature cell surface cMET receptor. cMET is expressed in cells of epithelial origin, as well as stem and progenitor cells and other cell types (e.g., various cancer cell types). Hepatocyte growth factor / scatter factor (HGF / SF) and its splicing isoforms (NK1, NK2) have been identified as ligands for cMET.
[0003] cMET is thought to be required for normal embryonic development, organogenesis, and wound healing. Aberrant expression and / or activity of cMET is associated with certain neoplastic disorders and cancers (e.g., renal, liver, stomach, breast, and brain cancers), and cMET is involved in tumor growth, angiogenesis, and metastasis. Overexpression of cMET and autoactivation by coexpression of its ligands are also involved in tumorigenesis.
[0004] Presented herein are novel anti-cMET binding agents (eg, monoclonal antibodies) conjugated to a cytotoxic payload, pharmaceutical compositions thereof, and methods of using same. Summary of the Invention [Means for solving the problem]
[0005] In some aspects, provided herein are binder-drug conjugates comprising a binder and a payload, wherein the payload comprises a pyrrolobenzodiazepine toxin, and the binder specifically binds to mesenchymal-epithelial transition factor (cMET). In some embodiments, the payload comprises a linking group, the pyrrolobenzodiazepine toxin is covalently linked to the linking group, and the linking group is covalently linked to the binder. In some embodiments, the binder is a monoclonal antibody or an antigen-binding portion thereof.
[0006] In some embodiments, provided herein are binder-drug conjugates comprising a binder and a payload. The binder comprises (i) two or more polypeptide sequences of a light chain complementarity determining region (CDR-L), namely, CDR-L1, CDR-L2, and CDR-L3, and (ii) two or more polypeptide sequences of a heavy chain complementarity determining region (CDR-H), namely, CDR-H1, CDR-H2, and CDR-H3, wherein CDR-L1 is selected from the amino acid sequences of SEQ ID NOs: 1-15, CDR-L2 is selected from the amino acid sequences of SEQ ID NOs: 16-25, and CDR-L3 is selected from the amino acid sequences of SEQ ID NOs: 26-36. wherein CDR-H1 is selected from the amino acid sequences of SEQ ID NOs: 50-61, CDR-H2 is selected from the amino acid sequences of SEQ ID NOs: 62-78, and CDR-H3 is selected from the amino acid sequences of SEQ ID NOs: 79-93; and the payload comprises a pyrrolobenzodiazepine toxin and a linking group; the pyrrolobenzodiazepine toxin is covalently linked to the linking group, the linking group is covalently linked to a binder, and the binder specifically binds to the extracellular domain of mesenchymal epithelial transition factor (cMET).
[0007] In certain embodiments, the pyrrolobenzodiazepine toxin has the formula (I): [ka] [In the formula, Z1 and Z2 are both N; Z3 and Z4 are both C; [ka] n is 1 to 12; Each of R3 and R4 is independently H or C 1-4 is alkoxyl; and R1 and R2 are each independently H, C 1-5 Alkyl, C 3-6 Cycloalkyl, C 2-5 selected from the group consisting of alkenyl and phenyl optionally substituted by R5; R5 is -NH2, -NHR6 and the structure: [ka] piperazinyl substituted with R7 having the formula R6 comprises a linking group, and R7 is H or C 1-5 is alkyl; X1 is null, a protecting group, or contains a linking group; X2 is null, a protecting group, or contains a linking group; Only one of X1, X2, R1 and R2 contains a linking group; and each of Y1 and Y2 is independently either null, OH, or SO3H; however, [ka] Null indicates that the moiety is absent or that one or more hydrogens are present to complete the required valence. Includes structure.
[0008] In some embodiments of pyrrolobenzodiazepine toxins having the structure of formula I, n is 3 or 5. In some embodiments of pyrrolobenzodiazepine toxins having the structure of formula I, R3 and R4 are both -O-CH3. In some embodiments of pyrrolobenzodiazepine toxins having the structure of formula I, R1 and R2 are both methyl, or R1 and R2 are both -CH=CH-CH3. In some embodiments of pyrrolobenzodiazepine toxins having the structure of formula I, R2 is cyclopropyl. In some embodiments of pyrrolobenzodiazepine toxins having the structure of formula I, R2 is phenyl substituted with 4-methylpiperazin-1-yl or phenyl optionally substituted with R5, R5 is -NHR6, and R6 comprises a linking group. [ka] In some embodiments of a pyrrolobenzodiazepine toxin having the structure of Formula I, the linking group is attached to the pyrrolobenzodiazepine toxin by a carbamate group or an amide group.
[0009] In one embodiment, the coupler has Formula A: [ka] wherein the asterisk indicates the point of attachment to the pyrrolobenzodiazepine toxin; the wavy line indicates the point of attachment to the binding agent; m is 1-20; q is 0-10; and E is a linking group. In some embodiments of the linking group of formula A, m is 4 or 8, and q is 0, 1, or 2. In some embodiments, m is 8, and q is 2.
[0010] In one embodiment, the linking group has Formula B: [ka] wherein the asterisk indicates the point of attachment to the pyrrolobenzodiazepine toxin; the wavy line indicates the point of attachment to the binding agent; E comprises the linking group; v is 0-10; and u is 0 or 1; when u is 1, t is 1-10. In some embodiments of a linking group of Formula B, v is 1. In some embodiments of a linking group of Formula B, u is 1 and t is 8. In some embodiments of a linking group of Formula B, u is 0 and v is 4.
[0011] In certain embodiments of linking groups of formulas A and B, the binding agent is attached to E by a thioether bond formed between a cysteine thiol residue of the binding agent and E. In some embodiments, E has formula C: [ka] where the wavy line indicates the point of attachment to the binder and the double asterisk indicates the point of attachment to the linking group. Includes the structure of
[0012] In some implementations of the pyrrolobenzodiazepine toxin of formula I, the protecting group has the following structure (D): [ka] where the asterisk indicates the point of attachment to the pyrrolobenzodiazepine toxin; and w is 1 to 5. In some embodiments, w is 2. In some embodiments, the protecting group is a cleavable protecting group.
[0013] In one embodiment, provided herein is a binder-drug conjugate comprising a binder and a payload, wherein the binder specifically binds to the extracellular domain of mesenchymal-epithelial transition factor (cMET), and the payload is covalently linked to the binder, wherein the payload comprises a structure selected from the group consisting of Formulas II, III, V, VI, and VII, wherein Formula II has the structure: [ka] wherein m is 8 and the wavy line indicates the point of attachment to the binder; Formula III has the structure: [ka] wherein m is 8, p is 2 or 3, X2 is a protecting group, and the wavy line indicates the point of attachment to the linking agent; Formula V has the structure: [ka] wherein m is 8 and the wavy line indicates the point of attachment to the binder; Formula VI has the structure: [ka] wherein t is 8, v is 1, and the wavy line indicates the point of attachment to the binder; Formula VI has the structure: [ka] where the wavy line indicates the point of attachment to the binder.
[0014] In one embodiment, the protecting group for X2 has the following structure (D): [ka] where the asterisk indicates the point of attachment to the payload; and w is 1-5.
[0015] In one embodiment, provided herein is a binder-drug conjugate comprising a monoclonal antibody, or antigen-binding portion thereof, and a payload. The monoclonal antibody, or antigen-binding portion thereof, comprises a CDR-L1 selected from the amino acid sequences of SEQ ID NOs: 2, 4, 6, 8, 10, 12, and 14; a CDR-L2 comprising the amino acid sequences of SEQ ID NOs: 17, 19, 21, 23, and 25; a CDR-L3 comprising the amino acid sequences of SEQ ID NOs: 27, 29, 31, 33, and 35; a CDR-H1 comprising the amino acid sequences of SEQ ID NOs: 51, 53, 55, 57, and 59; a CDR-H2 comprising the amino acid sequences of SEQ ID NOs: 63, 65, 67, 69, 73, and 75; and a CDR-H3 comprising the amino acid sequences of SEQ ID NOs: 80, 82, 84, 86, 88, 91, and 93.
[0016] In certain embodiments, the binder of the binder-drug conjugate described herein comprises a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or 14; a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 25; a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 35; a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 59; a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 71; and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 88.
[0017] In certain embodiments, the binder of the binder-drug conjugate described herein comprises a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 9 or 15; a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 24; a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 34; a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 58; a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 70 or 78; and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 87.
[0018] In some embodiments, the binding agent comprises a variable light chain region comprising an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 37-44. In some embodiments, the binding agent comprises a light chain variable sequence having at least 90% sequence identity or 100% sequence identity to any one of the amino acid sequences of SEQ ID NOs: 45-49. In some embodiments, the binding agent comprises a light chain variable sequence having at least 90% sequence identity to any one of the amino acid sequences of SEQ ID NOs: 37-49, wherein the light chain variable sequence comprises 1 to 5 amino acid modifications selected from an amino acid addition, an amino acid deletion, and an amino acid substitution.
[0019] In some embodiments, the binding agent comprises a heavy chain variable region comprising an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 94-103. In some embodiments, the binding agent comprises a heavy chain variable region having at least 90% sequence identity or 100% sequence identity to any one of the amino acid sequences of SEQ ID NOs: 104-108. In some embodiments, the binding agent comprises a heavy chain variable sequence having at least 90% sequence identity to any one of the amino acid sequences of SEQ ID NOs: 94-108, wherein the heavy chain variable sequence comprises 1 to 5 amino acid modifications selected from amino acid additions, amino acid deletions, and amino acid substitutions.
[0020] In one embodiment, the binding agent comprises a light chain variable sequence having at least 90% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 37-49 and a heavy chain variable sequence having at least 90% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 94-108.
[0021] In certain embodiments, the binding agent, monoclonal antibody, or antigen-binding portion thereof is chimeric or humanized. For example, in some embodiments, the binding agent comprises one or more humanized or human framework regions and / or one or more murine framework regions.
[0022] In an embodiment, the binding agent, monoclonal antibody, or antigen-binding portion thereof, comprises a heavy chain and a light chain having CDRs, respectively, that are the same as the CDRs of the heavy chain and light chain, respectively, of the antibody produced by hybridoma cell line F6B1P3D12, deposited with the ATCC on March 20, 2019.
[0023] In some embodiments, a binding agent that specifically binds to cMET or a portion thereof comprises an antigen-binding portion of an antibody or a single-chain antibody. For example, in certain embodiments, the binding agent of the binding agent-drug conjugate comprises a Fab, Fab', F(ab')2, Fv, or scFV fragment of an antibody.
[0024] In some embodiments, the binding agent specifically binds to mammalian cMET. In some embodiments, the binding agent specifically binds to human cMET, monkey cMET, and / or rat cMET. In some embodiments, the binding agent specifically binds to the extracellular domain of wild-type or mutant cMET. In some embodiments, the binding agent specifically binds to cMET induces the internalization and / or degradation of cMET on human cancer cells. In some embodiments, the binding agent specifically binds to cMET is a binding agent that is not a cMET agonist. Thus, a cMET binding agent that is not a cMET agonist is a binding agent that, upon binding to cell surface cMET, does not substantially induce signal transduction through cell surface cMET.
[0025] In one aspect, provided herein is a pharmaceutical composition comprising a binder-drug conjugate described herein and a pharmaceutically acceptable excipient, diluent, additive, or carrier.
[0026] In one aspect, a method for treating a subject having a neoplastic disorder or cancer is provided. The method comprises administering a therapeutically effective amount of a binding agent-drug conjugate to a subject having or suspected of having a neoplastic disorder or cancer. In some embodiments, administration of the binding agent-drug conjugate prevents, inhibits, ameliorate, abrogates, or suppresses cancer growth, viability, or metastasis. In some embodiments, administration of the binding agent-drug conjugate induces death, necrosis, or apoptosis in some or all of the cancer. In some embodiments, the neoplastic disorder or cancer comprises carcinoma, sarcoma, neuroblastoma, glioblastoma, myeloma, lymphoma, melanoma, or solid or soft tissue tumor. In some embodiments, the neoplastic disorder or cancer comprises bladder cancer, breast cancer, colorectal cancer, gastric cancer, pancreatic cancer (e.g., exocrine pancreatic cancer and pancreatic neuroendocrine cancer), esophageal cancer, liver cancer, hepatocellular carcinoma, hypopharyngeal cancer, lung cancer, adenocarcinoma, ovarian cancer, or kidney cancer. In certain embodiments, the neoplastic disorder or cancer comprises pancreatic adenocarcinoma, colorectal adenocarcinoma, small intestine malignancies, cholangiocarcinoma, non-small cell lung cancer (NSCLC), thyroid cancer, esophageal or gastroesophageal junction (EGJ) cancer, gastric adenocarcinoma, liver hepatocellular carcinoma, head and neck squamous cell carcinoma, female genital tract malignancies, breast cancer, small cell lung carcinoma, ovarian surface epithelial carcinoma, retroperitoneal or peritoneal sarcoma, prostate adenocarcinoma, neuroendocrine tumors, gastrointestinal stromal tumors, glioblastoma, or non-epithelial ovarian cancer. In certain embodiments, the cancer that can be treated by the methods described herein is a cancer comprising cells (e.g., malignant or neoplastic cells) that express a cMET polypeptide (e.g., cMET, e.g., expressed on the cell surface).
[0027] Certain aspects of the present technology are further described in the following description, examples, claims and drawings.
[0028] The drawings are illustrative of embodiments of the present technology and are not intended to be limiting. For clarity and ease of illustration, the drawings are not to scale and in some cases various aspects may be shown exaggerated or enlarged to aid in understanding particular embodiments. [Brief explanation of the drawings]
[0029] [Figure 1] Figure 1 shows an overview of the workflow used for the generation of monoclonal antibodies (exemplary binders) that specifically bind to cMET. The lead monoclonal Ab P3D12 was generated from mice immunized with the recombinant native extracellular domain of cMET fused to human Fc.
[0030] [Figure 2] Figure 2 shows the immunization scheme used to generate monoclonal antibodies (exemplary binders) that specifically bind cMET. Mice were initially immunized intraperitoneally (ip) with 100 μg of human cMET-Fc fusion protein (cMET-Fc) or 50–100 μg of KLH-conjugated cMET peptide in complete Freund's adjuvant (CFA), as indicated. cMET-Fc contains the extracellular domain of human cMET fused to the Fc portion of an antibody. The cMET peptide was strategically selected from a portion of the cMET extracellular domain. Immunized mice received one or multiple booster immunizations containing 25 μg or 50 μg of cMET-Fc or peptide in incomplete Freund's adjuvant (IFA), as indicated. Some mice received repeated immunizations (RIMMS) at multiple sites. Immunizations included Met-Fc fusion, peptide, conventional, and RIMMS. Spleens from immunized mice were harvested and fused with the appropriate fusion partner. Over 20,000 hybridoma clones were obtained and screened.
[0031] [Figure 3] Figure 3 shows the 3D structure of the MET SEMA domain bound to the Fab of the agonist Met-mAb antibody (5D5 Fab) and the HGF beta subunit (HGFβ or HGFb). The arrow below indicates the location of the portion of cMET used to design peptide 3.
[0032] [Figure 4]Figure 4 shows the characterization results from an exemplary fusion (FUSION 6B1, plate 3). Anti-cMet hybridomas were selected in part for the presence of specific binding to cMet, as assayed by ELISA (see the column labeled "MET binding ELISA OD450nm"), and for their ability to induce internalization of cMET in human cancer cell lines, as measured by flow cytometry (see the column labeled "FACS Geom. Mean"). A FACS Geom. Mean value lower than the negative control indicates internalization of cMet. The arrow indicates the lead hybridoma F6B1P3D12. [Figure 5] Figure 5 shows the results of the MET degradation assay. Anti-cMet antibodies isolated from the indicated wells (x-axis) were tested and selected for their ability to induce degradation of cMET in human cancer cell lines as measured by mesoscale (MSD) cMet protein quantitation. The relative values of Met degradation are shown on the y-axis as % control (% of control). Values below 100% control (negative control level) indicate internalization and degradation of cMet. Degradation indicates not only internalization but also lysosomal trafficking, an important characteristic of antibody-drug conjugates. The arrow indicates the results for the lead hybridoma F6B1P3D12. [Figure 6] Figure 6 shows the results of an ERK phosphorylation assay (P-ERK assay). This assay measures the agonistic activity of anti-cMET antibodies by indirectly measuring ERK phosphorylation induced by binding of anti-cMET antibodies to cMET on the cell surface. The amount of phosphorylated ERK (shown as a percentage of control, y-axis) detected in cell lysates after treatment of live cells with anti-cMET antibodies is shown. Anti-cMET antibodies produced by various anti-cMET hybridomas (x-axis) were tested at 6 μg / ml or 30 μg / ml (shown on the x-axis) and selected for their lack of activity in inducing significant ERK phosphorylation (i.e., no proliferation-inducing activity, i.e., no agonistic activity). The lead monoclonal antibody (mAb) P3D12 is indicated by an arrow.
[0033] [Figure 7]Figure 7 shows the results of six cMET monoclonal antibodies (mAbs) assayed by ELISA for binding to human, monkey (Cynomolgus Macaque, "Cyno"), dog, rat, and mouse cMET. All monoclonal antibodies bound to human and monkey cMET. P3D12 showed significant cross-reactivity with rat cMET. Various concentrations of each antibody are shown on the x-axis. Relative binding is shown on the y-axis (OD450nm).
[0034] [Figure 8] Figure 8A shows the amino acid sequence alignment of the light chain variable regions of nine mouse monoclonal anti-cMET antibodies. The names are shown to the left of each sequence. The sequence numbers are shown to the right of each sequence. The amino acid sequences of the light chain variable regions of LC F6B1P1E2 and F6BP3E2 are 100% identical. The amino acid sequences of the light chain variable regions of LC F6B1P3D12 and F6B1P3E9 are 100% identical.
[0035] Figure 8B shows the amino acid sequence alignment of the heavy chain variable regions of nine mouse monoclonal anti-cMET antibodies. The names are shown to the left of each sequence. The sequence numbers are shown to the right of each sequence. The amino acid sequences of the heavy chain variable regions of F6B1P3D12H7913 and F6B1P3E9 are 100% identical. The amino acid sequences of the heavy chain variable regions of F6B1P1E2H7819 and F6BP3E2 are 100% identical.
[0036] [Figure 9]Figures 9A and 9B show in vivo xenograft mouse model results evaluating the efficacy of the indicated anti-cMET antibody-drug conjugates (ADCs) using the MKN45 tumor model (cMet+ gastric cancer model) in nude mice. Animals were treated once with 2.5 mg / kg (9A) or 5.0 mg / kg (9B) of ADC. The efficacy of each drug-conjugated anti-cMET binder is compared to PBS or an irrelevant non-targeting monoclonal antibody (IgG-ADC). Tumor volume (y-axis) was measured at various time points after implantation (x-axis, days post-implantation). Inhibition of tumor growth indicates a positive effect. The anti-cMET binders and a non-targeting control monoclonal antibody (IgG) were conjugated to monomethyl auristatin F (MMAF).
[0037] [Figure 10] Figure 10 shows the results of an ERK phosphorylation assay (P-ERK assay). This assay measures the agonist activity of anti-cMET antibodies by indirectly measuring ERK phosphorylation induced by binding of anti-cMET antibodies to cMET on the cell surface. The amount of phosphorylated ERK (shown as a percentage of control, y-axis) detected in cell lysates after treatment of live cells with anti-cMET antibodies is shown. The heavy and light chain constant regions of an isolated mouse monoclonal antibody designated P3D12 were replaced with those of human IgG1 (P3D12(hIgG1)) or human IgG2 (P3D12(hIgG2)), as shown on the x-axis. Each antibody was tested at concentrations of 0.00064 μg / ml, 0.0032 μg / ml, 0.016 μg / ml, 0.08 μg / ml, 0.4 μg / ml, 2 μg / ml, 10 μg / ml, and 50 μg / ml, as shown on the x-axis. "Control" indicates an untreated negative control. HGF(EC90) is a positive control and represents cells treated with hepatocyte growth factor (HGF), the natural ligand of the cMET receptor. The data show that the human IgG2 isotype exhibits no detectable agonist activity.
[0038] [Figure 11]Figure 11 shows the results of an MET degradation assay. Degradation is a measure of cMET receptor internalization upon antibody binding. Chimeric anti-cMET antibodies were tested for their ability to induce cMET degradation in human cancer cell lines, as measured by mesoscale (MSD) cMET protein quantification. The relative value of Met degradation is shown on the y-axis as % control (% of control). Values lower than 100% control indicate cMet internalization and degradation. Chimeric antibodies were generated by replacing the heavy and light chain constant regions of an isolated murine monoclonal antibody designated P3D12 (P3D12(murine)) with the antibody constant regions of human IgG1 (P3D12(hIgG1)) or human IgG2 (P3D12(hIgG2)), as shown on the x-axis. Each antibody was tested at 0.00064 μg / ml, 0.0032 μg / ml, 0.016 μg / ml, 0.08 μg / ml, 0.4 μg / ml, 2 μg / ml, 10 μg / ml, and 50 μg / ml, as indicated on the x-axis. The P3D12 chimeric cMET antibody exhibited similar internalization / degradation activity as the parental murine P3D12 antibody.
[0039] [Figure 12] FIG. 12 shows a flow chart of the process development for testing and selection of lead anti-cMET monoclonal binders.
[0040] [Figure 13] Figure 13 shows the layout of five humanized light chain variable regions from the humanized version of murine anti-cMET clone P3D12, with their names and SEQ ID NOs indicated to the left of each sequence. Five independent methods were used to humanize the murine anti-cMET mAb. Two of the methods produced the same results. Thus, four different light chains are shown.
[0041] [Figure 14]Figure 14 shows the layout of five humanized heavy chain variable regions from the humanized version of murine clone P3D12, with their names and SEQ ID NOs indicated to the left of each sequence. Five independent methods were used to humanize the murine anti-cMET mAb. Two of the methods produced the same results. Thus, there are four different light chains (see Figure 13) and four different heavy chains, resulting in 16 different binder combinations.
[0042] [Figure 15] Figure 15 shows the results of an in vivo xenograft mouse model testing the efficacy of the indicated humanized anti-cMet antibody-drug conjugates (ADCs) at 2.5 mg / kg (2.5 mpk) or 5 mg / kg (5 mpk), demonstrated using the MKN45 tumor model (a cMet+ gastric cancer model). Animals were treated once with the indicated ADC at 2.5 mg / kg or 5.0 mg / kg. The efficacy of each anti-cMET binder is compared to PBS or the non-targeting monoclonal antibody rituximab (Retux). Rituximab is an anti-cancer monoclonal antibody that targets CD20, which is found primarily on the surface of immune system B cells. Tumor volume (y-axis) was measured at various time points after implantation (x-axis). Inhibition of tumor growth indicates a positive effect. The anti-cMET binders were conjugated to monomethyl auristatin F (MMAF).
[0043] [Figure 16]Figure 16 shows the binding of the anti-cMET monoclonal binder hD12 and a negative control antibody (denosumab) to cMET-Fc and mutant cMET (E168D) Fc recombinant fusion proteins. The anti-cMET monoclonal binder hD12 has heavy and light chain variable regions of SEQ ID NOs: 108 and 47 and a human IgG2 constant region. Denosumab does not bind to cMET. The E168D mutation is a somatic mutation found in small cell lung cancer (SCLC). The mutation resides in the Sema domain and results in constitutive activation of the cMet receptor. The abundance of somatic mutations in cMet is extremely low. E168D occurs in 0.8% to 3% of SCLC patients. Binding ELISAs were performed with human cMET or the E168D cMET extracellular domain fused to human IgG1 Fc. cMET protein was coated onto plates overnight, and samples were titrated and detected with goat anti-human IgG(H+L)-HRP. EC50 was determined by sigmoidal dose-response fit.
[0044] [Figure 17] Figure 17A shows the results of an ELISA-based cMET binding assay. Briefly, five representative antibody-drug conjugates (i.e., hD12-VI, hD12-II, hD12-VII, hD12-IV, and hD12-XI (see antibody nomenclature described in Example 3)) were tested at increasing concentrations for their ability to bind to plate-bound human cMET (x-axis, antibody-drug conjugate concentration (μg / ml)). Relative binding avidity is shown as luminescence (y-axis). A negative control antibody (denosumab) that does not bind to cMET was conjugated to each of the five payloads (i.e., payloads of formulas VI, II, IV, VII, and XI) (designated denosumab VI, denosumab II, denosumab IV, denosumab VII, and denosumab XI, respectively) and tested as a negative control. Figure 17B shows the IC50 values for each antibody tested in Figure 17A.
[0045] [Figure 18-1]Figures 18A-18D show the results of cytotoxicity assays of five representative antibody-drug conjugates (hD12-VI, hD12-II, hD12-VII, hD12-IV, and hD12-XI) against four cell lines expressing different amounts of cMET on their cell surface: SNU-1, no cMET expression (Figure 18A); SNU-16, moderate cMET expression (Figure 18B); SNU-620, high cMET expression (Figure 18C); and MKN-45, high cMET expression (Figure 18D). Viability is shown on the y-axis, and the amount of antibody-drug conjugate added (pM) is shown on the x-axis.
[0046] [Figure 18-2] Figure 18E summarizes the results showing relative IC50 values.
[0047] [Figure 19-1] Figures 19A-19E show the results of cytotoxicity assays of five representative antibody-drug conjugates (hD12-VI, hD12-II, hD12-VII, hD12-IV, and hD12-XI) against five cell lines expressing different amounts of cMET on their cell surface: H441, moderately expressing cMET (Figure 19A), H1373, moderately expressing cMET (Figure 19B), H1975, moderately expressing cMET (Figure 19C), SNU-5, highly expressing cMET (Figure 19D), and H1573, moderately expressing cMET (Figure 19E). Figure 19-1 provides Figures 19A-19D. [Figure 19-2] Figure 19E is provided. Viability is shown on the y-axis and the amount of antibody drug conjugate added is shown on the x-axis (pM). Figure 19F summarizes the results showing relative IC50 values.
[0048] [Figure 20-1]Figure 20 shows the results of an in vivo xenograft study. Mice were injected with H1975 tumor cells (moderate expression of cMET) and treated with either hD12-XI (Figures 20A, 20B, and 20C), hD12-VI (Figures 20A, 20B, and 20D), hD12-II (Figures 20A, 20B, and 20E), hD12-VII (Figures 20A, 20B, and 20F), or hD12-IV (Figures 20A, 20B, and 20G). Tumor volume (y-axis, Figures 20A and 20C-20G) or body weight (Figure 20B) was measured over time (i.e., days, x-axis). A negative control antibody (denosumab) conjugated to each of the five payloads (i.e., VI, II, IV, VII, and XI) was tested as a negative control. Figure 20-1 provides Figure 20A. [Figure 20-2] Figure 20-2 provides Figure 20B. [Figure 20-3] Figure 20-3 provides Figure 20C. [Figure 20-4] Figure 20-4 provides Figure 20D. [Figure 20-5] Figure 20-5 provides Figure 20E. [Figure 20-6] Figure 20-6 provides Figure 20F. [Figure 20-7] Figure 20-7 provides Figure 20G.
[0049] [Figure 21-1] Figure 21 shows the results of an in vivo xenograft study. Mice were injected with H1373 tumor cells (moderate expression of cMET) and treated with hD12-XI (Figure 21A), hD12-VI (Figure 21B), hD12-II (Figure 21C), hD12-VII (Figure 21D), and hD12-IV (Figure 21E), and tumor volume (y-axis) was determined over time (i.e., days, x-axis). A negative control antibody (denosumab) conjugated to II was tested as a negative control. Figure 21-1 provides Figures 21A and 21B. [Figure 21-2] Figure 21-2 provides Figure 21C. [Figure 21-3] Figure 21-3 provides Figure 21D. [Figure 21-4] Figure 21-4 provides Figure 21E.
[0050] [Figure 22] FIG. 22 shows the body weight (y-axis) over time (x-axis) of mice treated as in FIG.
[0051] [Figure 23] Figure 23 shows the serum concentrations (y-axis) of hD12-XI, hD12-VI, hD12-II, hD12-VII, hD12-IV, and denosumab-II after intravenous (iv) injection in mice. Time after injection (hours) is shown on the x-axis. The concentration of each antibody-drug conjugate was determined by ELISA.
[0052] [Figure 24] Figure 24 shows the results of an ELISA-based cMET binding assay, demonstrating the relative affinity of hD12 and four mutant forms of hD12 covalently linked to payload II (hD12-T289C, hD12-V442C, and hD12-V282C) for plate-bound human cMET. hD12-II was randomly stochastically linked to the payload at sulfhydryl groups. hD12-T289C-II, hD12-V442C-II, and hD12-V282C-II were site-specifically linked to the payload at mutated cysteine residues (i.e., T289C, V442C, and V282C, respectively). Antibody-drug conjugates were tested at increasing concentrations for their ability to bind to plate-bound human cMET (x-axis, antibody-drug conjugate concentration (μg / ml)). Relative binding intensities are shown as luminescence (y-axis). A negative control antibody (denosumab-II) was tested as a negative control. Figure 24B shows the IC50 values for each antibody tested in Figure 24A.
[0053] [Figure 25-1]Figure 25 shows the results of a cytotoxicity assay of the antibody conjugates of Figure 24 (i.e., hD12-II, hD12-T289C-II, hD12-V442C-II, and hD12-V282C-II) against four cell lines expressing different amounts of cMET on their cell surface: SNU-1, no expression of cMET (Figure 25A); SNU-16, moderate expression of cMET (Figure 25B); SNU-620, high expression of cMET (Figure 25C); MKN-45, high expression of cMET (Figure 25D); and N87, low expression of cMET (Figure 25E). Viability is shown on the y-axis, and the amount of antibody-drug conjugate added is shown on the x-axis (pM). Figure 25F summarizes the results, showing comparative relative IC50 values. The concentrations of the antibody-drug conjugates tested are shown in Figure 25G. Figure 25-1 provides Figure 25A. [Figure 25-2] Figure 25-2 provides Figure 25B. [Figure 25-3] Figure 25-3 provides Figure 25C. [Figure 25-4] Figure 25-4 provides Figure 25D. [Figure 25-5] Figure 25-5 provides Figure 25E. [Figure 25-6] Figure 25-2 provides Figure 25F and Figure 26G.
[0054] [Figure 26] Figure 26A shows the results of a cytotoxicity assay of the antibody conjugates of Figure 24 (i.e., hD12-II, hD12-T289C-II, hD12-V442C-II, and hD12-V282C-II) against a cMET-high expressing cell line (i.e., SNU-5). Viability is shown on the y-axis, and the amount of antibody-drug conjugate added is shown on the x-axis (pM). Figure 26B summarizes the results, showing relative IC50 values. The concentrations of antibody-drug conjugates tested are shown in Figure 26C.
[0055] [Figure 27-1]Figure 27 shows the results of a cytotoxicity assay of the antibody conjugates of Figure 24 (i.e., hD12-II, hD12-T289C-II, hD12-V442C-II, and hD12-V282C-II) against three cell lines (H1373, Figure 27A; H1573, Figure 27B; and H1975, Figure 27C) that express moderate levels of cMET on their cell surface. Viability is shown on the y-axis, and the amount of antibody-drug conjugate added is shown on the x-axis (pM). Figure 27D shows the concentrations of antibody-drug conjugates tested. Figure 27E summarizes the results, showing comparative IC50 values. Figure 27-1 provides Figure 27A. [Figure 27-2] Figure 27-2 provides Figure 27B. [Figure 27-3] Figure 27-3 provides Figure 27C. [Figure 27-4] Figure 27-4 provides Figures 27D and 27E.
[0056] [Figure 28-1] Figure 28 shows the results of an in vivo xenograft study. Mice were injected with H1975 tumor cells (moderate expression of cMET) and treated with the indicated concentrations of hD12-V442C-II (Figure 28A), hD12-T289C-II (Figure 28B), and hD12-V282C-II (Figure 28C). Mice were treated with stochastically complexed hD12-II as a positive control. Mice were treated with vehicle (PBS) or denosumab-II as a negative control. Tumor volume (y-axis) was determined over time (i.e., days, x-axis). Figure 28-1 provides Figure 28A. [Figure 28-2] Figure 28-2 provides Figure 28B. [Figure 28-3] Figure 28-3 provides Figure 28C.
[0057] [Figure 29] FIG. 29 shows the body weight (y-axis) over time (x-axis) of mice treated as in FIG.
[0058] [Figure 30]Figure 30 shows the serum concentrations (y-axis) of hD12-V442C-II (Figure 28A), hD12-T289C-II (Figure 28B), and hD12-V282C-II (Figure 28C) after intravenous injection in rats. Time after injection (hours) is shown on the x-axis. The concentration of each antibody-drug conjugate was determined by ELISA.
[0059] [Figure 31] FIG. 31 shows a table summarizing the pharmacokinetic data obtained from the study of FIG.
[0060] [Figure 32] Figure 32 shows the results of an in vivo patient-derived xenograft (PDX) study using human primary gastric cancer tissue (Figure 32A), human primary colorectal cancer tissue (Figure 32B), and human head and neck cancer tissue (Figure 32C). The percentage of tumor growth inhibition (TGI%) is shown on the y-axis, and the concentration of administered antibody conjugate (hD12-T289C-II) is shown on the x-axis. TGI% was calculated as described in Example 12.
[0061] [Figure 33-1] Figure 33A shows immunohistochemical staining of a cross section of gastric cancer PDX model GA3121 for human cMET protein. Figure 33B shows an enlarged view of the area indicated by the white inset box in Figure 33A. [Figure 33-2] Figure 33C shows tumor growth inhibition results for the patient-derived in vivo xenograft (PDX) model GA3121. Each data point represents one group of 10 mice. Mice were treated with vehicle (PBS) or secukinumab II as a negative control. Tumor volume (y-axis) was determined over time (i.e., days, x-axis). DETAILED DESCRIPTION OF THE INVENTION
[0062] In some embodiments, provided herein are binder-drug conjugates comprising a binder (e.g., a monoclonal antibody or antigen-binding portion thereof) and a payload (e.g., a cytotoxic payload). In some embodiments, the binder is a novel monoclonal antibody or antigen-binding portion thereof that specifically binds to cMET. In some embodiments, the payload comprises a pyrrolobenzodiazepine (PBD) toxin and a specific linking group. The novel binder-drug conjugates described herein are useful for treating cancer and / or neoplastic disorders.
[0063] The binding agents described herein are novel not only in the amino acid sequences of their antigen-binding regions (e.g., heavy and light chain variable regions) but also in their functional characteristics. For example, the anti-cMET binding agents described herein possess a distinct combination of features not found in other cMET antibodies. First, the anti-cMET binding agents described herein do not induce significant signaling (e.g., receptor tyrosine kinase activity) from the cMET receptor upon binding. Thus, upon binding, the cMET binding agents described herein do not induce undesirable oncogenic activity (e.g., growth, proliferation, metastasis, or angiogenesis). Second, the anti-cMET binding agents described herein can induce cMET degradation after binding and are internalized. An advantage of this property is that any toxic payload attached to the anti-cMET binding agent is brought inside the target cell, thereby reducing the payload's off-target, nonspecific toxicity. This feature also makes it possible to control or modulate the activity of the toxic payload. For example, in some embodiments, the toxic payloads described herein are substantially inactive until contacted with an intracellular protease. Third, certain anti-cMET binding agents described herein cross-react with non-human primates, rats, and / or mice, allowing for testing and optimization of antibody-drug conjugates using non-human animal models. Fourth, the anti-cMET binding agents described herein are soluble, exhibit long half-lives in vivo, and are stable upon storage.
[0064] Many cytotoxic payloads are known and can be attached to antibodies using known linkers to generate antibody-drug conjugates (ADCs) (see, e.g., U.S. Patent Application Publication No. 2014 / 0120118, U.S. Patent Application Publication No. 2014 / 0127239, U.S. Patent Application Publication No. 2016 / 0250344, U.S. Patent Application Publication No. 2016 / 0250345, and Tiberghien, et al., (2016) ACS Medicinal Chemistry Letters 7 (11):983-987). However, the biochemical function of antibody binding agents often changes after conjugation to a payload. Similarly, the biochemical properties of payloads after conjugation to an antibody cannot always be predicted. For example, the in vivo activity of known payloads can vary widely, ranging from lethal to no therapeutic effect, depending on the type of linker used and the location at which the linker is attached to the antibody. Therefore, combining a particular cMET-binding agent with an ideal linker, a selected toxic payload, and an optimal conjugation site of the linker to the antibody to generate an antibody-drug conjugate that provides optimal toxin delivery while minimizing adverse events (e.g., off-target toxicity) and maintaining the desired biofunctional properties of the binder is extremely challenging, time-consuming, and requires considerable inventive effort. The ADCs presented herein provide a unique combination of toxin, linker, and novel cMET-binding agent, resulting in a highly effective ADC that provides optimal therapeutic efficacy while substantially reducing or eliminating off-target toxicity.
[0065] cMET The term "MET" is used interchangeably herein. cMET is also known as hepatocyte growth factor receptor (HGFR). Human cMET (e.g., SEQ ID NO: 109) comprises a 1390 amino acid immature polypeptide sequence, including, counting from N- to C-terminus, an N-terminal sequence from amino acids 1 to 24, an extracellular domain of human cMET from about amino acids 24 to 932, a transmembrane domain from about amino acids 933 to 955, and a cytoplasmic domain from about amino acids 956 to 1390. Methods for identifying the leader sequence, extracellular domain, transmembrane domain, and cytoplasmic domain of the cMET receptor are known, and any suitable method can be used to identify such domains or regions within a cMET polypeptide sequence from a suitable mammalian species. Human cMET polypeptides can include several known variants (see, e.g., URL: http: / / www.uniprot.org / uniprot / P08581, accessed May 5, 2016; the cMET variants and alternative sequences disclosed therein are incorporated herein by reference). Non-limiting examples of naturally occurring variants of human cMET include amino acid substitutions at 143, 150, 156, 168, 238, 316, 320, 375, 385, 773, 970, 991, and / or 992 of human cMET (SEQ ID NO: 109). In some embodiments, cMET or the extracellular domain of cMET comprises an E to D substitution at position 168 of human cMET, referred to herein as E168D. In some embodiments, cMET or the extracellular domain of cMET comprises an N to S substitution at position 375 of human cMET, referred to herein as N375S.
[0066] In some embodiments, the cMET is mammalian cMET. In some embodiments, the cMET is primate cMET. In some embodiments, the cMET is human cMET. In some embodiments, the cMET is monkey cMET. In some embodiments, the cMET is rodent cMET (e.g., rat and / or mouse). In some embodiments, the cMET is canine cMET (e.g., dog cMET). Non-limiting examples of mammalian cMET are provided in Example 5 and / or the Sequence Listing of the present application. In some embodiments, the extracellular domain of cMET typically comprises the N-terminal portion of a cMET polypeptide expressed on the cell surface of a native mammalian cell. The extracellular domain of cMET can comprise two or more polypeptide chains derived from a MET translation product. In some embodiments, the extracellular domain of cMET can be expressed in a soluble form and / or a non-membrane-bound form that does not include the cytoplasmic and / or transmembrane domains. In some embodiments, the extracellular domain of cMET is expressed as a fusion protein, isolated, and / or purified. For example, the extracellular domain of a mammalian cMET can be engineered and expressed as a fusion protein with the Fc portion of an immunoglobulin (e.g., cMET-Fc). In certain embodiments, cMET and / or the extracellular domain of cMET contain one or more amino acid additions, deletions, or substitutions. A cMET polypeptide can be at least 80%, at least 85%, at least 90%, or at least 95% identical to a cMET polypeptide disclosed herein. In certain embodiments, a cMET polypeptide comprises a portion of a cMET protein (e.g., a subsequence thereof). In some embodiments, the portion of cMET comprises the extracellular domain of cMET or a portion thereof.
[0067] Binder In some embodiments, the binding agent comprises or consists of one or more polypeptides or one or more proteins that specifically bind to cMET or a portion thereof. In some embodiments, the binding agent comprises or consists of one or more proteins that specifically bind to cMET or a portion thereof. Binding agents often comprise at least one antigen-binding moiety (i.e., binding moiety). An antigen-binding moiety of a binding agent is a moiety that specifically binds to an antigen. In some embodiments, the binding moiety of a binding agent comprises or consists of a single polypeptide (e.g., a single-chain antibody). In some embodiments, the binding moiety of a binding agent comprises or consists of two polypeptides. In some embodiments, the binding moiety of a binding agent comprises or consists of two, three, four, or more polypeptides. In some embodiments, the binding agent comprises one or more structural moieties (e.g., a scaffold, a structural polypeptide, a constant region, and / or a framework region). In some embodiments, the binding agent or its binding moiety is attached to a substrate (e.g., a polymer, an inorganic material, silicon, a bead, etc.).
[0068] A binding agent may comprise one antigen-binding moiety or multiple antigen-binding moieties. For example, a binding agent comprising one binding moiety may be referred to as monovalent. A binding agent comprising two binding moieties may be referred to as bivalent. In some embodiments, a binding agent comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more binding moieties. In some embodiments, all of the binding moieties of a multivalent binding agent bind to the same antigen. In some embodiments, all of the binding moieties of a multivalent binding agent comprise one or more polypeptide sequences that are at least 90%, at least 95%, at least 99%, or 100% identical.
[0069] In certain embodiments, the two or more binding moieties of a binding agent bind to different antigens. Such binding agents are sometimes referred to as bispecific or multispecific binding agents (e.g., antibodies). Thus, in certain embodiments, a binding agent comprises a first antigen-binding moiety that specifically binds cMET or a portion thereof and a second antigen-binding moiety that specifically binds to another antigen (e.g., a polypeptide or portion thereof that is not cMET). In some embodiments, a binding agent that specifically binds cMET is covalently or noncovalently attached to another binding agent that does not specifically bind cMET or a portion thereof. In certain embodiments, a binding agent that specifically binds cMET comprises a second binding agent that specifically binds to another antigen.
[0070] In some embodiments, the binding agent comprises an antibody or a portion thereof (e.g., a binding portion thereof). In certain embodiments, the binding agent comprises or consists of a suitable antibody or an antigen-binding portion of an antibody. In some embodiments, the binding agent is an antibody (e.g., a monoclonal antibody and / or a recombinant antibody). The binding agent or antibody can be generated, manufactured, or produced by any suitable method. In some embodiments, the binding agent is monoclonal. In some embodiments, the binding agent is a monoclonal antibody derived from a suitable species. Some non-limiting examples of binding agents include monoclonal antibodies, chimeric antibodies, antibody-binding fragments (e.g., antigen-binding portions of antibodies), CDR-grafted antibodies, humanized antibodies, human antibodies, or portions thereof. Human antibodies can be obtained by any suitable method. For example, human antibodies can be obtained from transchromosomal animals engineered to produce fully human antibodies. In certain embodiments, the binding agent is not polyclonal, and the term "binding agent" does not refer to a polyclonal antibody.
[0071] In some embodiments, the binding agent is derived from, produced, obtained, isolated, and / or purified from a suitable species. In some embodiments, the binding agent is derived from, produced, obtained, isolated, and / or purified from, for example, rabbit, goat, horse, cow, rat, mouse, fish, bird, or llama. In some embodiments, the binding agent is derived from, produced, obtained, isolated, and / or purified from, a bird (e.g., a chicken or bird egg). In some embodiments, the binding agent is derived from, produced, obtained, isolated, and / or purified from, a plant (e.g., a recombinant binding agent produced by a genetically engineered plant). In some embodiments, the binding agent is derived from, produced, obtained, isolated, and / or purified from a suitable mammal. In certain embodiments, a suitable mammal is a genetically modified mammal (e.g., a transchromosomal or transgenic mammal) engineered to produce antibodies comprising human heavy chains and / or human light chains or portions thereof. In some embodiments, the binding agent is produced, obtained, isolated, or purified from a prokaryotic or eukaryotic cell (e.g., a recombinant binding agent produced by a genetically engineered cell). In some embodiments, the binding agent is produced, obtained, isolated, or purified from a virus (e.g., a recombinant binding agent produced by a genetically engineered virus). The binding agent can be expressed, isolated, and / or purified from a suitable expression system, non-limiting examples of which include suitable bacterial, phage, insect, viral, plant, or mammalian expression systems. For example, a nucleic acid encoding the binding agent can be introduced into a suitable mammalian cell line and the binding agent can be expressed and secreted into the cell culture medium.
[0072] In some embodiments, the binding agent is not found or produced in nature, e.g., in some embodiments, the binding agent is artificially produced in an animal by administering an emulsified cocktail containing the foreign recombinant antigen, a strong adjuvant, and often mineral oil and / or surfactant, thereby eliciting an artificial immune response to the foreign recombinant antigen (e.g., cMET, cMET-Fc).
[0073] In certain embodiments, a monoclonal antibody or monoclonal binding agent is a substantially homogenous population of binding agents or binding fragments thereof, with the exception of variants that may arise during production of the monoclonal binding agent, where each individual binding agent in the population is substantially identical and / or binds to the same epitope. In some embodiments, such variants may be generally absent or present in trace amounts. In contrast to polyclonal antibody preparations, which typically include a population of different antibodies directed against different determinants (epitopes), each binding agent in a population of monoclonal binding agents often binds to a single determinant on an antigen. Monoclonal binding agents are often free from contamination by other immunoglobulins. One or more different monoclonal binding agents may be intentionally added to a composition to form a mixture.
[0074] The modifier "monoclonal" should not be construed as requiring that the binding agent be produced by any particular method. Monoclonal binding agents can be produced by any suitable method. For example, in certain embodiments, monoclonal antibodies are made by the hybridoma method described in Kohler et al., Nature. (1975) 256:495, or modifications thereof. In some embodiments, monoclonal binding agents are made by suitable recombinant DNA methods. For example, monoclonal binding agents can be produced by any suitable method. For example, in certain embodiments, monoclonal antibodies can be made or modified by the methods described in U.S. Pat. No. 5,225,539 and / or Daugherty et al. (1991) Nucleic Acids Research 19(9): 2471-2476. Monoclonal binding agents can be made, for example, by screening recombinant libraries using a suitable expression system (e.g., a phage display expression system). In some embodiments, monoclonal binding agents are isolated from a phage library of binding agents by, for example, the techniques described in Clackson et al. (1991) Nature, 352: 624-628 and / or Marks et al. (1991) J. Mol Biol, 222: 581-597, or modifications thereof.
[0075] In certain embodiments, a binder comprises one or more structural or skeletal moieties, sometimes referred to as a scaffold. A binder may comprise a scaffold, non-limiting examples of which include scaffolds derived from antibodies, the Z domain of protein A, gamma-B crystals, ubiquitin, cystatin, Sac7d, triple helix coiled coils, lipocalins, ankyrin repeat motifs, the SH3 domain of Fyn, the Kunitz domain of a suitable protease inhibitor, a fibronectin domain, a nucleic acid polymer, or other moieties or combinations thereof. In some embodiments, a binder does not comprise a scaffold. In certain embodiments, a binder comprises one or more structural moieties of a mammalian antibody.
[0076] In certain embodiments, the binding agent comprises one or more constant regions (e.g., a constant region from an antibody, e.g., a mammalian antibody). In certain embodiments, the binding agent comprises a constant region of an antibody light chain and / or a constant region of an antibody heavy chain. There are at least two types of immunoglobulin light chains in mammalian antibodies, designated lambda (λ) and kappa (κ). The binding agent may comprise any suitable constant region of an antibody, or one or more portions thereof. In some embodiments, the binding agent comprises a lambda light chain constant region, or a portion thereof. In some embodiments, the binding agent comprises a kappa light chain constant region, or a portion thereof. In some embodiments, the binding agent comprises a polypeptide that is at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% identical to the polypeptide sequence of a light chain constant region, or portion thereof, of a mammalian antibody. In some embodiments, the binding agent comprises a polypeptide that is at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% identical to the polypeptide sequence of an antibody light chain constant region of a human antibody. In some embodiments, the binding agent does not comprise a light chain constant region.
[0077] In certain embodiments, the binding agent comprises the constant region of an antibody heavy chain. In mammals, antibodies can have at least five types / classes of Ig heavy chains, designated IgA, IgD, IgE, IgG, and IgM, which are determined by the presence of different heavy chain constant regions or portions thereof (e.g., CH1, CL, CH2, CH3 domains). The binding agent can comprise any suitable heavy chain constant region or portion thereof. In some embodiments, the binding agent comprises an IgG1, IgG2, IgG3, or IgG4 heavy chain constant region, or one or more portions thereof. In some embodiments, the binding agent comprises one or more heavy chain constant regions or portions thereof of the IgM, IgD, IgA, or IgE isotypes.
[0078] Unless otherwise specified herein, the numbering of amino acid residues in the constant region of an antibody is according to the EU numbering system described in Edelman, GM et al., Proc. Natl. Acad. USA, 63, 78-85 (1969). PMID: 5257969.
[0079] In some embodiments, the binding agent comprises a polypeptide that is at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% identical to the polypeptide sequence of a constant region of a heavy chain of a mammalian antibody, or a portion thereof. In some embodiments, the binding agent comprises a polypeptide that is at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% identical or 100% identical to the polypeptide sequence of a constant region of an antibody heavy chain of a human antibody. In some embodiments, the binding agent comprises one or more additions, deletions, and / or modifications of the constant region. The binding agent may be modified to change the antibody class or isotype of the binding agent. In some embodiments, the binding agent comprises one or more additions, deletions, and / or modifications (one or more amino acid substitutions, deletions, or additions) to alter one or more functions of the binding agent, e.g., to inhibit, enhance, or reduce serum half-life, Fc receptor binding, complement fixation (e.g., C1q binding), glycosylation, sialylation, cytotoxicity, antibody-dependent cell-mediated phagocytosis (ADCP), antibody-dependent cellular cytotoxicity (ADCC), etc. In some embodiments, the binding agent does not comprise one or more portions of a heavy chain constant region or a light chain constant region. In some embodiments, the binding agent does not comprise a heavy chain constant region.
[0080] In some embodiments, the binding agent comprises or consists of one or more variable regions or portions thereof of an antibody. In some embodiments, the binding agent comprises one or more light chain variable regions or portions thereof. In some embodiments, the binding agent comprises one or more heavy chain variable regions or portions thereof. In certain embodiments, the binding agent comprises at least one light chain variable region and at least one heavy chain variable region. The light chain variable region and the heavy chain variable region can be on the same or different polypeptides. In certain embodiments, the antigen-binding portion of the binding agent consists of one or more heavy chain variable regions. In certain embodiments, the antigen-binding portion of the binding agent consists of one or more light chain variable regions. In certain embodiments, the antigen-binding portion of the binding agent consists of one or more light chain variable regions and one or more heavy chain variable regions.
[0081] In some embodiments, the binding agent comprises or consists of a Fab, Fab', F(ab')2, Fv fragment, single-chain Fv (scFv), diabody (Dab), synbody, etc., and / or a combination or portion thereof. In some embodiments, the binding agent comprises or consists of a Fab, Fab', F(ab')2, Fv fragment, single-chain Fv (scFv), diabody (Dab), synbody, etc., and / or a combination or portion thereof (see, e.g., U.S. Patent Nos. 6,099,842 and 5,990,296). In some embodiments, the binding agent comprises a single-chain polypeptide comprising one or more antigen-binding moieties. For example, single-chain binding agents can be constructed by recombinant molecular biology processes by joining a heavy chain variable region, or its antigen-binding portion, to a light chain variable region, or its antigen-binding portion, with a linker (e.g., an amino acid, polypeptide linker). Such single-chain binding agents often exhibit similar specificity and affinity for antigen as the parent two-chain monoclonal binding agent. Binding agents often include engineered regions, such as CDR-grafted or humanized portions. In certain embodiments, the binding agent is a native two-chain immunoglobulin, while in other embodiments the binding agent is a Fab monomer or a Fab dimer.
[0082] Nucleic acids encoding the binding agent polypeptides, or portions thereof, may be cloned, subcloned, rearranged, or modified for recombinant expression by suitable cloning procedures, and then expressed in a suitable expression system by methods known to those of skill in the art (e.g., Maniatis et al. (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press; Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons (1987 and annual updates); Methods in molecular biology, edited by Benny KC Lo, Springer Science & Business Media, 2004; Antibody Engineering, Vol. 1, Roland E. Kontermann, Stefan Duebel, Edition 2, Publisher Springer Science & Business Media, 2010; Antibody Phage See Display: Methods and Protocols, Biomed Protocols, Vol. 178 of Methods in molecular biology, Editors Philippa M. O'Brien, Robert Aitken, Springer Science & Business Media, 2004).
[0083] In mammals, the heavy and light chain variable regions of an antibody contribute three CDRs (complementarity-determining regions), commonly referred to as CDR1, CDR2, and CDR3, respectively, separated and / or flanked by framework regions (e.g., FR1, FR2, FR3, and FR4). As used herein, the term "CDR" refers to the amino acid sequences of a polypeptide identified as complementarity-determining regions. In certain embodiments, definitive description of the CDR polypeptide sequences and identification of the residues comprising the binding site of a binding agent are achieved by solving the structure of the binding agent and / or the structure of a binding agent-antigen complex. In certain embodiments, this can be achieved by any suitable method, such as X-ray crystallography and / or computer modeling. In certain embodiments, various analytical methods can be used to identify or approximate the CDR sequences of a binding agent or antibody. For example, the amino acid sequences and / or locations of the CDRs in the polypeptide sequence of a binding agent, antibody, binding portion thereof, or variable region thereof can be identified by suitable methods. Non-limiting examples include the Kabat system (see, e.g., Kabat, EA, et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication No. 91-3242, as well as Johnson, G. and Wu, TT (2000) Nucleic Acids Research 28(1):214-8, and / or the Chothia numbering scheme (see, e.g., Chothia & Lesk, (1987) J. Mol. Biol, 196:901-917; Chothia et al. (1989) Nature 342:878-883; and Al-Lazikani et al. (1997) JMB 273,927-948)). In some embodiments, the amino acid sequences and / or locations of the CDRs of an antibody can be identified by the AbM method and / or the contact method.The "AbM" definition uses an integrated package of computer programs created by the Oxford Molecular Group to model antibody structures (see, e.g., Martin et al., (1989) Proc. Natl. Acad. Sci. (USA), 86:9268-9272; "AbM." TM , A Computer Program for Modeling Variable Regions of Antibodies,” Oxford, UK; Oxford Molecular, Ltd.). The AbM definition models the tertiary structure of antibodies from primary sequence using a combination of ab initio methods and knowledge databases as described by Samudrala et al., (1999) Proteins, Structure, Function and Genetics Suppl, 3:194-198 and Xia Y, et al. (2000) J Mol Biol. 300(1):171-85. In one embodiment, the contact definition is based on an analysis of available complex crystal structures (see, e.g., MacCallum et al., (1996) J. Mol. Biol, 5:732-45).
[0084] In some embodiments, the binding agent and / or antigen-binding portion of the binding agent comprises at least two, at least three, at least four, at least five, or at least six CDRs. In some embodiments, the binding agent comprises 3 to 60 CDRs (e.g., for binding agents with multiple antigen-binding portions). In some embodiments, the binding agent comprises 3 to 12 CDRs. In some embodiments, the antigen-binding portion of the binding agent comprises 1 to 6 CDR polypeptide sequences.
[0085] In certain embodiments, the binding agent and / or antigen-binding portion of the binding agent comprises one, two, or three CDRs of a light chain variable region. In some embodiments, the light chain variable region of the binding agent comprises one or more CDRs (e.g., one, two, three, or more CDRs). The amino acid sequences representing the CDRs in the light chain variable region of an antibody or binding agent are referred to as CDR-L1, CDR-L2, and CDR-L3, which are numbered consecutively (i.e., L1, L2, and L3) from the amino terminus (N-terminus) to the carboxy terminus (C-terminus) of the light chain variable region. For example, in a polypeptide representing a light chain variable region of a binding agent, CDR-L1, if present, is the N-terminal-most light chain CDR, CDR-L3, if present, is the C-terminal-most light chain CDR, and CDR-L2, if present, is located (i) between CDR-L1 and CDR-L3, (ii) N-terminal to CDR-L3, or (iii) C-terminal to CDR-L1 of the light chain variable region or binding portion of the binding agent. The terms "CDR-L1," "CDR-L2," and "CDR-L3" refer, in part, to the amino acid sequences of polypeptides identified as complementarity-determining regions (e.g., CDRs of a light chain variable region) of a binding agent or disclosed herein. Non-limiting examples of amino acid sequences of CDR-L1, CDR-L2, and CDR-L3 are set forth in Tables 1-3, respectively. The light chain variable region or antigen-binding portion of the binding agents described herein can comprise any combination of CDR-L1, CDR-L2, and CDR-L3 disclosed herein, wherein the binding agent retains specific binding to cMET or a portion thereof. In one embodiment, the light chain variable region or antigen-binding portion of the binding agents described herein comprises a single light chain CDR comprising an amino acid sequence at least 70% identical to a CDR-L3 selected from Table 3.
[0086] In certain embodiments, the light chain variable region or antigen-binding portion of a binding agent described herein comprises an amino acid sequence at least 70% identical to a CDR-L3 selected from Table 3, and any other suitable CDR-L2 and / or CDR-L1 polypeptide sequence, and the binding agent retains specific binding to cMET or a portion thereof. In certain embodiments, the light chain CDRs of the light chain variable region or antigen-binding portion of the binding agent consist of CDR-L3 and CDR-L2, wherein CDR-L3 comprises an amino acid sequence at least 70% identical to a CDR-L3 selected from Table 3, and CDR-L2 comprises an amino acid sequence at least 70% identical to a CDR-L2 selected from Table 2. In certain embodiments, the light chain variable region or antigen-binding portion of a binding agent described herein comprises an amino acid sequence at least 70% identical to a CDR-L3 selected from Table 3, and an amino acid sequence at least 70% identical to a CDR-L2 selected from Table 2, and any other suitable CDR-L1 polypeptide sequence, and the binding agent retains specific binding to cMET or a portion thereof. In one embodiment, the light chain variable region or antigen-binding portion of the binding agents described herein comprises three light chain CDRs consisting of an amino acid sequence at least 70% identical to a CDR-L3 selected from Table 3, an amino acid sequence at least 70% identical to a CDR-L2 selected from Table 2, and an amino acid sequence at least 70% identical to a CDR-L1 selected from Table 1. In one embodiment, the light chain variable region or antigen-binding portion of the binding agents described herein comprises an amino acid sequence at least 70% identical to a CDR-L3 selected from Table 3, an amino acid sequence at least 70% identical to a CDR-L2 selected from Table 2, and an amino acid sequence at least 70% identical to a CDR-L1 selected from Table 1, and the binding agent retains specific binding to cMET or a portion thereof.
[0087] In some embodiments, the binding agent comprises one or more light chain CDRs that are at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to any one of the CDR sequences listed in Table 1, Table 2, or Table 3. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L1 that is at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to any one of the sequences shown in Table 1. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L1 of any one of the sequences shown in Table 1. [Table 1]
[0088] The clone names referenced in Tables 1-10 indicate the fusion number ("F"), plate number ("P"), and 96-well plate well number (A1-H12) from which the clone originated. Thus, for example, clone F6AP12F12 originated from fusion 6A, plate 12, well F12. The fusion number for each clone corresponds to the fusion shown in Figure 2.
[0089] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L2 that is at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to any one of the sequences shown in Table 2. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L2 of any one of the sequences shown in Table 2. [Table 2]
[0090] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L3 that is at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to any one of the sequences shown in Table 3. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L3 of any one of the sequences shown in Table 3. [Table 3]
[0091] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a light chain variable region having at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identity to an amino acid sequence in Table 4. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a light chain variable region sequence in Table 4. [Table 4]
[0092] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a humanized light chain variable region having at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identity to a sequence in Table 5. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a humanized light chain variable region sequence in Table 5. Table 5
[0093] In certain embodiments, the binding agent and / or antigen-binding portion of the binding agent comprises one, two, or three CDRs of a heavy chain variable region. In some embodiments, the heavy chain variable region comprises one or more CDRs (e.g., one, two, three, or more CDRs). The amino acid sequences representing the CDRs in the heavy chain variable region of an antibody or binding agent are referred to as CDR-H1, CDR-H2, and CDR-H3, which are numbered consecutively (i.e., H1, H2, and H3) from the amino terminus (N-terminus) to the carboxy terminus (C-terminus) of the heavy chain variable region. For example, in a polypeptide representing the heavy chain variable region of a binding agent, CDR-H1, if present, is the N-terminal most CDR; CDR-H3, if present, is the C-terminal most CDR; and CDR-H2, if present, is located (i) between CDR-H1 and CDR-H3, (ii) N-terminal to CDR-H3, or (iii) C-terminal to CDR-H of the heavy chain variable region. The terms "CDR-H1," "CDR-H2," and "CDR-H3" refer, in part, to the amino acid sequences of a polypeptide identified as a complementarity determining region (e.g., a CDR of a heavy chain variable region of a binding agent) of a binding agent or disclosed herein. Non-limiting examples of amino acid sequences for CDR-H1, CDR-H2, and CDR-H3 are provided in Tables 6-8, respectively. The heavy chain variable region or antigen-binding portion of a binding agent described herein can comprise any combination of CDR-H1, CDR-H2, and CDR-H3 disclosed herein, provided the binding agent retains specific binding to cMET or a portion thereof. In certain embodiments, the heavy chain variable region or antigen-binding portion of a binding agent described herein comprises a single heavy chain CDR consisting of an amino acid sequence at least 70% identical to a CDR-H3 selected from Table 8. In one embodiment, the heavy chain variable region or antigen-binding portion of the binding agents described herein comprises an amino acid sequence at least 70% identical to a CDR-H3 selected from Table 8, and any other suitable CDR-H2 and / or CDR-H1 polypeptide sequence, and the binding agent retains specific binding to cMET or a portion thereof.In certain embodiments, the heavy chain CDRs of the heavy chain variable region or antigen-binding portion of the binding agent consist of CDR-H3 and CDR-H2, wherein CDR-H3 comprises an amino acid sequence at least 70% identical to a CDR-H3 selected from Table 8, and CDR-H2 comprises an amino acid sequence at least 70% identical to a CDR-H2 selected from Table 7. In certain embodiments, the heavy chain variable region or antigen-binding portion of the binding agent described herein comprises an amino acid sequence at least 70% identical to a CDR-H3 selected from Table 8 and an amino acid sequence at least 70% identical to a CDR-H2 selected from Table 7, as well as any other suitable CDR-H1 polypeptide sequence, and the binding agent retains specific binding to cMET or a portion thereof. In certain embodiments, the heavy chain variable region or antigen-binding portion of the binding agent described herein comprises three heavy chain CDRs consisting of an amino acid sequence at least 70% identical to a CDR-H3 selected from Table 8, an amino acid sequence at least 70% identical to a CDR-H2 selected from Table 7, and an amino acid sequence at least 70% identical to a CDR-H1 selected from Table 6. In one embodiment, the heavy chain variable region or antigen-binding portion of the binding agent described herein comprises an amino acid sequence at least 70% identical to a CDR-H3 selected from Table 8, an amino acid sequence at least 70% identical to a CDR-H2 selected from Table 7, and an amino acid sequence at least 70% identical to a CDR-H1 selected from Table 6, and the binding agent retains specific binding to cMET or a portion thereof.
[0094] In some embodiments, the binding agent comprises one or more heavy chain CDRs that are at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to any one of the CDRs in Table 6, Table 7, or Table 8. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-H1 that is at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to any one of the sequences set forth in Table 6. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-H1 of any one of the sequences set forth in Table 6. [Table 6]
[0095] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-H2 that is at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to any one of the sequences shown in Table 7. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-H2 of any one of the sequences shown in Table 7. [Table 7]
[0096] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-H3 that is at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identical to any one of the sequences shown in Table 8. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-H3 of any one of the sequences shown in Table 8. [Table 8]
[0097] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a heavy chain variable region having at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identity to a sequence in Table 9. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a heavy chain variable region sequence in Table 9. [Table 9]
[0098] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a humanized heavy chain variable region having at least 70%, 75%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least 99% identity to a sequence in Table 10. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a humanized heavy chain variable region sequence in Table 10. [Table 10]
[0099] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L3 (e.g., a CDR-L3 selected from Table 3) that comprises an amino acid sequence at least 70%, at least 75%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 26-36. and a CDR-H3 (e.g., a CDR-H3 sequence selected from Table 8) comprising an amino acid sequence at least 70%, at least 75%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 79-93. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L3 comprising an amino acid sequence at least 70%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 34 or 35 and a CDR-H3 comprising an amino acid sequence at least 70%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to the amino acid sequence of SEQ ID NO: 87, 88, 92, or 93.
[0100] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L3 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 26-36 (e.g., a CDR-L3 sequence selected from Table 3), a CDR-L2 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 16-25 (e.g., a CDR-L2 sequence selected from Table 2), a CDR-H3 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 79-93 (e.g., a CDR-H3 sequence selected from Table 8), and a CDR-H2 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 62-78 (e.g., a CDR-H2 sequence selected from Table 7). In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L3 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 34 or 35; a CDR-L2 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 24 or 25; a CDR-H3 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 87, 88, 92, or 93; and a CDR-H2 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 70, 71, or 78.
[0101] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L3 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 26-36 (e.g., a CDR-L3 sequence selected from Table 3), a CDR-L2 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 16-25 (e.g., a CDR-L2 sequence selected from Table 2), a CDR-L1 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 1-15 (e.g., a CDR-L2 sequence selected from Table 1). CDR-H1 sequences selected from Table 6), CDR-H2 sequences selected from Table 7), CDR-L1 sequences selected from Table 6), CDR-H3 sequences selected from Table 8), CDR-H2 sequences selected from Table 7), CDR-H1 sequences selected from Table 6), CDR-H1 sequences selected from Table 6), CDR-L1 sequences selected from Table 6), CDR-H2 sequences selected from Table 7), CDR-L1 sequences selected from Table 6), CDR-H1 sequences selected from Table 6), CDR-H2 sequences selected from Table 7), CDR-L1 sequences selected from Table 6), CDR-L2 sequences selected from Table 7), CDR-L1 sequences selected from Table 6), CDR-L2 sequences selected from Table 7), CDR-L3 sequences selected from Table 8), CDR-L1 sequences selected from Table 6), CDR-L2 sequences selected from Table 7 ...3 sequences selected from Table 8), CDR-L1 sequences selected from Table 8), CDR-L2 sequences selected from Table 8), CDR-L1 sequences selected from Table 8), CDR-L2 sequences selected from Table 8), CDR-L3 sequences selected from Table 8), CDR-L2 sequences selected from Table 8), CDR-L1 sequences selected from Table 8), CDR-L1 sequences selected from Table 8), CDR-L2 sequences selected from Table 8), CDR-L1 sequences selected from Table 8), CDR-L2 sequences selected from Table 8), CDR-L1 sequences selected from Table 8), CDR-L2 sequences selected from Table 8), CDR-L2 sequences selected from Table 8), CDR-L3 sequences selected from Table 8), CDR-L3 sequences selected from Table 8), CDR-L1 sequences selected In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a CDR-L3 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 34 or 35; a CDR-L2 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 24 or 25; a CDR-L1 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 9, 10, or 15; a CDR-H3 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 87 or 88; a CDR-H2 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 70, 71, or 78; and a CDR-H1 comprising an amino acid sequence at least 70%, at least 90%, or 100% identical to the amino acid sequence of SEQ ID NO: 58 or 59.
[0102] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a heavy chain variable region (e.g., a heavy chain variable region) that comprises an amino acid sequence at least 70%, at least 75%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 94-108 .... In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a heavy chain variable region comprising an amino acid sequence at least 70%, at least 75%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any one of the amino acid sequences of SEQ ID NOs: 37-49 (e.g., a light chain variable region selected from Table 4 and Table 5). In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises a heavy chain variable region comprising an amino acid sequence at least 90% identical to any one of the amino acid sequences of SEQ ID NOs: 104-108 (e.g., a heavy chain variable region selected from Table 10) and a light chain variable region comprising an amino acid sequence at least 90% identical to any one of the amino acid sequences of SEQ ID NOs: 45-49 (e.g., a light chain variable region selected from Table 5).
[0103] The abbreviations "abb," "sdr," "fra," "ven," and "cdr" used herein are explained below. The abbreviation "cdr" or "CDR" refers to complementarity-determining region. The abbreviation "abb" refers to a truncated CDR, e.g., as described in Padlan et al. (1995) FASEB J 9:133-139. In some embodiments, the truncated CDR is defined as residues 27D-34, 50-55, and 89-96 of the light chain and 31-35B, 50-58, and 95-101 of the heavy chain grafted onto an appropriate human scaffold. Key framework residues are often conserved. The abbreviation "sdr" refers to "specificity-determining residues," residues thought to be involved in antigen binding, e.g., as described in Padlan et al. (1995). The abbreviation "fra" refers to the "Frankenstein approach," as described, for example, in Wu and Kabat (1992) Mol Immunol 29:1141-1146. The abbreviation "ven" refers to the "veneering" approach, as described, for example, in Padlan (1991), Mol Immunol 28:489-498.
[0104] The term "% identical" or "% identity" refers to the sequence identity between two amino acid sequences. Identity can be determined by comparing positions in each sequence aligned for purposes of comparison. When an equivalent position in the compared sequences is occupied by the same amino acid, the molecules are identical at that position. When an equivalent position is occupied by the same or similar (e.g., similar in steric and / or electronic properties) amino acid residue, the molecules can be said to be homologous (similar) at that position. Expression as a percentage of homology, similarity, or identity refers to a function of the number of identical or similar amino acids at positions shared by the compared sequences. Expression as a percentage of homology, similarity, or identity refers to a function of the number of identical or similar amino acids at positions shared by the compared sequences. Various alignment algorithms and / or programs can be used, such as FASTA, BLAST, or ENTREZ. FASTA and BLAST are available as part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.) and can be used, for example, with default settings. ENTREZ is available through the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Md. In one embodiment, the percent identity of two sequences can be determined by the GCG program using a gap weight of 1, e.g., weighting each amino acid gap as if there were a single amino acid or nucleotide mismatch between the two sequences.
[0105] Other methods for alignment are described in Methods in Enzymology, vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., a division of Harcourt Brace & Co., San Diego, Calif., USA. In some embodiments, an alignment program that tolerates gaps in the sequence is utilized to align the sequences. Smith-Waterman is one type of algorithm that tolerates gaps in sequence alignment. See Meth. Mol. Biol. 70:173-187 (1997). The GAP program, which uses the Needleman and Wunsch alignment method, can also be used to align sequences. An alternative search strategy uses MPSRCH software running on a MASPAR computer. MPSRCH uses the Smith-Waterman algorithm to score sequences on a massively parallel computer. This approach improves the ability to capture distantly related combinations and can tolerate particularly small gaps and nucleotide sequence errors. Nucleic acid-encoded amino acid sequences can be used to search both protein and DNA databases.
[0106] In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises one or more CDRs selected from the light chain variable regions of Table 4 and Table 5. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises one or more CDRs selected from the heavy chain variable regions of Table 9 and Table 10. In some embodiments, the binding agent or antigen-binding portion of the binding agent comprises one or more CDRs selected from the light chain variable regions of Table 4 and Table 5 and one or more CDRs selected from the heavy chain variable regions of Table 9 and Table 10. In an embodiment, the binding agent or antigen-binding portion of the binding agent comprises CDR-L1, CDR-L2, and CDR-L3 selected from any one of the light chain variable regions of Table 4 and Table 5, respectively, and CDR-H1, CDR-H2, and CDR-H3 selected from any one of the heavy chain variable regions of Table 9 and Table 10, respectively. The amino acid sequences of the CDRs (e.g., CDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and CDR-H3) can be identified in the heavy or light chain variable regions disclosed herein by any suitable method described herein or known to those of skill in the art.
[0107] In one embodiment, a binding agent that specifically binds to cMET comprises (i) polypeptide sequences of light chain complementarity determining regions (CDR-L), CDR-L1, CDR-L2, and CDR-L3, and (ii) polypeptide sequences of heavy chain complementarity determining regions (CDR-H), CDR-H1, CDR-H2, and CDR-H3, wherein CDR-L1 is selected from the amino acid sequences of SEQ ID NOs: 1-15, CDR-L2 is selected from the amino acid sequences of SEQ ID NOs: 16-25, CDR-L3 is selected from the amino acid sequences of SEQ ID NOs: 26-36, CDR-H1 is selected from the amino acid sequences of SEQ ID NOs: 50-61, CDR-H2 is selected from the amino acid sequences of SEQ ID NOs: 62-78, and CDR-H3 is selected from the amino acid sequences of SEQ ID NOs: 79-93.
[0108] In some embodiments, the binding agents comprise one or more suitable sequences selected from Tables 1-10, and the selected polypeptide sequences comprise 0-5, 1-5, 0-10, 1-10, 0-15, or 1-15 amino acid modifications, which may be amino acid additions, deletions, and / or substitutions. In some embodiments, the binding agents comprise one or more suitable sequences selected from Tables 4, 5, 9, or 10, and the selected polypeptide sequences comprise 0-5, 1-5, 0-10, 1-10, 0-15, or 1-15 amino acid modifications in framework or constant regions, which may be amino acid additions, deletions, and / or substitutions. In some embodiments, the amino acid modifications are conservative amino acid substitutions. In some embodiments, the binding agents disclosed herein comprise one or more amino acid analogs, unnatural amino acids, or amino acid derivatives.
[0109] In certain embodiments, a binding agent or antigen-binding portion of a binding agent comprises one or more framework regions (FRs). Framework regions are often located between the CDRs and / or flank the CDR sequences of the heavy or light chain variable regions of the antibody or binding agent. In mammals, heavy chain variable regions often comprise four framework regions, and light chain variable regions often comprise four framework regions. Any suitable method can be used to identify one or more framework regions in an antibody, in an antibody variable region, or in a binding agent. As discussed below, binding agents may comprise unmodified or modified (e.g., optimized), synthetic, or naturally occurring framework regions.
[0110] In some embodiments, the binding agent or antigen-binding portion thereof is chimerized, grafted, and / or humanized. Chimerized, grafted, and / or humanized binding agents often contain altered or substituted constant and / or framework regions while maintaining binding specificity to cMET or a portion thereof. In some embodiments, the binding agent or antigen-binding portion thereof comprises a constant region, framework region, or portion thereof derived from a human antibody. In some embodiments, the binding agent or antigen-binding portion thereof comprises an entirely synthetic portion, one or more amino acids, or a sequence of amino acids not found in a native antibody molecule.
[0111] Naturally occurring framework regions or portions thereof can be obtained from any suitable species. In certain embodiments, the complementarity determining regions (CDRs) of the light and heavy chain variable regions of a binding agent or antigen-binding portion thereof are grafted onto framework regions from the same or another species. For example, one or more framework regions of a binding agent can be derived from a rodent (e.g., mouse or rat) or a primate (e.g., human).
[0112] In some embodiments, the CDRs of the light and / or heavy chain variable regions of a binding agent, or antigen-binding portion thereof, can be grafted into consensus human framework regions. To create a consensus human framework region, in some embodiments, framework regions from several human heavy or light chain amino acid sequences can be aligned to identify a consensus sequence. In some embodiments, the heavy or light chain framework region of an antibody or binding agent is replaced with one or more framework regions, or portions thereof, from different heavy or light chain variable regions. In some embodiments, the binding agent, or antigen-binding portion thereof, comprises one or more human framework regions. In some embodiments, the binding agent, or antigen-binding portion thereof, comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 human framework regions. In some embodiments, the binding agent, or antigen-binding portion thereof, comprises one or more murine framework regions. In some embodiments, the binding agent, or antigen-binding portion thereof, comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 murine framework regions. In some embodiments, the binding agent, or antigen-binding portion thereof, comprises one or more human framework regions and one or more murine framework regions.
[0113] Methods for generating chimeric, humanized, and / or optimized antibodies or binding agents, for example, by modifying, substituting, or deleting framework regions or portions thereof, are known. Non-limiting examples of CDR grafting are described, for example, in U.S. Patent Nos. 6,180,370, 6,054,297, 5,693,762, 5,859,205, 5,693,761, 5,565,332, 5,585,089, and 5,530,101, as well as Jones et al., Nature, (1986) 321:522-525; Verhoeyen et al., (1988) Science, 239:1534-1536; and Winter, (1998) FEBS Letts., 430:92-94. Further non-limiting examples of generating chimeric, grafted, and / or humanized binding agents include U.S. Pat. Nos. 5,530,101, 5,707,622, 5,994,524, 6,245,894, Queen et al., (1988) PNAS 86:10029-10033, Riechmann et al., (1988) Nature 332:323-327, Antibody Engineering: Methods and Protocols, Vol. 248 of Methods in molecular biology, edited by Benny K.C. Lo, Springer Science & Business Media, (2004), and Antibody Engineering, Vol. 1, Roland E. Kontermann, Stefan Duebel, 2nd edition, Publisher Springer Science & Business Media, (2010). In some embodiments, a binding agent can be humanized by replacing one or more framework regions or portions thereof (e.g., one or more amino acids) with one or more framework regions or portions thereof from a human antibody.In certain embodiments, antibodies or binding agents can be humanized or grafted by transferring one or more CDRs (e.g., one, two, three, four, five, or all six CDRs) from a donor binding agent (e.g., a murine monoclonal antibody) to an acceptor binding agent (e.g., a human antibody) while retaining the binding specificity of the donor binding agent. In certain embodiments, the process of creating a chimerized, grafted, or humanized binding agent involves making one or more amino acid substitutions, additions, or deletions in the constant or framework regions of the binding agent. In certain embodiments, techniques such as "reshaping," "hyperchimerization," or "veneering / resurfacing" can be used to produce humanized binding agents (see, e.g., Vaswami et al., (1998) Annals of Allergy, Asthma, & Immunol. 81:105; Roguska et al., (1996) Prot. Engin., 9:895-904; and U.S. Patent No. 6,072,035). In some embodiments, the binding agent is modified to reduce immunogenicity by the methods discussed above or by another suitable method (see, e.g., Gilliland et al., (1999) J. Immunol, 62(6):3663-71).
[0114] In certain embodiments, the amino acid sequence of a binding agent is modified to optimize binding affinity for a target (e.g., cMET), species cross-reactivity, solubility, and / or function (e.g., agonist activity, or lack thereof). In some embodiments, specific combinations of CDRs disclosed herein can be optimized for binding to cMET and / or to optimize the function or characteristics of the binding agents disclosed herein. For example, a characterized light chain variable region disclosed herein (e.g., the light chain variable region of SEQ ID NO: 48) can be co-expressed using a suitable expression system with a library of heavy chain variable regions comprising CDR-H1 and CDR-H2 of a characterized heavy chain variable region (e.g., the heavy chain variable region of SEQ ID NO: 107), with the CDR-H3 replaced with a library of CDR-H3 sequences, which may include, for example, one or more CDR-H3 regions from Table 8. The resulting light chain / heavy chain binders can be screened for binding to cMET and / or for a particular function. Optimized binders are identified, and the amino acid sequence of the CDR-H3 is identified by a suitable method. The above screening methods can be used to identify binding agents containing particular combinations of CDRs or particular optimized CDR sequences (e.g., CDR sequences containing amino acid substitutions, additions, or deletions) that may improve the binding specificity, binding affinity, and / or function of the binding agent. Such methods for screening and optimizing binding agents are known (see, e.g., Portolano et al. (1993) Journal of Immunology 150:880-887; and Clarkson et al. (1991) Nature 352:624-628). Such references teach how to produce antibodies that bind to specific antigens using known light chain variable regions, known heavy chain variable regions, or portions thereof (e.g., their CDRs) by screening libraries of complementary variable regions.
[0115] In certain embodiments, binders are modified to remove or add glycosylation sites to optimize the affinity and / or function of the binder (see, e.g., Co et al. (1993) Mol. Immunol. 30:1361-1367). In some embodiments, the number and / or type of glycosylation sites in a binder are modified or changed. N-linked glycosylation sites are often characterized by the sequence Asn-X-Ser or Asn-X-Thr, where the amino acid residue designated X can be any amino acid residue except proline. Substitution of amino acids to create this sequence provides a new potential site for the addition of an N-linked carbohydrate chain. Alternatively, substitution to eliminate this sequence will remove an existing N-linked carbohydrate chain. In certain embodiments, rearrangements of N-linked carbohydrate chains are also provided, in which one or more N-linked glycosylation sites (typically naturally occurring) are eliminated and one or more new N-linked sites are created. In some embodiments, the binding agent is modified by deleting one or more cysteine residues or substituting one or more cysteine residues with another amino acid (e.g., serine) compared to the unmodified binding agent. In certain embodiments, cysteine variants may be useful for optimizing expression, secretion, and / or solubility.
[0116] In certain embodiments, the binding agents are modified to include certain amino acid additions, substitutions, or deletions designed or intended to, for example, reduce the binding agent's susceptibility to proteolysis, reduce the binding agent's susceptibility to oxidation, increase serum half-life, and / or impart or modify other physicochemical, pharmacokinetic, or functional properties of the binding agent.
[0117] In some embodiments, the binding agent specifically binds to mammalian cMET or a portion thereof. In some embodiments, the binding agent specifically binds to the extracellular domain or extracellular region of mammalian cMET or a portion thereof. In certain aspects, the binding agent specifically binds to wild-type cMET produced by non-modified (genetically unaltered) mammalian cells as found in nature. In certain aspects, the binding agent specifically binds to naturally occurring cMET variants. In certain aspects, the binding agent specifically binds to cMET containing one or more amino acid substitutions, additions, or deletions. In certain embodiments, the binding agent specifically binds to cMET produced and / or expressed on the surface of human, non-human primate, canine, feline, or rodent (e.g., mouse or rat) cells. In certain embodiments, the binding agent specifically binds to one or more cMET polypeptides or portions thereof having the amino acid sequence of any one of SEQ ID NOs: 109-113. In certain embodiments, the binding agent specifically binds to human cMET. In certain embodiments, the binding agent specifically binds to the extracellular domain of human cMET. In certain embodiments, the binding agent specifically binds to human cMET and / or its extracellular domain, wherein the human cMET comprises an E168 to D168 substitution (i.e., the E168D mutant of cMET). In certain embodiments, the binding agent specifically binds to human cMET and / or its extracellular domain, wherein the human cMET comprises an N375 to S375 substitution (i.e., the N375S mutant of cMET).
[0118] The term "specifically binds" refers to a binding agent that binds to a target peptide preferentially over other molecules or other peptides, as determined, for example, by a suitable in vitro assay (e.g., ELISA, immunoblot, flow cytometry, etc.). A specific binding interaction distinguishes a non-specific binding interaction by at least about 2-fold, often at least about 10-fold, and sometimes at least about 100-fold, 1000-fold, 10,000-fold, 100,000-fold, or 1,000,000-fold.
[0119] In some embodiments, a binding agent that specifically binds to cMET or a portion thereof is a binding agent that binds to cMET or a portion thereof (e.g., the extracellular domain of cMET) with a binding affinity constant (KD) of 100 nM or less, 50 nM or less, 25 nM or less, 10 nM or less, 5 nM or less, 1 nM or less, 900 pM or less, 800 pM or less, 750 pM or less, 700 pM or less, 600 pM or less, 500 pM or less, 400 pM or less, 300 pM or less, 200 pM or less, or 100 pM or less. In some embodiments, a binding agent that specifically binds to cMET or a portion thereof is a binding agent that binds to human cMET or a portion thereof (e.g., the extracellular domain of human cMET) with a binding affinity constant (KD) of 100 nM or less, 50 nM or less, 25 nM or less, 10 nM or less, 5 nM or less, 1 nM or less, 900 pM or less, 800 pM or less, 750 pM or less, 700 pM or less, 600 pM or less, 500 pM or less, 400 pM or less, 300 pM or less, 200 pM or less, or 100 pM or less. In some embodiments, a binding agent that specifically binds to cMET or a portion thereof is a binding agent that specifically binds to cMET or a portion thereof from a non-human species (e.g., a non-human primate or a rodent, e.g., a mouse or rat) with a binding affinity constant (KD) of 100 nM or less, 50 nM or less, 25 nM or less, 10 nM or less, 5 nM or less, 1 nM or less, 900 pM or less, 800 pM or less, 750 pM or less, 700 pM or less, 600 pM or less, 500 pM or less, 400 pM or less, 300 pM or less, 200 pM or less, or 100 pM or less. In certain embodiments, a binding agent disclosed herein specifically binds to human cMET or a portion thereof and specifically binds to cMET or a portion thereof from a non-human primate. In certain embodiments, a binding agent disclosed herein specifically binds to human cMET or a portion thereof and specifically binds to cMET or a portion thereof from a rodent (e.g., a mouse or rat).In one embodiment, the binding agent (i) specifically binds to human cMET or a portion thereof (e.g., the extracellular domain of human cMET) with a KD of 10 nM or less, or 1 nM or less, and (ii) specifically binds to rat or mouse cMET or a portion thereof (e.g., the extracellular domain of rat or mouse cMET) with a KD of 100 nM or less, 90 nM or less, 80 nM or less, 70 nM or less, 60 nM or less, 50 nM or less, 40 nM or less, 30 nM or less, 20 nM or less, or 10 nM or less.
[0120] In some embodiments, the binding agent comprises one or more functional features. Thus, a binding agent can be described structurally and functionally (e.g., by what it does or what it can do). The binding agents disclosed herein can specifically bind to the extracellular portion of cMET, e.g., the extracellular portion of cMET present on the surface of a cell. In some embodiments, the cell is a human cancer cell or a human neoplastic cell that expresses cMET. In some embodiments, the binding agents disclosed herein induce internalization of cMET upon binding to cell surface cMET. The ability of a cMET-binding agent to induce internalization and / or degradation of cMET provides an advantage over other cMET-binding agents that lack this ability. A cMET-binding agent-drug conjugate that induces internalization and / or degradation of cMET after binding provides localized intracellular delivery of a cytotoxic drug. Furthermore, in some embodiments, the binding agent-drug conjugate is configured to release the PBD toxin from the binding agent only after internalization, e.g., by a lysosomal enzyme cleavage site incorporated into the linking group. Thus, the binding agent-drug conjugates described herein can specifically deliver toxins to the interior of cancer cells that express cMET in a subject, while minimizing nonspecific cytotoxicity to healthy cells in the subject. Consequently, the anti-cMET binding agent-drug conjugates described herein provide greater efficacy (e.g., target-specific cytotoxicity) and fewer adverse side effects (e.g., less nonspecific cytotoxicity). Thus, in certain embodiments, a binding agent-drug conjugate comprises a binding agent that specifically binds to cMET on the cell surface of a cell and induces internalization of cMET after binding. In some embodiments, the binding agent specifically binds to cMET or a portion thereof and induces degradation of cMET. Thus, in certain embodiments, a binding agent-drug conjugate comprises a binding agent that specifically binds to cMET on the cell surface of a cell and induces internalization and / or degradation of cMET after binding.The internalization and / or degradation of cell surface-bound receptors induced by ligand or binding agent binding can be detected, measured, and / or quantified using public assays known in the art. Thus, the ability of a binding agent to induce cMET internalization and / or degradation can be determined without undue burden through the use of public experimental assays. Thus, in some embodiments, the binding agents described herein are binding agents that specifically bind to cMET or portions thereof on the cell surface and induce the internalization and / or degradation of cMET.
[0121] Activation of cMET through binding of its cognate ligand is involved in tumor growth, angiogenesis, and metastasis. Agonistic anti-cMET antibodies often mimic ligand binding by cross-linking the cMET receptor and inducing cMET activation. Thus, binding agents that bind to cell surface cMET without activating the cMET receptor are more suitable for anti-cancer therapeutic applications. In some embodiments, the binding agent of a binding agent-drug conjugate specifically binds to cMET or a portion thereof on the cell surface and does not detectably induce or promote signal transduction (e.g., tyrosine kinase activity). In some embodiments, the binding agent of a binding agent-drug conjugate specifically binds to cMET or a portion thereof on the cell surface and does not substantially activate cMET (e.g., tyrosine kinase activity). In certain embodiments, the anti-cMET binding agents disclosed herein lack detectable cMET agonist activity. In certain embodiments, the anti-cMET binding agents lack agonist activity upon binding of cMET on the cell surface and / or are unable to induce or promote detectable tyrosine kinase activity upon binding of cMET on the cell surface. In some embodiments, anti-cMET binding agents are cMET antagonists. In certain embodiments, anti-cMET binding agents decrease, inhibit, reduce, interfere with, or prevent signaling through the cMET receptor and / or decrease, inhibit, reduce, interfere with, or prevent the cMET receptor from inducing or promoting detectable tyrosine kinase activity. In some embodiments, the anti-cMET binding agents disclosed herein decrease, inhibit, reduce, prevent, or interfere with the binding of cMET to its natural analog ligand (e.g., hepatocyte growth factor, or an isoform thereof).
[0122] In some embodiments, the binding agent comprises a label. As used herein, the term "label" or "labeled" refers to the incorporation of a detectable marker, for example, by incorporation of a labeled amino acid or attachment of a biotin moiety to the polypeptide that can be detected by labeled avidin (e.g., streptavidin containing a fluorescent marker or enzymatic activity that can be detected optically or colorimetrically). In certain embodiments, a label or marker can be attached to the binding agent to generate a therapeutic or diagnostic agent. The binding agent can be covalently or non-covalently attached to any suitable label or marker. A variety of methods for labeling polypeptides and glycoproteins are known to those of skill in the art and can be used. Non-limiting examples of labels for polypeptides include, but are not limited to, the following radioisotopes or radionuclides (e.g., 3 H, 14 C. 15 N, 35 S, 90 Y, 99 Tc, 125 I, 131 I), fluorescent labels, enzyme labels (e.g., horseradish peroxidase, β-galactosidase, luciferase, alkaline phosphatase), chemiluminescent labels, metal labels, chromophores, electrochemiluminescent labels, phosphorescent labels, quenchers (e.g., fluorophore quenchers), fluorescence resonance energy transfer (FRET) pairs (e.g., donor and acceptor), dyes, enzyme substrates, small molecules, mass tags, quantum dots, nanoparticles, biotinyl groups, predetermined polypeptide epitopes recognized by secondary reporters (e.g., leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags), others, and combinations thereof.
[0123] In some embodiments, the binder comprises a suitable carrier. The binder can be covalently or non-covalently attached to a suitable carrier. In certain embodiments, the carrier is an agent or molecule that alters or extends the in vivo half-life of the binder or improves its pharmacokinetic properties. Non-limiting examples of carriers include polyethylene glycol, glycogen (e.g., by glycosylation of the binder), dextran, and the carriers or vehicles described in U.S. Patent No. 6,660,843, among others, and combinations thereof.
[0124] payload PBD toxin In some embodiments, the binder-drug conjugate comprises a binder described herein (e.g., a binder that specifically binds to cMET) and a payload (e.g., a cytotoxic payload). The binder-drug conjugate is often covalently linked to the binder. In some embodiments, the payload comprises a pyrrolobenzodiazepine (PBD) toxin. In some embodiments, the payload comprises a linking group or a suitable linker. In some embodiments, the payload comprises a pyrrolobenzodiazepine (PBD) toxin and a linking group. In some embodiments, the payload comprises a pyrrolobenzodiazepine (PBD) toxin and a linking group, wherein the pyrrolobenzodiazepine is covalently linked to the linking group, and the linking group is covalently linked to a binder described herein.
[0125] Non-limiting examples of PBD toxins and methods of making PBD toxins are described in the following patent application publications: U.S. Patent Application Publication No. 2011 / 0256157, WO 2015 / 052322, U.S. Patent Application Publication No. 2016 / 0106861, U.S. Patent Application Publication No. 2007 / 0072846, U.S. Patent Application Publication No. 2011 / 0201803, U.S. Patent Application Publication No. 2010 / 0113425, U.S. Patent Application Publication No. 2008 / 0167 293, U.S. Patent Application Publication No. 2014 / 0127239, U.S. Patent Application Publication No. 2015 / 0158869, U.S. Patent Application Publication No. 2015 / 0344482, U.S. Patent Application Publication No. 2015 / 0111880, U.S. Patent Application Publication No. 2015 / 0315196, U.S. Patent Application Publication No. 2016 / 0015828, U.S. Patent Application Publication No. 2014 / 0088089, U.S. Patent Application Publication No. 2013 / 0035484 ...6 / 0015828, U.S. Patent Application Publication No. 2016 / 0015828, U.S. Patent Application Publication No. 2016 / 0015828, U.S. Patent Application Publication No. 2016 / 0015828, U.S. Patent Application Publication No. 2016 / 0015828, 011 / 0196148, U.S. Patent Application Publication No. 2013 / 0028919, U.S. Patent Application Publication No. 2013 / 0059800, U.S. Patent Application Publication No. 2014 / 0274907, U.S. Patent Application Publication No. 2014 / 0275522, U.S. Patent Application Publication No. 2014 / 0234346, U.S. Patent Application Publication No. 2013 / 0266595, U.S. Patent Application Publication No. 2014 / 0302066, U.S. Patent Application Publication No. 2014 / 0286970, U.S. Patent Application Publication No. 2014 / 0294868, U.S. Patent Application Publication No. 2016 / 0144052, U.S. Patent Application Publication No. 2016 / 0031887, U.S. Patent Application Publication No. 2014 / 0120118, U.S. Patent Application Publication No. 2016 / 0250344, WO 2017 / 137553, WO 2017 / 137555 and WO 2017 / 186894, the entire contents of which are incorporated herein by reference in their entireties.
[0126] In some embodiments, the pyrrolobenzodiazepine toxin has Formula I: [ka]
[0127] wherein Z1 and Z2 are both N; Z3 and Z4 are both C; [ka] n is 1 to 12; each of R3 and R4 is independently H or C 1-4 alkoxyl; and each of R and R is independently H, C 1-5 Alkyl, C 3-6 Cycloalkyl, C 2-5 alkenyl and phenyl optionally substituted with R5, wherein R5 is -NH2, -NHR6 and a group having the structure: [ka] piperazinyl substituted with R7 having the formula R6 comprises a linking group, and R7 is null or C 1-5 X1 is null, a protecting group, or comprises a linking group; X2 is null, a protecting group, or comprises a linking group; only one of X1, X2, R1, and R2 comprises a linking group; and each of Y1 and Y2 is independently either null, OH, or SO3H; provided that [ka] Includes the structure of
[0128] In some embodiments, a PBD toxin includes only one linking group. For example, in Formula I, only one of X1, X2, R1, and R2 can include a linking group. For example, if X1 includes a linking group, then X2, R1, and R2 do not include a linking group.
[0129] In some embodiments of PBD toxins of Formula I, n is 1-12. In some embodiments of PBD toxins of Formula I, n is 1-10, 1-9, 1-7, 1-5, or 1-3. In some embodiments of PBD toxins of Formula I, n is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12. In some embodiments, n is 1, 3, or 5. In some embodiments, n is 3 or 5.
[0130] In some embodiments of the PBD toxin of formula I, R3 and R4 are independently C 1-4 In some embodiments of a PBD toxin of formula I, R3 and R4 are independently selected from -O-CH2CH3 or -O-CH3. In some embodiments of a PBD toxin of formula I, R3 and R4 are both -O-CH3.
[0131] In some embodiments of the PBD toxin of formula I, R and R are independently H, C, 1-5 Alkyl, C3-C6 cycloalkyl and C 2-5 R1 and R2 are selected from the group consisting of C1-C3 alkyl and C2-C3 alkenyl. R1 and R2 can be the same or different. In some embodiments, R1 and R2 are independently selected from C1-C3 alkyl and C2-C3 alkenyl. In certain embodiments, R1 and R2 are independently selected from -CH2CH2CH3 and -CH3. In certain embodiments, R1 and R2 are both -CH2CH2CH3 or -CH3.
[0132] In some embodiments of the PBD toxin of formula I, R1 and R2 are independently selected from C3-C6 cycloalkyl and phenyl optionally substituted with R5, where R5 is -NH2, -NHR6, and the structure: [ka] piperazinyl substituted with R7 having the formula R6 comprises a linking group, and R7 is null or C 1-5In certain embodiments, R1 and R2 are different and independently selected from (i) C3-C6 cycloalkyl and (ii) phenyl optionally substituted with R5, where R5 is selected from -NH2 and -NHR6, and R6 comprises a linking group. In certain embodiments, R1 and R2 are different and independently selected from (i) C3 cycloalkyl and (ii) phenyl substituted with -NH2 or -NHR6, and R6 comprises a linking group. In certain embodiments, R1 and R2 are different and independently selected from (i) phenyl optionally substituted with R5 (where R5 is -NH2 and -NHR6, and R6 comprises a linking group) and (ii) piperazinyl substituted with R7 (where R7 is null or C1-C2 alkyl) having the structure: In certain embodiments, R1 and R2 are different and independently selected from (i) phenyl substituted with R5 (where R5 is -NH2 and -NHR6, and R6 comprises a linking group) and (ii) piperazinyl substituted with R7 (where R7 is null or C1-C2 alkyl). In certain embodiments, R1 and R2 are different and independently selected from (i) phenyl substituted with R5 (where R5 is -NH2 and -NHR6, and R6 comprises a linking group) and (ii) piperazinyl substituted with R7 (where R7 is null or C1-C2 alkyl). [ka] [R7 is -CH3] In one embodiment, R2 is phenyl substituted with 4-methylpiperazin-1-yl.
[0133] In some embodiments of a PBD toxin of formula I, X1 is null, Y1 is null, Z1Z3 is N=C, X2 is null, Y2 is null, and Z2Z4 is N=C. In some embodiments of a PBD toxin of formula I, X1 comprises a linking group, Y1 is OH, Z2Z4 is N=C, X2 is null, and Y2 is null. In some embodiments of a PBD toxin of formula I, X1 comprises a linking group, Y1 is OH, Z2Z4 is NC, X2 is a protecting group, and Y2 is OH.
[0134] In some embodiments, the PBD toxin has Formula VII, as shown below: [ka] [wherein X1 contains a linking group].
[0135] In some embodiments, the PBD toxin has Formula VIII, as shown below: [ka] [wherein X1 contains a linking group].
[0136] In some embodiments, the PBD toxin has Formula IX, shown below: [ka] [wherein R6 contains a linking group].
[0137] In some embodiments, the PBD toxin has the formula X shown below: [ka] [wherein R6 contains a linking group].
[0138] In some embodiments, the PBD toxin is attached (e.g., covalently linked) to the linking group by a suitable bond, moiety, or group. In some embodiments, the PBD toxin is attached (e.g., covalently linked) to the linking group by a carbonyl bond or an amide bond. In some embodiments, the PBD toxin is attached (e.g., covalently linked) to the linking group by a carbamate group. In some embodiments, the PBD toxin is attached (e.g., covalently linked) to the linking group by an amide group. Non-limiting examples of attachment of PBD toxins to linking groups are described in U.S. Patent Application Publication Nos. 2017 / 0002096, 2016 / 0331842, 2015 / 0250896, 2017 / 0080103, 2016 / 0136300, 2017 / 0152274, 2015 / 0209444, and ...136300, 2017 / 0152274, 2015 / 0209444, and 2015 / 0209446. Publication No. 2013 / 0274091, U.S. Patent Application Publication No. 2017 / 0095570, U.S. Patent Application Publication No. 2017 / 0157264, U.S. Patent Application Publication No. 2015 / 0125474, U.S. Patent Application Publication No. 2011 / 0256157, International Publication No. 2015 / 052322, U.S. Patent Application Publication No. 2016 / 0106861, U.S. Patent Application Publication No. 2007 / 0072846, U.S. Patent Application Publication No. 2011 / 0256157 0201803, U.S. Patent Application Publication No. 2010 / 0113425, U.S. Patent Application Publication No. 2008 / 0167293, U.S. Patent Application Publication No. 2014 / 0127239, U.S. Patent Application Publication No. 2015 / 0158869, U.S. Patent Application Publication No. 2015 / 0344482, U.S. Patent Application Publication No. 2015 / 0111880, U.S. Patent Application Publication No. 2015 / 0315196, U.S. Patent Application Publication No. 2016 / 0015 828, U.S. Patent Application Publication No. 2014 / 0088089, U.S. Patent Application Publication No. 2013 / 0035484, U.S. Patent Application Publication No. 2011 / 0196148, U.S. Patent Application Publication No. 2013 / 0028919, U.S. Patent Application Publication No. 2013 / 0059800, U.S. Patent Application Publication No. 2014 / 0274907, U.S. Patent Application Publication No. 2014 / 0275522, U.S. Patent Application Publication No. 2014 / 0234346,Nos. 2013 / 0266595, 2014 / 0302066, 2014 / 0286970, 2014 / 0294868, 2016 / 0144052, 2016 / 0031887, 2014 / 0120118, 2016 / 0250344, WO 2017 / 137553, WO 2017 / 137555, and WO 2017 / 186894, the entire contents of which are incorporated herein by reference in their entireties.
[0139] As used herein, the term "null" means that the depicted moiety is not present in the structure; the depicted moiety may be substituted or occupied with one or more hydrogen atoms to complete the required valence. Additionally, with respect to any structure depicted herein, one or more hydrogens may be present to complete the required valence of a carbon, nitrogen, or oxygen atom depicted in the structure. Thus, if not explicitly shown, one or more hydrogen atoms may be present.
[0140] linking group In some embodiments, the payload comprises a linking group that partially facilitates the linkage between the binding agent and the PBD toxin. In certain embodiments, any suitable linking group can be used to link the PBD toxin to the binding agent. Non-limiting examples of linking groups and methods of making linking groups are described in International Publication No. WO 2015 / 052322, U.S. Patent Application Publication No. 2015 / 0158869, U.S. Patent Application Publication No. 2015 / 0344482, U.S. Patent Application Publication No. 2014 / 0127239, U.S. Patent Application Publication No. 2017 / 0002096, U.S. Patent Application Publication No. 2016 / 0331842, U.S. Patent Application Publication No. 2015 / 0250896, U.S. Patent Application Publication No. 2017 / 00801 03, U.S. Patent Application Publication No. 2016 / 0136300, U.S. Patent Application Publication No. 2017 / 0152274, U.S. Patent Application Publication No. 2015 / 0209444, U.S. Patent Application Publication No. 2013 / 0274091, U.S. Patent Application Publication No. 2017 / 0095570, U.S. Patent Application Publication No. 2017 / 0157264, and U.S. Patent Application Publication No. 2015 / 0125474, which are incorporated by reference in their entireties. In some embodiments, the linking group comprises a C1-C20 alkyl, a C1-C20 alkenyl, a C1-C20 alkoxyl, one or more amino acids or amino acid derivatives, a peptide comprising 1 to 20 amino acids, a phenyl group, a suitable polymer (e.g., polyethylene glycol), or a combination thereof.
[0141] In some embodiments, the linking group has Formula A: [ka] [wherein the asterisk indicates the point of attachment of the linking group to the pyrrolobenzodiazepine toxin, the wavy line indicates the point of attachment of the linking group to the binding agent, m is 0-20, q is 0-10, and E is a linking group. In some embodiments of a linking group of Formula A, m is 1-20, 1-10, 1-8, 1-6, 1-4, 2-8, or 4 or 8. In some embodiments of a linking group of Formula A, m is selected from 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments of a linking group of Formula A, q is 1-10, 1-8, 1-6, or 1-4. In some embodiments of a linking group of Formula A, q is selected from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments of a linking group of Formula A, q is ... In some embodiments of the linking group of Formula A, m is 8 and q is 2.
[0142] In some embodiments, the linking group has formula B: [ka] wherein the asterisk indicates the point of attachment of the linking group to the pyrrolobenzodiazepine toxin, the wavy line indicates the point of attachment of the linking group to the binder, v is 0-10, and u is 0 or 1; when u is 1, t is 1-10, and E is a linking group. In some embodiments of a linking group of Formula B, v is 1-10, 1-8, 1-4, or 0-4, 21. In some embodiments of a linking group of Formula B, v is selected from 0, 1, 2, 3, 4, 5, 6, 7, or 8. In some embodiments of a linking group of Formula B, when u is 1, t is 1-8, 1-5, 1-4, or 2-5. In some embodiments of a linking group of Formula B, when u is 1, t is selected from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments of the linking group of formula B, t is 8, u is 1, and v is 2. In some embodiments of the linking group of formula B, u is 0, and v is 4.
[0143] The linking group E of Formulas A and B can comprise any suitable bond, linker, or moiety, non-limiting examples of which include a disulfide bond, a thioether bond, a thioester bond, an amide bond, an amine, a ketone, a carboxylate ether, a carbamate, an ester, a thioester, etc., or a combination thereof. In certain embodiments, E comprises a covalent bond between the linking group and the binding agent. In some embodiments, E comprises a covalent bond. In some embodiments, E comprises a reacted moiety that remains after a suitable conjugation reaction has been performed. Many conjugation reactions are known in the art, any of which can be used to covalently link the linking groups disclosed herein to the binding agents disclosed herein.Any suitable conjugation chemistry can be used to covalently attach the linking group to the binding group, either stochastically or site-specifically, non-limiting examples of which include Shan S. Wong (published June 18, 1991) Chemistry of Protein Conjugation and Cross-Linking, CRC Press; Greg T. Hermanson (Copyright 2013) Bioconjugate Techniques, Third Edition, Elsevier Inc.; and Thiol-X Chemistries in Polymer and Materials Science, RSC Polymer Chemistry Series No. 6 (2013) edited by Andrew B. Lowe and Christopher N. Bowman, RCS. Publishing, International Publication No. 2015 / 052322, U.S. Patent Application Publication No. 2015 / 0158869, U.S. Patent Application Publication No. 2015 / 0344482, U.S. Patent Application Publication No. 2014 / 0127239, U.S. Patent Application Publication No. 2017 / 0002096, U.S. Patent Application Publication No. 2016 / 0331842, U.S. Patent Application Publication No. 2015 / 0250896, U.S. Patent Application Publication No. 2017 / 0080103, U.S. Patent Application Publication No. 2017 / 0080103 Nos. 2016 / 0136300, 2017 / 0152274, 2015 / 0209444, 2013 / 0274091, 2017 / 0095570, 2017 / 0157264 and 2015 / 0125474, the entire contents of which are incorporated herein by reference in their entireties.Other non-limiting examples of conjugating a payload or linking group to a binder include conjugating an amine or amino group to an N-hydroxysuccinimide (NHS) ester, succinimidyl succinate, succinimidyl succinamide, succinimidyl propionate, succinimidyl carbonate, oxycarbonylimidazole, nitrophenyl carbonate, trichlorophenyl carbonate, tresylate, maleic anhydride, methylmaleic anhydride, imido ester, pentafluorophenyl (PFP) ester, hydroxymethylphosphine, oxirane or reacting with other carbonyl moieties; reacting carboxyl moieties with carbodiimides; reacting sulfhydryl moieties with maleimides, haloacetyls, pyridyl disulfides, orthopyridyl disulfides and / or vinyl sulfones; reacting aldehyde moieties with hydrazines or hydrazides; reacting non-selective groups with diazirines and / or aryl azides; reacting hydroxyl moieties with isocyanates; reacting hydroxylamine moieties with carbonyl moieties; and others, and combinations thereof.
[0144] Thus, E is often defined by the chemistry used to conjugate the linking group to the binder. In some embodiments, E comprises a suitable moiety configured to attach the linking group to the binder. In some embodiments, the linking group is covalently attached to the binder via a suitable sulfhydryl-sulfhydryl reaction, for example, by use of a maleimide or pyridyldithiol reactive group that reacts with reduced cysteine to form a stable thioether bond. Further non-limiting examples of reactive sulfhydryl-reactive moieties include haloacetyl, aziridine, acryloyl, arylating agents, vinyl sulfone, pyridyl disulfide, and TNB-thiol. In some embodiments, the binder is attached to E via a thioether bond formed between a cysteine thiol residue (e.g., thiol) of the binder and E. Thus, in some embodiments, E comprises a disulfide or thioether bond. In some embodiments, the binder is covalently linked to the binder using, for example, a maleimide reaction, and E has the chemical formula C: [ka] wherein the wavy line indicates the point of attachment to the linking agent and the double asterisk (**) indicates the point of attachment to the linking group. In one embodiment, the double asterisk in Formula C represents a thioether bond.
[0145] The payload, linking group, or linking group can be stochastically or site-specifically conjugated to any suitable amino acid of the binder. In some embodiments, the payload, linking group, or linking group is conjugated to one or more suitable cysteines of the binder. In some embodiments, the payload, linking group, or linking group is conjugated to one or more suitable lysine residues of the binder. In certain embodiments, one or more amino acids of the binder are substituted with an amino acid suitable for conjugation to a payload, linking group, or linking group. Non-limiting examples of amino acids that can be substituted with a thiol-containing amino acid residue or lysine residue include A118, S119, S239, V282, T289, N361, and V422 of IgG2, S115, S252, V289, T306, and N384 of IgG1, or corresponding positions in IgG1, IgG2, IgG3, or IgG4. Incorporation of cysteine into an antibody by mutagenesis allows for direct conjugation of a payload, linking group, or linking group to a specific site on the antibody, for example, via a disulfide bond or thioether bond. For example, one or more amino acids of a binding agent can be substituted with cysteine, which can then be used for site-specific conjugation of a payload, linking group, or linking group using appropriate chemical reactions. Any suitable amino acid in the constant region of an antibody can be mutated to cysteine or lysine for site-specific conjugation to a payload, linking group, or linking group. The stability of the antibody-drug conjugate resulting from site-specific conjugation can be evaluated by methods known in the art.
[0146] In some embodiments, the linking group comprises a suitable enzymatic cleavage site. In certain embodiments, the enzymatic cleavage site comprises an enzymatic recognition site for a mammalian protease. Thus, in some embodiments, the linking group, or a portion thereof, can be cleaved by a mammalian protease. The linking group can be cleaved by an enzyme present at or near the target site (e.g., at or near the cMET protein). The enzyme present at or near the target site can be intracellular, membrane-bound, membrane-associated, or extracellular (e.g., secreted). For example, the linking group can be configured to be cleaved by a cell-surface protease, a secreted protease, or an intracellular protease (e.g., a lysosomal protease). Non-limiting examples of enzymatic cleavage sites include protease recognition sites for lysosomal cysteine proteases and / or lysosomal aspartic proteases. Non-limiting examples of lysosomal proteases include cathepsin B, C, H, I, J, K, L, M, N, O, P, S, T and X, as well as cathepsin D, E, F, G and / or cathepsin A (carboxypeptidase A).
[0147] protecting group In some embodiments, the PBD toxin comprises a suitable protecting group. Non-limiting examples of protecting groups and methods of making protecting groups are described in the following patent application publications: U.S. Patent Application Publication No. 2011 / 0256157, WO 2015 / 052322, U.S. Patent Application Publication No. 2011 / 0201803, U.S. Patent Application Publication No. 2008 / 0167293, U.S. Patent Application Publication No. 2014 / 0127239, U.S. Patent Application Publication No. 2015 / 0158869, U.S. Patent No. 2015 / 0344482, U.S. Patent Application Publication No. 2015 / 0315196, U.S. Patent Application Publication No. 2015 / 0315196, U.S. Patent Application Publication No. 2014 / 0302066, U.S. Patent Application Publication No. 2006 / 0264622 and U.S. Patent Application Publication No. 2015 / 0133435, the entire contents of which are incorporated herein by reference in their entireties.
[0148] In some embodiments, the protecting group has the following formula D: [ka] wherein the asterisk indicates the point of attachment to the pyrrolobenzodiazepine toxin; and w is 0-10. In some embodiments, w is 0-8, 0-6, 0-4, 1-10, 1-8, 1-5, or 1-4. In some embodiments, w is selected from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10. In some embodiments, w is 2.
[0149] In some embodiments, the protecting group is removable. In certain embodiments, the protecting group is cleavable using suitable chemistry.
[0150] In some embodiments, the payload has Formula II: [ka] wherein m is 8 and the wavy line indicates the point of attachment to the binder.
[0151] In some embodiments, the payload has Formula III: [ka] wherein m is 8, p is 1 or 3, X2 is null or a protecting group, and the wavy line indicates the point of attachment to the linking agent. In one embodiment, the payload comprises a structure of Formula IV: [ka] The structure includes [the wavy line indicates the point attached to the binder].
[0152] In some embodiments, the payload has formula V': [ka] wherein m is 8, E is a suitable linking group, and the wavy line indicates the point of attachment to the linking agent. In some embodiments, E comprises structure C: [ka] wherein the wavy line indicates the point of attachment to the linking agent and the double asterisk indicates the point of attachment to the payload of formula V. A payload of formula V containing a linking group of structure C may be referred to herein as formula XI.
[0153] In some embodiments, the payload has Formula VI: [ka] where t is 8, v is 1, and the wavy line indicates the point of attachment to the binder.
[0154] In some embodiments, the payload has Formula VII: [ka] wherein the wavy line indicates the point of attachment to the binder.
[0155] In some embodiments, the binder-drug conjugate comprises a binder comprising a payload comprising a structure selected from any one of formulas II, III, IV, V, VI, VII, and XI, and a CDR-L1 selected from the amino acid sequences set forth in SEQ ID NOs: 2, 4, 6, 8, 10, 12, and 14; a CDR-L2 selected from the amino acid sequences set forth in SEQ ID NOs: 17, 19, 21, 23, and 25; a CDR-L3 selected from the amino acid sequences set forth in SEQ ID NOs: 27, 29, 31, 33, and 35; a CDR-H1 selected from the amino acid sequences set forth in SEQ ID NOs: 51, 53, 55, 57, and 59; a CDR-H2 selected from the amino acid sequences set forth in SEQ ID NOs: 63, 65, 67, 69, 71, 73, and 75; and a CDR-H3 selected from the amino acid sequences set forth in SEQ ID NOs: 80, 82, 84, 86, 88, 91, and 93.
[0156] In some embodiments, the binder-drug conjugate comprises a payload comprising a structure selected from any one of formulas II, III, IV, V, VI, VII, and XI, and a binder comprising CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or 14, CDR-L2 comprising the amino acid sequence of SEQ ID NO: 21, CDR-L3 comprising the amino acid sequence of SEQ ID NO: 35, CDR-H1 comprising the amino acid sequence of SEQ ID NO: 59, CDR-H2 comprising the amino acid sequence of SEQ ID NO: 71, and CDR-H3 comprising the amino acid sequence of SEQ ID NO: 88.
[0157] In some embodiments, the binder-drug conjugate comprises a payload comprising a structure selected from any one of formulas II, III, IV, V, VI, VII, and XI, and a binder comprising CDR-L1 comprising the amino acid sequence of SEQ ID NO: 9, CDR-L2 comprising the amino acid sequence of SEQ ID NO: 24, CDR-L3 comprising the amino acid sequence of SEQ ID NO: 34, CDR-H1 comprising the amino acid sequence of SEQ ID NO: 58, CDR-H2 comprising the amino acid sequence of SEQ ID NO: 70, and CDR-H3 comprising the amino acid sequence of SEQ ID NO: 87.
[0158] In some embodiments, the binder-drug conjugate comprises a payload comprising a structure selected from any one of formulas II, III, IV, V, VI, VII, and XI, and a binder comprising a light chain variable region having at least 90% sequence identity to an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 37-44, and a heavy chain variable region having at least 90% sequence identity to an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 94-103.
[0159] In some embodiments, the binder-drug conjugate comprises a payload comprising a structure selected from any one of formulas II, III, IV, V, VI, VII, and XI, and a binder comprising a light chain variable region having an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 37-44, and a heavy chain variable region having an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 94-103.
[0160] In some embodiments, the binder-drug conjugate comprises a payload comprising a structure selected from any one of formulas II, III, IV, V, VI, VII, and XI, and a binder comprising a light chain variable region having at least 90% sequence identity to an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 45-49, and a heavy chain variable region having at least 90% sequence identity to an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 104-108.
[0161] In some embodiments, the binder-drug conjugate comprises a payload comprising a structure selected from any one of Formulas II, III, IV, V, VI, VII, and XI, and a binder comprising a light chain variable region comprising an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 45-49, and a heavy chain variable region comprising an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 104-108.
[0162] Pharmaceutical Composition In some embodiments, a composition or pharmaceutical composition comprises a binder-drug conjugate described herein. In some embodiments, a pharmaceutical composition comprises a binder-drug conjugate and a pharmaceutically acceptable excipient, diluent, additive, or carrier.
[0163] Pharmaceutical compositions can be formulated for a suitable route of administration. In some embodiments, pharmaceutical compositions are formulated for subcutaneous (sc), intradermal, intramuscular, intraperitoneal, and / or intravenous administration. In certain embodiments, pharmaceutical compositions may contain formulation materials to modify, maintain, or preserve, for example, pH, osmolality, viscosity, clarity, color, isotonicity, odor, sterility, stability, rate of dissolution or release, adsorption or penetration of the composition. In certain embodiments, suitable formulation materials include, but are not limited to, amino acids (such as glycine, glutamine, asparagine, arginine, or lysine), antimicrobial agents, antioxidants (such as ascorbic acid, sodium sulfite, or sodium bisulfite), buffers (such as borate, bicarbonate, Tris-HCl, citrate, phosphate (e.g., phosphate buffered saline), or suitable organic acids), bulking agents (such as mannitol or glycine), chelating agents (such as ethylenediaminetetraacetic acid (EDTA)), complexing agents (such as caffeine, polyvinylpyrrolidone, beta-cyclodextrin, or hydroxypropyl-beta-cyclodextrin), proteins (such as serum albumin, gelatin, or immunoglobulins), colorants, flavorings, and diluents, emulsifiers, hydrophilic polymers (such as polyvinylpyrrolidone), low molecular weight polypeptides, salt-forming counterions (such as sodium), solvents (such as glycerin, propylene glycol, or polyethylene glycol), diluents, excipients, and / or pharmaceutical adjuvants. In particular, the pharmaceutical composition may include any suitable carrier, formulation, or ingredient, or combinations thereof, such as those listed in "Remington: The Science And Practice Of Pharmacy" Mack Publishing Co., Easton, PA, 19th Edition, (1995) (hereinafter Remington '95) or "Remington: The Science And Practice Of Pharmacy", Pharmaceutical Press, Easton, PA, 22nd Edition, (2013) (hereinafter Remington 2013), the contents of which are incorporated herein by reference.The various materials listed herein may be incorporated into or used with materials described in Remington '95 or Remington 2013, either alone or in combination. Any suitable techniques, carriers, and excipients may be used, including those understood by those skilled in the art, such as those described in Remington '95 or Remington 2013.
[0164] In certain embodiments, the pharmaceutical composition comprises suitable excipients, non-limiting examples of which include anti-adherents (e.g., magnesium stearate), binders, fillers, monosaccharides, disaccharides, other carbohydrates (e.g., glucose, mannose, or dextrin), sugar alcohols (e.g., mannitol or sorbitol), coatings (e.g., cellulose, hydroxypropylmethylcellulose (HPMC), microcrystalline cellulose, synthetic polymers, shellac, gelatin, corn protein zein, enteric or other polysaccharides), starches (e.g., potato, maize, or or wheat starch), silica, colorants, disintegrants, flavorings, lubricants, preservatives, adsorbents, sweeteners, vehicles, suspending agents, surfactants and / or wetting agents (such as pluronics, PEG, sorbitan esters, polysorbates such as Polysorbate 20, Polysorbate 80, Triton, tromethamine, lecithin, cholesterol, tyloxapal, etc.), stability enhancers (such as sucrose or sorbitol), and tonicity enhancers (such as alkali metal halides, sodium or potassium chloride, mannitol, sorbitol), and / or any excipients disclosed in Remington '95 or Remington 2013. As used herein, the term "binder" refers to a compound or ingredient that helps keep a pharmaceutical mixture combined. Suitable binders, often used in the preparation of pharmaceutical tablets, capsules, and granules to make pharmaceutical formulations, are known to those skilled in the art. For clarity, the term "binding agent" as used herein does not refer to the "binders" used in certain pharmaceutical formulations, although in certain embodiments, pharmaceutical compositions may include binding agents as well as binders that specifically bind to cMET.
[0165] In some embodiments, the pharmaceutical composition comprises a suitable pharmaceutically acceptable additive and / or carrier. Non-limiting examples of suitable additives include suitable pH adjusters, buffers, sulfur-containing reducing agents, antioxidants, etc. Non-limiting examples of sulfur-containing reducing agents include reducing agents having a sulfhydryl group (e.g., thiol), such as N-acetylcysteine, N-acetylhomocysteine, thioctic acid, thiodiglycol, thioethanolamine, thioglycerol, thiosorbitol, thioglycolic acid and its salts, sodium thiosulfate, glutathione, and C1-C7 thioalkanoic acids. Non-limiting examples of antioxidants include erythorbic acid, dibutylhydroxytoluene, butylhydroxyanisole, alpha-tocopherol, tocopherol acetate, L-ascorbic acid and its salts, L-ascorbyl palmitate, L-ascorbyl stearate, sodium bisulfite, sodium sulfite, triamyl gallate and propyl gallate, and chelating agents such as disodium ethylenediaminetetraacetic acid (EDTA), sodium pyrophosphate and sodium metaphosphate. Additionally, diluents, additives and excipients may contain other commonly used ingredients, for example, inorganic salts such as sodium chloride, potassium chloride, calcium chloride, sodium phosphate, potassium phosphate and sodium bicarbonate, and organic salts such as sodium citrate, potassium citrate and sodium acetate.
[0166] The pharmaceutical compositions used herein may be stable for extended periods of time, for example, months or years. In some embodiments, the pharmaceutical compositions contain one or more suitable preservatives. Non-limiting examples of preservatives include benzalkonium chloride, benzoic acid, salicylic acid, thimerosal, phenethyl alcohol, methylparaben, propylparaben, chlorhexidine, sorbic acid, hydrogen peroxide, and / or combinations thereof. Preservatives may include quaternary ammonium compounds such as benzalkonium chloride, benzoxonium chloride, benzethonium chloride, cetrimide, sepazonium chloride, cetylpyridinium chloride, or domiphen bromide (BRADOSOL®). Preservatives may include alkylmercuric salts of thiosalicylic acid, such as thimerosal, phenylmercuric nitrate, phenylmercuric acetate, or phenylmercuric borate. Preservatives may include parabens, such as methylparaben or propylparaben. Preservatives may include alcohols, such as chlorobutanol, benzyl alcohol, or phenylethyl alcohol. The preservative may include a biguanide derivative, such as chlorhexidine or polyhexamethylene biguanide. The preservative may include sodium perborate, imidazolidinyl urea, and / or sorbic acid. The preservative may include a stabilized oxychloro complex commercially available under the trade name PURITE®. The preservative may include a polyglycol-polyamine condensation resin commercially available under the trade name POLYQUART® from Henkel KGaA. The preservative may include stabilized hydrogen peroxide. The preservative may be benzalkonium chloride. In some embodiments, the pharmaceutical composition is preservative-free.
[0167] In some embodiments, the composition, pharmaceutical composition, or binder-drug conjugate is substantially free of contaminants (e.g., blood cells, platelets, polypeptides, minerals, blood-derived compounds or chemicals, viruses, bacteria, other pathogens, toxins, etc.). In some embodiments, the composition, pharmaceutical composition, or binder-drug conjugate is substantially free of serum and serum contaminants (e.g., serum proteins, serum lipids, serum carbohydrates, serum antigens, etc.). In some embodiments, the composition, pharmaceutical composition, or binder-drug conjugate is substantially free of pathogens (e.g., viruses, parasites, or bacteria). In some embodiments, the composition, pharmaceutical composition, or binder-drug conjugate is substantially free of endotoxins. In some embodiments, the composition, pharmaceutical composition, or binder-drug conjugate is sterile. In certain embodiments, the composition or pharmaceutical composition comprises a binder-drug conjugate that specifically binds to the extracellular domain of cMET and a suitable diluent (e.g., phosphate buffered saline).
[0168] The pharmaceutical compositions described herein can be configured for administration to a subject in any suitable form and / or amount depending on the treatment for which they are used. For example, pharmaceutical compositions configured for parenteral administration (e.g., by injection or infusion) may take the form of a suspension, solution, or emulsion in an oily or aqueous vehicle and may include formulating agents, excipients, additives, and / or diluents, such as aqueous or non-aqueous solvents, cosolvents, suspending agents, preservatives, stabilizers, and / or dispersing agents. In some embodiments, a pharmaceutical composition suitable for parenteral administration may include one or more excipients. In some embodiments, the pharmaceutical composition is lyophilized to a dry powder form. In some embodiments, the pharmaceutical composition is lyophilized to a dry powder form suitable for reconstitution with a suitable pharmaceutical solvent (e.g., water, saline, isotonic buffer solution (e.g., PBS), etc.). In certain embodiments, the reconstituted form of the lyophilized pharmaceutical composition is suitable for parenteral administration (e.g., intravenous administration) to a mammal.
[0169] In certain embodiments, the pharmaceutical composition is adapted for oral administration and may be formulated as a tablet, microtablet, minitablet, micropellet, powder, granule, capsule (e.g., capsule filled with microtablets, micropellets, powder, or granules), emulsion, or solution. Pharmaceutical compositions adapted for oral administration may include a suitable coating that delays or sustains the release of the active ingredient (e.g., binder), non-limiting examples of which include enteric coatings such as fatty acids, waxes, shellac, plastics, methyl acrylate-methacrylic acid copolymer, cellulose acetate phthalate (CAP), cellulose acetate succinate, hydroxypropyl methylcellulose phthalate, hydroxypropyl methylcellulose acetate succinate (hypromellose succinate), polyvinyl acetate phthalate (PVAP), methyl methacrylate-methacrylic acid copolymer, cellulose acetate trimellitate, sodium alginate, zein, vegetable fibers, etc., and combinations thereof.
[0170] In some embodiments, the pharmaceutical compositions described herein may be configured for topical administration and may include one or more of a binder and / or lubricant, polymeric glycol, gelatin, cocoa butter, or other suitable wax or fat. In some embodiments, the pharmaceutical compositions described herein are incorporated into a topical formulation, which generally includes a topical carrier suitable for topical drug administration and includes any suitable material known to those skilled in the art. In certain embodiments, the topical formulation of the pharmaceutical composition is formulated for administration of the binder from a topical patch.
[0171] In certain embodiments, the optimal pharmaceutical composition will be determined by one of skill in the art based on, for example, the intended route of administration, delivery format, and desired dosage (see, e.g., Remington '95 or Remington 2013, supra). In certain embodiments, such compositions can influence the physical state, stability, rate of in vivo release, and rate of in vivo clearance of the antibodies of the invention. Pharmaceutical compositions can be manufactured in any suitable manner, including, for example, by conventional mixing, dissolving, granulating, dragee-making, milling, emulsifying, encapsulating, entrapping, or tabletting processes (see, e.g., methods described in Remington '95 or Remington 2013).
[0172] Secondary medical use In some embodiments, provided herein are compositions or pharmaceutical compositions for use as medicaments for treating cancer or a neoplastic disorder in a subject, wherein the composition or pharmaceutical composition comprises a binding agent-drug conjugate described herein. In some embodiments, provided herein are compositions or pharmaceutical compositions comprising a binding agent-drug conjugate described herein for use in treating cancer or a neoplastic disorder.
[0173] Treatment method In some embodiments, the compositions, pharmaceutical compositions, or binding agent-drug conjugates described herein are used to treat a subject having or suspected of having a neoplastic disorder or cancer. In certain embodiments, the binding agent-drug conjugates or pharmaceutical compositions described herein are used in treating a neoplastic disorder or cancer in a subject, wherein the binding agent-drug conjugate specifically binds to the extracellular domain of human cMET. In some embodiments, methods of treating a subject having or suspected of having a neoplastic disorder or cancer are provided herein. In certain embodiments, the methods of treating a subject having or suspected of having a neoplastic disorder or cancer comprise administering to the subject a therapeutically effective amount of a composition, pharmaceutical composition, or binding agent described herein. In certain embodiments, the methods comprise contacting cells (e.g., one or more cells) of the subject with a therapeutically effective amount of a composition, pharmaceutical composition, or binding agent-drug conjugate described herein. In certain embodiments, the methods comprise contacting cancer cells or neoplastic cells of the subject with a therapeutically effective amount of a composition, pharmaceutical composition, or binding agent-drug conjugate described herein. In certain embodiments, the method involves contacting a cell (e.g., one or more cells) of a subject with a therapeutically effective amount of a binding agent-drug conjugate that specifically binds to the extracellular domain of human cMET or a variant thereof. In certain embodiments, the method involves contacting a cancer cell or neoplastic cell with a therapeutically effective amount of a binding agent-drug conjugate that specifically binds to the extracellular domain of human cMET or a variant thereof, wherein the cell expresses cMET on its cell surface. The cell of the subject is often a cell that expresses the extracellular portion of cMET. The cell contacted with the binding agent-drug conjugate may be found inside the subject (e.g., in vivo) or outside the subject (e.g., in vitro or ex vivo).
[0174] In some embodiments, the binding agent-drug conjugate prevents, inhibits, ameliorates, abolishes, or suppresses the growth, growth rate, or metastasis of cancer or cancer cells. In some embodiments, the binding agent-drug conjugate induces death, necrosis, or apoptosis of cancer or cancer cells. In some embodiments, contacting a subject's cells with a binding agent-drug conjugate disclosed herein induces or promotes cell death, necrosis, or apoptosis. In some embodiments, contacting a subject's cells with a binding agent-drug conjugate disclosed herein induces or promotes cell death by ADCC, ADCP, or complement-dependent cytotoxicity (CDCC) processes. In some embodiments, contacting a subject's cells with a binding agent-drug conjugate disclosed herein decreases, inhibits, or reduces cell mitosis. In some embodiments, contacting a subject's cancer or cancer cells with a binding agent-drug disclosed herein decreases, inhibits, or reduces cancer or cancer cell metastasis.
[0175] subject The term "subject" refers to a mammal. Any suitable mammal can be treated by the methods or compositions described herein. Non-limiting examples of mammals include humans, non-human primates (e.g., apes, gibbons, chimpanzees, orangutans, monkeys, macaques, etc.), domestic animals (e.g., dogs, cats), livestock (e.g., horses, cows, goats, sheep, pigs), and laboratory animals (e.g., mice, rats, rabbits, guinea pigs). In some embodiments, the mammal is a human. The mammal can be of any age or at any stage of development (e.g., an adult, teenager, child, newborn, or mammal in utero). The mammal can be male or female. The mammal can be a pregnant female.
[0176] In some embodiments, the subject is in need of a treatment or composition described herein. In some embodiments, the subject has or is suspected of having a neoplastic disorder or cancer. In some embodiments, the subject in need of a treatment or composition described herein has or is suspected of having a neoplastic disorder or cancer. In some embodiments, the binding agent-drug conjugate or composition described herein is used to treat a subject having or suspected of having a neoplastic disorder or cancer.
[0177] Type of cancer The compositions, pharmaceutical compositions, or binder-drug conjugates disclosed herein can be used to treat neoplastic disorders or cancers, non-limiting examples of which include carcinomas, sarcomas, neuroneoplasias, lymphomas, myelomas, leukemias, melanomas, mesotheliomas, solid or soft tissue tumors, and secondary cancers (e.g., cancers secondary to the primary site). Non-limiting examples of carcinomas include respiratory system cancer, digestive system cancer, genitourinary system cancer, testicular cancer, prostate cancer, endocrine system cancer, basal cell carcinoma of the skin, cancer of unknown primary site, bile duct carcinoma, ductal carcinoma in situ (DCIS), Merkel cell carcinoma, lung cancer, thymic carcinoma and thymic carcinoma, midline carcinoma, small cell lung carcinoma, thyroid cancer, hepatocellular carcinoma, squamous cell carcinoma, squamous cell carcinoma of the head and neck, breast cancer, epithelial carcinoma, adrenocortical carcinoma, ovarian surface epithelial carcinoma, and others, as well as carcinomas of the uterus, cervix, colon, pancreas, kidney, esophagus, stomach, and ovary. Non-limiting examples of sarcomas include Ewing's sarcoma, lymphosarcoma, liposarcoma, osteosarcoma, breast sarcoma, soft tissue sarcoma, Kaposi's sarcoma, rhabdomyosarcoma, uterine sarcoma, chondrosarcoma, leiomyosarcoma, fibrosarcoma, etc. Non-limiting examples of neuro-oncologies include glioma, glioblastoma, meningioma, neuroblastoma, retinoblastoma, astrocytoma, oligodendroglioma, etc. Non-limiting examples of lymphomas, myelomas, and leukemias include acute and chronic lymphoblastic leukemia, myeloblastic leukemia, multiple myeloma, poorly differentiated acute leukemia (e.g., erythroblastic leukemia and acute megakaryoblastic leukemia), acute promyelocytic leukemia (APML), acute myeloid leukemia (AML), chronic myelogenous leukemia (CML), acute lymphoblastic leukemia (ALL), including B-lineage ALL and T-lineage ALL, chronic myeloma, and acute myeloma. These include chronic lymphocytic leukemia (CLL), prolymphocytic leukemia (PLL), hairy cell leukemia (HLL), Waldenstrom's macroglobulinemia (WM), non-Hodgkin's lymphoma and its variants, peripheral T-cell lymphoma, adult T-cell leukemia / lymphoma (ATL), cutaneous T-cell lymphoma (CTCL), large granular lymphocytic leukemia (LGF), Hodgkin's disease, and Reed-Sternberg disease.Non-limiting examples of soft or solid tissue tumors include visceral tumors, seminoma, hepatocellular carcinoma, and other tumors of the breast, liver, lung, pancreas, uterus, ovaries, testes, head, neck, eyes, brain, mouth, pharynx, vocal cords, ear, nose, esophagus, stomach, intestines, colon, adrenal glands, kidneys, bone, bladder, urethra, carcinoma, lung, muscle, skin, feet, hands, and soft tissues. In some embodiments, the neoplastic disorder or cancer that can be treated with the pharmaceutical compositions or binder-drug conjugates disclosed herein is selected from bladder cancer, breast cancer, colorectal cancer, cervical cancer, gastric cancer, liver cancer, hepatocellular carcinoma, hypopharyngeal cancer, lung cancer, adenocarcinoma, ovarian cancer, and kidney cancer. In some embodiments, the neoplastic disorder or cancer that may be treated by the pharmaceutical compositions or binding agent-drug conjugates disclosed herein is selected from pancreatic cancer (e.g., pancreatic adenocarcinoma, exocrine pancreatic cancer, or pancreatic neuroendocrine carcinoma), colorectal cancer (e.g., colorectal adenocarcinoma), small intestine malignancies, bile duct carcinoma, non-small cell lung cancer (NSCLC), thyroid cancer, esophageal or esophagogastric junction (EGJ) cancer, gastric adenocarcinoma, liver hepatocellular carcinoma, head and neck squamous cell carcinoma, female reproductive tract malignancies, breast cancer, small cell lung carcinoma, ovarian surface epithelial carcinoma, retroperitoneal or peritoneal sarcoma, prostate adenocarcinoma, neuroendocrine tumors, gastrointestinal stromal tumors, glioblastoma, or non-epithelial ovarian cancer. In some embodiments, the neoplastic disorder or cancer that can be treated by the pharmaceutical compositions or binding agent-drug conjugates disclosed herein is breast cancer, non-limiting examples of which include ductal carcinoma in situ (DCIS), invasive ductal carcinoma (IDC) (e.g., tubular carcinoma of the breast, medullary carcinoma of the breast, mucinous carcinoma of the breast, papillary carcinoma of the breast, and cribriform carcinoma of the breast), invasive lobular carcinoma (ILC), inflammatory breast cancer, lobular carcinoma in situ (LCIS), male breast cancer, molecular subtypes of breast cancer (luminal B or hormone receptor-positive breast cancer, triple-negative breast cancer, HER2-enriched breast cancer, and normal-like breast cancer), Paget's disease of the nipple, phyllodes tumor of the breast, and metastatic breast cancer. In some embodiments, the neoplastic disorder or cancer that can be treated by the pharmaceutical compositions or binding agent-drug conjugates disclosed herein is triple-negative breast cancer.
[0178] In some embodiments, the effectiveness of the treatments described herein can be determined or predicted, in part, by the amount of cMET expressed by the cancer or neoplasia. Many cancer and tumor types are known to express cMET, including, but not limited to, certain bladder, breast, colorectal, gastric, hepatocellular, HNSCC, hypopharyngeal, lung, adenocarcinoma, ovarian, and renal cancers (see, e.g., Ariyawutyakorn et al. (2016) Journal of Cancer 7(6):633-649), and the amount of cMET expressed in many cancer types is known (see, e.g., Arguello et al. (2013) Annual Meeting of the Association for Molecular Pathology (AMP) Abstract No. 294319). Additionally, neoplastic or cancer cells can be rapidly assayed for cMET expression using a suitable method (e.g., whole-cell ELISA, FAC, any suitable immunoassay, etc.) using an appropriate anti-cMET binding agent (e.g., an antibody). Thus, in some embodiments, a method of treating a subject having or suspected of having cancer comprises administering to the subject a therapeutically effective amount of a binding agent-drug conjugate described herein or a pharmaceutical composition comprising a binding agent-drug conjugate described herein, wherein the cancer expresses a detectable level of cMET. In certain embodiments, a cancer expressing a detectable level of cMET can be a cancer known or reported to express cMET, or a cancer suspected of expressing cMET (e.g., by having a similar genotype or phenotype to another cancer known to express cMET). In some embodiments, a cancer expressing or suspected of expressing cMET is a cancer that expresses an RNA transcript encoding cMET, or a portion thereof. In some embodiments, a cancer expressing or suspected of expressing cMET is a cancer that expresses cMET on the cell surface.
[0179] Route of administration Any suitable method of administering a composition, pharmaceutical composition, or binder-drug conjugate to a subject can be used. The exact formulation and route of administration of a composition for use in the methods of the invention described herein can be selected by a medical professional (e.g., a physician) in view of the patient's medical condition (see, e.g., Fingl et al. 1975, "The Pharmacological Basis of Therapeutics," incorporated herein by reference in its entirety). Any suitable route of administration can be used to administer a pharmaceutical composition or binder-drug conjugate described herein. Non-limiting examples of routes of administration include topical or local (e.g., transdermal or dermal (e.g., on the skin or epidermis), ocular or supraocular, intranasal, transmucosal, intraaural, intraaural (e.g., behind the tympanic membrane)), enteral (e.g., delivery via the gastrointestinal tract, e.g., oral (e.g., tablet, capsule, granule, liquid, emulsion, lozenge, or combination thereof), sublingual, gastric feeding tube, rectal, etc.), parenteral administration (e.g., parenteral, e.g., intravenous, intraarterial, intramuscular, intraperitoneal, intradermal, subcutaneous, intracavitary, intracranial, intraarticular, intrajoint space, intramyocardial (intracardiac), intracavity injection, intralesional (intracutaneous lesion), intraosseous infusion (intramedullary), intrathecal (intraspinal canal), intrauterine, intravaginal, intravesical infusion, intravitreal), etc., or combinations thereof.
[0180] In some embodiments, a composition described herein is provided to a subject. The composition provided to the subject may be for self-administration or for administration to the subject by another person (e.g., a person other than a medical professional). For example, a composition described herein may be provided as instructions (e.g., a prescription) written by a clinician authorizing a patient to receive a composition or treatment described herein. In another example, a composition is provided to a subject, and the subject self-administers the composition orally, intravenously, or by, for example, inhalation.
[0181] Alternatively, compositions for use in accordance with the methods of the invention may be administered locally rather than systemically, for example by direct application to the skin, mucous membranes, or desired area for treatment, including using depot or sustained release formulations.
[0182] In some embodiments, a pharmaceutical composition comprising a binder-drug conjugate can be administered alone (e.g., as a single active ingredient (AI) or, e.g., as a single active pharmaceutical ingredient (API)). In other embodiments, a pharmaceutical composition comprising a binder-drug conjugate can be administered in combination with one or more additional AIs / APIs, e.g., as two different compositions or as a single composition in which one or more additional AIs / APIs are mixed or formulated with the binder-drug conjugate in the pharmaceutical composition.
[0183] In some embodiments, the cMET-binding agent-drug conjugate is delivered to a cell (e.g., a mammalian cell). The cMET-binding agent-drug conjugate can be delivered to a cell using any suitable method. In some embodiments, delivering the cMET-binding agent-drug conjugate to a cell comprises contacting a mammalian cell with the cMET-binding agent-drug conjugate in vitro or in vivo under conditions that allow the binding of the binding agent-drug conjugate to the cell.
[0184] Dosage and Therapeutically Effective Amount In some embodiments, the amount of binder-drug conjugate in the composition is a therapeutically effective amount. In some embodiments, a therapeutically effective amount of the binder-drug conjugate is administered to a subject. In some embodiments, the therapeutically effective amount of the binder-drug conjugate in the composition is the amount necessary to achieve an effective therapeutic result. In certain embodiments, the amount of binder-drug conjugate in the composition (e.g., pharmaceutical composition) is an amount sufficient to prevent, treat, reduce the severity of, delay the onset of, and / or alleviate the symptoms of a neoplastic disorder or cancer, as contemplated herein.
[0185] A "therapeutically effective amount" is an amount sufficient to obtain an effective therapeutic result and / or to prevent, treat, reduce the severity of, delay the onset of, and / or alleviate the symptoms of a neoplastic disorder or cancer. In some embodiments, a "therapeutically effective amount" refers to an amount sufficient to stop and / or slow the growth of a tumor or cancer. In some embodiments, a "therapeutically effective amount" refers to an amount sufficient to inhibit replication and / or induce the death of one or more tumor or cancer cells. Determination of a therapeutically effective amount is well within the capabilities of those skilled in the art, especially in light of the detailed disclosure provided herein.
[0186] In some embodiments, a therapeutically effective amount is an amount that is high enough to provide effective therapeutic effects and low enough to minimize undesirable side effects. Thus, in some embodiments, the therapeutically effective amount of the binder-drug conjugate may often vary from subject to subject, depending on the subject's age, weight, and general condition, the severity of the condition to be treated, and the specific combination of drugs administered. Thus, in some embodiments, the therapeutically effective amount is determined empirically. Thus, the therapeutically effective amount of the binder-drug conjugate used to treat a subject can be determined by those skilled in the art based on, for example, the amount found to be effective in animal tests or clinical trials, the physician's experience, and the suggested dosage range or dosing guidelines.
[0187] In certain embodiments, the amount of binder-drug conjugate (e.g., binder in a pharmaceutical composition) is administered in a suitable therapeutically effective amount or dose (e.g., in a suitable volume and concentration, which may depend in part on the particular route of administration). In certain embodiments, the therapeutically effective amount of the binder-drug conjugate is selected from one or more doses of an amount between about 0.01 mg / kg (e.g., per kg of subject body weight) and 500 mg / kg, 0.1 mg / kg and 500 mg / kg, 0.1 mg / kg and 400 mg / kg, 0.01 mg / kg and 300 mg / kg, 0.1 mg / kg and 300 mg / kg, 0.1 mg / kg and 200 mg / kg, 0.1 mg / kg and 150 mg / kg, 0.1 mg / kg and 100 mg / kg, 0.1 mg / kg and 75 mg / kg, 0.1 mg / kg and 50 mg / kg, 0.1 mg / kg and 25 mg / kg, 0.1 mg / kg and 10 mg / kg, 0.1 mg / kg and 5 mg / kg, 0.1 mg / kg and 1 mg / kg, and combinations thereof. In some aspects, a therapeutically effective amount of the binder-drug conjugate comprises one or more doses of between about 10 mg / kg, 9 mg / kg, 8 mg / kg, 7 mg / kg, 6 mg / kg, 5 mg / kg, 4 mg / kg, 3 mg / kg, 2 mg / kg, 1 mg / kg, 0.9 mg / kg, 0.8 mg / kg, 0.7 mg / kg, 0.6 mg / kg, 0.5 mg / kg, 0.4 mg / kg, 0.3 mg / kg, 0.2 mg / kg, and 0.1 mg / kg, and combinations thereof. In some embodiments, a therapeutically effective amount of the binder-drug conjugate is between about 0.1 mg / kg and 100 mg / kg, or between about 1 mg / kg and about 50 mg / kg.
[0188] In some embodiments, administering a therapeutically effective amount of a binder-drug conjugate or a pharmaceutical composition comprising a binder-drug conjugate comprises administering a suitable dose at a frequency or interval necessary to achieve an effective therapeutic result. In some embodiments, administering a therapeutically effective amount of a binder-drug conjugate or a pharmaceutical composition comprising a binder-drug conjugate comprises administering a suitable dose hourly, every 2 hours, every 4 hours, every 6 hours, three times a day, twice a day, once a day, six times a week, five times a week, four times a week, three times a week, twice a week, weekly, combinations thereof, and / or at regular or irregular intervals, and / or simply at a frequency or interval as needed or recommended by a healthcare professional.
[0189] kit Pharmaceutical compositions containing amounts or doses of binder-drug conjugates can be provided in kits, packs, or dispensing devices, which can contain one or more doses of binder, if desired. In some embodiments, the kit includes a pack and / or a dispensing device. Non-limiting examples of packs include metal, glass, or plastic containers or blister packs containing the binder-drug conjugates or compositions described herein. In certain embodiments, the kit includes a dispensing device, such as a syringe or inhaler. The pack or dispensing device may be accompanied by instructions for administration. The pack or dispenser may be accompanied by notice associated with the container in a form prescribed by a government agency regulating the manufacture, use, or sale of pharmaceuticals, reflecting approval by the agency of the drug form for human or veterinary administration. Such notice may be, for example, labeling approved by the U.S. Food and Drug Administration for prescription drugs or an approved product insert.
[0190] In some embodiments, the kit or pack contains a sufficient amount of binding agent-drug conjugate to treat a patient for 1 day to 1 year, 1 day to 180 days, 1 day to 120 days, 1 day to 90 days, 1 day to 60 days, 1 day to 30 days, 1 hour to 24 hours, 1 hour to 12 hours, 1 hour to 4 hours, or any time in between.
[0191] A kit may include a product label and / or one or more package inserts providing descriptions of the components therein or directions for in vitro, in vivo, or ex vivo use of the components. Exemplary instructions include instructions for a diagnostic method, treatment protocol, or therapeutic regimen. In certain embodiments, a kit includes packaging, which refers to the physical structure that houses the components of the kit. The packaging can keep the components sterile and may be made from materials commonly used for such purposes (e.g., paper, corrugated fiber, glass, plastic, foil, ampoules, vials, tubes, etc.). Product labels or package inserts include "printed matter," such as paper or cardboard, either individually or affixed to the component, kit, or packaging material (e.g., a box), or attached to an ampoule, tube, or vial containing the kit components. A label or package insert may also include computer-readable media, electronic storage media such as CD- or DVD-ROM / RAM, DVD, optical disks such as MP3, magnetic tape, or hybrids thereof such as RAM and ROM, or magnetic / optical storage media, FLASH media, or memory-type cards, etc. The product label or package insert may include identification information for one or more components therein, dosage, mechanism of action, clinical pharmacology of the active ingredients, including pharmacokinetics (PK) and pharmacodynamics (PD). The product label or package insert may include information identifying the manufacturer, lot number, manufacturing location, manufacturing date, and information regarding the indicated condition, disorder, disease, or symptom for which the kit components are used. The product label or package insert may include instructions for a physician or subject for using one or more kit components in a method, treatment protocol, or therapeutic regimen. The instructions may include dosage, frequency, or duration, and instructions for practicing any of the methods, treatment protocols, or therapeutic regimens described herein. Thus, the kits of the present invention may further include labels or instructions for practicing any of the methods and uses of the present invention described herein. The product label or package insert may include information and / or warnings regarding possible side effects. [Example]
[0192] Example 1 - Antibody generation To elicit antibody responses against cMET, mice were immunized with cMET-Fc or cMET peptides as shown in Figures 1 and 2. In some embodiments, peptides derived from strategic regions were selected for immunization. An example of a structural loop on MET that inspired the design of peptide 3 is shown in Figure 3. Spleens from immunized mice were obtained, and splenocytes were fused with a suitable fusion partner to generate hybridomas using standard protocols. Hybridoma clones were isolated, and hybridoma culture media were tested for their ability to bind to MET and / or induce internalization of cMET on human cancer cell lines as measured by flow cytometry (Figure 4). Selected hybridoma antibodies were screened for their ability to induce degradation of MET (Figure 5) or lack of ability to induce phosphorylation of ERK (Figure 6). The lead hybridoma F6B1P3D12 was deposited with the American Type Culture Collection, Patent Depository, 10801 University Boulevard, Manassas, VA 20110-2209, USA on March 20, 2019. The deposit was made under the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure and its Regulations (Budapest Treaty). An ATCC number has not yet been assigned.
[0193] Additional assays were performed to select ideal anti-cMET antibody candidates. For example, the species cross-reactivity of anti-cMET antibodies was tested by measuring the binding ability of the antibodies to human cMET, monkey cMET (e.g., Macaca fascicularis, i.e., Cynomolgus Macaque), rat cMET, and mouse cMET, as measured by ELISA (Figure 7 and Table 11). In vivo half-life and other pharmacokinetic properties were also evaluated (data not shown). The efficacy and specificity of antibody-drug conjugates (ADCs) were also determined in high-, moderate-, and non-cMET-expressing cell lines using anti-cMET antibodies conjugated to MMAF (Figures 9 and 15, Tables 11 and 12). The in vivo efficacy of the ADCs was tested using the MKN45 xenograft model. [Table 11] SPR = surface plasmon resonance MSD = Mesoscale Discovery Platform NHP = non-human primate (i.e., Cynomolgus macaque) 5D5 = agonist positive control ABF46 = MET ADC, positive control
[0194] Example 2 - Summary of properties of selected humanized monoclonal binding agents Humanized and isotype-switched monoclonal binders containing the heavy and light chain CDRs of murine monoclonal antibody P3D12 were generated. Sixteen different heavy chain (HC) and light chain (LC) combinations were tested for solubility in PBS, binding to human cMET, binding to rat cMET, binding affinity to human and rat cMET as measured by surface plasmon resonance (SPR), presence of agonist activity as reported by the Mesoscale Discovery Platform (MSD), and degradation of cMET. The results are summarized in Table 12 below.
[0195] [Table 12] The present inventors selected a humanized monoclonal antibody of the IgG2 isotype containing a humanized light chain variable region of SEQ ID NO: 47 and a humanized heavy chain variable region of SEQ ID NO: 108 as a representative humanized anti-cMET antibody, designated hD12, and used the antibody in the following examples.
[0196] Example 3 - Binding Assays hD12, a representative humanized anti-cMET antibody comprising the humanized heavy chain sequence of SEQ ID NO: 108 and the humanized light chain sequence of SEQ ID NO: 47, was stochastically conjugated to five representative payloads (i.e., payloads of formulas II, IV, VI, VII, and XI). Each payload contains a pyrrolobenzodiazepine toxin and a linking group. In this example, the payload linking group was stochastically conjugated to the hD12 antibody using disulfide chemistry. Briefly, the hD12 antibody was first reduced with glutathione (GSH), removing any unreacted GSH, and then a linking group containing a reactive maleimide group was reacted with one or more free sulfhydryl groups (i.e., thiol groups) on the antibody. Using this approach, one or more payloads were covalently conjugated to the hD12 antibody at random positions occupied by cysteine residues. Therefore, this method is referred to as stochastic conjugation.
[0197] The resulting hD12 antibody-drug conjugates (i.e., hD12-II (antibody hD12 attached to a payload of Formula II)); hD12-IV (antibody hD12 attached to a payload of Formula IV); hD12-VI (antibody hD12 attached to a payload of Formula VI); hD12-VII (antibody hD12 attached to a payload of Formula VII); and hD12-XI (antibody hD12 attached to a payload of Formula XI)) were assayed for binding to plate-bound cMET by ELISA. Denosumab conjugated to each of the five payloads was used as a negative control because the monoclonal antibody denosumab specifically binds to RANK ligand (RANKL) and not cMET. The results of the ELISA binding studies are shown in Figures 17A and 17B. There were no significant differences in binding to cMET among the five hD12-drug conjugates. As expected, the isotype control conjugate of denosumab did not bind to cMET.
[0198] Materials: High-binding 384-well plate (ThermoFisher #:8755), blocking buffer (SkyTek Lab #AAA500), recombinant human c-Met-10X His (1.04 mg / ml, in-house made, lot #140924TA), HRP-conjugated anti-human kappa light chain (1 mg / ml, Brthyl #AP80-219P), 1x KPL wash buffer in water (20x, 200 ml, KPL #50-63-01), TMB (100 ml, KPL #53-00-00), and stop solution (Cell Signaling #7002L).
[0199] Example 4 - Cytotoxicity Assay The cytotoxicity of the five hD12 antibody-drug conjugates in Example 3 was tested against cells expressing different levels of surface cMET. Denosumab conjugated to each of the five representative payloads was used as a negative control (data not shown). The denosumab conjugates showed little or no cell-killing effect on cMET-expressing cell lines.
[0200] The results of the cytotoxicity assay are shown in Figures 18A-18E and 19A-19F. The cell lines tested were SNU-1 (ATCC, no cMET expression, Figure 18A), SNU-16 (ATCC, moderate cMET expression, Figure 18B), SNU-620 (KCLB, high cMET expression, Figure 18C), MKN-45 (DSMZ, high cMET expression, Figure 18D), H441 (ATCC, moderate cMET expression, Figure 19A), H1373 (ATCC, moderate cMET expression, Figure 19B), H1975 (ATCC, moderate cMET expression, Figure 19C), SNU-5 (ATCC, high cMET expression, Figure 19D), and H1573 (ATCC, moderate cMET expression, Figure 19E). hD12-II and hD12-VII were slightly more effective in some media and in cell lines with high cMET expression.
[0201] Example 5 - Xenograft studies Two in vivo xenograft studies were conducted to evaluate the efficacy of the five hD12 antibody-drug conjugates (i.e., hD12-VI, hD12-II, hD12-VII, and hD12-XI) described in Example 3. Note that the terms hD12-vc-XI, hD12-vc-VI, hD12-vc-II, hD12-vc-VII, and hD12-vc-IV shown in Figures 20-22 are used synonymously with hD12-XI, hD12-VI, hD12-II, hD12-VII, and hD12-IV, respectively. Additionally, denosumab-* (e.g., denosumab-II) is used synonymously with the term denosumab-vc-* (e.g., denosumab-vc-II) shown in the figures. The "vc" designation is not construed as significant. The term "denosumab-II" refers to the monoclonal antibody "denosumab" attached to a payload of formula II.
[0202] The first H1975 in vivo xenograft study was designed, with 10 mice per group (Nu / nu: (Charles River)). Each mouse was inoculated with H1975 cells and then treated with one of the designated antibody-drug conjugates or PBS. On day 1, the antibody-drug conjugates were administered as a single dose via tail vein intravenous injection. Two doses (0.5 mg / kg and 0.125 mg / kg) of each antibody-drug conjugate were tested. Denosumab-II was used as a negative control. Tumor volume and weight were measured three times weekly. The results of the H1975 in vivo xenograft study are shown in Figures 20A-20G.
[0203] All animals tolerated the antibody-drug conjugates well. No significant weight loss was observed in any group (see, for example, Figure 20B). hD12-VII demonstrated the highest efficacy at both dose levels of all ADCs tested (Figures 20A and 20F). hD12-II and hD12-VI were slightly less effective than hD12-VII in the lower dose group (0.125 mg / kg) (Figures 20E and 20D). hD12-3315 and hD12-XI were least effective in the lower dose group (Figures 20G and 20C). The isotype control denosumab-II demonstrated some efficacy at the 0.5 mg / kg dose. Because H1975 possesses the RANK-RANKL signaling pathway (Journal of Thoracic Oncol., 2014, 9(3) 345-54), denosumab may have demonstrated tumor growth inhibition. In summary, all five hD12-drug conjugates showed significant efficacy against H1975 xenografts, with hD12-VII, hD12-II, and hD12-VI showing the highest therapeutic efficacy, and VII slightly superior to the other two.
[0204] A second H1373 in vivo xenograft study was conducted to further evaluate the efficacy of the five hD12 antibody-drug conjugates (i.e., hD12-VI, hD12-II, hD12-VII, and hD12-XI) described in Example 3. The H1373 in vivo xenograft study was designed with 10 mice (Nu / nu: (Charles River)) in each group. Each mouse was inoculated with H1373 cells and then treated with one of the designated antibody-drug conjugates or PBS. The antibody-drug conjugates were administered as a single dose via tail vein intravenous injection on day 7. Two doses (0.5 mg / kg and 0.125 mg / kg) of each antibody-drug conjugate were tested. Denosumab II was used as a negative control. Tumor volume and weight were measured three times weekly. The results of the H1373 in vivo xenograft study are shown in Figures 21A-213 and 22.
[0205] All animals tolerated the antibody-drug conjugates well. No significant weight loss was observed in any group (see, e.g., Figure 22). As seen in the first H1975 xenograft model, hD12-VII showed slightly greater efficacy in the low-dose group (0.125 mg / kg) compared to hD12-II and hD12-VI (Figures 21C and 21B) (Figure 21D). As previously observed (Figure 21E), hD12-IV was the least effective drug.
[0206] Example 6 - PK studies in mice The circulating half-lives of the hD12-drug conjugates of Example 3 (i.e., hD12-VI, hD12-II, hD12-VII, and hD12-XI) were evaluated in five groups of three mice over a 72-hour period. Mice in each group received a single intravenous injection of 1 mg / kg of either hD12-II, hD12-IV, hD12-VI, hD12-XI, or denosumab-II. Blood was collected at 0.5, 2, 6, 24, 48, and 72 hours. Serum samples were prepared and analyzed for the amount of each of the indicated antibody-drug conjugates (Figure 23). Serum antibodies were captured with an anti-Fc-specific antibody and detected using goat anti-human IgG(H+L)-HRP.
[0207] Example 7 - Site-specific conjugation of payload to hD12 The coding region of hD12 was mutated at various sites to introduce cysteine residues into the heavy chain constant region of an IgG2 antibody, resulting in the following hD12 mutant antibodies: hD12-T289C (T at position 289 mutated to cysteine), hD12-V442C (V at position 442 mutated to cysteine), hD12-V282C (V at position 282 mutated to cysteine), and hD12-S119C (S at position 119 mutated to cysteine). The mutation sites are located in the constant region of hD12 and are defined according to the EU numbering system described in Edelman, GM et al., Proc. Natl. Acad. USA, 63, 78-85 (1969). PMID: 5257969. A payload of Formula II was site-specifically conjugated to each of the mutated cysteine residues using maleimide chemistry. The quality and extent of conjugation were assessed by measuring total recovery, aggregate content, monomer content, and drug-to-antibody ratio (DAR). Optimal conjugation was observed for the hD12 conjugates hD12-T289C-II, hD12-V442C-II, and hD12-V282C-II. The relative binding affinities of these three site-specific conjugates to cMET were compared to stochastically conjugated hD12-II using the cMET binding ELISA described in Example 3. The results of the cMET binding assay are shown in Figures 24A and 24B. All site-specific compounds successfully bound to human cMET with similar affinities. The site-specific conjugates bound with similar or slightly better affinities than stochastically conjugated hD12-II.
[0208] Example 8 - Cytotoxicity evaluation of site-specific conjugation to cMET-expressing cell lines. We assayed the cytotoxic potency of site-specifically conjugated II complexes (i.e., hD12-T289C-II, hD12-V442C-II, and hD12-V282C-II) in comparison with stochastically conjugated hD12-II as a benchmark against eight cMET-expressing cell lines: SNU-16 (Figure 25B), SNU-620 (Figure 25C), MKN-45 (Figure 25D), NCI-N87 (Figure 25E), SNU-5 (Figure 26A), H1373 (Figure 27A), H1573 (Figure 27B), H1975 (Figure 27C), and the cMET-negative cell line, SNU-1 (Figure 25A). Cytotoxicity results are summarized in Figures 25F, 26B, and 27E. Administered doses are shown in Figures 25G, 26C, and 27D.
[0209] All site-specifically conjugated antibodies demonstrated comparable cytotoxicity to the stochastically conjugated hD12-II control against the MKN-45, SNU-620, SNU-5, SNU-16, NCI-N87, and H1975 cell lines. The EC50 values for the site-specific conjugates for the H1373 and H1573 cell lines could not be determined due to the complex killing curves, which differed significantly from sigmoidal curves. The complex shape of the killing curves was more pronounced for the site-specific conjugates and was reproducible in duplicate experiments. Overall, the cytotoxic potency of the site-specific hD12 conjugates appeared superior to that of the stochastically conjugated hD12-II.
[0210] Example 9 - In vivo xenograft analysis of site-specific conjugates The site-specific conjugates hD12-T289C-II, hD12-V442C-II, and hD12-V282C-II, as well as stochastically conjugated hD12-II, were evaluated in the H1975 (moderate cMET expression) xenograft tumor model. Denosumab II was used as a negative control. Mice were inoculated with H1975 cells (day 0) and then treated with one of the designated antibody-drug conjugates or PBS. The antibody-drug conjugates were administered via tail vein intravenous injection as a single dose on day 14 after tumor cell inoculation. Two doses of each antibody-drug conjugate (0.5 mg / kg and 0.125 mg / kg) were tested. Ten mice were tested for each treatment. Tumor volume and weight were measured three times weekly. The results of the H1975 in vivo xenograft study are shown in Figures 28A-28C.
[0211] All high-dose groups using site-specific ADCs and stochastically conjugated II (0.5 mg / kg) demonstrated high efficacy in the H1975 model. Tumors completely regressed (Figures 28A-28C). The low-dose group (0.125 mg / kg) demonstrated tumor regression with hD12-II (stochastic) and hD12-T289C-II, with hD12-V422C-II being the most effective. hD12-V282C-II was the least effective. The denosumab control showed a moderate effect at higher doses, as seen in previous H1975 models using stochastically conjugated ADCs. All administered test articles were well tolerated, and no significant weight loss was observed (Figure 29).
[0212] Example 10 - Pharmacokinetics in rats using hD12 site-specific conjugates (total antibody detection) The circulating half-lives of the site-specific hD12 conjugates hD12-V422C-II, hD12-V282C-II, and hD12-T289C-II were evaluated in rats for 21 days. Each group of rats (3 rats / group) received a single intravenous injection of 1 mg / kg of the designated antibody-drug conjugate (Figure 30). Blood samples were collected at 0.5, 2, 6, 24, 48, 72, 168, 312, and 480 hours post-injection. Antibody levels in serum samples were analyzed by PK ELISA using a capture antibody (anti-Fc specific) and a goat anti-human IgG (H+L)-HRP detection antibody. The results are summarized in Figure 31. Pharmacokinetic (PK) parameters of the site-specific conjugates were determined using WinNonlin software. All three site-specific conjugates exhibited similarly shaped concentration-time curves. The calculated half-lives ranged from 12 to 18 days. The variants could not be distinguished from each other based on total antibody pharmacokinetic data alone. Based on the results of this experiment, there were no significant differences in pharmacokinetics between hD12-V422C-II, hD12-V282C-II, and hD12-T289C-II.
[0213] Example 11 - Tolerance in non-human primates Stochastically conjugated hD12-II and site-directed mutants hD12-V282C-II and hD12-T289C-II were tested for tolerability in non-human primates at doses up to 1 mg / kg. Overall, all antibody-drug conjugates were well tolerated. No severe weight loss was observed by the end of the study (day 21).
[0214] Example 12 - PDX Models, Methods and Results Patient-derived xenografts (PDX) are cancer models in which tissue or cells from a patient's tumor are transplanted into immunocompromised mice. PDX models are often used to create an environment similar to the natural growth of cancer for the study of cancer progression and treatment. Multiple Crown Bio HuPrime® gastric, colorectal, and head and neck (H&N) PDX models were performed to evaluate the efficacy of hD12-T289C-II. PDX models were selected for a range of c-Met expression (low to high).
[0215] Briefly, 14- to 15-week-old female BALB / c nude mice were subcutaneously inoculated into the right flank with human primary tumor fragments (gastric, colorectal, or H&N carcinoma, 2-3 mm in size) for tumor formation. Tumor size was 200 mm in average volume. 3 Upon reaching 100 mg / kg, mice were randomized into groups (6 treatment groups). Each group consisted of 10 mice. The test article was administered intravenously to tumor-bearing mice as a single dose on day 0. A second dose was administered as needed. A non-targeting antibody linked to a Formula II payload (Secukinumab) (Secukinumab-II) was administered at a dose of 1 mg / kg. hD12-T289C-II was administered at single doses of 1.0 mg / kg, 0.5 mg / kg, 0.25 mg / kg, and 0.125 mg / kg, except as noted in Figure 34. The vehicle control group received a single intravenous dose of 1x PBS.
[0216] After randomization, tumor size was measured twice weekly in two dimensions using a calispa. Tumor volume (mm 3 ) was calculated as TV = 0.5a × b2, where a and b are the major and minor diameters of the tumor surface. Body weight was measured and updated along with tumor measurements.
[0217] The tumor size was then used to calculate TGI% according to the following formula: TGI% = ((mean value (C) - mean value (C0)) - (mean value (T) - mean value (T0)) / (mean value (C) - mean value (C0)) × 100% [T is the current group value; T0 is the initial value of the current group; C is the value of the control group; C0 is the initial value of the control group].
[0218] The results of the PDX study are shown in Figures 1 and 2. Each data point represents one PDX model group consisting of 10 mice inoculated with a single PDX tumor. TGI% was calculated as described above. Mice were treated with vehicle (PBS) or Secukinumab-II as a negative control. Tumor volume (y-axis) was determined over time (i.e., days, x-axis; Figure 33C). The results in Figures 32 and 33 show that hD12-T289C-II effectively inhibits the growth of human tumor tissues derived from gastric, colorectal, or H&N cancer in a dose-dependent manner.
[0219] Example 13 A human subject has multiple metastatic cancers of 2 cm or greater present in the liver and lungs. A biopsy is performed to determine whether the cancer cells express cMET on their cell surface. The presence of cell surface cMET expression is confirmed by the biopsy results.
[0220] A human subject is administered a binder-drug conjugate described herein that specifically binds to the extracellular domain of human cMET. The binder may comprise human kappa and IgG2 heavy chain constant regions, a light chain variable region of SEQ ID NO: 41, and a heavy chain variable region of SEQ ID NO: 98. The binder-drug conjugate may be administered intravenously at a dose of 15 mg / kg over 1 hour in a volume of 100 ml once daily for 6 weeks. Follow-up biopsies and ultrasounds determine the presence, size, and viability of tumors. After 2 weeks of treatment, tumor size and number are substantially reduced. After 6 weeks of treatment, the subject is deemed to be in remission.
[0221] Example 14 The human subject exhibits colorectal adenocarcinoma with a solid tumor measuring 2 cm in diameter. The human subject is administered a binder-drug conjugate described herein. The binder of the binder-drug conjugate is a humanized monoclonal antibody of the IgG2 isotype comprising a light chain variable region of SEQ ID NO: 47 and a humanized heavy chain variable region of SEQ ID NO: 108. The drug of the binder-drug conjugate is a payload having the structure of Formula II. The binder is administered intravenously at a dose of 1 mg / kg in a volume of 50 ml over 30 minutes once daily for 6 weeks. After 2 weeks of treatment, the tumor size is reduced by 50% or more. After 6 weeks of treatment, the subject is deemed to be in remission.
[0222] Example 15 - cMET sequence SEQ ID NO: 109 (Human cMET-UniProtKB-P08581(MET_HUMAN)) *Residues E168 and N375 are bold and underlined TIFF2025170277000049.tif77164 TIFF2025170277000050.tif102164
[0223] SEQ ID NO: 110 (rat cMET-UniProtKB-P97523 (MET_RAT) TIFF2025170277000051.tif132164 TIFF2025170277000052.tif49164
[0224] SEQ ID NO: 111 (mouse cMET-UniProtKB-P16056(MET_MOUSE) TIFF2025170277000053.tif177164
[0225] SEQ ID NO: 112 (canine cMET) TIFF2025170277000054.tif176164
[0226] SEQ ID NO: 113 (Macaca mulatta, rhesus cMET - NCBI Reference Sequence: NP_001162100.1) TIFF2025170277000055.tif43164 TIFF2025170277000056.tif136164
[0227] Example 16 - Humanized Monoclonal Antibody hD12 SEQ ID NO: 114 Heavy chain sequence of hD12 TIFF2025170277000057.tif62164
[0228] SEQ ID NO: 115 Light chain sequence of hD12 TIFF2025170277000058.tif16164 TIFF2025170277000059.tif15164
[0229] SEQ ID NO: 116 Heavy chain sequence of hD12T289C (residue C289 is underlined) TIFF2025170277000060.tif62164
[0230] Each patent, patent application, publication, or any other reference or document cited herein is hereby incorporated by reference in its entirety. In the case of conflict, the present specification, including definitions, will control.
[0231] Citation of any patent, patent application, publication, or any other document is not an admission that any of them is pertinent prior art, nor does it constitute any admission as to the contents or date of such publication or document.
[0232] Unless otherwise defined, 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. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described herein.
[0233] All of the features disclosed herein may be combined in any combination. Each feature disclosed herein may be replaced by an alternative feature serving the same, equivalent, or similar purpose. Thus, unless expressly stated otherwise, a disclosed feature (e.g., an antibody) is an example of a genus of equivalent or similar features.
[0234] As used herein, all numerical values or ranges of values include integers and fractions of values within the range, unless the context clearly dictates otherwise. Furthermore, when a list of values is provided herein (e.g., about 50%, 60%, 70%, 80%, 85%, or 86%), the list includes all intermediate values and fractions thereof (e.g., 54%, 85.4%). Thus, illustratively, a reference to 80% or greater identity includes 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, etc., as well as 81.1%, 81.2%, 81.3%, 81.4%, 81.5%, etc., 82.1%, 82.2%, 82.3%, 82.4%, 82.5%, etc., etc.
[0235] References to integers with greater than or less than include any number greater than or less than the referenced number, respectively. Thus, for example, a reference to less than 100 includes 99, 98, 97, etc., all the way up to the digit 1, and a reference to less than 10 includes 9, 8, 7, etc., all the way up to the digit 1.
[0236] As used herein, all numerical values or ranges include values within that range and integer fractions and integer fractions within that range, unless the context clearly dictates otherwise. Thus, for illustrative purposes, a reference to a numerical range such as 1 to 10 includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, as well as 1.1, 1.2, 1.3, 1.4, 1.5, etc. Thus, a reference to a range of 1 to 50 includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, etc., up to and including 50, as well as 1.1, 1.2, 1.3, 1.4, 1.5, etc., 2.1, 2.2, 2.3, 2.4, 2.5, etc.
[0237] References to continuous ranges include ranges combining the limits of different ranges within that series. Thus, for example, 1 to 10, 10 to 20, 20 to 30, 30 to 40, 40 to 50, 50 to 60, 60 to 75, 75 to 100, 100 to 150, 150 to 200, 200 to 250, 250 to 300, 300 to 400, 400 to 500, 500 to 750, 750 to 1,000, 1,000 to 1,500, 1,500 to 2,000, 2,000 to 2,500, 2,500 References to continuous ranges of up to 3,000, 3,000 to 3,500, 3,500 to 4,000, 4,000 to 4,500, 4,500 to 5,000, 5,500 to 6,000, 6,000 to 7,000, 7,000 to 8,000, or 8,000 to 9,000 include ranges such as 10 to 50, 50 to 100, 100 to 1,000, 1,000 to 3,000, 2,000 to 4,000, etc.
[0238] Modifications can be made to the above without departing from the basic aspects of the present technology. Although the technology has been described in substantial detail with reference to one or more specific embodiments, those skilled in the art will recognize that modifications can be made to the embodiments specifically disclosed in this application. However, these modifications and improvements are within the scope and spirit of the present technology.
[0239] The present invention is generally disclosed herein using affirmative language to describe various embodiments and aspects. The present invention also specifically includes embodiments that exclude, in whole or in part, certain subject matter, such as substances or materials, methods and conditions, protocols or procedures. For example, certain embodiments or aspects of the present invention exclude materials and / or method steps. Thus, even if the present invention does not generally state herein what it does not exclude, aspects of the present invention that are not expressly excluded are nevertheless disclosed herein.
[0240] The technology illustratively described herein can suitably be practiced without any element not specifically disclosed herein. Thus, for example, any of the terms "comprising," "consisting essentially of," and "consisting of" in each instance herein can be replaced with either of the other two terms. The terms and expressions used are used as terms of description, not of limitation. The use of such terms and expressions does not exclude any equivalents of the disclosed and described features or portions thereof, and various modifications are possible within the scope of the claimed technology. The terms "a" or "an" can refer to one or more of the elements it modifies (e.g., "reagent" can refer to one or more reagents), unless the context clearly indicates that one or more of the elements are being described. As used herein, the term "about" means a value within 10% (i.e., plus or minus 10%) of the underlying parameter, and the use of the term "about" at the beginning of a numerical series modifies each of the numerical values (e.g., "about 1, 2, and 3" means about 1, about 2, and about 3). For example, a weight of "about 100 grams" can include a weight of 90 grams to 110 grams. As used herein, the term "substantially" refers to a value modifier meaning "at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%, and can include 100%. For example, a composition that is substantially free of X can contain less than 5%, less than 4%, less than 3%, less than 2%, or less than 1% X, and / or X can be absent or undetectable in the composition.
[0241] Thus, while the present technology has been specifically disclosed in terms of exemplary embodiments and optional features, it should be understood that modifications and variations of the concepts disclosed herein may be made by those skilled in the art, and such modifications and variations are considered to be within the scope of the present technology.
Claims
1. A binder-drug conjugate comprising a binder and a payload, The binder is (i) two or more of the polypeptide sequences of the light chain complementarity determining region (CDR-L): CDR-L1, CDR-L2, and CDR-L3; and (ii) two or more of the heavy chain complementarity determining region (CDR-H) polypeptide sequences CDR-H1, CDR-H2, and CDR-H3; CDR-L1 is selected from the amino acid sequences of SEQ ID NOs: 1-15, CDR-L2 is selected from the amino acid sequences of SEQ ID NOs: 16-25, and CDR-L3 is selected from the amino acid sequences of SEQ ID NOs: 26-36; CDR-H1 is selected from the amino acid sequences of SEQ ID NOs: 50-61, CDR-H2 is selected from the amino acid sequences of SEQ ID NOs: 62-78, and CDR-H3 is selected from the amino acid sequences of SEQ ID NOs: 79-93; and The payload comprises a pyrrolobenzodiazepine toxin and a linking group; A pharmaceutical composition, wherein the pyrrolobenzodiazepine toxin is covalently linked to a linking group, the linking group is covalently linked to a binding agent, and the binding agent specifically binds to the extracellular domain of mesenchymal epithelial transition factor (cMET).
2. Pyrrolobenzodiazepine toxins have the chemical formula I: 【Chemistry 1】 [In the formula, Z 1 and Z 2 are both N; Z 3 and Z 4 are both C; 【Chemistry 2】 n is 1 to 10; R 3 and R 4 each independently represents H or C 1-4 alkoxyl; and R 1 and R 2 Each of the groups independently represents H, C 1-5 Alkyl, C 3-6 Cycloalkyl, C 2-5 alkenyl and R 5 phenyl optionally substituted with R 5 is -NH 2 , -NHR 6 and structure: 【Transformation 3】 R with 7 piperazinyl substituted with R 6 comprises a linking group, and R 7 is H or C 1-5 is alkyl; X 1 is null, a protecting group, or contains a linking group; X 2 is null, a protecting group, or contains a linking group; X 1 , X 2 , R 1 and R 2 Only one of Y contains a linking group; and Y 1 and Y 2 each independently being null, OH, or SO 3 H; however, 【Chemistry 4】 Null indicates that the moiety is absent or that one or more hydrogens are present to complete the required valence.
2. The binder-drug conjugate of claim 1, comprising the structure:
3. 3. The binder-drug conjugate of claim 2, wherein n is 3, 4, or 5.
4. R 3 and R 4 Both are O-CH 3 The binder-drug conjugate of claim 2 or 3, wherein
5. R 1 and R 2 The binder-drug conjugate of any one of claims 2 to 4, wherein both are methyl.
6. R 1 and R 2 Both are -CH=CH-CH 3 The binder-drug conjugate of any one of claims 2 to 4, wherein
7. R 2 The binder-drug conjugate of any one of claims 2 to 4, wherein is cyclopropyl.
8. R 2 The binder-drug conjugate of any one of claims 2 to 4, wherein is phenyl substituted with 4-methylpiperazin-1-yl.
9. R 1 is R 5 phenyl optionally substituted with R 5 Ga-NHR 6 and R 6 The binder-drug conjugate of claim 7 or 8, wherein comprises a linking group.
10. X 1 is null and Y 1 is null, and 【Transformation 5】 The binder-drug conjugate of any one of claims 2 to 9.
11. X 1 contains a linking group, and Y 1 is OH, 【Transformation 6】 The binder-drug conjugate of any one of claims 2 to 8.
12. X 1 contains a linking group, and Y 1 is OH, 【Transformation 7】 The binder-drug conjugate of any one of claims 2 to 8.
13. 13. The binder-drug conjugate of any one of claims 1 to 12, wherein the linking group is attached to the pyrrolobenzodiazepine toxin by a carbamate group.
14. 13. The binder-drug conjugate of any one of claims 1 to 12, wherein the linking group is attached to the pyrrolobenzodiazepine toxin by an amide group.
15. The linking group is of formula A: 【Transformation 8】 [In the formula, Asterisks indicate points of attachment to the pyrrolobenzodiazepine toxin; The wavy line indicates the point of attachment to the linking agent; m is 1 to 20; q is 0 to 10; and E is a linking group. The binder-drug conjugate of any one of claims 1 to 14, comprising the structure:
16. 16. The binder-drug conjugate of claim 15, wherein m is 4 or 8.
17. 17. The binder-drug conjugate of claim 15 or 16, wherein q is 0, 1 or 2.
18. 16. The binder-drug conjugate of claim 15, wherein m is 8 and q is 2.
19. The linking group is of formula B: 【Chemistry 9】 [In the formula, The asterisk indicates the point of attachment to the pyrrolobenzodiazepine toxin; the wavy line indicates the point of attachment to the binding agent; E is the linking group; v is 0-10; and u is 0 or 1; when u is 1, t is 1-10. The binder-drug conjugate of any one of claims 1 to 14, comprising the structure:
20. 20. The binder-drug conjugate of claim 19, wherein v is 1.
21. 21. The binder-drug conjugate of claim 19 or 20, wherein u is 1 and t is 8.
22. 20. The binder-drug conjugate of claim 19, wherein u is 0 and v is 4.
23. 23. The binder-drug conjugate of any one of claims 15 to 22, wherein the binder is attached to E by a thioether bond formed between a cysteine thiol residue of the binder and E.
24. E is a compound of formula C: 【Chemistry 10】 where the wavy line indicates the point of attachment to the binder and the double asterisk indicates the point of attachment to the linking group. The binder-drug conjugate of any one of claims 15 to 23, comprising the structure:
25. The protecting group has the following structure (D): 【Chemistry 11】 where the asterisk indicates the point of attachment to the pyrrolobenzodiazepine toxin; and w is 1 to 5. The binder-drug conjugate of any one of claims 2 to 24, having the formula:
26. 26. The binder-drug conjugate of claim 25, wherein w is 2.
27. 27. The binder-drug conjugate of any one of claims 2 to 26, wherein the protecting group is a cleavable protecting group.
28. The payload is 【Chemistry 12】 wherein m is 8; 【Chemistry 13】 wherein m is 8, p is 3, and X 2 is a protecting group; 【Chemistry 14】 wherein m is 8; 【Chemistry 15】 wherein t is 8 and v is 1; and 【Chemistry 16】 where the wavy lines indicate the points of attachment to the binder.
2. The binder-drug conjugate of claim 1, comprising a structure selected from the group consisting of:
29. X 2 The protecting group has the following structure (D): 【Chemistry 17】 where the asterisk indicates the point of attachment to the payload; and w is 1 to 5.
29. The binder-drug conjugate of claim 28, having the formula:
30. 30. The binding agent-drug conjugate of any one of claims 1 to 29, wherein CDR-L1 is selected from the amino acid sequences of SEQ ID NOs: 2, 4, 6, 8, 9, 10, 12, 14 and 15.
31. 31. The binder-drug conjugate of any one of claims 1 to 30, wherein CDR-L2 is selected from the amino acid sequences of SEQ ID NOs: 17, 19, 21, 23, 24 and 25.
32. 32. The binder-drug conjugate of any one of claims 1 to 31, wherein CDR-L3 is selected from the amino acid sequences of SEQ ID NOs: 27, 29, 31, 33, 34 and 35.
33. 33. The binding agent-drug conjugate of any one of claims 1 to 32, wherein CDR-H1 is selected from the amino acid sequences of SEQ ID NOs: 51, 53, 55, 57, 58 and 59.
34. 34. The binding agent-drug conjugate of any one of claims 1 to 33, wherein CDR-H2 is selected from the amino acid sequences of SEQ ID NOs: 63, 65, 67, 69, 70, 71, 73, 75 and 78.
35. 35. The binding agent-drug conjugate of any one of claims 1 to 34, wherein CDR-H3 is selected from the amino acid sequences of SEQ ID NOs: 80, 82, 84, 86, 87, 88, 91 and 93.
36. 36. The binding agent-drug conjugate of any one of claims 1 to 35, wherein the binding agent is an antibody or a binding fragment thereof.
37. 37. The binding agent-drug conjugate of claim 36, wherein the binding agent is a monoclonal antibody or a binding fragment thereof.
38. 38. The binder-drug conjugate of any one of claims 1 to 37, wherein the binder comprises an IgG1, IgG2, IgG3, or IgG4 constant region.
39. 39. The binder-drug conjugate of claim 38, wherein the binder comprises an IgG2 constant region.
40. 38. The binder-drug conjugate of any one of claims 1 to 37, wherein the binder comprises a constant region of IgD, IgE, IgA, or IgM.
41. 41. The binder-drug conjugate of any one of claims 1 to 40, wherein the binder is humanized.
42. 42. The binder-drug conjugate of any one of claims 1 to 41, wherein the binder comprises at least one humanized or human framework region.
43. 43. The binder-drug conjugate of claim 42, wherein the binder comprises at least three humanized or human framework regions.
44. 44. The binder-drug conjugate of any one of claims 1 to 43, wherein the binder comprises at least one murine framework region.
45. 45. The binder-drug conjugate of claim 44, wherein the binder comprises at least three murine framework regions.
46. 46. The binder-drug conjugate of any one of claims 1 to 45, wherein the binder is a Fab, Fab', F(ab')2, Fv, or scFv fragment of an antibody.
47. 47. The binder-drug conjugate of any one of claims 1 to 46, wherein the binder comprises a single-chain polypeptide.
48. 48. The binder-drug conjugate of any one of claims 1 to 47, wherein the binder comprises a light chain variable region having an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 37 to 44.
49. 49. The binder-drug conjugate of any one of claims 1 to 48, wherein the binder comprises a heavy chain variable region having an amino acid sequence selected from the amino acid sequences of SEQ ID NOs: 94 to 103.
50. 50. The binder-drug conjugate of any one of claims 1 to 49, wherein the binder comprises a light chain sequence having at least 90% sequence identity or 100% sequence identity to any one of the amino acid sequences of SEQ ID NOs: 46-49.
51. 51. The binder-drug conjugate of any one of claims 1 to 50, wherein the binder comprises a heavy chain sequence having at least 90% sequence identity or 100% sequence identity to any one of the amino acid sequences of SEQ ID NOs: 105-108.
52. 52. The binding agent-drug conjugate of claim 50 or 51, wherein the light chain sequence or the heavy chain sequence comprises 1 to 5 amino acid modifications selected from amino acid additions, amino acid deletions, and amino acid substitutions.
53. 53. The binding agent-drug conjugate of any one of claims 1 to 52, wherein the binding agent induces internalization of cMET on human cancer cells.
54. 54. The binder-drug conjugate of any one of claims 1 to 53, wherein the binder induces degradation of cMET on human cancer cells.
55. 55. The binder-drug conjugate of any one of claims 1 to 54, wherein the binder is not a cMET agonist.
56. 56. The binding agent-drug conjugate of any one of claims 1 to 55, wherein the binding agent specifically binds to mammalian cMET.
57. 57. The binding agent-drug conjugate of claim 56, wherein the mammalian cMET is human cMET, monkey cMET, or rat cMET.
58. 58. The binding agent-drug conjugate of claim 57, wherein the binding agent specifically binds to human cMET.
59. 59. The binding agent-drug conjugate of claim 57 or 58, wherein the binding agent specifically binds to human cMET, monkey cMET, and rat cMET.
60. 60. The binding agent-drug conjugate of any one of claims 1 to 59, wherein the binding agent specifically binds to the extracellular domain of wild-type cMET.
61. 61. The binding agent-drug conjugate of any one of claims 1 to 60, wherein the binding agent specifically binds to the extracellular domain of a cMET mutant.
62. 62. The binder-drug conjugate of claim 61, wherein the cMET mutant comprises the E168D or N375S mutant of cMET.
63. 63. The binder-drug conjugate of any one of claims 1 to 62, wherein at least one amino acid of the binder is mutated to a cysteine, and the cysteine is covalently linked to the linking group by a thiol ether bond.
64. The binder CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or 14; CDR-L2 comprising the amino acid sequence of SEQ ID NO: 25; CDR-L3 comprising the amino acid sequence of SEQ ID NO: 35; CDR-H1 comprising the amino acid sequence of SEQ ID NO: 59; CDR-H2 comprising the amino acid sequence of SEQ ID NO: 71; and CDR-H3 comprising the amino acid sequence of SEQ ID NO: 88 64. The binder-drug conjugate of any one of claims 1 to 63, comprising:
65. The binder CDR-L1 comprising the amino acid sequence of SEQ ID NO: 9 or 15; CDR-L2 comprising the amino acid sequence of SEQ ID NO: 24; CDR-L3 comprising the amino acid sequence of SEQ ID NO: 34; CDR-H1 comprising the amino acid sequence of SEQ ID NO: 58; CDR-H2 comprising the amino acid sequence of SEQ ID NO: 70 or 78; and CDR-H3 comprising the amino acid sequence of SEQ ID NO: 87 65. The binder-drug conjugate of claim 64, comprising:
66. The binder CDR-L1 comprising the amino acid sequence of SEQ ID NO: 9 or 10; CDR-L2 comprising the amino acid sequence of SEQ ID NO: 24 or 25; CDR-L3 comprising the amino acid sequence of SEQ ID NO: 34 or 35; CDR-H1 comprising the amino acid sequence of SEQ ID NO: 58 or 59; CDR-H2 comprising the amino acid sequence of SEQ ID NO: 70 or 71; and CDR-H3 comprising the amino acid sequence of SEQ ID NO: 87 or 88 64. The binder-drug conjugate of any one of claims 1 to 63, comprising:
67. 67. The binder-drug conjugate of any one of claims 1 to 66, having a heavy chain variable region comprising an amino acid sequence selected from SEQ ID NOs: 105, 106, 107, and 108, and a light chain variable region comprising an amino acid sequence selected from SEQ ID NOs: 46, 47, 48, and 49.
68. 68. The binding agent-drug conjugate of any one of claims 1 to 67, wherein the light chain sequence comprises SEQ ID NO:47 and the heavy chain sequence comprises SEQ ID NO:
108.
69. Chemical formula (II): [Chemistry 18] where m is 8 and the wavy line indicates the point of attachment to the thiol group of the linking agent.
69. The binder-drug conjugate of any one of claims 1 to 68, comprising a payload having the structure:
70. The binder CDR-L1 comprising the amino acid sequence of SEQ ID NO: 9 or 10; CDR-L2 comprising the amino acid sequence of SEQ ID NO: 24 or 25; CDR-L3 comprising the amino acid sequence of SEQ ID NO: 34 or 35; CDR-H1 comprising the amino acid sequence of SEQ ID NO: 58 or 59; CDR-H2 comprising the amino acid sequence of SEQ ID NO: 70 or 71; and CDR-H3 comprising the amino acid sequence of SEQ ID NO: 87 or 88 70. The binder-drug conjugate of claim 69, comprising:
71. 70. The binder-drug conjugate of claim 69, wherein the binder comprises a heavy chain of SEQ ID NO: 114 or SEQ ID NO: 116 and a light chain of SEQ ID NO:
115.
72. 72. A pharmaceutical composition comprising the binder-drug conjugate of any one of claims 1 to 71 and a pharmaceutically acceptable excipient, diluent, additive or carrier.
73. a) identifying subjects having or suspected of having a neoplastic disorder or cancer; b) A method of treating a subject having a neoplastic disorder or cancer, comprising administering to said subject a therapeutically effective amount of a binder-drug conjugate of any one of claims 1 to 71, or a composition of claim 72.
74. 74. The method of claim 73, wherein after administration, the binding agent-drug conjugate prevents, inhibits, ameliorate, abolishes or suppresses cancer growth, viability or metastasis.
75. 74. The method of claim 72 or 73, wherein after administration, the binding agent-drug conjugate induces death, necrosis or apoptosis of some or all of the cancer.
76. 76. The method of any one of claims 73 to 75, wherein the neoplastic disorder or cancer comprises carcinoma, sarcoma, neuroblastoma, glioblastoma, myeloma, lymphoma, melanoma or solid or soft tissue tumor.
77. 77. The method of claim 76, wherein the neoplastic disorder or cancer comprises bladder cancer, breast cancer, colorectal cancer, gastric cancer, pancreatic cancer, esophageal cancer, liver cancer, hepatocellular carcinoma, hypopharyngeal cancer, lung cancer, adenocarcinoma, ovarian cancer or renal cancer.
78. 78. The method of claim 76 or 77, wherein the neoplastic disorder or cancer comprises pancreatic adenocarcinoma, pancreatic neuroendocrine carcinoma, colorectal adenocarcinoma, small intestine malignancy, bile duct carcinoma, non-small cell lung cancer (NSCLC), thyroid cancer, esophageal or esophagogastric junction (EGJ) cancer, gastric adenocarcinoma, liver hepatocellular carcinoma, head and neck squamous cell carcinoma, female genital tract malignancy, breast cancer, triple-negative breast cancer, small cell lung cancer, ovarian surface epithelial carcinoma, retroperitoneal or peritoneal sarcoma, prostate adenocarcinoma, neuroendocrine tumor, gastrointestinal stromal tumor, glioblastoma, or non-epithelial ovarian cancer.
79. A binder-drug conjugate comprising a binder and a payload, the binding agent comprises a heavy chain and a light chain having the same CDRs, respectively, as the heavy chain and light chain CDRs of the antibody produced by hybridoma cell line F6B1P3D12 deposited with the ATCC on March 20, 2019; and the payload comprises a pyrrolobenzodiazepine toxin and a linking group; A binder-drug conjugate, wherein the pyrrolobenzodiazepine toxin is covalently linked to a linking group, the linking group is covalently linked to a binder, and the binder specifically binds to the extracellular domain of mesenchymal epithelial factor (cMET).
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