Search

BR-122025023595-A2 - Antigen-binding protein, conjugate or fusion protein, pharmaceutical composition, methods of production, nucleic acid and uses.

BR122025023595A2BR 122025023595 A2BR122025023595 A2BR 122025023595A2BR-122025023595-A2

Abstract

The present invention relates to antigen-binding proteins that bind to Claudin6 (CLDN6). In several respects, the antigen-binding proteins bind to Extracellular Loop 2 (EL2) of the extracellular domain of CLDN6. Polypeptides, nucleic acids, vectors, host cells, and related conjugates are further provided herein. Kits and pharmaceutical compositions comprising such entities are further provided. Methods for producing an antigen-binding protein and methods for treating an individual who has cancer are also provided.

Inventors

  • Dylan Conklin
  • Dennis Slamon
  • NEIL O'BRIEN
  • MIKE PALAZZOLO
  • Erika Von Euw

Assignees

  • THE REGENTS OF THE UNIVERSITY OF CALIFORNIA

Dates

Publication Date
20260317
Application Date
20180918
Priority Date
20170918

Claims (20)

  1. 1. Antigen-binding protein, characterized in that it binds to a human Claudin6 (CLDN6) protein (SEQ ID NO: 200), wherein: a) the antigen-binding protein binds to Extracellular Loop 2 (EL2) of an extracellular domain (ECD) of CLDN6 and does not bind to Extracellular Loop 1 (EL1) of the ECD of CLDN6; or b) it does not bind to any of Claudin3 (CLDN3), Claudin4 (CLDN4) and Claudin9 (CLDN9) and inhibits the binding of a reference antibody to CLDN6 endogenously expressed by OVCA429 cells with less than about 1200 nM; or c) a combination thereof.
  2. 2. Antigen-binding protein according to claim 1, characterized in that: a) the antigen-binding protein binds to an epitope within the amino acid sequence of WTAHAIIRDFYNPLVAEAQKREL (SEQ ID NO: 2); b) the antigen-binding protein does not bind to any one or more of Claudin3 (CLDN3), Claudin4 (CLDN4) and Claudin9 (CLDN9); or c) the reference antibody comprises a variable light chain sequence of SEQ ID NO: 181 and a variable heavy chain sequence of SEQ ID NO: 182 or a variable light chain sequence of SEQ ID NO: 185 and a variable heavy chain sequence of SEQ ID NO: 186.
  3. 3. Antigen-binding protein according to claim 2, characterized in that: a) it binds to the amino acid sequence TAHAIIRDFYNPL (SEQ ID NO: 3) or LVAEAQKREL (SEQ ID NO: 4) of CLDN 6; or b) an antigen-binding protein that: (1) does not bind to CLDN3; (2) does not bind to CLDN3, and binds to CLDN6, CLDN4 and CLDN9; (3) does not bind to CLDN3 and CLDN9; (4) does not bind to CLDN3 and CLDN9, and binds to CLDN6 and CLDN4; (5) does not bind to CLDN3 and CLDN4; or (6) does not bind to CLDN3 and CLDN4, and binds to CLDN6 and CLDN9.
  4. 4. Antigen-binding protein, according to any one of claims 1 to 3, characterized in that it comprises: a) a heavy chain CDR1 amino acid sequence presented in Table A, Table A1, or a sequence selected from the group consisting of: SEQ ID NOs: 11, 17, 23, 29, 35, 41, 47, 53, 59, 65, 71, 77, 83, 89, 95, 101, 107, 113, 119, 125, 131, 452, 455, 461, 465, and 472; or a variant sequence thereof that differs only by one or two amino acids or that has at least or about 70% sequence identity; (b) a heavy chain CDR2 amino acid sequence presented in Table A, Table A1, or a sequence selected from the group consisting of: SEQ ID NOs: 12, 18, 24, 30, 36, 42, 48, 54, 60, 66, 72, 78, 84, 90, 86, 102, 108, 114, 120, 126, 132, 475, 456, 462, 466, 468, and 473; or a variant sequence thereof that differs by only one or two amino acids or that has at least or approximately 70% sequence identity; (c) a heavy chain CDR3 amino acid sequence presented in Table A, Table A1, or a sequence selected from the group consisting of: SEQ ID NOs: 13, 19, 25, 31, 37, 43, 49, 55, 61, 67, 73, 79, 85, 91, 97, 103, 109, 115, 121, 127, 133, 453, 457, 463, 467, 469, and 474; or a variant sequence thereof that differs by only one or two amino acids or that has at least or approximately 70% sequence identity; (d) an amino acid sequence of CDR1 light chain presented in Table A, Table A1, or a sequence selected from the group consisting of: SEQ ID NOs: 8, 14, 20, 32, 38, 44, 50, 56, 62, 68, 74, 80, 86, 92, 98, 104, 110, 116, 122, 128, 449, 476, 458, 464, and 470; or a variant sequence thereof that differs by only one or two amino acids or that has at least or about 70% sequence identity; (e) a CDR2 light chain amino acid sequence presented in Table A, Table A1, or a sequence selected from the group consisting of: SEQ ID NOs: 9, 15, 21, 27, 33, 39, 45, 51, 57, 63, 69, 75, 81, 87, 93, 99, 105, 111, 117, 123 and 129 or a variant sequence thereof that differs by only one or two amino acids or that has at least or approximately 70% sequence identity; f) a CDR3 light chain amino acid sequence presented in Table A, Table A1, or a sequence selected from the group consisting of: SEQ ID NOs: 10, 16, 22, 28, 34, 40, 46, 52, 58, 64, 70, 76, 82, 88, 94, 100, 106, 112, 118, 124, 130, 451, 454, and 460, or a variant sequence thereof that differs by only one or two amino acids or that has at least or about 70% sequence identity; or g) a combination of any two or more of (a) to (f).
  5. 5. Antigen-binding protein according to claim 4, characterized in that the variant sequence has at least about 80%; at least or about 85%; at least or about 90%; or at least or about 95% sequence identity.
  6. 6. Antigen-binding protein according to claim 4, characterized in that: a) it comprises a CDR1 light chain amino acid sequence, a CDR2 light chain amino acid sequence and a CDR3 light chain amino acid sequence presented in Table A or Table A1; and 1 or 2 of the CDR heavy chain amino acid sequences presented in Table A or Table A1; b) it comprises a CDR1 heavy chain amino acid sequence, a CDR2 heavy chain amino acid sequence and a CDR3 heavy chain amino acid sequence presented in Table A or Table A1; and 1 or 2 of the CDR light chain amino acid sequences presented in Table A or Table A1; or c) it comprises six CDR amino acid sequences selected from the group consisting of: (1) SEQ ID NOs: 74-79; (2) SEQ ID NOs: 50-55; (3) SEQ ID NOs: 122-127; (4) SEQ ID NOs: 26-31; (5) SEQ ID NOs: 128-133; (6) SEQ ID NOs: 38-43; (7) SEQ ID NOs: 62-67; (8) SEQ ID NOs: 80-85; (9) SEQ ID NOs: 44-49; (10) SEQ ID NOs: 86-91; (11) SEQ ID NOs: 104-109; (12) SEQ ID NOs: 56-61; (13) SEQ ID NOs: 32-37; (14) SEQ ID NOs: 110-115; (15) SEQ ID NOs: 98-103; (16) SEQ ID NOs: 92-97; (17) SEQ ID NOs: 116-121; (18) SEQ ID NOs: 8-13; (19) SEQ ID NOs: 68-73; (20) SEQ ID NOs: 14-19; (21) SEQ ID NOs: 20-25; (22) SEQ ID NOs: 449-453 and 475; (23) SEQ ID NOs: 476-477, 454-457; (24) SEQ ID NOs: 458-463; (25) SEQ ID NOs: 57, 58, 464-467; (26) SEQ ID NOs: 68-71 and 468-469; and (27) SEQ ID NOs: 112, and 470-474.
  7. 7. Antigen-binding protein, according to any one of claims 4 to 6, characterized in that it comprises: a) an amino acid sequence of variable heavy chain region presented in Table B, or Table B1; or a sequence selected from the group consisting of: 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 478, 480, 482, 484, 486, and 488; or a variant sequence thereof that differs only by one or two amino acids or that has at least or about 70% sequence identity; or b) a variable region light chain amino acid sequence presented in Table B, or Table B1; or a sequence selected from the group consisting of: 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 479, 481, 483, 485, 487, and 489; or a variant sequence thereof that differs by only one or two amino acids or that has at least or about 70% sequence identity; or c) both (a) and (b).
  8. 8. Antigen-binding protein according to claim 7, characterized in that: a) the variant sequence has at least or about 80%; at least or about 85%; at least or about 90%; or at least or about 95% sequence identity; or b) comprises a pair of amino acid sequences selected from the group consisting of: (1) SEQ ID NOs: 156 and 157; (2) SEQ ID NOs: 148 and 149; (3) SEQ ID NOs: 172 and 173; (4) SEQ ID NOs: 140 and 141; (5) SEQ ID NOs: 174 and 175; (6) SEQ ID NOs: 144 and 145; (7) SEQ ID NOs: 152 and 153; (8) SEQ ID NOs: 158 and 159; (9) SEQ ID NOs: 146 and 147; (10) SEQ ID NOs: 160 and 161; (11) SEQ ID NOs: 166 and 167; (12) SEQ ID NOs: 150 and 151; (13) SEQ ID NOs: 142 and 143; (14) SEQ ID NOs: 168 and 169; (15) SEQ ID NOs: 164 and 165; (16) SEQ ID NOs: 162 and 163; (17) SEQ ID NOs: 170 and 171; (18) SEQ ID NOs: 134 and 135; (19) SEQ ID NOs: 154 and 155; (20) SEQ ID NOs: 136 and 137; (21) SEQ ID NOs: 138 and 139; (22) SEQ ID NOs: 478 and 479; (23) SEQ ID NOs: 480 and 481; (24) SEQ ID NOs: 482 and 483; (25) SEQ ID NOs: 484 and 485; (26) SEQ ID NOs: 486 and 487; and (27) SEQ ID NO: 488 and 489.
  9. 9. Antigen-binding protein, according to any one of claims 1 to 9, characterized in that: a) it is an antibody; b) it inhibits at least about 50% of colony growth in 3D soft agar proliferation assays; or c) it inhibits tumor growth in xenograft mice injected with human cancer cells.
  10. 10. Antigen-binding protein, according to claim 9, characterized in that: a) it is a monoclonal antibody or an IgG; or b) it inhibits tumor growth in xenograft mice injected with ovarian cancer cells, melanoma cancer cells, bladder cancer cells or endometrial cancer cells, optionally wherein it inhibits at least 50% of tumor growth in xenograft mice injected with ovarian cancer cells, bladder cancer cells or endometrial cancer cells.
  11. 11. Antigen-binding protein characterized in that it comprises: a) an amino acid sequence of variable heavy chain region presented in Table C or a sequence selected from the group consisting of: SEQ ID NOs: 376 to 379, 384 to 387, 391 to 396, 403 to 408, 412 to 413, 416 to 419, and 422 to 427 or a variant sequence thereof that differs by only one or two amino acids or that has at least or about 70% sequence identity; or b) a variable region light chain amino acid sequence presented in Table C or a sequence selected from the group consisting of: SEQ ID NOs: 380 to 383, 388 to 390, 397 to 402, 409 to 411, 414 to 415 and 420 to 421 or a variant sequence thereof that differs by only one or two amino acids or that has at least or about 70% sequence identity; or c) both (a) and (b).
  12. 12. Antigen-binding protein according to claim 11, characterized in that the variant sequence has at least or about 85%; at least or about 90%; at least or about 95% sequence identity.
  13. 13. Antigen-binding protein, characterized in that it comprises a pair of amino acid sequences selected from the group consisting of: a. SEQ ID NOs: 376 and 380; b. SEQ ID NOs: 377 and 380; c. SEQ ID NOs: 377 and 381; d. SEQ ID NOs: 377 and 382; e. SEQ ID NOs: 377 and 383; f. SEQ ID NOs: 378 and 381; g. SEQ ID NOs: 378 and 382; h. SEQ ID NOs: 378 and 383; i. SEQ ID NOs: 379 and 381; j. SEQ ID NOs: 379 and 382; k. SEQ ID NOs: 379 and 383; l. SEQ ID NOs: 384 and 388; m. SEQ ID NOs: 385 and 388; n. SEQ ID NOs: 385 and 389; the. SEQ ID NOs: 386 and 388; p. SEQ ID NOs: 386 and 389; q. SEQ ID NOs: 387 and 389; r. SEQ ID NOs: 422 and 389; s. SEQ ID NOs: 391 and 397; t. SEQ ID NOs: 392 and 397; u. SEQ ID NO: 393 and 398; v. SEQ ID NO: 394 and 398; w. SEQ ID NO: 395 and 398; x. SEQ ID NO: 396 and 398; y. SEQ ID NO: 423 and 398; z. SEQ ID NO: 424 and 398; aa. SEQ ID NO: 425 and 398; bb. SEQ ID NO: 426 and 398 cc. SEQ ID NO: 427 and 398; dd. SEQ ID NO: 403 and 409; ee. SEQ ID NO: 404 and 409; ff. SEQ ID NO: 405 and 410; gg. SEQ ID NO: 405 and 411; hh. SEQ ID NO: 406 and 410; ii. SEQ ID NO: 406 and 411; jj. SEQ ID NO: 407 and 410; lol. SEQ ID NO: 407 and 411; ll. SEQ ID NO: 408 and 410; mm. SEQ ID NO: 408 and 411; no. SEQ ID NO: 412 and 414; oo. SEQ ID NO: 413 and 414; pp. SEQ ID NO: 416 and 420; whatever. SEQ ID NO: 417 and 420; rr. SEQ ID NO: 417 and 421; ss. SEQ ID NO: 418 and 420; tt. SEQ ID NO: 418 and 421; uu. SEQ ID NO: 419 and 420; and vv. SEQ ID NO: 419 and 421;
  14. 14. Antigen-binding protein, characterized in that it comprises: (A) an HC CDR1 comprising the amino acid sequence YTFTXYT, wherein X is T, V, D or S (SEQ ID NO: 452), optionally comprising the amino acid sequence YTFTTYT (SEQ ID NO: 11); (B) an HC CDR2 comprising the amino acid sequence IXPSSGYT, wherein X is Q, S, A or N (SEQ ID NO: 475), optionally comprising the amino acid sequence INPSSGYT (SEQ ID NO: 12); (C) an HC CDR3 comprising the amino acid sequence AXGDYYVAY, wherein X is N, Q, H, or D (SEQ ID NO: 453), optionally comprising the amino acid sequence ANGDYYVAY (SEQ ID NO: 13); (D) an LC CDR1 comprising the amino acid sequence SSVSSXY, wherein X is T, V, F, or D (SEQ ID NO: 449), optionally comprising the amino acid sequence SSVSSTY (SEQ ID NO: 8); (E) an LC CDR2 comprising the amino acid sequence XTX, wherein X at position 1 is S, T, Q, or A and X at position 3 is S, T, D, or Q (SEQ ID NO: 450), optionally comprising the amino acid sequence STS (SEQ ID NO: 9); and (F) a CDR3 of LC comprising the amino acid sequence of HXYXRSPLT, wherein X at position 2 is Q, H or S and X at position 4 is H, Y, Q or S (SEQ ID NO: 451), optionally comprising the amino acid sequence of HQYHRSPLT (SEQ ID NO: 10).
  15. 15. Antigen-binding protein, characterized in that it comprises: (A) a CDR1 of HC comprising the amino acid sequence FTFSXYX, wherein X at position 5 is N, S, R, Q or A and X at position 7 is W, H, Y, F (SEQ ID NO: 455), optionally comprising the amino acid sequence FTFSNYW (SEQ ID NO: 23); (B) a CDR2 of HC comprising the amino acid sequence IRLKXDXYAT, wherein X at position 5 is S, N, A or T and X at position 7 is Q, S, A, N (SEQ ID NO: 456), optionally comprising the amino acid sequence IRLKSDNYAT (SEQ ID NO: 24); (C) a CDR3 of HC comprising the amino acid sequence of XDGPPSGX, wherein X at position 1 is N, D, or T and X at position 8 is S, T, A, C, or Y (SEQ ID NO: 457), optionally comprising the amino acid sequence of NDGPPSGC (SEQ ID NO: 25); (D) a CDR1 of LC comprising the amino acid sequence of EXIYSY, wherein X is Q, S, A, D, or N (SEQ ID NO: 476), optionally comprising the amino acid sequence of ENIYSY (SEQ ID NO: 20); (E) a CDR2 of LC comprising the amino acid sequence of XAK, wherein X at position 1 is Q, S, A, D, or N (SEQ ID NO: 477), optionally comprising the amino acid sequence of NAK (SEQ ID NO: 21); and (F) a CDR3 of LC comprising the amino acid sequence QXHYXVPWT, wherein X at position 2 is H, Q, S or T and X at position 5 is T, S, N or G (SEQ ID NO: 454), optionally comprising the amino acid sequence QHHYTVPWT (SEQ ID NO: 22).
  16. 16. Antigen-binding protein, characterized in that it comprises: (A) a CDR1 of HC comprising the amino acid sequence YTXTXYT, wherein X at position 3 is F, Y, S or T and X at position 5 is S, T, Y or D (SEQ ID NO: 461), optionally comprising the amino acid sequence YTFTSYT (SEQ ID NO: 29); (B) a CDR2 of HC comprising the amino acid sequence IXPSSXYT, wherein X at position 2 is Q, S, A or N and X at position 6 is T, S, V, D or G (SEQ ID NO: 462), optionally comprising the amino acid sequence INPSSTYT (SEQ ID NO: 30); (C) a CDR3 of HC comprising the amino acid sequence of XRGEXGGFAY, wherein X at position 1 is S, A, T or V and X at position 5 is L, V or F (SEQ ID NO: 463), optionally comprising the amino acid sequence of SRGELGGFAY (SEQ ID NO: 31); (D) a CDR1 of LC comprising the amino acid sequence of QSLVHSXGXTY, wherein X at position 7 is D, N, E, Q, S or A and X at position 9 is Q, S, A, D or N (SEQ ID NO: 458), optionally comprising the amino acid sequence of QSLVHSDGNTY (SEQ ID NO: 26); (E) an LC CDR2 comprising the amino acid sequence XVX, wherein X at position 1 is K, Q, or R and X at position 3 is S, T, or V (SEQ ID NO: 459), optionally comprising the amino acid sequence KVS (SEQ ID NO: 27); and (F) an LC CDR3 comprising the amino acid sequence SXXTHVPYT, wherein X at position 2 is Q, H, or T and X at position 3 is S, G, T, or D (SEQ ID NO: 460), optionally comprising the amino acid sequence SQSTHVPYT (SEQ ID NO: 28).
  17. 17. Conjugate or fusion protein, characterized in that it comprises an antigen-binding protein, as defined in any one of claims 1 to 16.
  18. 18. Nucleic acid, characterized in that it encodes (a) an antigen-binding protein, as defined in any one of claims 1 to 16, (ii) a conjugate, as defined in claim 17, or a fusion protein, as defined in claim 17; vector comprising said nucleic acid; or host cell comprising said nucleic acid or said vector.
  19. 19. Method for producing an antigen-binding protein or a fusion protein that binds to a Claudin6 protein (CLDN6) characterized in that it comprises (i) culturing the host cell, as defined in claim 18, in a cell culture medium, and (ii) collecting the antigen-binding protein or fusion protein from the cell culture medium.
  20. 20. A method for producing a pharmaceutical composition, characterized in that it comprises combining an antigen-binding protein, as defined in any one of claims 1 to 16, a conjugate, as defined in claim 17, a fusion protein, as defined in claim 17, a nucleic acid, as defined in claim 18, a vector, as defined in claim 18, a host cell, as defined in claim 18, or a combination thereof, and a pharmaceutically acceptable excipient, diluent or vehicle.

Description

[001] A computer-readable listing of nucleotide/amino acid sequences submitted with this document and identified as follows is incorporated herein by reference in its entirety: 315,776-byte ASCII (Text) file named "51836_SeqListing.txt"; created on September 18, 2018. BACKGROUND [002] Antibodies are potent therapeutic agents characterized by limited side effects due to their ability to specifically target a distinct antigen on a cell, bacteria, virus, or toxin. In 1986, the first therapeutic monoclonal antibody, OKT3 Orthoclone, was introduced to the market. Since then, this class of biopharmaceutical products has grown significantly. By the end of 2014, forty-seven monoclonal antibody products had received approval in the U.S. or Europe for the treatment of a variety of diseases, including cancer and inflammatory, cardiovascular, respiratory, and infectious diseases. [003] More than a dozen monoclonal antibodies are currently approved by the U.S. Food and Drug Administration (FDA) to treat cancers. Among these agents are alemtuzumab (Campath®), which is indicated for chronic lymphocytic leukemia (CLL), and trastuzumab (Herceptin®), which is used to treat breast cancer. Some antibodies are identified with chemotherapeutic drugs, including, for example, brentuximab vedotin (Adcetris®) and ado-trastuzumab emtansine (Kadcyla®). Other antibody products, such as blinatumomab (Blincyto), are designed to recognize and bind to two different antigens. Despite the commercial availability of such antibody products, the current incidence of cancer and cancer deaths remain high. It has been reported that the incidence of cancer is greater than 450 per 100,000 men and women per year, and cancer mortality is just above 170 per 100,000 men and women per year. SUMMARY [004] Antigen-binding proteins that bind to Claudin6 (CLDN6) are provided in this document. In several respects, the antigen-binding protein of the present invention binds to a human CLDN6 and optionally binds to a mouse CLDN6. In several respects, the antigen-binding protein binds to the extracellular domain (ECD) of CLDN6. In several respects, the antigen-binding protein binds to Extracellular Loop 2 (EL2) of the CLDN6 ECD. In several respects, the antigen-binding protein binds to EL2 and does not bind to Extracellular Loop 1 (EL1) of the CLDN6 ECD. In several respects, the antigen-binding protein binds to additional members of the human Claudin family, including, for example, Claudin-3 (CLDN3), Claudin-4 (CLDN4), and Claudin-9 (CLDN9). In several respects, the antigen-binding protein binds to CLDN6 and at least one of CLDN4 and CLDN9. In several cases, the antigen-binding protein binds to CLDN6 and does not bind to any other member of the Claudin family. In several respects, the antigen-binding protein binds to CLDN6 endogenously expressed by human ovarian cancer cells, for example, OVCA429 cells, and exhibits an IC50 lower than about 1200 nM in a FACS affinity assay with OVCA429 cells. In several cases, the antigen-binding proteins of the present invention inhibit tumor growth in an individual, for example, a human being, without any other chemical moiety attached to the antigen-binding protein. In several cases, antigen-binding proteins not conjugated to a heterologous chemical moiety (for example, not conjugated to any chemotherapeutic agent, drug, or toxic chemical moiety) inhibit tumor growth in an individual, for example, a human being. [005] In several respects, the antigen-binding protein binds to CLDN6 expressed by human cancer cells. In several respects, the antigen-binding protein inhibits a binding interaction between human CLDN6 and a reference anti-CLDN6 antibody. Without adhering to a particular theory, the inhibitory action of the antigen-binding proteins provided in this document allows such entities to be useful in methods to reduce tumor growth and treat an individual with a tumor or cancer. As further discussed in this document, in several respects, the antigen-binding protein is an antibody, antigen-binding antibody fragment thereof, or antibody protein product. [006] The present invention also provides antigen-binding proteins comprising at least 3, 4, 5, or all amino acid sequences of a specified group of amino acid sequences. In several respects, the antigen-binding proteins comprise at least 3, 4, 5, or 6 amino acid sequences of the complementarity-determining region (CDR) of CLDN6 antibodies disclosed herein. [007] The present invention further provides antigen-binding proteins comprising amino acid sequences as detailed herein. In several respects, the antigen-binding protein comprises an amino acid sequence of a SEQ ID NO: listed in Tables A, A1, B, B1, C or D, or a combination thereof, as further described herein. [008] Polypeptides, nucleic acids, vectors, host cells and related conjugates are additionally provided in this document. Kits and pharmaceutical compositions comprising such entities are additionally contemplated. [00