IP Library › Granted Patent US 11,753,466

Granted Patent B2

US 11,753,466 · App. 16/723,809 · Granted Sep 12, 2023

Anti-CD166 antibodies, activatable anti-CD166 antibodies, and methods of use thereof

Inventors: James William West (Bend, OR); Jason Gary Sagert (San Mateo, CA); Jonathan Alexander Terrett (Lexington, MS); Annie Yang Weaver (San Mateo, CA); Luc Roland Desnoyers (San Francisco, CA); Shweta Singh (Fremont, CA)

C07K16/2803 A61K31/537 A61K47/6873 A61K2039/505 C07K2317/24 C07K2317/73 C07K2317/732 C07K2317/76 C07K2317/92 C07K2319/50 C07K2319/55

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Quick Facts

Patent No.: US 11,753,466
App. No.: 16/723,809
Granted: Sep 12, 2023
Kind: B2

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Abstract

The invention relates generally to antibodies that bind CD166, activatable antibodies that specifically bind to CD166 and methods of making and using these anti-CD166 antibodies and anti-CD166 activatable antibodies in a variety of therapeutic, diagnostic and prophylactic indications.

Claims (186)

1. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease in a subject in which diseased cells express CD166 or the disorder or disease is associated with cells expressing CD166, comprising:

administering to the subject a therapeutically effective amount of a conjugated activatable antibody that in an activated state binds CD166, the conjugated activatable antibody comprising:

an activatable antibody conjugated to an agent, the activatable antibody comprising:

an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian CD166, wherein the AB specifically binds human CD166 and cynomolgus monkey CD166, wherein the AB comprises the VH CDR1 amino acid sequence GFSLSTYGMGVG (SEQ ID NO: 127); the VH CDR2 amino acid sequence NIWWSEDKH (SEQ ID NO: 128); the VH CDR3 amino acid sequence IDYGNDYAFTY (SEQ ID NO: 129); the VL CDR1 amino acid sequence RSSKSLLHSNGITYLY (SEQ ID NO: 130) or RSSQSLLHSNGITYLY (SEQ ID NO: 131); the VL CDR2 amino acid sequence QMSNLAS (SEQ ID NO: 132) or QMSNRAS (SEQ ID NO: 133); and the VL CDR3 amino acid sequence AQNLELPYT (SEQ ID NO: 134);

a masking moiety (MM) that inhibits the binding of the AB to CD166 when the activatable antibody is in an uncleaved state, wherein the MM comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 135-238; and

a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease, the CM comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 18-87 and 318-358.

2. The method of claim 1 , wherein the disorder or disease associated with cells expressing CD166 is cancer.

3. The method of claim 2 , wherein the cancer is an adenocarcinoma, a bile duct (biliary) cancer, a bladder cancer, a bone cancer, a breast cancer, a Her2-negative breast cancer, a triple-negative breast cancer (TNBC), an endometrial cancer, an estrogen receptor-positive breast cancer, a carcinoid, a cervical cancer, a cholangiocarcinoma, a colorectal cancer, a colon cancer, a glioma, a head and neck cancer, a head and neck squamous cell cancer (HNSCC), a leukemia, a liver cancer, a lung cancer, a non-small cell lung cancer (NSCLC), a small cell lung cancer (SCLC), a lymphoma, a melanoma, an oropharyngeal cancer, an ovarian cancer, a pancreatic cancer, a prostate cancer, a metastatic castration-resistant prostate carcinoma, a renal cancer, a sarcoma, a skin cancer, a squamous cell cancer, a stomach cancer, a testis cancer, a thyroid cancer, a urogenital cancer, or a urothelial cancer.

4. The method of claim 2 , wherein the cancer is a Her2-negative breast cancer.

5. The method of claim 2 , wherein the cancer is an estrogen receptor-positive breast cancer.

6. The method of claim 2 , wherein the cancer is a triple-negative breast cancer (TNBC).

7. The method of claim 1 , wherein the AB comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 121 or SEQ ID NO: 122, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 123-126.

8. The method of claim 1 , wherein the antigen binding fragment thereof is selected from the group consisting of a Fab fragment, a F(ab′)2 fragment, a scFv, a scAb, and a dAb.

9. The method of claim 1 , wherein the MM is linked to the CM such that the activatable antibody in an uncleaved state comprises the structural arrangement from N-terminus to C-terminus as follows: MM-CM-AB or AB-CM-MM.

10. The method of claim 9 , wherein the activatable antibody comprises a first linking peptide (LP1) and a second linking peptide (LP2), wherein the activatable antibody in the uncleaved state has the structural arrangement from N-terminus to C-terminus as follows: MM-LP1-CM-LP2-AB or AB-LP2-CM-LP1-MM, and wherein each of LP1 and LP2 is a peptide of about 1 to 20 amino acids in length.

11. The method of claim 10 , wherein the two linking peptides are not identical to each other.

12. The method of claim 1 , wherein the agent has one or more of the characteristics selected from the group consisting of:

(a) the agent is a toxin or a fragment thereof;

(b) the agent is a microtubule inhibitor;

(d) the agent is a dolastatin;

(e) the agent is an auristatin;

(f) the agent is a maytansinoid;

(g) the agent is a duocarmycin;

(h) the agent is a calicheamicin;

(i) the agent is a pyrrolobenzodiazepine;

(j) the agent is auristatin E;

(k) the agent is monomethyl auristatin E (MMAE);

(l) the agent is monomethyl auristatin D (MMAD);

(m) the agent is the maytansinoid DM1;

(n) the agent is the maytansinoid DM4;

(o) the agent is a detectable moiety; and

(p) the agent is a diagnostic agent.

13. The method of claim 1 , wherein the agent is conjugated to the AB via a linker.

14. The method of claim 1 , wherein the linker with which the agent is conjugated to the AB comprises an SPDB moiety, a vc moiety, or a PEG2-vc moiety.

15. The method of claim 1 , wherein the agent is a toxin conjugated to the AB via a linker, and wherein the linker and the toxin conjugated to the AB comprise a moiety selected from the group consisting of: an SPDB-DM4 moiety, a vc-MMAD moiety, a vc-MMAE moiety, a vc-duocarmycin moiety, or a PEG2-vc-MMAD moiety.

16. The method of claim 13 , wherein the linker is a cleavable linker.

17. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease in a subject in which diseased cells express CD166 or the disorder or disease is associated with cells expressing CD166, comprising:

administering to the subject a therapeutically effective amount of a conjugated activatable antibody that in an activated state binds CD166, the conjugated activatable antibody comprising:

an activatable antibody conjugated to an agent, the activatable antibody comprising:

an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian CD166, wherein the AB specifically binds human CD166 and cynomolgus monkey CD166;

a masking moiety (MM) that inhibits the binding of the AB to CD166 when the activatable antibody is in an uncleaved state; and

a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease,

wherein the activatable antibody comprises a heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 121 and 122, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 123-126, 363-370, 373, 374, 377, 378, 381, 382, 385, 386, 389, 390, 393, 394, 397, 398, 401, 402, 405, 406, 409, 410, 413, 414, 417, 418, 421, 422, 425, 426, 429, 430, 433, 434, 437, 438, 441, 442, 445, 446, 449, 450, 453, 454, 457, 458, 461, 462, 465, 466, 469, 470, 473, and 474.

18. The method of claim 17 , wherein the disorder or disease associated with cells expressing CD166 is cancer.

19. The method of claim 18 , wherein the cancer is an adenocarcinoma, a bile duct (biliary) cancer, a bladder cancer, a bone cancer, a breast cancer, a Her2-negative breast cancer, a triple-negative breast cancer (TNBC), an endometrial cancer, an estrogen receptor-positive breast cancer, a carcinoid, a cervical cancer, a cholangiocarcinoma, a colorectal cancer, a colon cancer, a glioma, a head and neck cancer, a head and neck squamous cell cancer (HNSCC), a leukemia, a liver cancer, a lung cancer, a non-small cell lung cancer (NSCLC), a small cell lung cancer (SCLC), a lymphoma, a melanoma, an oropharyngeal cancer, an ovarian cancer, a pancreatic cancer, a prostate cancer, a metastatic castration-resistant prostate carcinoma, a renal cancer, a sarcoma, a skin cancer, a squamous cell cancer, a stomach cancer, a testis cancer, a thyroid cancer, a urogenital cancer, or a urothelial cancer.

20. The method of claim 18 , wherein the cancer is a Her2-negative breast cancer.

21. The method of claim 18 , wherein the cancer is an estrogen receptor-positive breast cancer.

22. The method of claim 18 , wherein the cancer is a triple-negative breast cancer (TNBC).

23. The method of claim 17 , wherein the activatable antibody comprises the heavy chain comprising an amino acid sequence of SEQ ID NO: 239 and a light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 240, 242, 244, 246, 248, 303, 310, 312, 314, 316, 371, 372, 375, 376, 379, 380, 383, 384, 387, 388, 391, 392, 395, 396, 399, 400, 403, 404, 407, 408, 411, 412, 415, 416, 419, 420, 423, 424, 427, 428, 431, 432, 435, 436, 439, 440, 443, 444, 447, 448, 451, 452, 455, 456, 459, 460, 463, 464, 467, 468, 471, and 472.

24. The method of claim 17 , wherein the agent has one or more of the characteristics selected from the group consisting of:

(a) the agent is a toxin or a fragment thereof;

(b) the agent is a microtubule inhibitor;

(d) the agent is a dolastatin;

(e) the agent is an auristatin;

(f) the agent is a maytansinoid;

(g) the agent is a duocarmycin;

(h) the agent is a calicheamicin;

(i) the agent is a pyrrolobenzodiazepine;

(j) the agent is auristatin E;

(k) the agent is monomethyl auristatin E (MMAE);

(l) the agent is monomethyl auristatin D (MMAD);

(m) the agent is the maytansinoid DM1;

(n) the agent is the maytansinoid DM4;

(o) the agent is a detectable moiety; and

(p) the agent is a diagnostic agent.

25. The method of claim 17 , wherein the agent is conjugated to the AB via a linker.

26. The method of claim 17 , wherein the linker with which the agent is conjugated to the AB comprises an SPDB moiety, a vc moiety, or a PEG2-vc moiety.

27. The method of claim 17 , wherein the agent is a toxin conjugated to the AB via a linker, and wherein the linker and the toxin conjugated to the AB comprise a moiety selected from the group consisting of: an SPDB-DM4 moiety, a vc-MMAD moiety, a vc-MMAE moiety, a vc-duocarmycin moiety, or a PEG2-vc-MMAD moiety.

28. The method of claim 25 , wherein the linker is a cleavable linker.

29. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease in a subject in which diseased cells express CD166 or the disorder or disease is associated with cells expressing CD166, comprising:

administering to the subject a therapeutically effective amount of a conjugated activatable antibody that in an activated state binds CD166, the conjugated activatable antibody comprising:

an activatable antibody conjugated to an agent, the activatable antibody comprising:

an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian CD166, wherein the AB specifically binds human CD166 and cynomolgus monkey CD166;

a masking moiety (MM) that inhibits the binding of the AB to CD166 when the activatable antibody is in an uncleaved state; and

a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease,

wherein the activatable antibody comprises a combination of amino acid sequences, wherein the combination of amino acid sequences is selected from a single row in Table A, wherein for a given combination,

(i) the heavy chain of the AB comprises the amino acid sequences of the VH CDR sequences corresponding to the given combination in the single row listed in Table A,

(ii) the light chain of the AB comprises the amino acid sequences of the VL CDR sequences corresponding to the given combination in the single row listed in Table A,

(iii) the MM comprises the amino acid sequence of the mask sequence (MM) corresponding to the given combination in the single row listed in Table A, and

(iv) the CM comprises the amino acid sequence of the substrate sequence (CM) corresponding to the given combination in the single row listed in Table A.

30. The method of claim 29 , wherein the disorder or disease associated with cells expressing CD166 is cancer.

31. The method of claim 30 , wherein the cancer is an adenocarcinoma, a bile duct (biliary) cancer, a bladder cancer, a bone cancer, a breast cancer, a Her2-negative breast cancer, a triple-negative breast cancer (TNBC), an endometrial cancer, an estrogen receptor-positive breast cancer, a carcinoid, a cervical cancer, a cholangiocarcinoma, a colorectal cancer, a colon cancer, a glioma, a head and neck cancer, a head and neck squamous cell cancer (HNSCC), a leukemia, a liver cancer, a lung cancer, a non-small cell lung cancer (NSCLC), a small cell lung cancer (SCLC), a lymphoma, a melanoma, an oropharyngeal cancer, an ovarian cancer, a pancreatic cancer, a prostate cancer, a metastatic castration-resistant prostate carcinoma, a renal cancer, a sarcoma, a skin cancer, a squamous cell cancer, a stomach cancer, a testis cancer, a thyroid cancer, a urogenital cancer, or a urothelial cancer.

32. The method of claim 30 , wherein the cancer is a Her2-negative breast cancer.

33. The method of claim 30 , wherein the cancer is an estrogen receptor-positive breast cancer.

34. The method of claim 30 , wherein the cancer is a triple-negative breast cancer (TNBC).

35. The method of claim 29 , wherein the AB comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 122, and a light chain variable region comprising an amino acid sequence of SEQ ID NO: 123.

36. The method of claim 29 , wherein the antigen binding fragment thereof is selected from the group consisting of a Fab fragment, a F(ab′)2 fragment, a scFv, a scAb, and a dAb.

37. The method of claim 29 , wherein the MM is linked to the CM such that the activatable antibody in an uncleaved state comprises the structural arrangement from N-terminus to C-terminus as follows: MM-CM-AB or AB-CM-MM.

38. The method of claim 29 , wherein the activatable antibody comprises a first linking peptide (LP1) and a second linking peptide (LP2), wherein the activatable antibody in the uncleaved state has the structural arrangement from N-terminus to C-terminus as follows: MM-LP1-CM-LP2-AB or AB-LP2-CM-LP1-MM, and wherein each of LP1 and LP2 is a peptide of about 1 to 20 amino acids in length.

39. The method of claim 30 , wherein the two linking peptides are not identical to each other.

40. The method of claim 29 , wherein the agent has one or more of the characteristics selected from the group consisting of:

(a) the agent is a toxin or a fragment thereof;

(b) the agent is a microtubule inhibitor;

(d) the agent is a dolastatin;

(e) the agent is an auristatin;

(f) the agent is a maytansinoid;

(g) the agent is a duocarmycin;

(h) the agent is a calicheamicin;

(i) the agent is a pyrrolobenzodiazepine;

(j) the agent is auristatin E;

(k) the agent is monomethyl auristatin E (MMAE);

(l) the agent is monomethyl auristatin D (MMAD);

(m) the agent is the maytansinoid DM1;

(n) the agent is the maytansinoid DM4;

(o) the agent is a detectable moiety; and

(p) the agent is a diagnostic agent.

41. The method of claim 29 , wherein the agent is conjugated to the AB via a linker.

42. The method of claim 29 , wherein the linker with which the agent is conjugated to the AB comprises an SPDB moiety, a vc moiety, or a PEG2-vc moiety.

43. The method of claim 29 , wherein the agent is a toxin conjugated to the AB via a linker, and wherein the linker and the toxin conjugated to the AB comprise a moiety selected from the group consisting of: an SPDB-DM4 moiety, a vc-MMAD moiety, a vc-MMAE moiety, a vc-duocarmycin moiety, or a PEG2-vc-MMAD moiety.

44. The method of claim 29 , wherein the linker is a cleavable linker.

45. A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease in a subject in which diseased cells express CD166 or the disorder or disease is associated with cells expressing CD166, comprising:

administering to the subject a therapeutically effective amount of a conjugated activatable antibody that in an activated state binds CD166, the conjugated activatable antibody comprising:

an activatable antibody conjugated to an agent, the activatable antibody comprising:

an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian CD166, wherein the AB specifically binds human CD166 and cynomolgus monkey CD166;

a masking moiety (MM) that inhibits the binding of the AB to CD166 when the activatable antibody is in an uncleaved state; and

a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease,

wherein the activatable antibody comprises a combination of amino acid sequences, wherein for a given combination of amino acid sequences,

(i) the heavy chain of the AB comprises the amino acid sequences of the VH sequence or VH CDR sequences selected from the group consisting of: the VH sequence or VH CDR sequences listed in the corresponding column of Table B,

(ii) the light chain of the AB comprises the amino acid sequences of the VL sequence or VL CDR sequences selected from the group consisting of: the VL sequence or VL CDR sequences listed in the corresponding column of Table B,

(iii) the MM comprises the amino acid sequence of the mask sequence (MM) selected from the group consisting of: the MM sequences listed in the corresponding column of Table B, and

(iv) the CM comprises the amino acid sequence of the substrate sequence (CM) selected from the group consisting of: the CM sequences listed in the corresponding column of Table B.

46. The method of claim 45 , wherein the disorder or disease associated with cells expressing CD166 is cancer.

47. The method of claim 46 , wherein the cancer is an adenocarcinoma, a bile duct (biliary) cancer, a bladder cancer, a bone cancer, a breast cancer, a Her2-negative breast cancer, a triple-negative breast cancer (TNBC), an endometrial cancer, an estrogen receptor-positive breast cancer, a carcinoid, a cervical cancer, a cholangiocarcinoma, a colorectal cancer, a colon cancer, a glioma, a head and neck cancer, a head and neck squamous cell cancer (HNSCC), a leukemia, a liver cancer, a lung cancer, a non-small cell lung cancer (NSCLC), a small cell lung cancer (SCLC), a lymphoma, a melanoma, an oropharyngeal cancer, an ovarian cancer, a pancreatic cancer, a prostate cancer, a metastatic castration-resistant prostate carcinoma, a renal cancer, a sarcoma, a skin cancer, a squamous cell cancer, a stomach cancer, a testis cancer, a thyroid cancer, a urogenital cancer, or a urothelial cancer.

48. The method of claim 46 , wherein the cancer is a Her2-negative breast cancer.

49. The method of claim 46 , wherein the cancer is an estrogen receptor-positive breast cancer.

50. The method of claim 46 , wherein the cancer is a triple-negative breast cancer (TNBC).

51. The method of claim 45 , wherein the AB comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 121 or SEQ ID NO: 122, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 123-126.

52. The method of claim 45 , wherein the antigen binding fragment thereof is selected from the group consisting of a Fab fragment, a F(ab′)2 fragment, a scFv, a scAb, and a dAb.

53. The method of claim 45 , wherein the MM is linked to the CM such that the activatable antibody in an uncleaved state comprises the structural arrangement from N-terminus to C-terminus as follows: MM-CM-AB or AB-CM-MM.

54. The method of claim 45 , wherein the activatable antibody comprises a first linking peptide (LP1) and a second linking peptide (LP2), wherein the activatable antibody in the uncleaved state has the structural arrangement from N-terminus to C-terminus as follows: MM-LP1-CM-LP2-AB or AB-LP2-CM-LP1-MM, and wherein each of LP1 and LP2 is a peptide of about 1 to 20 amino acids in length.

55. The method of claim 54 , wherein the two linking peptides are not identical to each other.

56. The method of claim 45 , wherein the agent has one or more of the characteristics selected from the group consisting of:

(a) the agent is a toxin or a fragment thereof;

(b) the agent is a microtubule inhibitor;

(d) the agent is a dolastatin;

(e) the agent is an auristatin;

(f) the agent is a maytansinoid;

(g) the agent is a duocarmycin;

(h) the agent is a calicheamicin;

(i) the agent is a pyrrolobenzodiazepine;

(j) the agent is auristatin E;

(k) the agent is monomethyl auristatin E (MMAE);

(l) the agent is monomethyl auristatin D (MMAD);

(m) the agent is the maytansinoid DM1;

(n) the agent is the maytansinoid DM4;

(o) the agent is a detectable moiety; and

(p) the agent is a diagnostic agent.

57. The method of claim 45 , wherein the agent is conjugated to the AB via a linker.

58. The method of claim 45 , wherein the linker with which the agent is conjugated to the AB comprises an SPDB moiety, a vc moiety, or a PEG2-vc moiety.

59. The method of claim 45 , wherein the agent is a toxin conjugated to the AB via a linker, and wherein the linker and the toxin conjugated to the AB comprise a moiety selected from the group consisting of: an SPDB-DM4 moiety, a vc-MMAD moiety, a vc-MMAE moiety, a vc-duocarmycin moiety, or a PEG2-vc-MMAD moiety.

60. The method of claim 57 , wherein the linker is a cleavable linker.

61. A pharmaceutical composition comprising a conjugated activatable antibody that in an activated state binds CD166, and a carrier, the conjugated activatable antibody comprising:

an activatable antibody conjugated to an agent, the activatable antibody comprising:

62. A pharmaceutical composition comprising a conjugated activatable antibody that in an activated state binds CD166, and a carrier, the conjugated activatable antibody comprising:

an activatable antibody conjugated to an agent, the activatable antibody comprising:

an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian CD166, wherein the AB specifically binds human CD166 and cynomolgus monkey CD166;

a masking moiety (MM) that inhibits the binding of the AB to CD166 when the activatable antibody is in an uncleaved state; and

a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease,

63. A pharmaceutical composition comprising a conjugated activatable antibody that in an activated state binds CD166, and a carrier, the conjugated activatable antibody comprising: