Anti-nectin-4 antibodies and conjugates thereof
Anti-Nectin-4 antibodies and ADCs with enhanced binding affinity and cytotoxicity address the need for safer and more effective cancer treatments by targeting Nectin-4, showing potent cytotoxicity and anti-tumor effects in cancer models.
Patent Information
- Application Number
- PCT/CN2025/120924
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2024-09-12
- Filing Date
- 2025-09-12
- Publication Date
- 2026-03-19
AI Technical Summary
There is a need for more efficacious and safer clinical candidates targeting Nectin-4 for the treatment of various cancers, as existing antibody-drug conjugates (ADCs) require careful attention to components like target selection, antibody-linkage, and cytotoxic payload to enhance safety and efficacy.
Development of anti-Nectin-4 antibodies and antigen-binding fragments with enhanced binding affinity in the presence of adenosine-containing compounds, conjugated with cytotoxic payloads via specific linkers, forming antibody-drug conjugates that induce cytotoxicity in cancer cells and exhibit in vivo anti-tumor effects.
The anti-Nectin-4 antibodies and ADCs demonstrate potent cytotoxicity in cancer cell lines and effective anti-tumor responses in multiple tumor models, with improved binding affinity and internalization capabilities.
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Abstract
Description
ANTI-NECTIN-4 ANTIBODIES AND CONJUGATES THEREOFCROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of PCT Application No. PCT / CN2024 / 118427, filed September 12, 2024, the content of which is hereby incorporated by reference in its entirety. REFERENCE TO AN ELECTRONIC SEQUENCE LISTING
[0002] The content of the electronic sequence listing (397675. xml; Size: 171,878 bytes; and Date of Creation: September 11, 2025) is herein incorporated by reference in its entirety.BACKGROUND
[0003] Nectin-4 (also known as PVRL4, poliovirus receptor-like molecule 4) is a type I transmembrane glycoprotein having a molecular mass of 66 kD, and belongs to the Nectin family of Ig superfamily proteins. Nectin-4 has an extracellular region with three immunoglobulin-like (Ig-like) domains (VCC) ; and serves a role in the formation and maintenance of adhesion connection together with cadherin. Nectin-4 is a tumor-associated antigen found on the surface of many cancers, such as urothelial carcer, bladder cancer, ovarian cancer, lung cancer, etc. Therefore, Nectin-4 has become an important target for the diagnosis and treatment of a plurality of solid tumors.
[0004] Antibody-drug conjugates (ADC) are one of the fast-growing anticancer drugs. This approach includes a mAb conjugated to the cytotoxic payload via a chemical linker that directed toward a target antigen expressed on the cancer cell surface, reducing systemic exposure and therefore toxicity. ADCs are complex molecules that require careful attention to various components. Selection of an appropriate target, an mAb, cytotoxic payload, and the manner in which the antibody is linked to the payload are key determinants of the safety and efficacy of ADCs.
[0005] There is a need to develop more efficacious and safer clinical candidates targeting the Nectin-4.SUMMARY
[0006] Provided herein are antibodies or antigen-binding fragment thereof specifically binds to Nectin-4, and antibody-drug conjugates (ADC) thereof. The anti-Nectin-4 antibodies or antigen-binding fragment thereof provided herein are ANP dependent, and specifically binds to Nectin-4 with comparable binding affinity to the benchmark Enfortumab. The anti-Nectin-4 antibodies or antigen-binding fragment thereof bind to Nectin 4 overexpressing cells and Nectin-4 expressing cancer cells, and induce antibody internalization in various cancer cell lines. The Nectin-4 targeting ADCs exhibit potent cytotoxicity in the cancer cell lines and in vivo anti-tumor effects in several tumor models.
[0007] Also provided, in some embodiments, are compositions including the antibodies or antigen-binding fragment thereof or ADCs, and a pharmaceutically acceptable carrier.
[0008] Methods and uses for the treatment of diseases and conditions are also provided. In one embodiment, provided is a method of treating cancer in a patient in need thereof, including administering to the patient the antibodies or antigen-binding fragment thereof or ADCs of the present disclosure.
[0009] In one aspect, the present disclosure provides an antibody or antigen-binding fragment thereof that has binding specificity to a human Nectin-4 protein, which has a higher binding affinity to human Nectin-4 in the presence of the adenosine-containing compound (ANP) than in the absence of the ANP.
[0010] In certain embodiments, the concentration of the ANP is at least about 50 μM.
[0011] In certain embodiments, the binding affinity to human Nectin-4 protein is at least about 1-fold higher in the presence of the ANP than in the absence of the ANP, when the ANP is present at a concentration of at least about 100 μM.
[0012] In certain embodiments, the antibody or the fragment thereof comprises a heavy chain variable region (VH) comprising heavy chain complementarity determining regions (CDR) VH CDR1, VH CDR2, and VH CDR3, and a light chain variable region (VL) comprising VL CDR1, VL CDR2, and VL CDR3, and wherein the VH CDR1 comprises the amino acid sequence of SEQ ID NO: 144, the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 145, the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 146, the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 147, the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 148, and the VL CDR3 comprises the amino acid sequence of SEQ ID NO: 149;
[0013] In certain embodiments, the VH CDR1 comprises the amino acid sequence of SEQ ID NO: 13, or 20-33, the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 14 or 34-49, the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 15 or 50-55, the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 16 or 56-58, the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 17 or 59-61, and the VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18 or 62.
[0014] In certain embodiments, the VH comprises an amino acid sequence of any one of SEQ ID NO: 8, 72-90, 92-108, and 110-137, or a peptide having at least 90%sequence identity to the amino acid sequence of any one of SEQ ID NO: 8, 72-90, 92-108, and 110-137, and the VL comprises an amino acid sequence of any one of SEQ ID NO: 7, 63-71, 91 and 109, or a peptide having at least 90%sequence identity to the amino acid sequence of any one of SEQ ID NO: 7, 63-71, 91 and 109.
[0015] In certain embodiments, the VH CDR1 comprises the amino acid sequence of SEQ ID NO: 13, or 20-25, the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 14 or 34-49, the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 15 or 50, the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 16 or 56-58, the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 17 or 59-61, and the VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18 or 62.
[0016] In certain embodiments, the VH comprises an amino acid sequence of any one of SEQ ID NO: 8, 72-90, and 92-108, or a peptide having at least 90%sequence identity to the amino acid sequence of any one of SEQ ID NO: 8, 72-90, and 92-108, and the VL comprises an amino acid sequence of any one of SEQ ID NO: 7, 63-71, 91 and 109, or a peptide having at least 90%sequence identity to the amino acid sequence of any one of SEQ ID NO: 7, 63-71, 91 and 109.
[0017] In certain embodiments, the VH / VL pair comprise the amino acid sequences of SEQ ID NO: 8 / 7, 8 / 63, 8 / 64, 8 / 65, 8 / 66, 8 / 67, 8 / 68, 8 / 69, 8 / 70, 8 / 71, 72 / 7, 73 / 7, 74 / 7, 75 / 7, 76 / 7, 77 / 7, 78 / 7, 79 / 7, 80 / 7, 81 / 7, 82 / 7, 83 / 7, 84 / 7, 85 / 7, 86 / 7, 87 / 7, 88 / 7, 89 / 7, 90 / 7, 83 / 67, 84 / 67, 85 / 67, 86 / 67, 87 / 67, 8 / 91, 72 / 67, 74 / 67, 75 / 67, 79 / 67, 92 / 67, 93 / 67, 94 / 67, 95 / 67, 96 / 67, 97 / 67, 98 / 67, 74 / 68, 99 / 67, 100 / 67, 101 / 67, 102 / 67, 103 / 67, 104 / 67, 105 / 67, 106 / 67, 107 / 67, 108 / 67, 105 / 109, 106 / 109, 107 / 109, 108 / 109, 102 / 109, or 103 / 109, respectively.
[0018] In certain embodiments, the VH CDR1 comprises the amino acid sequence of SEQ ID NO: 22, the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 34, the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 15, the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 56, the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 60, and the VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18.
[0019] In certain embodiments, the VH comprises the amino acid sequence of SEQ ID NO: 93, and the VL comprises the amino acid sequence of SEQ ID NO: 67.
[0020] In certain embodiments, the VH CDR1 comprises the amino acid sequence of SEQ ID NO: 26-33, the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 34, the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 51-55, the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 56, the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 60, and the VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18.
[0021] In certain embodiments, the VH comprises an amino acid sequence of any one of SEQ ID NO: 110-137, and the VL comprises the amino acid sequence of SEQ ID NO: 67.
[0022] In certain embodiments, the VH CDR1 comprises the amino acid sequence of SEQ ID NO: 27, the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 34, the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 53, the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 56, the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 60, and the VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18.
[0023] In certain embodiments, the VH comprises the amino acid sequence of SEQ ID NO: 121, and the VL comprises the amino acid sequence of SEQ ID NO: 67.
[0024] In certain embodiments, the antibody or antigen-binding fragment thereof provided herein is a F (ab') 2, a F (ab) 2, a Fab', a Fab, a Fv, or a scFv.
[0025] In certain embodiments, the antibody or antigen-binding fragment thereof further comprises a heavy chain constant region, a light chain constant region, an Fc region, or the combination thereof.
[0026] In certain embodiments, the antibody or antigen-binding fragment thereof is of an isotype of IgG1, IgG2, IgG3 or IgG4.
[0027] In certain embodiments, the antibody or antigen-binding fragment thereof is of an isotype of human IgG1.
[0028] In certain embodiments, the antibody or antigen-binding fragment thereof provided herein is conjugated.
[0029] In one aspect, provided herein is a multifunctional molecule, comprising a first antigen-binding portion having specificity to a human Nectin-4 protein and a second antigen-binding portion having specificity to a second antigen, wherein the first antigen-binding portion comprises the antibody or antigen-binding fragment thereof of the present disclosure.
[0030] In one aspect, provided herein is an antibody-drug conjugate, comprising the antibody or antigen-binding fragment thereof or the multifunctional molecule of the present disclosure, and a drug moiety.
[0031] In certain embodiments, the drug moiety is a cytotoxin, an immunosuppressive agent, a radioisotope, or a toxin.
[0032] In certain embodiments, the drug moiety is a cytotoxin selected from the group consisting of auristatins, maytansinoids, macrocyclic ketone analogues, topoisomerase inhibitors, benzodiazepines, tubulysins, duocarmycin, camptothecin, calicheamicins, exatecans, irinotecans (SN38) , doxorubicin, anthracycline, the pyrrolobenzodiazepenes (PBD) , TLR agonist, STING agonists, pseudomonas aeruginosa exotoxin PE38, diphtheria toxin, staphylococcus aureus enterotoxin A / E-120, antibacterial antibiotic, shigatoxin, ricin, and urease.
[0033] In certain embodiments, the drug moiety is a cytotoxin selected from the group consisting of monomethyl auristatin E (MMAE) , monomethyl auristatin F (MMAF) , maytansine, mertansine (DM1) , ravtansine (DM4) , tublysin A, DXd, 7-ethyl-10-hydroxycamptothecin (SN-38) , DGN462, Amberstatin269, anthramycin, SG3199 / SCX, 700DX, TLR7 / 8 agonist, diABZI STING agonist-2, or any derivative thereof.
[0034] In certain embodiments, the drug moiety comprises MMAE, MMAF, or DXd.
[0035] In certain embodiments, the antibody or antigen-binding fragment thereof or the multifunctional molecule is conjugated to the drug moiety via a linker.
[0036] In certain embodiments, the linker comprises succinimidyl-4- (N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) , sulfo-SMCC, p-carboxycyclo hexylmethylmaleimide, maleimide-caproyl (MC) -Valine-citrulline (VC) -para-aminobenzyloxycarbamoyl (PABC) , CL2A, maleimide-caproyl (MC) , MC-glycine-glycine-phenylalanine-glycine (GGFG) , MC-PEG8-GGFG, MC-PEG8-GGFG-PAB, or maleimide propoyl (MP) -PEG8-Valine-alanine (VA) -PABC.
[0037] In certain embodiments, the drug-antibody ratio (DAR) is 1-20.
[0038] In certain embodiments, the drug-antibody ratio (DAR) is 4-8.
[0039] In one aspect, provided herein is a chimeric antigen receptor (CAR) having specificity to the human FOLR1 protein, comprising an antigen-binding fragment thereof or a multifunctional molecule of the present disclosure, a transmembrane domain, and an intracellular activating domain.
[0040] In certain embodiments, the antigen-binding fragment is a single chain fragment (scFv) .
[0041] In certain embodiments, the transmembrane domain is a transmembrane domain of 4-1BB, an alpha chain of a T cell receptor, a beta chain of a T cell receptor, a zeta chain of a T cell receptor, CD3 epsilon, CD4, CD5, CD8 alpha, CD9, CD16, CD19, CD22, CD28, CD33, CD37, CD45, CD64, CD80, CD86, CD134, CD137, or CD154.
[0042] In certain embodiments, the chimeric antigen receptor comprises an intracellular activation domain that is a signaling domain derived from CD3 zeta, CD3 epsilon, CD3 delta, and CD3 gamma.
[0043] In certain embodiments, the CAR further comprises one or more costimulatory domains selected from a signaling domain (or other suitable portion) of CD28, OX-40, 4-1BB / CD137, CD2, CD7, CD27, CD30, CD40, Programmed Death-1 (PD-1) , inducible T cell costimulator (ICOS) , lymphocyte function-associated antigen-1 (LFA-1, CD1-1a / CD18) , CD3 gamma, CD3 delta, CD3 epsilon, CD247, CD276 (B7-H3) , LIGHT, (TNFSF14) , NKG2C, Ig alpha (CD79a) , DAP-10, Fc gamma receptor, MHC class 1 molecule, TNF receptor proteins, an Immunoglobulin protein, cytokine receptor, integrins, Signaling Lymphocytic Activation Molecules (SLAM proteins) , activating NK cell receptors, BTLA, a Toll ligand receptor, ICAM-1, B7-H3, CDS, ICAM-1, GITR, BAFFR, LIGHT, HVEM (LIGHTR) , KIRDS2, SLAMF7, NKp80 (KLRF1) , NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL-2R beta, IL-2R gamma, IL-7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD1 1d, ITGAE, CD103, ITGAL, CD1 la, LFA-1, ITGAM, CD1 1b, ITGAX, CD1 1c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, TNFR2, TRANCE / RANKL, DNAM1 (CD226) , SLAMF4 (CD244, 2B4) , CD84, CD96 (Tactile) , CEACAM1, CRT AM, Ly9 (CD229) , CD160 (BY55) , PSGL1, CD100 (SEMA4D) , CD69, SLAMF6 (NTB-A, Ly108) , SLAM (SLAMF1, CD150, IPO-3) , BLAME (SLAMF8) , SELPLG (CD162) , LTBR, LAT, GADS, SLP-76, PAG / Cbp, CD19a, a ligand that specifically binds with CD83, or any combination thereof.
[0044] In certain embodiments, the CAR further comprises a hinge domain selected from a hinge domain of IgG1, IgG2, IgG3, IgG4, IgA, IgD, IgE, IgM, CD28, or CD8 alpha, any truncation thereof, or any combination thereof.
[0045] In one aspect, provided herein is a nucleic acid encoding the antibody or antigen-binding fragment thereof, the multifunctional molecule, or the CAR of the present disclosure.
[0046] In one aspect, provided herein is a vector comprising the nucleic acid of the present disclosure.
[0047] In one aspect, provided herein is an isolated cell comprising the nucleic acid of the present disclosure, or the vector of the present disclosure.
[0048] In one aspect, provided herein is a pharmaceutical composition comprising the antibody or antigen-binding fragment thereof, the multifunctional molecule, the antibody-drug conjugate, or the CAR of the present disclosure, and a pharmaceutically acceptable carrier.
[0049] In one aspect, provided herein is a method of treating cancer in a patient in need thereof, comprising administering to the patient the antibody or antigen-binding fragment thereof, the multifunctional molecule, the antibody-drug conjugate, or the CAR, or the pharmaceutical composition of the present disclosure.
[0050] In one aspect, provided herein is use of the antibody or antigen-binding fragment thereof, the multifunctional molecule, the antibody-drug conjugate, or the CAR, or the pharmaceutical composition of the present disclosure for the preparation of a medicament for treating cancer.
[0051] In one aspect, provided herein is the antibody or antigen-binding fragment thereof, the multifunctional molecule, the antibody-drug conjugate, or the CAR, or the pharmaceutical composition of the present disclosure for use in the treatment of cancer in a patient in need thereof.
[0052] In certain embodiments, the cancer is selected from the group consisting of bladder cancer, liver cancer, colon cancer, rectal cancer, endometrial cancer, leukemia, lymphoma, pancreatic cancer, small cell lung cancer, non-small cell lung cancer, breast cancer, urethral cancer, head and neck cancer, gastrointestinal cancer, stomach cancer, oesophageal cancer, ovarian cancer, renal cancer, melanoma, prostate cancer and thyroid cancer.BRIEF DESCRIPTION OF THE DRAWINGS
[0053] FIG. 1A-1B show the binding affinity of the anti-Nectin-4 antibodies to the human Nectin-4 expressing CHOK1 cells in the presence or absence of ANP, as measured by FACS.
[0054] FIG. 2A-2K show the binding affinity of the P004E08 variants to the human Nectin-4 expressing CHOK1 cells in the presence or absence of ANP, as measured by FACS.
[0055] FIG. 3 shows the binding affinity of the affinity matured P004E08-mut040 antibodies to the human Nectin-4 expressing CHOK1 cells in the presence or absence of ANP, as measured by FACS.
[0056] FIG. 4A-4D show the binding affinity of the P004E08-mut040-PTM12 to the human / cyno / mouse Nectin-4 expressing CHOK1 cells in the presence or absence of ANP, as measured by FACS.
[0057] FIG. 5A-5D show the binding affinity of the P004E08-mut040-PTM12 in IgG format and the antibody-drug conjugate thereof to the tumor cell lines in the presence or absence of ANP, as measured by FACS.
[0058] FIG. 6A-6D show the internalization of the P004E08-mut040-PTM12 in the human Nectin-4 expressing CHOK1 cells and the tumor cell lines, respectively, in the presence or absence of ANP, as measured by FACS.
[0059] FIG. 7 shows the result of cytotoxicity assay on NCI-H2122 cell line using P004E08-mut040-PTM12 conjugated to MMAE.
[0060] FIG. 8A-8B show the in vivo anti-tumor effect of the ADC of P004E08-mut040 conjugated to MMAE in the MDA-MB-468 CDX model.
[0061] FIG. 9A-9B show the in vivo anti-tumor effect of the ADC of P004E08-mut040-PTM12 conjugated to MMAE in the HCI-H322 CDX model.
[0062] FIG. 10A-10B show the in vivo anti-tumor efficacy and tolerability of the tested ADCs against a breast cancer animal model.
[0063] FIG. 11A-11B show the in vivo anti-tumor efficacy and tolerability of the tested ADCs against a bladder cancer animal model.
[0064] FIG. 12A-12B show the in vivo anti-tumor efficacy and tolerability of the tested ADCs against a esophageal cancer animal model.
[0065] FIG. 13A-13B show the in vivo anti-tumor efficacy and tolerability of the tested ADCs against a head and neck cancer animal model.
[0066] FIG. 14A-14B show the in vivo anti-tumor efficacy and tolerability of the tested ADCs against a cervical cancer animal model.DETAILED DESCRIPTIONDefinitions
[0067] It is to be noted that the term “a” or “an” entity refers to one or more of that entity; for example, “an antibody, ” is understood to represent one or more antibodies. As such, the terms “a” (or “an” ) , “one or more, ” and “at least one” can be used interchangeably herein.
[0068] The term “about” as used herein refers to the usual error range for the respective value readily known to the skilled person in this technical field. Reference to “about” a value or parameter herein includes (and describes) embodiments that are directed to that value or parameter per se. In case of doubt, or should there be no art recognized common understanding regarding the error range for a certain value or parameter, “about” means ± 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, or 10%of this value or parameter.
[0069] As used herein, the term “polypeptide” is intended to encompass a singular “polypeptide” as well as plural “polypeptides, ” and refers to a molecule composed of monomers (amino acids) linearly linked by amide bonds (also known as peptide bonds) . The term “polypeptide” refers to any chain or chains of two or more amino acids, and does not refer to a specific length of the product. Thus, peptides, dipeptides, tripeptides, oligopeptides, “protein, ” “amino acid chain, ” or any other term used to refer to a chain or chains of two or more amino acids, are included within the definition of “polypeptide, ” and the term “polypeptide” may be used instead of, or interchangeably with any of these terms. The term “polypeptide” is also intended to refer to the products of post-expression modifications of the polypeptide, including without limitation glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting / blocking groups, proteolytic cleavage, or modification by non-naturally occurring amino acids. A polypeptide may be derived from a natural biological source or produced by recombinant technology, but is not necessarily translated from a designated nucleic acid sequence. It may be generated in any manner, including by chemical synthesis.
[0070] The terms “Nectin-4, ” “Nectin-4 polypeptide, ” or “Nectin-4 protein” encompasses a polypeptide ( “polypeptide” and “protein” are used interchangeably herein) , including any native polypeptide, from any vertebrate source, including mammals such as primates (e.g., humans and cynomolgus monkeys (cynos) ) , dogs, and rodents (e.g., mice and rats) , unless otherwise indicated. In certain embodiments, the terms include “related Nectin-4 polypeptides, ” including SNP variants thereof. The term “Nectin-4” also encompasses “full-length, ” unprocessed Nectin-4 as well as any form of Nectin-4 that results from processing in the cell. Nectin-4 has GenBankTM accession number NM_030916 (mRNA) , NG_028109 (genomic DNA) , Gene ID 81607 (gene) , NP_112178 (precursor amino acid sequences) provides exemplary human Nectin-4 nucleic acid or amino acid sequences.
[0071] “Homology” or “identity” or “similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. An “unrelated” or “non-homologous” sequence shares less than 40%identity, though preferably less than 25%identity, with one of the sequences of the present disclosure.
[0072] A polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) has a certain percentage (for example, 60 %, 65 %, 70 %, 75 %, 80 %, 85 %, 90 %, 95 %, 98 %or 99 %) of “sequence identity” to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences.
[0073] The term “an equivalent nucleic acid or polynucleotide” refers to a nucleic acid having a nucleotide sequence having a certain degree of homology, or sequence identity, with the nucleotide sequence of the nucleic acid or complement thereof. A homolog of a double stranded nucleic acid is intended to include nucleic acids having a nucleotide sequence which has a certain degree of homology with or with the complement thereof. In one aspect, homologs of nucleic acids are capable of hybridizing to the nucleic acid or complement thereof. Likewise, “an equivalent polypeptide” refers to a polypeptide having a certain degree of homology, or sequence identity, with the amino acid sequence of a reference polypeptide. In some aspects, the sequence identity is at least about 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99%. In some aspects, the equivalent polypeptide or polynucleotide has one, two, three, four or five addition, deletion, substitution and their combinations thereof as compared to the reference polypeptide or polynucleotide. In some aspects, the equivalent sequence retains the activity (e.g., epitope-binding) or structure (e.g., salt-bridge) of the reference sequence.
[0074] As used herein, an “antibody” or “antigen-binding polypeptide” refers to a polypeptide or a polypeptide complex that specifically recognizes and binds to an antigen. An antibody can be a whole antibody and any antigen binding fragment or a single chain thereof. Thus the term “antibody” includes any protein or peptide containing molecule that includes at least a portion of an immunoglobulin molecule having biological activity of binding to the antigen. Examples of such include, but are not limited to a complementarity determining region (CDR) of a heavy or light chain or a ligand binding portion thereof, a heavy chain or light chain variable region, a heavy chain or light chain constant region, a framework (FR) region, or any portion thereof, or at least one portion of a binding protein.
[0075] The terms “antibody fragment” or “antigen-binding fragment” , as used herein, is a portion of an antibody such as F (ab') 2, F (ab) 2, Fab', Fab, Fv, scFv and the like. Regardless of structure, an antibody fragment binds with the same antigen that is recognized by the intact antibody. The term “antibody fragment” includes aptamers, spiegelmers, and diabodies. The term “antibody fragment” also includes any synthetic or genetically engineered protein that acts like an antibody by binding to a specific antigen to form a complex.
[0076] A “single-chain variable fragment” or “scFv” refers to a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins. In some aspects, the regions are connected with a short linker peptide of ten to about 25 amino acids. The linker can be rich in glycine for flexibility, as well as serine or threonine for solubility, and can either connect the N-terminus of the VH with the C-terminus of the VL, or vice versa. This protein retains the specificity of the original immunoglobulin, despite removal of the constant regions and the introduction of the linker. ScFv molecules are known in the art and are described, e.g., in US patent 5, 892, 019.
[0077] The term antibody encompasses various broad classes of polypeptides that can be distinguished biochemically. Those skilled in the art will appreciate that heavy chains are classified as gamma, mu, alpha, delta, or epsilon (γ, μ, α, δ, ε) with some subclasses among them (e.g., γl-γ4) . It is the nature of this chain that determines the “class” of the antibody as IgG, IgM, IgA IgG, or IgE, respectively. The immunoglobulin subclasses (isotypes) e.g., IgG1, IgG2, IgG3, IgG4, IgG5, etc. are well characterized and are known to confer functional specialization. Modified versions of each of these classes and isotypes are readily discernable to the skilled artisan in view of the instant disclosure and, accordingly, are within the scope of the instant disclosure. All immunoglobulin classes are clearly within the scope of the present disclosure, the following discussion will generally be directed to the IgG class of immunoglobulin molecules. With regard to IgG, a standard immunoglobulin molecule includes two identical light chain polypeptides of molecular weight approximately 23, 000 Daltons, and two identical heavy chain polypeptides of molecular weight 53, 000-70, 000. The four chains are typically joined by disulfide bonds in a “Y” configuration wherein the light chains bracket the heavy chains starting at the mouth of the “Y” and continuing through the variable region.
[0078] Antibodies, antigen-binding polypeptides, variants, or derivatives thereof of the disclosure include, but are not limited to, polyclonal, monoclonal, multispecific, human, humanized, primatized, or chimeric antibodies, single chain antibodies, epitope-binding fragments, e.g., Fab, Fab'a nd F (ab') 2, Fd, Fvs, single-chain Fvs (scFv) , single-chain antibodies, disulfide-linked Fvs (sdFv) , fragments including either a VK or VH domain, fragments produced by a Fab expression library, and anti-idiotypic (anti-Id) antibodies (including, e.g., anti-Id antibodies to LIGHT antibodies disclosed herein) . Immunoglobulin or antibody molecules of the disclosure can be of any type (e.g., IgG, IgE, IgM, IgD, IgA, and IgY) , class (e.g., IgG1, IgG2, IgG3, IgG4, IgAl and IgA2) or subclass of immunoglobulin molecule.
[0079] Light chains are classified as either kappa or lambda (K, λ) . Each heavy chain class may be bound with either a kappa or lambda light chain. In general, the light and heavy chains are covalently bonded to each other, and the “tail” portions of the two heavy chains are bonded to each other by covalent disulfide linkages or non-covalent linkages when the immunoglobulins are generated either by hybridomas, B cells or genetically engineered host cells. In the heavy chain, the amino acid sequences run from an N-terminus at the forked ends of the Y configuration to the C-terminus at the bottom of each chain.
[0080] Both the light and heavy chains are divided into regions of structural and functional homology. The terms “constant” and “variable” are used functionally. In this regard, it will be appreciated that the variable domains of both the light (VK) and heavy (VH) chain portions determine antigen recognition and specificity. Conversely, the constant domains of the light chain (CK) and the heavy chain (CH1, CH2 or CH3) confer important biological properties such as secretion, transplacental mobility, Fc receptor binding, complement binding, and the like. By convention the numbering of the constant region domains increases as they become more distal from the antigen-binding site or amino-terminus of the antibody. The N-terminal portion is a variable region and at the C-terminal portion is a constant region; the CH3 and CK domains actually include the carboxy-terminus of the heavy and light chain, respectively.
[0081] As indicated above, the variable region allows the antibody to selectively recognize and specifically bind epitopes on antigens. That is, the VK domain and VH domain, or subset of the complementarity determining regions (CDRs) , of an antibody combine to form the variable region that defines a three-dimensional antigen-binding site. This quaternary antibody structure forms the antigen-binding site present at the end of each arm of the Y. More specifically, the antigen-binding site is defined by three CDRs on each of the VH and VK chains (i.e., CDR-H1, CDR-H2, CDR-H3, CDR-L1, CDR-L2 and CDR-L3) . In some instances, e.g., certain immunoglobulin molecules derived from camelid species or engineered based on camelid immunoglobulins, a complete immunoglobulin molecule may consist of heavy chains only, with no light chains. See, e.g., Hamers-Casterman et al., Nature 363: 446-448 (1993) .
[0082] In naturally occurring antibodies, the six “complementarity determining regions” or “CDRs” present in each antigen-binding domain are short, non-contiguous sequences of amino acids that are specifically positioned to form the antigen-binding domain as the antibody assumes its three-dimensional configuration in an aqueous environment. The remainder of the amino acids in the antigen-binding domains, referred to as “framework” regions, show less inter-molecular variability. The framework regions largely adopt a β-sheet conformation and the CDRs form loops which connect, and in some cases form part of, the β-sheet structure. Thus, framework regions act to form a scaffold that provides for positioning the CDRs in correct orientation by inter-chain, non-covalent interactions. The antigen-binding domain formed by the positioned CDRs defines a surface complementary to the epitope on the immunoreactive antigen. This complementary surface promotes the non-covalent binding of the antibody to its cognate epitope. The amino acids including the CDRs and the framework regions, respectively, can be readily identified for any given heavy or light chain variable region by one of ordinary skill in the art, since they have been precisely defined (see “Sequences of Proteins of Immunological Interest, ” Kabat, E., et al., U.S. Department of Health and Human Services, (1983) ; and Chothia and Lesk, J. MoI. Biol., 196: 901-917 (1987)) .
[0083] In the case where there are two or more definitions of a term which is used and / or accepted within the art, the definition of the term as used herein is intended to include all such meanings unless explicitly stated to the contrary. A specific example is the use of the term “complementarity determining region” ( “CDR” ) to describe the non-contiguous antigen combining sites found within the variable region of both heavy and light chain polypeptides. This particular region has been described by Kabat et al., U.S. Dept. of Health and Human Services, “Sequences of Proteins of Immunological Interest” (1983) and by Chothia et al., J. MoI. Biol. 196: 901-917 (1987) , which are incorporated herein by reference in their entireties. The CDR definitions according to Kabat and Chothia include overlapping or subsets of amino acid residues when compared against each other. Nevertheless, application of either definition to refer to a CDR of an antibody or variants thereof is intended to be within the scope of the term as defined and used herein. The appropriate amino acid residues which encompass the CDRs as defined by each of the above cited references are set forth in the table below as a comparison. The exact residue numbers which encompass a particular CDR will vary depending on the sequence and size of the CDR. Those skilled in the art can routinely determine which residues include a particular CDR given the variable region amino acid sequence of the antibody.
[0084] Kabat et al. also defined a numbering system for variable domain sequences that is applicable to any antibody. One of ordinary skill in the art can unambiguously assign this system of “Kabat numbering” to any variable domain sequence, without reliance on any experimental data beyond the sequence itself. As used herein, “Kabat numbering” refers to the numbering system set forth by Kabat et al., U.S. Dept. of Health and Human Services, “Sequence of Proteins of Immunological Interest” (1983) .
[0085] Antibodies disclosed herein may be from any animal origin including birds and mammals. Preferably, the antibodies are human, murine, donkey, rabbit, goat, guinea pig, camel, llama, horse, or chicken antibodies. In another embodiment, the variable region may be condricthoid in origin (e.g., from sharks) .
[0086] As used herein, the term “heavy chain constant region” includes amino acid sequences derived from an immunoglobulin heavy chain. A polypeptide including a heavy chain constant region includes at least one of: a CH1 domain, a hinge (e.g., upper, middle, and / or lower hinge region) domain, a CH2 domain, a CH3 domain, or a variant or fragment thereof. For example, an antigen-binding polypeptide for use in the disclosure may include a polypeptide chain including a CH1 domain; a polypeptide chain including a CH1 domain, at least a portion of a hinge domain, and a CH2 domain; a polypeptide chain including a CH1 domain and a CH3 domain; a polypeptide chain including a CH1 domain, at least a portion of a hinge domain, and a CH3 domain, or a polypeptide chain including a CH1 domain, at least a portion of a hinge domain, a CH2 domain, and a CH3 domain. In another embodiment, a polypeptide of the disclosure includes a polypeptide chain including a CH3 domain. Further, an antibody for use in the disclosure may lack at least a portion of a CH2 domain (e.g., all or part of a CH2 domain) . As set forth above, it will be understood by one of ordinary skill in the art that the heavy chain constant region may be modified such that they vary in amino acid sequence from the naturally occurring immunoglobulin molecule.
[0087] The heavy chain constant region of an antibody disclosed herein may be derived from different immunoglobulin molecules. For example, a heavy chain constant region of a polypeptide may include a CH1 domain derived from an IgG1 molecule and a hinge region derived from an IgG3 molecule. In another example, a heavy chain constant region can include a hinge region derived, in part, from an IgG1 molecule and, in part, from an IgG3 molecule. In another example, a heavy chain portion can include a chimeric hinge derived, in part, from an IgG1 molecule and, in part, from an IgG4 molecule.
[0088] As used herein, the term “light chain constant region” includes amino acid sequences derived from antibody light chain. Preferably, the light chain constant region includes at least one of a constant kappa domain or constant lambda domain.
[0089] A “light chain-heavy chain pair” refers to the collection of a light chain and heavy chain that can form a dimer through a disulfide bond between the CL domain of the light chain and the CH1 domain of the heavy chain.
[0090] As previously indicated, the subunit structures and three-dimensional configuration of the constant regions of the various immunoglobulin classes are well known. As used herein, the term “VH domain” includes the amino terminal variable domain of an immunoglobulin heavy chain and the term “CH1 domain” includes the first (most amino terminal) constant region domain of an immunoglobulin heavy chain. The CH1 domain is adjacent to the VH domain and is amino terminal to the hinge region of an immunoglobulin heavy chain molecule.
[0091] As used herein the term “CH2 domain” includes the portion of a heavy chain molecule that extends, e.g., from about residue 244 to residue 360 of an antibody using conventional numbering schemes (residues 244 to 360, Kabat numbering system; and residues 231-340, EU numbering system; see Kabat et al., U.S. Dept. of Health and Human Services, “Sequences of Proteins of Immunological Interest” (1983) . The CH2 domain is unique in that it is not closely paired with another domain. Rather, two N-linked branched carbohydrate chains are interposed between the two CH2 domains of an intact native IgG molecule. It is also well documented that the CH3 domain extends from the CH2 domain to the C-terminal of the IgG molecule and includes approximately 108 residues.
[0092] As used herein, the term “hinge region” includes the portion of a heavy chain molecule that joins the CH1 domain to the CH2 domain. This hinge region includes approximately 25 residues and is flexible, thus allowing the two N-terminal antigen-binding regions to move independently. Hinge regions can be subdivided into three distinct domains: upper, middle, and lower hinge domains (Roux et al., J. Immunol 161: 4083 (1998)) .
[0093] As used herein the term “disulfide bond” includes the covalent bond formed between two sulfur atoms. The amino acid cysteine includes a thiol group that can form a disulfide bond or bridge with a second thiol group. In most naturally occurring IgG molecules, the CH1 and CK regions are linked by a disulfide bond and the two heavy chains are linked by two disulfide bonds at positions corresponding to 239 and 242 using the Kabat numbering system (position 226 or 229, EU numbering system) .
[0094] As used herein, the term “chimeric antibody” will be held to mean any antibody wherein the immunoreactive region or site is obtained or derived from a first species and the constant region (which may be intact, partial or modified in accordance with the instant disclosure) is obtained from a second species. In certain embodiments the target binding region or site will be from a non-human source (e.g., mouse or primate) and the constant region is human.
[0095] As used herein, “percent humanization” is calculated by determining the number of framework amino acid differences (i.e., non-CDR difference) between the humanized domain and the germline domain, subtracting that number from the total number of amino acids, and then dividing that by the total number of amino acids and multiplying by 100.
[0096] By “specifically binds” or “has specificity to, ” it is generally meant that an antibody binds to an epitope via its antigen-binding domain, and that the binding entails some complementarity between the antigen-binding domain and the epitope. According to this definition, an antibody is said to “specifically bind” to an epitope when it binds to that epitope, via its antigen-binding domain more readily than it would bind to a random, unrelated epitope. The term “specificity” or “binding specificity” is used herein to qualify the relative affinity by which a certain antibody binds to a certain epitope. For example, antibody “A” may be deemed to have a higher specificity for a given epitope than antibody “B, ” or antibody “A” may be said to bind to epitope “C” with a higher specificity than it has for related epitope “D. ”
[0097] “Binding affinity” as used herein, it is one of the most important indicators for evaluating how strong of a small molecule binds to its targets. As of an antibody, binding affinity is determined by the non-covalent interactions (such as hydrogen bonds, van der Waals forces, and electrostatic interactions) between the antigen-binding site on the antibody (the paratope) and the specific part of the antigen (the epitope) it recognizes and binds to. Measurement of affinity includes, Isothermal Titration Calorimetry (ITC) , Surface Plasmon Resonance (SPR) , Microscale Thermophoresis (MST) , Bio-Layer Interferometry (BLI) , Differential Scanning Fluorometry (DSF) , Fluorescence Polarization (FP) and Nuclear Magnetic Resonance (NMR) . The binding affinity can also be determined by flow cytometry.
[0098] The binding affinity is usually quantitatively expressed as the equilibrium dissociation constant (Kd) , which is the concentration of antigen at which half of the antibody binding sites are occupied in a given condition, and is defined as the ratio k off / k on . A lower Kd value indicates a higher binding affinity, meaning the antibody binds more tightly to its antigen. High-affinity antibodies are particularly important in the immune response because they are more effective at neutralizing pathogens and targeting them for destruction by other components of the immune system.
[0099] As used herein, the terms “treat” or “treatment” refer to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) an undesired physiological change or disorder, such as the progression of cancer. Beneficial or desired clinical results include, but are not limited to, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total) , whether detectable or undetectable. “Treatment” can also mean prolonging survival as compared to expected survival if not receiving treatment. Those in need of treatment include those already with the condition or disorder as well as those prone to have the condition or disorder or those in which the condition or disorder is to be prevented.
[0100] By “subject” or “individual” or “animal” or “patient” or “mammal, ” is meant any subject, particularly a mammalian subject, for whom diagnosis, prognosis, or therapy is desired. Mammalian subjects include humans, domestic animals, farm animals, and zoo, sport, or pet animals such as dogs, cats, guinea pigs, rabbits, rats, mice, horses, cattle, cows, and so on.
[0101] As used herein, phrases such as “to a patient in need of treatment” or “a subject in need of treatment” includes subjects, such as mammalian subjects, that would benefit from administration of an antibody or composition of the present disclosure used, e.g., for detection, for a diagnostic procedure and / or for treatment. Anti-Nectin-4 Antibody
[0102] In accordance with one embodiment of the present disclosure, therefore, provided are antibodies and antigen-binding fragments thereof that are able to bind to Nectin-4.
[0103] Exemplary antibodies include those listed in Table 1A (e.g., P001-C12, P003-C2, P003-E5, P004-E8, P006-F1, P008-C8) . Also included are those that include the same CDRs as illustrated herein. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as those illustrated here, and those that compete with the instantly disclosed in binding to Nectin-4. Table 1A. VH / VL sequence of the mutant antibodies Table 1B. CDR Sequences
[0104] In one embodiment, the CDRs are those of P001-C12, as exemplified in Table 1B. In one embodiment, the VH CDR1 includes the amino acid sequence of SEQ ID NO: 153 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR2 includes the amino acid sequence of SEQ ID NO: 154 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR3 includes the amino acid sequence of SEQ ID NO: 155 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR1 includes the amino acid sequence of SEQ ID NO: 150 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR2 includes the amino acid sequence of SEQ ID NO: 151 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, and the VL CDR3 includes the amino acid sequence of SEQ ID NO: 152 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof.
[0105] Also provided, in some embodiments, are those that include the same CDRs as P001-C12. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as P001-C12, and those that compete with any of them in binding to Nectin-4.
[0106] In some embodiments, the heavy chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 2, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence of SEQ ID NO: 2.
[0107] In some embodiments, the light chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 1, or a peptide having at least 80% (e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 1.
[0108] In some embodiments, the heavy chain variable region includes the amino acid sequence of SEQ ID NO: 2 and the light chain variable region includes the amino acid sequence of any one of SEQ ID NO: 1.
[0109] In one embodiment, the CDRs are those of P003-C2, as exemplified in Table 1B. In one embodiment, the VH CDR1 includes the amino acid sequence of SEQ ID NO: 159 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR2 includes the amino acid sequence of SEQ ID NO: 160 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR3 includes the amino acid sequence of SEQ ID NO: 161 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR1 includes the amino acid sequence of SEQ ID NO: 156 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR2 includes the amino acid sequence of SEQ ID NO: 157 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, and the VL CDR3 includes the amino acid sequence of SEQ ID NO: 158 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof.
[0110] Also provided, in some embodiments, are those that include the same CDRs as P003-C2. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as P003-C2, and those that compete with any of them in binding to Nectin-4.
[0111] In some embodiments, the heavy chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 4, or a peptide having at least 80% (e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence of SEQ ID NO: 4.
[0112] In some embodiments, the light chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 3, or a peptide having at least 80% (e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 3.
[0113] In some embodiments, the heavy chain variable region includes the amino acid sequence of SEQ ID NO: 4 and the light chain variable region includes the amino acid sequence of any one of SEQ ID NO: 3.
[0114] In one embodiment, the CDRs are those of P003-E5, as exemplified in Table 1B. In one embodiment, the VH CDR1 includes the amino acid sequence of SEQ ID NO: 165 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR2 includes the amino acid sequence of SEQ ID NO: 166 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR3 includes the amino acid sequence of SEQ ID NO: 167 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR1 includes the amino acid sequence of SEQ ID NO: 162 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR2 includes the amino acid sequence of SEQ ID NO: 163 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, and the VL CDR3 includes the amino acid sequence of SEQ ID NO: 164 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof.
[0115] Also provided, in some embodiments, are those that include the same CDRs as P003-E5. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as P003-E5, and those that compete with any of them in binding to Nectin-4.
[0116] In some embodiments, the heavy chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 6, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence of SEQ ID NO: 6.
[0117] In some embodiments, the light chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 5, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 5.
[0118] In some embodiments, the heavy chain variable region includes the amino acid sequence of SEQ ID NO: 6 and the light chain variable region includes the amino acid sequence of any one of SEQ ID NO: 5.
[0119] In one embodiment, the CDRs are those of P004-E8, as exemplified in Table 1B. In one embodiment, the VH CDR1 includes the amino acid sequence of SEQ ID NO: 13 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR2 includes the amino acid sequence of SEQ ID NO: 14 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR3 includes the amino acid sequence of SEQ ID NO: 15 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR1 includes the amino acid sequence of SEQ ID NO: 16 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR2 includes the amino acid sequence of SEQ ID NO: 17 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, and the VL CDR3 includes the amino acid sequence of SEQ ID NO: 18 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof.
[0120] Also provided, in some embodiments, are those that include the same CDRs as P004-E8. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as P004-E8, and those that compete with any of them in binding to Nectin-4.
[0121] In some embodiments, the heavy chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 8, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence of SEQ ID NO: 8.
[0122] In some embodiments, the light chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 7, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 7.
[0123] In some embodiments, the heavy chain variable region includes the amino acid sequence of SEQ ID NO: 8 and the light chain variable region includes the amino acid sequence of any one of SEQ ID NO: 7.
[0124] In some embodiments, the binding affinity of P004-E8 antibody is adenosine-containing compound (ANP) dependent, as illustrated in Example 2. Unlike the benchmark Enfortumab, which is ANP insensitive, the activity of P004-E8 antibody is ANP sensitive. In the presence of ANP (such as ATP / AMP / ADP) , P004-E8 exhibits prominent activity such as binding to Nectin-4, antibody internalization, and in vivo anti-tumor efficacy, even linked with a payload.
[0125] The term “ANP” as used herein means any adenosine-containing compounds, such as ATP, AMP, cAMP or ADP, or the mixture thereof. The adenosine triphosphate (ATP) , adenosine monophosphate (AMP) and adenosine diphosphate (ADP) can be interconverted to each other and plays an important role in many cellular metabolic processes. Adenosine is a ubiquitous extracellular signaling molecule with essential functions in human physiology. Due to the widespread expression of adenosine receptors, it has far-reaching effects across many different organ systems. Adenosine is a naturally occurring endogenous purine nucleoside composed of an adenine molecule attached to a ribose sugar moiety (ribofuranose) via a beta-N9-glycosidic bond (6-amino-9-β-d-ribofuranosyl-9-H-purine) . It is the nucleoside base of both ATP and the signaling molecule cyclic adenosine monophosphate (cAMP) . Adenosine is rapidly transported into vascular endothelial cells and erythrocytes where it is catabolized by adenosine deaminase to inosine. It is (re) phosphorylated by adenine kinase forming adenosine monophosphate (AMP) , which is incorporated into the high-energy phosphate pool.
[0126] In certain embodiments, the ANP is present at a concentration of at least about 10 μM (e.g., at least about 20 μM, 30 μM, 40 μM, 50 μM, 60 μM, 70 μM, 80 μM, 90 μM, 100 μM, 150 μM, 200 μM, 250 μM, 300 μM, 350 μM, 400 μM, 450 μM, 500 μM, 600 μM, 700 μM, 800 μM, 900 μM, 1000 μM, or higher) .
[0127] In certain embodiments, with the presence of the ANP, the P004-E8 antibody or the variants thereof of the present disclosure can bind to the human Nectin-4 with the binding specificity at least about 1-fold (e.g., at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 50-fold, at least about 100-fold, at least about 150-fold, at least about 200-fold, or more) higher than the absence of the ANP.
[0128] In certain embodiments, with the presence of the ANP at the concentration of 300 μM, the P004-E8 antibody or the variants of the present disclosure can bind to the human Nectin-4 with an EC50 less than 1x10-6 M, 1x10-7 M, 1x10-8 M, 1x10-9 M, 1x10-10 M, or 1x10-11 M, as measured by FACS.
[0129] In one embodiment, the CDRs are those of P006-F1, as exemplified in Table 1B. In one embodiment, the VH CDR1 includes the amino acid sequence of SEQ ID NO: 171 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR2 includes the amino acid sequence of SEQ ID NO: 172 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR3 includes the amino acid sequence of SEQ ID NO: 173 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR1 includes the amino acid sequence of SEQ ID NO: 168 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR2 includes the amino acid sequence of SEQ ID NO: 169 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, and the VL CDR3 includes the amino acid sequence of SEQ ID NO: 170 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof.
[0130] Also provided, in some embodiments, are those that include the same CDRs as P006-F1. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as P006-F1, and those that compete with any of them in binding to Nectin-4.
[0131] In some embodiments, the heavy chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 10, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence of SEQ ID NO: 10.
[0132] In some embodiments, the light chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 9, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 9.
[0133] In some embodiments, the heavy chain variable region includes the amino acid sequence of SEQ ID NO: 10 and the light chain variable region includes the amino acid sequence of any one of SEQ ID NO: 9.
[0134] In one embodiment, the CDRs are those of P008-C8, as exemplified in Table 1B. In one embodiment, the VH CDR1 includes the amino acid sequence of SEQ ID NO: 177 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR2 includes the amino acid sequence of SEQ ID NO: 178 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR3 includes the amino acid sequence of SEQ ID NO: 179 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR1 includes the amino acid sequence of SEQ ID NO: 174 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR2 includes the amino acid sequence of SEQ ID NO: 175 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, and the VL CDR3 includes the amino acid sequence of SEQ ID NO: 176 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof.
[0135] Also provided, in some embodiments, are those that include the same CDRs as P008-C8. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as P008-C8, and those that compete with any of them in binding to Nectin-4.
[0136] In some embodiments, the heavy chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 12, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence of SEQ ID NO: 12.
[0137] In some embodiments, the light chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 11, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 11.
[0138] In some embodiments, the heavy chain variable region includes the amino acid sequence of SEQ ID NO: 12 and the light chain variable region includes the amino acid sequence of any one of SEQ ID NO: 11.
[0139] It is appreciated that CDRs can be modified to include those having one, two or three amino acid addition, deletion and / or substitutions. In some embodiments, the CDRs and / or adjacent framework region are mutated by substitution to improve the binding affinity to the target antigen. Such as the CDR sequences are as in Table 1C below, which is based on the CDR sequences of P004-E8.
[0140] In certain embodiments, one or more amino acid residues in the heavy chain variable region of P004-E8 are selected from the group consisting of: D27, N32, N37, R56, D62, Y63, A64, S69 and I115 are mutated by substitution. In certain embodiments, one or more amino acid residues in the light chain variable region of P004-E8 are selected from the group consisting of: G28, S52, S53 and S96 are mutated by substitution. Table 1C. CDR sequences of P004-E8 antibody
[0141] Exemplary mutations are summarized in Table 1D. Table 1D. CDR mutations of P004-E8
[0142] The CDR combinations and heavy chain and light chain variable regions so generated are illustrated in Table 3A in Example 2. Also provided, in some embodiments, are those that include the same CDRs as the mutants in Table 1D. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as the antibodies in Table 3A-3B, and those that compete with any of them in binding to Nectin-4. In some embodiments, the disclosed heavy chain and light chain variable regions include those that have at least 80% (e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence as illustrated in Table 3A-3B.
[0143] All the generated P004E08 mutants (e.g., mut01-mut62) exhibit ANP (ATP) dependent antibody activity. Among them, the P004E08-mut40 reveals much improved binding affinity to human Nectin-4 (comparable with Enfortumab) in the presence of ANP. While in the absence of ANP, P004E08-mut40 has much lower binding affinity (Example 2) .
[0144] For example, the sequences of CDR and variable regions of P004-E8-mut40 are summarized in Table 1E. Table 1E. Sequences of CDR and variable regions of P004-E8-mut40
[0145] In one embodiment, the CDRs and variable regions are those of P004-E8-mut40, as exemplified in Table 1E. In one embodiment, the VH CDR1 includes the amino acid sequence of SEQ ID NO: 22 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR2 includes the amino acid sequence of SEQ ID NO: 34 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR3 includes the amino acid sequence of SEQ ID NO: 15 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR1 includes the amino acid sequence of SEQ ID NO: 56 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR2 includes the amino acid sequence of SEQ ID NO: 60 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, and the VL CDR3 includes the amino acid sequence of SEQ ID NO: 18 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof.
[0146] Also provided, in some embodiments, are those that include the same CDRs as P004-E8-mut40. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as P004-E8-mut40, and those that compete with any of them in binding to Nectin-4.
[0147] In some embodiments, the heavy chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 93, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence of SEQ ID NO: 93.
[0148] In some embodiments, the light chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 67, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 67.
[0149] In some embodiments, the heavy chain variable region includes the amino acid sequence of SEQ ID NO: 93 and the light chain variable region includes the amino acid sequence of any one of SEQ ID NO: 67.
[0150] In certain embodiments, one or more post-translation modification (PTM) residues in the heavy chain variable region of P004E08-mut40 are selected from the group consisting of: N32, S33, S105, and S106 are removed by substitution. Exemplary mutations are summarized in Table 1F. Table 1F. PTM removal in the CDRs of P004-E8-mut40
[0151] The CDR combinations and heavy chain and light chain variable regions so generated are illustrated in Table 5 in Example 2. Also provided, in some embodiments, are those that include the same CDRs as the mutants in Table 1F. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as the antibodies in Table 1F and Table 5, and those that compete with any of them in binding to Nectin-4. In some embodiments, the disclosed heavy chain variable regions include those that have at least 80% (e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence as illustrated in Table 5.
[0152] For example, the sequences of CDR and variable regions of P004-E8-mut40-PTM12 are summarized in Table 1G. Table 1G. Sequences of CDR and variable regions of P004-E8-mut40-PTM12
[0153] In one embodiment, the CDRs are those of P004-E8-mut40-PTM12, as exemplified in Table 1G. In one embodiment, the VH CDR1 includes the amino acid sequence of SEQ ID NO: 27 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR2 includes the amino acid sequence of SEQ ID NO: 34 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VH CDR3 includes the amino acid sequence of SEQ ID NO: 53 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR1 includes the amino acid sequence of SEQ ID NO: 56 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, the VL CDR2 includes the amino acid sequence of SEQ ID NO: 60 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof, and the VL CDR3 includes the amino acid sequence of SEQ ID NO: 18 or a variant thereof having one, two, or three deletions, additions, substitutions or the combinations thereof.
[0154] Also provided, in some embodiments, are those that include the same CDRs as P004-E8-mut40-PTM. In some embodiments, the disclosed antibodies and fragments include those that bind to the same epitope as P004-E8-mut40-PTM, and those that compete with any of them in binding to Nectin-4.
[0155] In some embodiments, the heavy chain variable region includes an amino acid sequence selected from the group consisting of SEQ ID NO: 121, or a peptide having at least 80%(e.g., at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%) sequence identity to an amino acid sequence of SEQ ID NO: 121.
[0156] In some embodiments, the heavy chain variable region includes the amino acid sequence of SEQ ID NO: 121 and the light chain variable region includes the amino acid sequence of any one of SEQ ID NO: 67.
[0157] In accordance with one embodiment of the present disclosure, provided is an antibody or antigen-binding fragments thereof that includes the heavy chain and light chain variable domains with the CDR regions disclosed herein, as well as their biological equivalents.
[0158] In some embodiments, the substitutions can be conservative substitutions. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art, including basic side chains (e.g., lysine, arginine, histidine) , acidic side chains (e.g., aspartic acid, glutamic acid) , uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine) , nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan) , beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine) . Thus, a nonessential amino acid residue in an immunoglobulin polypeptide is preferably replaced with another amino acid residue from the same side chain family. In another embodiment, a string of amino acids can be replaced with a structurally similar string that differs in order and / or composition of side chain family members.
[0159] Non-limiting examples of conservative amino acid substitutions are provided in the table below, where a similarity score of 0 or higher indicates conservative substitution between the two amino acids. Table A. Amino Acid Similarity Matrix Table B. Conservative Amino Acid Substitutions
[0160] It will also be understood by one of ordinary skill in the art that antibodies as disclosed herein may be modified such that they vary in amino acid sequence from the naturally occurring binding polypeptide from which they were derived. For example, a polypeptide or amino acid sequence derived from a designated protein may be similar, e.g., have a certain percent identity to the starting sequence, e.g., it may be 60%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99%identical to the starting sequence.
[0161] According to specific embodiments, the antibody is a humanized antibody. Humanized forms of non-human (e.g., murine) antibodies are chimeric molecules of immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab’ , F (ab’ ) 2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues form a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity. In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also include residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will include substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will include at least a portion of an immunoglobulin constant region (Fc) , typically that of a human immunoglobulin (Jones et al., Nature, 321: 522-525 (1986) ; Riechmann et al., Nature, 332: 323-329 (1988) ; and Presta, Curr. Op. Struct. Biol., 2: 593-596 (1992)) .
[0162] In certain embodiments, the antibody provided herein is a F (ab') 2 fragment, a F (ab) 2 fragment, a Fab'fragment, a Fab fragment, a single-chain variable fragment (scFv) , or a Fv fragment.
[0163] In certain embodiments, the antibody and antigen-binding fragment thereof targeting Nectin-4 provided herein, or the multifunctional molecule targeting Nectin-4 and a second antigen provided herein further includes a heavy chain constant region, a light chain constant region, an Fc region, or the combination thereof.
[0164] The Fc region can be engineered to enhance or eliminate effector function. IgG antibodies can induce direct anti-tumor effects by way of indirect anti-tumor effects via the Fc-mediated effector functions that engage other immune cells or killer mechanisms. “Effector functions” or “antibody effector functions” as used herein refer to biological activities attributable to the binding of Fc region of an antibody to its effectors such as C1 complex and Fc receptor (FcγRIIa or FcγRIIIa) . Exemplary effector functions include: complement dependent cytotoxicity (CDC) induced by interaction of antibodies and C1q on the C1 complex; antibody-dependent cell-mediated cytotoxicity (ADCC) induced by binding of Fc region of an antibody to Fc receptor on an effector cell; and antibody dependent cell mediated phagocytosis (ADCP) , where nonspecific cytotoxic cells that express FcγRs recognize bound antibody on a target cell and subsequently cause phagocytosis of the target cell. Among the four IgG subclasses, IgG1 and IgG3 induce the strongest Fc-effector functions. However, since IgG1 has the longest half-life and is more stable than IgG3, most therapeutic antibodies with Fc-mediated functions are of IgG1 isotype.
[0165] In certain embodiments, the antibody or antigen-binding fragment thereof provided herein is of an isotype of IgG1, IgG2, IgG3 or IgG4. In certain embodiments, the antibody or antigen-binding fragment thereof is of an isotype of IgG1. In certain embodiments, the antibody or antigen-binding fragment thereof is of human IgG1.
[0166] IgG2 and IgG4 isotypes have significantly lower binding affinity to FcγRs. Recent evidence suggests that the IgG2 isotype is not completely devoid of effector function, whereas the IgG4 isotype can undergo in vivo Fab arm exchange leading to bispecific antibody and off-target effects.
[0167] In certain embodiments, the Fc region of the antibodies provided herein is engineered to enhance the effector function, such as ADCC or CDC. Various methods (mainly Fc mutations) can be found to enhance the Fc-mediated effector function, such as those described in the PCT publications WO2007024249A2 and WO2011044368A1, which are incorporated herein by reference in their entireties. In certain embodiments, the Fc region is engineered to include S298A / E333A / K334A mutations in human IgG1. Such Fc mutation combination is reported to enhance binding to FcγRIIIa, thus enhancing ADCC (See Shields R.L. et al, J. Biol. Chem 276: 6591-6604 (2001) ) . Multi-functional Molecules
[0168] Multi-functional molecules that include an antibody or antigen-binding fragment specific to Nectin-4, such as those disclosed herein, and one or more antibody or antigen-binding fragment having specificity to a second antigen. In certain embodiments, the multi-functional molecules are bifunctional molecules.
[0169] In some embodiments, the second antigen is a protein expressed on an immune cell, such as a T cell, a B cell, a monocyte, a macrophage, a neutrophil, a dendritic cell, a phagocyte, a natural killer cell, an eosinophil, a basophil, and a mast cell.
[0170] In some embodiments, the second antigen is CD3, CD47, PD1, LAG3, TIM3, CTLA4, VISTA, CSFR1, A2AR, CD73, CD39, CD40, CEA, HER2, CMET, 4-1BB, OX40, SIRPA CD16, CD28, ICOS, CTLA4, BTLA, TIGIT, HVEM, CD27, EGFR, VEGFR, or VEGF.
[0171] In some embodiments, the second antigen is a protein expressed on tumor cells, such as a tumor antigen.
[0172] In some embodiments, the tumor antigen includes, but is not limited to MUC16, ENPP3, ROR1, SLC7A11, SLC34A2, DLL3, B7H4, EPHA2, CD318, CLDN6, HER2, Nectin-4, EGFR, 5T4, GPC3, MSLN, FAP, CLDN18.2, PD-L1, PD-L2, ILT-4, B7-H3, CS1, CD19, CD2, CD4, CD5, CD7, CD8, CD20, CD22, CD25, CD28, CD30, CD33, CD38, CD44V6, CD47, CD52, CD56, CD57, CD58, CD79b, CD81, CD123, CD133, CD151, CD171, CD276, CLL1, BCMA, VEGFR-2, GPC3, PMSA, CEACAM6, c-Met, ErbB3, HER3, ErbB4 / HER-4, IGF1R, GD2, O-acetyl GD2, O-acetyl GD3, GHRHR, GHR, Flt1, KDR, Flt4, Flt3, CEA, BTLA, TGFBR1, TGFBR2, TGFBR1, IL6R, gp130, Lewis, TNFR1, TNFR2, PD1, PSCA, HVEM, PSMA, RANK, TNFRSF4, TWEAK-R, LTPR, LIFRP, LRP5, MUC1, PTCH1, WT-1, Robo1, Frizzled, Notch-1-4, APRIL, MAGE3, Folate receptor α, Folate receptor β, GPC2, CD70, BAFF-R, or TROP-2.
[0173] In some embodiments, the second antigen is a tumor associated antigen. Chimeric Antigen Receptors (CAR)
[0174] The present disclosure provides a chimeric antigen receptor (CAR) or an engineered T cell receptors (TCRs) comprising the anti-Nectin-4 antigen-binding fragment thereof provided herein.
[0175] CARs and TCRs are genetically engineered receptors. These engineered receptors can be readily inserted into and expressed by immune cells, such as T cells. A CAR can recognize a specific antigen and, when bound to that antigen, activate the immune cell to attack and destroy the cell bearing that antigen. When these antigens exist on tumor cells, an immune cell that expresses the CAR can target and kill the tumor cell.
[0176] CARs can be engineered to bind to an antigen (such as a cell-surface antigen) by incorporating an antigen binding molecule that interacts with that targeted antigen. Preferably, the antigen binding molecule is an antibody fragment thereof, and more preferably one or more single chain antibody fragment ( “scFv” ) . An scFv is a single chain antibody fragment having the variable regions of the heavy and light chains of an antibody linked together. It will be appreciated that the antigen binding molecule is typically contained within the extracellular portion of the CAR such that it is capable of recognizing and binding to the antigen of interest. Bispecific and multispecific CARs are contemplated within the scope of the invention, with specificity to more than one target of interest.
[0177] An example CAR includes, in addition to the antigen binding molecule, a transmembrane domain and an activation domain. In some embodiments, the CAR can further include an extracellular domain between the antigen binding molecule and the transmembrane domain. The extracellular domain may comprise a hinge domain. In some embodiments, the CAR can further include a co-stimulatory domain. A. Antigen Binding Molecule
[0178] The antigen binding portion of the CAR of the instant disclosure can be an antibody or antigen binding fragment (in particular a scFv) targeting human Nectin-4, as disclosed herein. B. Extracellular Domain and Transmembrane Domain Extracellular Domains
[0179] Chimeric antigen receptors may comprise an extracellular domain. Extracellular domains of particular use in this invention may be derived from (i.e., comprise) all or some of CD28, OX-40, 4-1BB / CD137, CD2, CD7, CD27, CD30, CD40, programmed death-1 (PD-1) , inducible T cell costimulator (ICOS) , lymphocyte function-associated antigen-1 (LFA-1, CD1-1a / CD18) , CD3 gamma, CD3 delta, CD3 epsilon, CD247, CD276 (B7-H3) , LIGHT, (TNFSF14) , NKG2C, Ig alpha (CD79a) , DAP-10, Fc gamma receptor, MHC class 1 molecule, TNF receptor proteins, an Immunoglobulin protein, IgG1, IgG2, IgG3, IgG4, IgA, IgD, IgE, IgM, cytokine receptor, integrins, Signaling Lymphocytic Activation Molecules (SLAM proteins) , activating NK cell receptors, BTLA, a Toll ligand receptor, ICAM-1, B7-H3, CDS, ICAM-1, GITR, BAFFR, LIGHT, HVEM (LIGHTR) , KIRDS2, SLAMF7, NKp80 (KLRF1) , NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL-2R beta, IL-2R gamma, IL-7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, TNFR2, TRANCE / RANKL, DNAM1 (CD226) , SLAMF4 (CD244, 2B4) , CD84, CD96 (Tactile) , CEACAM1, CRT AM, Ly9 (CD229) , CD160 (BY55) , PSGL1, CD100 (SEMA4D) , CD69, SLAMF6 (NTB-A, Lyl08) , SLAM (SLAMF1, CD150, IPO-3) , BLAME (SLAMF8) , SELPLG (CD162) , LTBR, LAT, GADS, SLP-76, PAG / Cbp, CD19a, a ligand that specifically binds with CD83, or any combination thereof. The extracellular domain may be derived either from a natural or from a synthetic source.
[0180] Extracellular domains often comprise the hinge portion, sometimes referred to as the “spacer” region. A variety of hinges can be employed in accordance with the invention, including portions or derivatives of the molecules as listed above. In certain embodiments, the hinge portion is a hinge region of IgG1, IgG2, IgG3, IgG4, IgA, IgD, IgE, IgM, CD28, or CD8 alpha, any truncation thereof, or any combination thereof. Transmembrane Domain
[0181] The CAR can be designed with a transmembrane domain that is fused to the extracellular domain of the CAR. It can similarly be fused to the intracellular domain of the CAR. In some instances, the transmembrane domain can be selected or modified by amino acid substitution to avoid binding of such domains to the transmembrane domains of the same or different surface membrane proteins to minimize interactions with other members of the receptor complex. The transmembrane domain may be derived either from a natural or from a synthetic source. Where the source is natural, the domain may be derived from any membrane-bound or transmembrane protein.
[0182] Non-limiting examples of such proteins include CD28, CD8alpha, CD8beta, 4-1BB, B7-H3, BAFFR, BLAME, BTLA, CD100, CD103, CD11a, CD11b, CD11c, CD11d, CD160, CD18, CD19, CD19a, CD2, CD247, CD27, CD276, CD29, CD3 delta, CD3 epsilon, CD3 gamma, CD30, CD4, CD40, CD49a, CD49D, CD49f, CD69, CD7, CD79a, CD84, CD96, CDS, CEACAM1, CRT AM, DAP-10, DNAM1, Fc gamma receptor, GADS, GITR, HVEM, IA4, ICAM-1, ICOS, IL-2R beta, IL-2R gamma, IL-7R alpha, ITGA4, ITGA6, ITGAD, ITGAE, ITGAL, ITGAM, ITGAX, ITGB1, ITGB2, ITGB7, KIRDS2, LAT, LFA-1, LIGHT, LTBR, Ly9, NKG2C, NKG2D, NKp30, NKp44, NKp46, NKp80, OX-40, PAG, PD-1, PSGL1, SELPLG, SLAM, SLAMF4, SLAMF6, SLAMF7, SLP-76, TNFR2, TNFSF14, TRANCE, VLA1, VLA-6, a cytokine receptor, a MHC class 1 molecule, a SLAM protein, a TNF receptor protein, a Toll ligand receptor, an activating NK cell receptor, an immunoglobulin protein, and an integrin. C. Intracellular Domain---Costimulatory Domain and Activation Domain
[0183] The intracellular (cytoplasmic) domain of the engineered T cells of the invention can provide activation of at least one of the normal effector functions of the immune cell. Effector function of a T cell, for example, may refer to cytolytic activity or helper activity, including the secretion of cytokines. The intracellular domain may include at least an activation domain. The intracellular domain can also include one or more costimulatory domains. Costimulatory Domains
[0184] A “costimulatory domain” as used herein refers to a molecule that provides a signal which mediates a T cell response, including, but not limited to, proliferation, activation, differentiation, and the like. Costimulatory domain can provide a signal in addition to the primary signal provided by an activating molecule as described herein.
[0185] Chimeric antigen receptors may incorporate costimulatory (signaling) domains to increase their potency. See U.S. Patent Nos. 7,741,465, and 6,319,494, as well as Krause et al. and Finney et al. (supra) , Song et al., Blood 119: 696-706 (2012) ; Kalos et al., Sci Transl. Med. 3: 95 (2011) ; Porter et al., N. Engl. J. Med. 365: 725-33 (2011) , and Gross et al., Annu. Rev. Pharmacol. Toxicol. 56: 59–83 (2016) . For example, CD28 is a costimulatory protein found naturally on T-cells. A variety of costimulatory molecules are set forth herein, but it will be appreciated that additional costimulatory molecules are also included within the scope of this invention.
[0186] It will be appreciated that suitable costimulatory domains within the scope of the invention include the signaling domain (or other suitable portion) of CD28, OX-40, 4-1BB / CD137, CD2, CD7, CD27, CD30, CD40, Programmed Death-1 (PD-1) , inducible T cell costimulator (ICOS) , lymphocyte function-associated antigen-1 (LFA-1, CD1-1a / CD18) , CD3 gamma, CD3 delta, CD3 epsilon, CD247, CD276 (B7-H3) , LIGHT, (TNFSF14) , NKG2C, Ig alpha (CD79a) , DAP-10, Fc gamma receptor, MHC class 1 molecule, TNF receptor proteins, an Immunoglobulin protein, cytokine receptor, integrins, Signaling Lymphocytic Activation Molecules (SLAM proteins) , activating NK cell receptors, BTLA, a Toll ligand receptor, ICAM-1, B7-H3, CDS, ICAM-1, GITR, BAFFR, LIGHT, HVEM (LIGHTR) , KIRDS2, SLAMF7, NKp80 (KLRF1) , NKp44, NKp30, NKp46, CD19, CD4, CD8alpha, CD8beta, IL-2R beta, IL-2R gamma, IL-7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD1 1d, ITGAE, CD103, ITGAL, CD1 la, LFA-1, ITGAM, CD1 1b, ITGAX, CD1 1c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, TNFR2, TRANCE / RANKL, DNAM1 (CD226) , SLAMF4 (CD244, 2B4) , CD84, CD96 (Tactile) , CEACAM1, CRT AM, Ly9 (CD229) , CD160 (BY55) , PSGL1, CD100 (SEMA4D) , CD69, SLAMF6 (NTB-A, Ly108) , SLAM (SLAMF1, CD150, IPO-3) , BLAME (SLAMF8) , SELPLG (CD162) , LTBR, LAT, GADS, SLP-76, PAG / Cbp, CD19a, a ligand that specifically binds with CD83, or fragments or any combination thereof. It will be appreciated that additional costimulatory molecules, or fragments thereof, not listed above are within the scope of the invention. Activating Domains
[0187] An “activation domain” refers to a molecule on a T cell, e.g., the TCR / CD3 complex that specifically binds with a cognate stimulatory ligand present on an antigen present cell. Suitable activating molecules are described herein. The activation domain is part of the intracellular (cytoplasmic) portion of a CAR. The intracellular domain of a CAR can provide activation of at least one of the normal effector functions of the immune cell. Effector function of a T cell, for example, may refer to cytolytic activity or helper activity, including the secretion of cytokines.
[0188] CD3 is an element of the T cell receptor on native T cells, and has been shown to be an important intracellular activating element in CARs. In a preferred embodiment, the CD3 is CD3 zeta, CD3 epsilon, CD3 delta, or CD3 gamma. CAR-Immune Cells
[0189] Immune cells enclosing a CAR of the present disclosure or one or more polynucleotides encoding the CAR are also provided.
[0190] As described, an engineered receptors can be inserted into and expressed by an immune cell, such as T cell, which can recognize a specific antigen and, when bound to that antigen, activate the immune cell to attack and destroy the cell bearing that antigen.
[0191] Various types of immune cells have been tested for expressing CARs. Non-limiting examples include T cells, NK cells, macrophages and monocytes. A T cell, in some embodiment, may be an alpha beta T cell. In some embodiments, the T cell is a gamma delta T cell. Antibody-Drug Conjugates
[0192] The present disclosure provides antibody-drug conjugates including the antibodies or antigen-binding fragments thereof, or the multifunctional molecules provided herein.
[0193] The antibody-drug conjugate includes the antibody or the antigen-binding fragment thereof conjugated to a drug (or payload) via a linker. The drugs can be connected to the antibodies via a cysteine residue or a lysine residue on the antibodies. The ADC can be constructed via chemical approach such as stochastic conjugation on pre-existing lysine or cysteine residues via appropriate coupling reactions, such as amide coupling (of lysine) and sulfhydryl coupling (of cysteine) . An active carboxylic acid ester (when available in the linker) is used to connect payloads to lysine residues on the antibody. The primary amine in Lys easily reacts with N-hydroxysuccinimide (NHS) esters introduced into the linker, forming a stable amide. A typical IgG1 antibody molecule has roughly 90 Lys residues, of which approximately 30 can be modified for conjugation, implying that between 1 and 30 payloads can be covalently coupled to the antibody. As for cysteine, after reduction, the disulfide bond could transform to expose free cysteine residues which are accessible for coupling reactions, such as Michael additions, disulfide formation, and a-halo carbonyl alkylations.
[0194] The ADC can also be constructed via enzymatic approach such as site-specific conjugation. The site-specific conjugation includes introduction of engineered reactive cysteine residues, disulfide re-bridging, unnatural amino acids, enzyme-assisted ligation, or glycan remodeling, glycoconjugation or click chemistry. Details of the methods of conjugation can be found in the art, such as Fu et al., Signal Transduction and Targeted Therapy 7: 93 (2022) .
[0195] The drug-antibody ratio (DAR) for an ADC can be more than 2, more than 4, more than 6, more than 8, more than 10, more than 16, more than 20, or more than 30. In certain embodiments, the drug-antibody ratio (DAR) can be from 1-30, from 1-20, from 1-16, from 1-10, from 1-8, such as, 4-8, or 2-4. In certain embodiments, the drug-antibody ratio (DAR) can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 20, or 30. In certain embodiments, the DAR is homogenous.
[0196] The linker contained in the drug-linker compound can be non-cleavable linker and cleavable linker. The cleavable linker mainly includes enzyme-cleavable linkers and chemically sensitive linkers.
[0197] Non-cleavable linkers consist of stable bonds that resist proteolytic degradation and ensure greater plasma stability. The mechanism of action of non-cleavable linkers is based on the internalization of the ADC complex followed by degradation of the mAb component in the lysosome, resulting in the release of a cytotoxic drug that kills tumor cells. They do not unleash cytotoxic agents at off-target sites and thus do not harm healthy cells. Non-cleavable linkers are divided into two groups, namely thioether or maleimidocaproyl (MC) . Examples of the non-cleavable linkers include, but not limited to, 4-maleimidomethyl cyclohexane-1-carboxylate (MCC) , succinimidyl-4- (N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) , maleimidecaproyl (MC) , and p-carboxycyclo hexylmethylmaleimide.
[0198] Cleavable linkers mainly include chemically sensitive linkers those are usually cleaved by environmental differences (such as redox potential, pH) and enzyme-cleavable linkers which are cleaved by specific enzymes in response to extracellular and intracellular environments.
[0199] Chemically sensitive linkers include, but not limited to, types of pH-sensitive linkers, and glutathione-sensitive disulfide linkers (See Khongorzul et al., Mol Cancer Res; 18 (1) (2020)) .
[0200] PH-sensitive linkers are a group of linkers that are sensitive to the acidic environment but are stable in the alkaline environment such as systemic circulation, such as hydrozone based linker. One successful example of ADC design using pH-sensitive linker is the IMMU-110 which is composed of a humanized anti-CD74 mAb conjugated to doxorubicin via acid-labile hydrazone.
[0201] Glutathione-sensitive disulfide linkers utilize difference in reduction potential in the cytoplasm in contrast to plasma. A high concentration of glutathione can be found in cancer cells than normal cells. Glutathione-sensitive linkers are stable in the blood flow and particularly cleaved by the elevated intracellular concentration of glutathione in the tumor cell, releasing the active drugs at the tumor sites from the nontoxic prodrugs (see supra) .
[0202] Enzyme-cleavable linkers include, but not limited to, peptide based linkers, β-glucuronide based linkers and phosphate based linkers.
[0203] Peptide based linkers, also known as protease-sensitive linkers, are the most commonly used ADC linkers. These linkers can be cleaved by specific proteases extracellularly and / or intracellularly. For intracellular cleavage, as tumor cells exhibit high expression of lysosomal proteases like cathepsin B compared with the normal cells, therefore, proteases–sensitive peptide linker ADCs are selectively bound to and transformed into cancerous cells through receptor mediated endocytosis. The peptide linkers are stable in the systemic circulation and only unleash the drug in the target cells (see supra) . Examples are Valine-citrulline (VC or Val-Cit) , Valine-alanine (VA) , phenylalanine-lysine (PL) , and glycine-glycine-phenylalanine-glycine (GGFG) .
[0204] β-glucuronide based linkers are recognized and hydrolyzed by β-glucuronidase or β-galactosidase for the drug release, while the β-glucuronidase and β-galactosidase are enriched in lysosomes and tumor necrotic regions. β-glucuronidase is inactive at physiologic pH (blood circulation) and active at lysosomal pH. Such selective site of action allows for the cleavage of the glycosidic linkage of the β-glucuronidase–sensitive β-glucuronide linker, thereby enabling the selective release of cytotoxic payloads (see supra) .
[0205] Phosphate based linkers are a class of enzyme-cleavable linkers expressed exclusively to target enzymes in the lysosomal compartment. These linkers target pyrophosphatase and acid phosphatase enzymes, which hydrolyze pyrophosphates and terminal monophosphates into their respective alcohols.
[0206] Moieties that can be introduced as part of the linkers to facilitate the drug-linker connection or antibody-linker connection include maleimidocaproyl, maleimide-caproyl (MC) moiety, maleimide-methylene-cyclohexyl carbonyl moiety spacer, maleimide propoyl (MP) , para-aminobenzylcarbamate (PAB) spacer, para-aminobenzyloxycarbamoyl (PABC) spacer, aminomethoxy methylenecarbonyl (-NH-CH2-O-CH2-CO-) spacer, 4- (4’ -acetylphenoxy) butanoic acid moiety, acylhydrazide (–CO–NH–NH2) and thiol (–SH) moieties, Lys-PABC, PEG chain and PEG8.
[0207] Examples of the linkers include, but not limited to succinimidyl-4- (N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) , sulfo-SMCC, MC-VC-PABC, CL2A, MC-GGFG, MC, MC-PEG8-GGFG, MC-PEG8-GGFG-PAB, or MP-PEG8-VA-PABC.
[0208] The drug or payload can be a cytotoxin, a therapeutic peptide or polypeptide.
[0209] The peptide or polypeptide may be any peptide or polypeptide which has therapeutic properties, for example antinociceptive, antidiabetes, antitumor or antiviral activity. Additionally, or alternatively, the drug preferably includes an amine group, a thiol group, or a carboxylic acid group, as these types of groups provide ideal sites for conjugation of the drug with the linker of the present disclosure. Examples of biologics drug are pseudomonas aeruginosa exotoxin PE38, diphtheria toxin, staphylococcus aureus enterotoxin A / E-120, shigatoxin, ricin, and urease.
[0210] The cytotoxin are activated after release from ADC inside the cytoplasm of tumor cells and are able to destroy the tumor cells. There are two main classes of cytotoxins that can be used in the ADC designs: microtubule-disrupting agents (such as auristatins and maytansinoids) and DNA-damaging agents (such as calicheamicins, duocarmycin, and doxorubicin) . Examples included, but not limited to includes auristatins, maytansinoids, benzodiazepines, tubulysins, duocarmycin, calicheamicins, exatecans, irinotecans (SN38) , doxorubicin, anthracycline, pyrrolobenzodiazepenes (PBD) , TLR agonist, and STING agonists.
[0211] Auristatins are synthetic antineoplastic agents derived from the natural product dolastatin 10. They block the tubulin polymerization process resulting in cell-cycle arrest and apoptosis. Examples include monomethyl auristatin E (MMAE) and monomethyl auristatin F (MMAF) .
[0212] Maytansinoids are isolated from the maytansine, a benzoansamacrolide. These drugs inhibit tubulin polymerization. Examples include DM1 and DM4.
[0213] Calicheamicins are a class of enediyne antitumor antibiotics derived from the bacterium Micromonospora echinospora. Calicheamicin recognizes the minor groove of DNA and halts DNA replication resulting in mitotic arrest and cell death. One example is N-acetyl-calicheamicin, a derivative of calicheamicin.
[0214] Duocarmycin is a natural product derivative extracted from the bacteria Streptomyces strains. Duocarmycins are another class of DNA minor groove–binding alkylating agents. This class of drugs shows its action by binding to the minor groove of DNA and subsequently cause irreparable alkylation of DNA that disrupts the nucleic acid architecture and structural integrity.
[0215] Doxorubicin shows its action by intercalation of DNA that inhibits DNA synthesis. One example is IMMU-110.
[0216] Exatecans are synthetic derivatives of the natural cytotoxin, camptothecin, isolated from the Chinese tree Camptotheca acuminata. Like camptothecin, exatecan binds to the topoisomerase 1-DNA complex, preventing DNA re-ligation which results in the accumulation of DNA strand breaks and ultimately leads to cell death. Examples of exatecans are DX-8951f and DXd. 7-ethyl-10-hydroxycamptothecin (SN-38) is also a derivative of camptothecin.
[0217] Further examples of the cytotoxin includes, without limitation, macrocyclic ketone analogue, topoisomerase inhibitors, tublysin A, camptothecin, DGN462, Amberstatin269, anthramycin, SG3199 / SCX, 700DX, TLR7 / 8 agonist, diABZI STING agonist-2.
[0218] The cytotoxin may be a chemotherapeutic agent which may be categorized by their mechanism of action into, for example, the following groups: - anti-metabolites / anti-cancer agents such as pyrimidine analogs floxuridine, capecitabine, and cytarabine; - purine analogs, folate antagonists, and related inhibitors; - antiproliferative / antimitotic agents including natural products such as vinca alkaloid (vinblastine, vincristine) and microtubule such as taxane (paclitaxel, docetaxel) , vinblastin, nocodazole, epothilones, vinorelbine and epipodophyllotoxins (etoposide, teniposide) ; - DNA damaging agents such as actinomycin, amsacrine, busulfan, carboplatin, chlorambucil, cisplatin, cyclophosphamide dactinomycin, daunorubicin, doxorubicin, epirubicin, iphosphamide, melphalan, merchlorethamine, mitomycin, mitoxantrone, nitrosourea, procarbazine, taxol, taxotere, teniposide, etoposide, and triethylenethiophosphoramide; - antibiotics such as dactinomycin, daunorubicin, doxorubicin, idarubicin, anthracyclines, mitoxantrone, bleomycins, plicamycin (mithramycin) , and mitomycin; - enzymes such as L-asparaginase which systemically metabolizes L-asparagine and deprives cells which do not have the capacity to synthesize their own asparagine; - antiplatelet agents; - antiproliferative / antimitotic alkylating agents such as nitrogen mustards cyclophosphamide and analogs (melphalan, chlorambucil, hexamethylmelamine, and thiotepa) , alkyl nitrosoureas (carmustine) and analogs, streptozocin, and triazenes (dacarbazine) ; - antiproliferative / antimitotic antimetabolites such as folic acid analogs (methotrexate) ; - platinum coordination complexes (cisplatin, oxiloplatinim, and carboplatin) , procarbazine, hydroxyurea, mitotane, and aminoglutethimide; - hormones, hormone analogs (estrogen, tamoxifen, goserelin, bicalutamide, and nilutamide) , and aromatase inhibitors (letrozole and anastrozole) ; - anticoagulants such as heparin, synthetic heparin salts, and other inhibitors of thrombin; - fibrinolytic agents such as tissue plasminogen activator, streptokinase, urokinase, aspirin, dipyridamole, ticlopidine, and clopidogrel; - antimigratory agents; - antisecretory agents (breveldin) ; - immunosuppressives tacrolimus, sirolimus, azathioprine, and mycophenolate; - compounds (TNP-470, genistein) and growth factor inhibitors (vascular endothelial growth factor inhibitors and fibroblast growth factor inhibitors) ; - angiotensin receptor blockers, nitric oxide donors; - anti-sense oligonucleotides; - antibodies such as trastuzumab and rituximab; - cell cycle inhibitors and differentiation inducers such as tretinoin; - inhibitors, topoisomerase inhibitors (doxorubicin, daunorubicin, dactinomycin, eniposide, epirubicin, etoposide, idarubicin, irinotecan, mitoxantrone, topotecan, and irinotecan) , and corticosteroids (cortisone, dexamethasone, hydrocortisone, methylprednisolone, prednisone, and prednisolone) ; - growth factor signal transduction kinase inhibitors; - dysfunction inducers; - toxins such as Cholera toxin, ricin, Pseudomonas exotoxin, Bordetella pertussis adenylate cyclase toxin, diphtheria toxin, and caspase activators; - and chromatin.
[0219] Further examples of chemotherapeutic agents include: - alkylating agents such as thiotepa and cyclophosphamide - alkyl sulfonates such as busulfan, improsulfan, and piposulfan; - aziridines such as benzodopa, carboquone, meturedopa, and uredopa; - emylerumines and memylamelamines including alfretamine, triemylenemelamine, triethylenephosphoramide, triethylenethiophosphoramide, and trimemylolomelamine; - acetogenins, especially bullatacin and bullatacinone; - a camptothecin, including synthetic analog topotecan; - bryostatin; - callystatin; - CC-1065, including its adozelesin, carzelesin, and bizelesin synthetic analogs; - cryptophycins, particularly cryptophycin 1 and cryptophycin 8; - dolastatin; - duocarmycin, including the synthetic analogs KW-2189 and CBI-TMI; - eleutherobin; - pancratistatin; - a sarcodictyin; - spongistatin; - nitrogen mustards such as chlorambucil, chlornaphazine, cyclophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, and uracil mustard; - nitrosoureas such as carmustine, chlorozotocin, foremustine, lomustine, nimustine, and ranimustine; - antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammaII and calicheamicin phiI1) , dynemicin including dynemicin A, bisphosphonates such as clodronate, an esperamicin, neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromomophores, aclacinomycins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, carrninomycin, carzinophilin, chromomycins, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin, and deoxydoxorubicin) , epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, porfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, and zorubicin; - anti-metabolites such as methotrexate and 5-fluorouracil (5-FU) ; - folic acid analogs such as demopterin, methotrexate, pteropterin, and trimetrexate; - purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, and thioguanine; - pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, and floxuridine; - androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, and testolactone; - anti-adrenals such as aminoglutethimide, mitotane, and trilostane; - folic acid replinishers such as frolinic acid; - trichothecenes, especially T-2 toxin, verracurin A, roridin A, and anguidine; - taxoids such as paclitaxel and docetaxel - platinum analogs such as cisplatin and carboplatin; - aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; hestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elformthine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; leucovorin; lonidamine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidamol; nitracrine; pentostatin; phenamet; pirarubicin; losoxantrone; fluoropyrimidine; folinic acid; podophyllinic acid; 2-ethylhydrazide; procarbazine; polysaccharide-K (PSK) ; razoxane; rhizoxin; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2, 2', 2” -tricUorotriemylamine; urethane; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside ( “Ara-C” ) ; cyclophosphamide; thiopeta; chlorambucil; gemcitabine 6-thioguanine; mercaptopurine; methotrexate; vinblastine; platinum; etoposide (VP-16) ; ifosfamide; mitroxantrone; vancristine; vinorelbine novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeoloda; ibandronate; CPT-11; topoisomerase inhibitor RFS 2000; difluoromethylornithine (DFMO) ; retinoids such as retinoic acid; capecitabine; FOLFIRI (fluorouracil, leucovorin, and irinotecan) ; - and pharmaceutically acceptable salts, acids, or derivatives of any of the above.
[0220] In certain embodiments of the present disclosure, the drug and the linker form a drug-linker compound. In certain embodiments, the drug-linker compound can be ozogamicin (derivatives of calicheamicin, see U.S. Pat. No. 5773001) , vedotin (MC-VC-PABC-MMAE, see U.S. Pat. No. 7659241) , mafodotin (MC-MMAF, see U.S. Pat. No. 7498298) , emtansine (SMCC-DM1, U.S. Pat. No. 5208020) , deruxtecan (MC-GGFG-DXd, see U.S. Pat. No. 10195288) , govitecan (CL2A-SN38, see U.S. Pat. No. 8420086) , or tesirine (MP-PEG8-VA-PABC-SG3199 / SCX, see U.S. Pat. No. 9889207) , which are hereby incorporated by reference in their entirety.
[0221] Further examples of the drug-linker compound includes pasudotox (PE38) , soravtansine (DM4) , ravtansine (DM4) , and mertansine (DM1) .
[0222] In certain embodiments of the present disclosure, the drug-linker compound includes LM-D01 having Formula I
[0223] In certain embodiments of the present disclosure, the drug-linker compound includes LM-D02 having Formula II
[0224] In certain embodiments of the present disclosure, the drug-linker compound includes LM-D03 having Formula III
[0225] In certain embodiments of the present disclosure, the drug-linker compound includes vedotin having Formula IV
[0226] In certain embodiments of the present disclosure, the drug-linker compound includes deruxtecan having Formula V
[0227] In certain embodiments of the present disclosure, the drug-linker compound includes ozogamicin having Formula VI
[0228] In certain embodiments of the present disclosure, the drug-linker compound includes mafodotin having Formula VII
[0229] In certain embodiments of the present disclosure, the drug-linker compound includes emtansine having Formula VIII
[0230] In certain embodiments of the present disclosure, the drug-linker compound includes govitecan having Formula IX
[0231] In certain embodiments of the present disclosure, the drug-linker compound includes tesirine having Formula X Polynucleotides Encoding the Antibodies and Methods of Preparing the Antibodies
[0232] The present disclosure also provides isolated polynucleotides or nucleic acid molecules encoding the antibodies, variants or derivatives thereof of the disclosure. The polynucleotides of the present disclosure may encode the entire heavy and light chain variable regions of the antigen-binding polypeptides, variants or derivatives thereof on the same polynucleotide molecule or on separate polynucleotide molecules. Additionally, the polynucleotides of the present disclosure may encode portions of the heavy and light chain variable regions of the antigen-binding polypeptides, variants or derivatives thereof on the same polynucleotide molecule or on separate polynucleotide molecules.
[0233] Methods of making antibodies are well known in the art and described herein. In certain embodiments, both the variable and constant regions of the antigen-binding polypeptides of the present disclosure are fully human. Fully human antibodies can be made using techniques described in the art and as described herein. For example, fully human antibodies against a specific antigen can be prepared by administering the antigen to a transgenic animal which has been modified to produce such antibodies in response to antigenic challenge, but whose endogenous loci have been disabled. Exemplary techniques that can be used to make such antibodies are described in U.S. patents: 6,150,584; 6,458,592; 6,420,140 which are incorporated by reference in their entireties. Compositions
[0234] The present disclosure also provides pharmaceutical compositions. Such compositions include an effective amount of an antibody or ADC, and an acceptable carrier. In some embodiments, the composition further includes a second anticancer agent (e.g., an immune checkpoint inhibitor) .
[0235] In a specific embodiment, the term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. Further, a “pharmaceutically acceptable carrier” will generally be a non-toxic solid, semisolid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type.
[0236] The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a preferred carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents such as acetates, citrates or phosphates. Antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; and agents for the adjustment of tonicity such as sodium chloride or dextrose are also envisioned. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Examples of suitable pharmaceutical carriers are described in Remington's Pharmaceutical Sciences by E.W. Martin, incorporated herein by reference. Such compositions will contain a therapeutically effective amount of the antigen-binding polypeptide, preferably in purified form, together with a suitable amount of carrier so as to provide the form for proper administration to the patient. The formulation should suit the mode of administration. The parental preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
[0237] In an embodiment, the composition is formulated in accordance with routine procedures as a pharmaceutical composition adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic such as lignocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachet indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.
[0238] The antibodies or ADCs of the disclosure can be formulated as neutral or salt forms. Pharmaceutically acceptable salts include those formed with anions such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with cations such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc. Treatment Methods
[0239] As described herein, the antibodies or antigen-binding fragments thereof, multifunctional molecules, antibody-drug conjugates of the present disclosure may be used in certain treatment and diagnostic methods.
[0240] The present disclosure is further directed to antibody-based therapies which involve administering the antibodies or antigen-binding fragments thereof, multifunctional molecules, or the ADCs of the disclosure to a patient such as an animal, a mammal, and a human for treating one or more of the disorders or conditions described herein.
[0241] The antibodies or antigen-binding fragments thereof, multifunctional molecules, or the ADCs of the disclosure can also be used to treat or inhibit cancer. In some embodiments, the cancer cells in the patient express or overexpress Nectin-4. Inhibition of Nectin-4 has been shown to be useful for treating the tumors.
[0242] Accordingly, in some embodiments, provided are methods for treating a cancer in a patient in need thereof. The method, in one embodiment, entails administering to the patient an effective amount of an antibody of the present disclosure. In some embodiments, at least one of the cancer cells (e.g., stromal cells) in the patient over-express Nectin-4.
[0243] In some embodiments, the cell was isolated from the cancer patient him-or her-self. In some embodiments, the cell was provided by a donor or from a cell bank. When the cell is isolated from the cancer patient, undesired immune reactions can be minimized.
[0244] Non-limiting examples of cancers include bladder cancer, breast cancer, colorectal cancer, endometrial cancer, esophageal cancer, head and neck cancer, kidney cancer, leukemia, liver cancer, lung cancer, lymphoma, melanoma, pancreatic cancer, prostate cancer, and thyroid cancer. In some embodiments, the cancer is one or more of gastric, pancreatic, esophageal, ovarian, and lung cancers.
[0245] Additional diseases or conditions associated with increased cell survival, that may be treated, prevented, diagnosed and / or prognosed with the antibodies or variants, or derivatives thereof of the disclosure include, but are not limited to, progression, and / or metastases of malignancies and related disorders such as leukemia (including acute leukemias (e.g., acute lymphocytic leukemia, acute myelocytic leukemia (including myeloblastic, promyelocytic, myelomonocytic, monocytic, and erythroleukemia) ) and chronic leukemias (e.g., chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia) ) , polycythemia vera, lymphomas (e.g., Hodgkin's disease and non-Hodgkin's disease) , multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumors including, but not limited to, sarcomas and carcinomas such as fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyo sarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, melanoma, neuroblastoma and retinoblastoma.
[0246] A specific dosage and treatment regimen for any particular patient will depend upon a variety of factors, including the particular antibodies or ADCs used, the patient's age, body weight, general health, sex, and diet, and the time of administration, rate of excretion, drug combination, and the severity of the particular disease being treated. Judgment of such factors by medical caregivers is within the ordinary skill in the art. The amount will also depend on the individual patient to be treated, the route of administration, the type of formulation, the characteristics of the compound used, the severity of the disease, and the desired effect. The amount used can be determined by pharmacological and pharmacokinetic principles well known in the art.
[0247] Methods of administration of the antibodies or ADCs or compositions include but are not limited to intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, and oral routes. The antigen-binding polypeptides or compositions may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc. ) and may be administered together with other biologically active agents. Thus, pharmaceutical compositions containing the antigen-binding polypeptides of the disclosure may be administered orally, rectally, parenterally, intracistemally, intravaginally, intraperitoneally, topically (as by powders, ointments, drops or transdermal patch) , bucally, or as an oral or nasal spray.
[0248] The term “parenteral” as used herein refers to modes of administration which include intravenous, intramuscular, intraperitoneal, intrasternal, subcutaneous and intra-articular injection and infusion.
[0249] Administration can be systemic or local. In addition, it may be desirable to introduce the antibodies of the disclosure into the central nervous system by any suitable route, including intraventricular and intrathecal injection; intraventricular injection may be facilitated by an intraventricular catheter, for example, attached to a reservoir, such as an Ommaya reservoir. Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent.
[0250] It may be desirable to administer the antibodies or ADCs or compositions of the disclosure locally to the area in need of treatment; this may be achieved by, for example, and not by way of limitation, local infusion during surgery, topical application, e.g., in conjunction, with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers. Preferably, when administering a protein, including an antibody, of the disclosure, care must be taken to use materials to which the protein does not absorb.
[0251] The amount of the antibodies or ADCs or compositions of the disclosure which will be effective in the treatment, inhibition and prevention of an immune or malignant disease, disorder or condition can be determined by standard clinical techniques. In addition, in vitro assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the seriousness of the disease, disorder or condition, and should be decided according to the judgment of the practitioner and each patient's circumstances. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems.
[0252] As a general proposition, the dosage administered to a patient of the antibodies or ADCs of the present disclosure is typically 0.1 mg / kg to 100 mg / kg of the patient's body weight, between 0.1 mg / kg and 20 mg / kg of the patient's body weight, or 1 mg / kg to 10 mg / kg of the patient's body weight. Generally, human antibodies have a longer half-life within the human body than antibodies from other species due to the immune response to the foreign polypeptides. Thus, lower dosages of human antibodies and less frequent administration is often possible. Further, the dosage and frequency of administration of the antibodies or ADCs of the disclosure may be reduced by enhancing uptake and tissue penetration (e.g., into the brain) of the antibodies or ADCs by modifications such as, for example, lipidation.
[0253] In an additional embodiment, the antibodies or ADCs or compositions of the disclosure are administered in combination with cytokines. Cytokines that may be administered with the compositions of the disclosure include, but are not limited to, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-10, IL-12, IL-13, IL-15, anti-CD40, CD40L, and TNF-α.
[0254] In additional embodiments, the antibodies or ADCs or compositions of the disclosure are administered in combination with other therapeutic or prophylactic regimens, such as, for example, radiation therapy. Diagnostic Methods
[0255] Over-expression of Nectin-4 is observed in certain tumor samples, and patients having Nectin-4-over-expressing cells are likely responsive to treatments with the anti-Nectin-4 antibodies of the present disclosure. Accordingly, the antibodies of the present disclosure can also be used for diagnostic and prognostic purposes.
[0256] A sample that preferably includes a cell can be obtained from a patient, which can be a cancer patient or a patient desiring diagnosis. The cell be a cell of a tumor tissue or a tumor block, a blood sample, a urine sample or any sample from the patient. Upon optional pre-treatment of the sample, the sample can be incubated with an antibody of the present disclosure under conditions allowing the antibody to interact with a Nectin-4 protein potentially present in the sample. Methods such as ELISA can be used, taking advantage of the anti-Nectin-4 antibody, to detect the presence of the Nectin-4 protein in the sample.
[0257] Presence of the Nectin-4 protein in the sample (optionally with the amount or concentration) can be used for diagnosis of cancer, as an indication that the patient is suitable for a treatment with the antibody, or as an indication that the patient has (or has not) responded to a cancer treatment. For a prognostic method, the detection can be done at once, twice or more, at certain stages, upon initiation of a cancer treatment to indicate the progress of the treatment. EXAMPLES Example 1: Monoclonal antibodies against human Nectin-4 1.1 Antibody generation
[0258] A number of anti-human Nectin-4 antibodies were generated (Table 2A) . Table 2A. Sequences of variable regions of the anti-human Nectin-4 antibodies 1.2 Binding dependency of ATP
[0259] The anti-Nectin-4 antibodies were tested by flow cytometry for the binding to human Nectin 4 expressing CHOK1 cells in the presence or absence of ANP (300μM) (ATP / ADP / AMP) . As illustrated in FIG. 1A and Table 2B, all the tested anti-Nectin-4 antibodies showed binding affinity to the hNectin-4-CHOK1 cell independent of ANP. Table 2B. Binding affinity to human Nectin 4 expressing CHOK1 cells
[0260] However, P004-E8 showed ANP dependent binding to hNectin-4-CHOK1 cell, but with a weak binding affinity (FIG. 1B) . The control Enfortumab showed ANP independent binding to human Nectin-4 (Table 2C) . Table 2C. Binding affinity to human Nectin 4 expressing CHOK1 cells Example 2. Improved binding Affinity of the anti-Nectin-4 antibodies
[0261] As can been see from Example 1, P004-E08 showed ANP (ATP) dependent activity, but with weak binding affinity to human Nectin-4. Therefore, mutations are made to the CDRs or adjacent regions to improve the binding affinity. 2.1 Antibody variants.
[0262] Antibody variants of P004-E8 were generated to improve the binding affinity to the human Nectin 4. Table 3A. Mutation strategy to P004-E8 Table 3B. Sequences of variable regions of P004-E8 mutants
[0263] As can be seen from FIG. 2A-2B and 2H-2K and Table 4A-4B and 4H-4K, some variants greatly improved the binding affinity (FACS) to human Nectin-4, while some variants showed slight improvements (see FIG. 2C-2G and Table 2C-2G) . Among the variants, P004E08-mut40 showed similar binding affinity to the benchmark antibody Enfortumab (NEC4BMK003) . Table 4A. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4B. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4C. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4D. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4E. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4F. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4G. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4H. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4I. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4J. Binding affinity to human Nectin 4 expressing CHOK1 cells Table 4K. Binding affinity to human Nectin 4 expressing CHOK1 cells 2.2 Removal of Post-Translational Modification (PTM)
[0264] P004-E8-mut40 antibodies with affinity improvement by removal of PTM were further generated. Table 5. Sequences of heavy chain variable regions of P004-E8-mut40 after PTM removal
[0265] As can be seen in FIG. 3 and Table 6, all the antibodies with PTM showed comparable binding affinity as Enfortumab to the NCI-H322 cell (non-small cell carcinoma) in the presence of ANP. Table 6. Binding affinity to tumor cells 2.3 Antibody internalization
[0266] The antibody internalization of P004E08-mut40-PTM12 and Enfortumab in the human Nectin-4 expressing cells or tumor cells (NCI-H2122, NCI-H322, MDA-MB-468) was also investigated by FACS. As can be seen from FIG. 6A-6D, P004E08-mut40-PTM12 exhibited ATP dependent internalization, while Enfortumab is ATP independent. Example 3. Antibody-drug conjugates 3.1 Binding affinity
[0267] The anti-Nectin-4 antibodies (e.g., P004E08-mut40-PTM12 and Enfortumab) were conjugated with MMAE to form antibody-drug conjugates (ADCs) , which were tested for the binding affinity to Nectin-4 of different species. Briefly, the antibodies or ADCs were 4-fold diluted from 100 nM and incubated with CHOK1 cells expressing human Nectin-4, cyno Nectin-4 or mouse Nectin-4, respectively, in the presence or absence of ANP (300 μM) , at 4℃ for 1 hr. A anti-hFc_647 secondary antibody was then added with 1: 500 dilution and incubated at 4℃ for 0.5 hr. The cell binding were then measured by FACS.
[0268] As shown in FIG. 4A-4D and Table 7, both the P004E08-mut40-PTM12 antibody and ADC showed comparable binding affinity, as compared to Enfortumab, to human Nectin-4 and cyno Nectin-4 overexpressing CHOK1 cells in the presence of ANP (FIG. 4A-4B) , while the antibodies and ADCs showed much higher binding affinity than Enfortumab to mouse Nectin-4 expressing CHOK1 cells in the presence of ANP (FIG. 4C) .
[0269] The antibodies and ADCs were further tested in tumor cells with the same protocol as above. As shown in FIG. 5A-5C and Table 8A, both the P004E08-mut40-PTM12 antibody and ADC thereof showed comparable binding affinity, as compared with Enfortumab, to tumor cells HT1376 (FIG. 5A) , MDA-MB-468 (FIG. 5B) and NCI-H2122 cells (FIG. 5C) , which are ANP dependent. Similarly, the P004E08-mut40-PTM12 antibody and ADC thereof also showed ANP dependent binding to NCI-H322 cell, with similar binding affinity to Enfortumab (FIG. 5D and Table 8B) . Table 8B. Binding affinity of P004E08-mut40-PTM12 and ADC 3.2 Cytotoxicity
[0270] In the cell killing assay, the P004E08-mut40-PTM12 antibody and ADC thereof also showed ANP dependent cytotoxicity on the NCI-H2122 cells (FIG. 7 and Table 9) . Table 9. Cytotoxicity to tumor cells Example 4. In vivo efficacy of the antibody-drug conjugates
[0271] The ADC of P004E08-mut40-PTM12 antibody was tested in the animal models inoculated with MDA-MB-468 and NCI-H322 cells, respectively. 4.1 MDA-MB-468
[0272] The MMAE ADCs of P004E08-mut40 and Enfortumab (3 mpk or 10 mpk) were i. v. injected to the CDX model of NOG mice inoculated with MDA-MB-468 cells once every week for 3 weeks. The tumor volume and body weight were measured at day 0, 3, 7, 10, 14, 17 and 21 from the first injection.
[0273] The tumor growth inhibition (TGI%) was shown in FIG. 8A and Table 10 and the change of body weight was shown in FIG. 8B. As illustrated, all the ADCs were effective in inhibiting the tumor growth, while the 10 mpk treatment groups (P004E08-mut40-MMAE and Enfortumab-MMAE) showed higher TGI%than the 3 mpk treatment groups. The body weight change remained comparable among groups. Table 10. TGI%after ADC treatment 4.2 NCI-H322
[0274] The ADCs of P004E08-mut40-PTM12 and Enfortumab (1 mpk or 3 mpk) were i. v. injected with a single dose to the CDX model of NOG mice inoculated with NCI-H322 cells. The tumor volume and body weight were measured at day 0, 2, 5, 8, 11, 15, 19, 22, and 25 from the injection.
[0275] As seen in the results in FIG. 9A-9B, the 3 mpk treatment groups (P004E08-mut40-PTM12 and Enfortumab) showed better TGI%than the 1 mpk group (Enfortumab) , while the body weight does not show difference. Example 5. Extended in vivo Testing of ADC
[0276] This example tested the in vivo efficacy of four ADC molecules, as listed in Table 11 below. Table 11. Tested ADCs
[0277] In a first assay, LM002 ADC (P004E08 mut040-DXd) was administered to the CDX model of NOG mice inoculated with MDA-MB-468 cells once every week, at 3 mg / kg or 6 mg / kg. The tumor volume and body weight were measured as indicated in FIG. 10A-B. As shown in the figures, at both doses, LM002 ADC quickly reduced tumor size without having impact on body weight growth.
[0278] In a second assay, Benchmark ADC, LM001 ADC and LM002 ADC were administered to a bladder cancer animal model of SXBL004, at 3 or 6 mg / kg (FIG. 11A-B) . As shown in the figures, both LM001 ADC and LM002 ADC exhibited higher tumor inhibition efficacy than the benchmark, while all of them were well tolerated by the animals.
[0279] In a third assay, LM002 ADC and LM003 ADC were tested in an esophageal cancer animal model (6 mg / kg) . As shown in FIG. 12A-B, both tested ADC exhibited excellent inhibition efficacy of tumor growth.
[0280] In a fourth assay, LM002 ADC and LM003 ADC were tested in a head and neck cancer animal model (6 mg / kg) . As shown in FIG. 13A-B, both tested ADC exhibited excellent inhibition efficacy of tumor growth.
[0281] In a fifth assay, LM002 ADC (single dose, or once per week for 3 weeks) was tested in a cervical cancer animal model. Surprisingly, even a single dose of LM002 ADC exhibited potent and lasting tumor inhibition activities (FIG. 14A-B) . ***
[0282] The present disclosure is not to be limited in scope by the specific embodiments described which are intended as single illustrations of individual aspects of the disclosure, and any compositions or methods which are functionally equivalent are within the scope of this disclosure. It will be apparent to those skilled in the art that various modifications and variations can be made in the methods and compositions of the present disclosure without departing from the spirit or scope of the disclosure. Thus, it is intended that the present disclosure cover the modifications and variations of this disclosure provided they come within the scope of the appended claims and their equivalents.
[0283] All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
Claims
1.An antibody or antigen-binding fragment thereof that has binding specificity to a human Nectin-4 protein, which has a higher binding affinity to human Nectin-4 in the presence of the adenosine-containing compound (ANP) than in the absence of the ANP.2.The antibody or antigen-binding fragment thereof of claim 2, wherein the concentration of the ANP is at least about 50 μM.3.The antibody or antigen-binding fragment thereof of anyone of claims 1-3, wherein the binding affinity to human Nectin-4 protein is at least about 1-fold higher in the presence of the ANP than in the absence of the ANP, when the ANP is present at a concentration of at least about 100 μM.4.The antibody or antigen-binding fragment thereof of any one of claims 1-3, wherein the antibody or the fragment thereof comprises a heavy chain variable region (VH) comprising heavy chain complementarity determining regions (CDR) VH CDR1, VH CDR2, and VH CDR3, and a light chain variable region (VL) comprising VL CDR1, VL CDR2, and VL CDR3, and whereinthe VH CDR1 comprises the amino acid sequence of SEQ ID NO: 144,the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 145,the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 146,the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 147,the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 148, andthe VL CDR3 comprises the amino acid sequence of SEQ ID NO: 149;5.The antibody or antigen-binding fragment thereof of claim 4, whereinthe VH CDR1 comprises the amino acid sequence of SEQ ID NO: 13, or 20-33,the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 14 or 34-49,the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 15 or 50-55,the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 16 or 56-58,the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 17 or 59-61, andthe VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18 or 62.6.The antibody or antigen-binding fragment thereof of claim 5, wherein the VH comprises an amino acid sequence of any one of SEQ ID NO: 8, 72-90, 92-108, and 110-137, or a peptide having at least 90%sequence identity to the amino acid sequence of any one of SEQ ID NO: 8, 72-90, 92-108, and 110-137, and the VL comprises an amino acid sequence of any one of SEQ ID NO: 7, 63-71, 91 and 109, or a peptide having at least 90%sequence identity to the amino acid sequence of any one of SEQ ID NO: 7, 63-71, 91 and 109.7.The antibody or antigen-binding fragment thereof of claim 5, whereinthe VH CDR1 comprises the amino acid sequence of SEQ ID NO: 13, or 20-25,the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 14 or 34-49,the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 15 or 50,the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 16 or 56-58,the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 17 or 59-61, andthe VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18 or 62.8.The antibody or antigen-binding fragment thereof of claim 7, wherein the VH comprises an amino acid sequence of any one of SEQ ID NO: 8, 72-90, and 92-108, or a peptide having at least 90%sequence identity to the amino acid sequence of any one of SEQ ID NO: 8, 72-90, and 92-108, and the VL comprises an amino acid sequence of any one of SEQ ID NO: 7, 63-71, 91 and 109, or a peptide having at least 90%sequence identity to the amino acid sequence of any one of SEQ ID NO: 7, 63-71, 91 and 109.9.The antibody or antigen-binding fragment thereof of claim 8, wherein the VH / VL pair comprise the amino acid sequences of SEQ ID NO: 8 / 7, 8 / 63, 8 / 64, 8 / 65, 8 / 66, 8 / 67, 8 / 68, 8 / 69, 8 / 70, 8 / 71, 72 / 7, 73 / 7, 74 / 7, 75 / 7, 76 / 7, 77 / 7, 78 / 7, 79 / 7, 80 / 7, 81 / 7, 82 / 7, 83 / 7, 84 / 7, 85 / 7, 86 / 7, 87 / 7, 88 / 7, 89 / 7, 90 / 7, 83 / 67, 84 / 67, 85 / 67, 86 / 67, 87 / 67, 8 / 91, 72 / 67, 74 / 67, 75 / 67, 79 / 67, 92 / 67, 93 / 67, 94 / 67, 95 / 67, 96 / 67, 97 / 67, 98 / 67, 74 / 68, 99 / 67, 100 / 67, 101 / 67, 102 / 67, 103 / 67, 104 / 67, 105 / 67, 106 / 67, 107 / 67, 108 / 67, 105 / 109, 106 / 109, 107 / 109, 108 / 109, 102 / 109, or 103 / 109, respectively.10.The antibody or antigen-binding fragment thereof of claim 7, whereinthe VH CDR1 comprises the amino acid sequence of SEQ ID NO: 22,the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 34,the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 15,the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 56,the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 60, andthe VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18.11.The antibody or antigen-binding fragment thereof of claim 10, wherein the VH comprises the amino acid sequence of SEQ ID NO: 93, and the VL comprises the amino acid sequence of SEQ ID NO: 67.12.The antibody or antigen-binding fragment thereof of claim 5, whereinthe VH CDR1 comprises the amino acid sequence of SEQ ID NO: 26-33,the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 34,the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 51-55,the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 56,the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 60, andthe VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18.13.The antibody or antigen-binding fragment thereof of claim 12, wherein the VH comprises an amino acid sequence of any one of SEQ ID NO: 110-137, and the VL comprises the amino acid sequence of SEQ ID NO: 67.14.The antibody or antigen-binding fragment thereof of claim 12, whereinthe VH CDR1 comprises the amino acid sequence of SEQ ID NO: 27,the VH CDR2 comprises the amino acid sequence of SEQ ID NO: 34,the VH CDR3 comprises the amino acid sequence of SEQ ID NO: 53,the VL CDR1 comprises the amino acid sequence of SEQ ID NO: 56,the VL CDR2 comprises the amino acid sequence of SEQ ID NO: 60, andthe VL CDR3 comprises the amino acid sequence of SEQ ID NO: 18.15.The antibody or antigen-binding fragment thereof of claim 14, wherein the VH comprises the amino acid sequence of SEQ ID NO: 121, and the VL comprises the amino acid sequence of SEQ ID NO: 67.16.The antibody or antigen-binding fragment thereof of any one of claims 1-15, which is a F(ab') 2, a F (ab) 2, a Fab', a Fab, a Fv, or a scFv.17.The antibody or antigen-binding fragment thereof of any one of claims 1-16, wherein the antibody or antigen-binding fragment thereof further comprises a heavy chain constant region, a light chain constant region, an Fc region, or the combination thereof.18.The antibody or antigen-binding fragment thereof of any one of claims 1-17, wherein the antibody or antigen-binding fragment thereof is of an isotype of IgG1, IgG2, IgG3 or IgG4.19.The antibody or antigen-binding fragment thereof of claim 18, wherein the antibody or antigen-binding fragment thereof is of an isotype of human IgG1.20.The antibody or antigen-binding fragment thereof of any one of claims 1-19, which is conjugated.21.A multifunctional molecule, comprising a first antigen-binding portion having specificity to a human Nectin-4 protein and a second antigen-binding portion having specificity to a second antigen, wherein the first antigen-binding portion comprises the antibody or antigen-binding fragment thereof of any one of claims 1-20.22.An antibody-drug conjugate, comprising the antibody or antigen-binding fragment thereof of any one of claims 1-20 or the multifunctional molecule of claim 21, and a drug moiety.23.The antibody-drug conjugate of claim 22, wherein the drug moiety is a cytotoxin, an immunosuppressive agent, a radioisotope, or a toxin.24.The antibody-drug conjugate of claim 23, wherein the drug moiety is a cytotoxin selected from the group consisting of auristatins, maytansinoids, macrocyclic ketone analogues, topoisomerase inhibitors, benzodiazepines, tubulysins, duocarmycin, camptothecin, calicheamicins, exatecans, irinotecans (SN38) , doxorubicin, anthracycline, the pyrrolobenzodiazepenes (PBD) , TLR agonist, STING agonists, pseudomonas aeruginosa exotoxin PE38, diphtheria toxin, staphylococcus aureus enterotoxin A / E-120, antibacterial antibiotic, shigatoxin, ricin, and urease.25.The antibody-drug conjugate of claim 23, wherein the drug moiety is a cytotoxin selected from the group consisting of monomethyl auristatin E (MMAE) , monomethyl auristatin F (MMAF) , maytansine, mertansine (DM1) , ravtansine (DM4) , tublysin A, DXd, 7-ethyl-10-hydroxycamptothecin (SN-38) , DGN462, Amberstatin269, anthramycin, SG3199 / SCX, TLR7 / 8 agonist, diABZI STING agonist-2, or any derivative thereof.26.The antibody-drug conjugate of any one of claims 22-25, wherein the drug moiety comprises MMAE, MMAF, or DXd.27.The antibody-drug conjugate of any one of claims 22-26, wherein the antibody or antigen-binding fragment thereof or the multifunctional molecule is conjugated to the drug moiety via a linker.28.The antibody-drug conjugate of any one of claims 27, wherein the linker comprises succinimidyl-4- (N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) , sulfo-SMCC, p-carboxycyclo hexylmethylmaleimide, maleimide-caproyl (MC) -Valine-citrulline (VC) -para-aminobenzyloxycarbamoyl (PABC) , CL2A, maleimide-caproyl (MC) , MC-glycine-glycine-phenylalanine-glycine (GGFG) , MC-PEG8-GGFG, MC-PEG8-GGFG-PAB, or maleimide propoyl (MP) -PEG8-Valine-alanine (VA) -PABC.29.The antibody-drug conjugate of any one of claims 22-28, wherein the drug-antibody ratio (DAR) is 1-20.30.The antibody-drug conjugate of any one of claims 22-28, wherein the drug-antibody ratio (DAR) is 4-8.31.A chimeric antigen receptor (CAR) having specificity to the human FOLR1 protein, comprising an antigen-binding fragment thereof any one of claims 1-20 or a multifunctional molecule of claim 21, a transmembrane domain, and an intracellular activating domain.32.A nucleic acid encoding the antibody or antigen-binding fragment thereof of any one of claims 1-20, the multifunctional molecule of claim 21, or the CAR of claim 31.33.A vector comprising the nucleic acid of claim 32.34.An isolated cell comprising the nucleic acid of claim 32, or the vector of claim 33.35.A pharmaceutical composition comprising the antibody or antigen-binding fragment thereof of any one of claims 1-20, the multifunctional molecule of claim 21, the antibody-drug conjugate of any one of claims 22-30, or the CAR of claim 31, and a pharmaceutically acceptable carrier.36.A method of treating cancer in a patient in need thereof, comprising administering to the patient the antibody or antigen-binding fragment thereof of any one of claims 1-20, the multifunctional molecule of claim 21, the antibody-drug conjugate of any one of claims 22-30, or the CAR of claim 31, or the pharmaceutical composition of claim 35.37.Use of the antibody or antigen-binding fragment thereof of any one of claims 1-20, the multifunctional molecule of claim 21, the antibody-drug conjugate of any one of claims 22-30, or the CAR of claim 31, or the pharmaceutical composition of claim 35 for the preparation of a medicament for treating cancer.38.The antibody or antigen-binding fragment thereof of any one of claims 1-20, the multifunctional molecule of claim 21, the antibody-drug conjugate of any one of claims 22-30, or the CAR of claim 31, or the pharmaceutical composition of claim 35 for use in the treatment of cancer in a patient in need thereof.39.The method of claim 36 or the use of claim 37 or the antibody or antigen-binding fragment thereof, multifunctional molecule, antibody-drug conjugate, CAR or pharmaceutical composition for use of claim 38, wherein the cancer is selected from the group consisting of bladder cancer, liver cancer, colon cancer, rectal cancer, endometrial cancer, leukemia, lymphoma, pancreatic cancer, small cell lung cancer, non-small cell lung cancer, breast cancer, urethral cancer, head and neck cancer, gastrointestinal cancer, stomach cancer, oesophageal cancer, ovarian cancer, renal cancer, melanoma, prostate cancer and thyroid cancer.
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