ANTI-CLL-1 ANTIBODIES AND METHODS OF USE

• US 20160368994A1
• Filed: 06/14/2016
• Published: 12/22/2016
• Est. Priority Date: 06/16/2015
• Status: Active Grant

• Current Assignee: Genentech, Inc. (Roche Holding AG)
• Original Assignee: Genentech, Inc. (Roche Holding AG)
• Inventors: Mathieu, Mary, Kelley, Robert F., Leong, Steven R., Liang, Wei-Ching, Polson, Andrew G., Zheng, Bing, Chen, Xiaocheng, Chiu, Cecilia Pui Chi, Dennis, Mark S., Ebens, Allen, Wu, Yan
• Granted Patent: US 10,501,545 B2
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A61K 2039/505 comprising antibodies
• CPC Class Codes: A61K 2039/507 Comprising a combination of two or more separate antibodies
• CPC Class Codes: A61K 2039/57 characterised by the type of response, e.g. Th1, Th2
• CPC Class Codes: A61K 39/3955 against proteinaceous materials, e.g. enzymes, hormones, lymphokines
• CPC Class Codes: A61K 45/06 Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/02 specific for leukemia
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 37/04 Immunostimulants
• CPC Class Codes: C07K 16/2803 against the immunoglobulin superfamily
• CPC Class Codes: C07K 16/2809 against the T-cell receptor (TcR)-CD3 complex
• CPC Class Codes: C07K 16/2827 against B7 molecules, e.g. CD80, CD86
• CPC Class Codes: C07K 16/2851 against the lectin superfamily, e.g. CD23, CD72
• CPC Class Codes: C07K 16/3061 Blood cells
• CPC Class Codes: C07K 2317/14 Specific host cells or culture conditions, e.g. components, pH or temperature
• CPC Class Codes: C07K 2317/24 containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• CPC Class Codes: C07K 2317/31 multispecific
• CPC Class Codes: C07K 2317/33 Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
• CPC Class Codes: C07K 2317/34 Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
• CPC Class Codes: C07K 2317/40 characterized by post-translational modification
• CPC Class Codes: C07K 2317/41 : Glycosylation, sialylation, or fucosylation
• CPC Class Codes: C07K 2317/52 : Constant or Fc region; Isotype
• CPC Class Codes: C07K 2317/526 : CH3 domain
• CPC Class Codes: C07K 2317/55 : Fab or Fab'
• CPC Class Codes: C07K 2317/56 : variable (Fv) region, i.e. VH and/or VL
• CPC Class Codes: C07K 2317/73 : Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
• CPC Class Codes: C07K 2317/76 : Antagonist effect on antigen, e.g. neutralization or inhibition of binding
• CPC Class Codes: C07K 2317/77 : Internalization into the cell
• CPC Class Codes: C07K 2317/90 : characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
• CPC Class Codes: C07K 2317/92 : Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
• CPC Class Codes: C07K 2317/94 : Stability, e.g. half-life, pH, temperature or enzyme-resistance

Abstract

The present invention relates to anti-CLL-1 antibodies including anti-CLL-1 antibodies comprising a CLL-1 binding domain and a CD3 binding domain (e.g., anti-CLL-1/CD3 T cell dependent bispecific (TDB) antibody) and methods of using the same.

Claims

1. An isolated anti-CLL-1 antibody, wherein the antibody comprises

(i) a CLL-1 binding domain, wherein the CLL-1 binding domain binds a CLL-1 epitope and/or binds an overlapping CLL-1 epitope comprising amino acids of SEQ ID NO:

49 and does not bind an epitope comprising SEQ ID NO;

50 and/or SEQ ID NO;

51; and

(ii) a CD3 binding domain, wherein the CD3 binding domain binds a human CD3ε

polypeptide and a cyno CD3ε

polypeptide, the CD3 binding domain binds to a CD3 epitope within a fragment of the human CD3ε

polypeptide consisting of amino acids 1-26 (SEQ ID NO;

86) or 1-27 (SEQ ID NO;

87) of human CD3ε

, and amino acid residue Glu5 of the human CD3ε

polypeptide is not required for binding of the CD3 binding domain.

2. The anti-CLL-1 antibody of claim 1, wherein the CLL-1 epitope is determined by hydroxyl radical footprinting.

3. The anti-CLL-1 antibody of claim 1, wherein the CLL-1 binding domain comprises the following six hypervariable regions (HVRs):

(a) an HVR-H1 comprising the amino acid sequence of SEQ ID NO;

8;

(b) an HVR-H2 comprising the amino acid sequence of SEQ ID NO;

45;

(c) an HVR-H3 comprising the amino acid sequence of SEQ ID NO;

10;

(d) an HVR-L1 comprising the amino acid sequence of SEQ ID NO;

5;

(e) an HVR-L2 comprising the amino acid sequence of SEQ ID NO;

6; and

(f) an HVR-L3 comprising the amino acid sequence of SEQ ID NO;

7.

4. The anti-CLL-1 antibody of claim 3, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:

9.

5. The anti-CLL-1 antibody of claim 3, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:

47.

6. The anti-CLL-1 antibody of claim 5, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:

11.

7. The anti-CLL-1 antibody of claim 5, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:

43.

8. The anti-CLL-1 antibody of claim 5, wherein the CLL-1 binding domain comprises HVR-H2 comprising the amino acid sequence of SEQ ID NO:

44.

9. The anti-CLL-1 antibody of claim 3, wherein the antibody comprises a CLL-1 binding domain comprising:

a) a heavy chain variable region comprising the sequence of SEQ ID NO;

33 and a light chain variable region comprising the sequence of SEQ ID NO;

32;

b) a heavy chain variable region comprising the sequence of SEQ ID NO;

34 and a light chain variable region comprising the sequence of SEQ ID NO;

32;

c) a heavy chain variable region comprising the sequence of SEQ ID NO;

46 and a light chain variable region comprising the sequence of SEQ ID NO;

32;

or

d) a heavy chain variable region comprising the sequence of SEQ ID NO;

48 and a light chain variable region comprising the sequence of SEQ ID NO;

32.

10. The anti-CLL-1 antibody of any one of claim 1, wherein the CLL-1 binding domain comprises the following six HVRs:

(a) HVR-H1 comprising the amino acid sequence of SEQ ID NO;

21;

(b) HVR-H2 comprising the amino acid sequence of SEQ ID NO;

22;

(c) HVR-H3 comprising the amino acid sequence of SEQ ID NO;

23;

(d) HVR-L1 comprising the amino acid sequence of SEQ ID NO;

18;

(e) HVR-L2 comprising the amino acid sequence of SEQ ID NO;

19; and

(f) HVR-L3 comprising the amino acid sequence of SEQ ID NO;

20.

11. The anti-CLL-1 antibody of claim 9, wherein the antibody comprises a CLL-1 binding domain comprising:

(a) a heavy chain variable region comprising the sequence of SEQ ID NO;

40 and (b) a light chain variable region comprising the sequence of SEQ ID NO;

39.

12. The anti-CLL-1 antibody of claim 1, wherein the antibody comprises a CLL-1 binding domain has one or more of the following characteristics:

a. binds to recombinant human CLL-1;

b. binds to recombinant cynomolgus monkey CLL-1;

c. binds to endogenous CLL-1 on the surface of human peripheral blood mononucleocytes (PBMCs);

d. binds to endogenous CLL-1 on the surface of cynomolgus monkey PBMCs;

e. binds to endogenous CLL-1 on the surface of a cancer cell;

f. binds to endogenous CLL-1 on the surface of an AML cancer cell;

g. binds to endogenous CLL-1 on the surface of HL-60 cells;

h. binds to endogenous CLL-1 on the surface of EOL-1 cells;

i. binds to CLL-1 comprising a K244Q mutation;

j. competes for human CLL-1 binding with R&

D clone 687317antibody;

k. binds to endogenous human CLL-1 with a Kd of less than 15 nM, less than 10 nM, less than 7 nM, less than 5 nM, or less than 3 nM;

l. binds to recombinant human CLL-1 with a Kd of less than 10 nM, less than 7 nM, less than 5 nM, or less than 3 nM; and

/or m. binds to recombinant cynomolgus monkey CLL-1 with a Kd of less than 10 nM, less than 7 nM, less than 5 nM, or less than 3 nM, less than 2 nM, or less than 1 nM.

13. The anti-CLL-1 antibody of claim 1, wherein the antibody comprises a CD3 binding domain which binds a CD3 epitope comprising and/or consisting of Gln1, Asp2, Glu6, and Met7 of human CD3ε

polypeptide.

14. The anti-CLL-1 antibody of claim 1, wherein the antibody comprises a CD3 binding domain comprises the following six HVRs:

(a) HVR-H1 comprising the amino acid sequence of SEQ ID NO;

88;

(b) HVR-H2 comprising the amino acid sequence of SEQ ID NO;

89;

(c) HVR-H3 comprising the amino acid sequence of SEQ ID NO;

90;

(d) HVR-L1 comprising the amino acid sequence of SEQ ID NO;

74;

(e) HVR-L2 comprising the amino acid sequence of SEQ ID NO;

91; and

(f) HVR-L3 comprising the amino acid sequence of SEQ ID NO;

92.

15. The anti-CLL-1 antibody of claim 1, wherein the CD3 binding domain comprises (a) HVR-H1 comprising the amino acid sequence of SEQ ID NO:

71;

(b) HVR-H2 comprising the amino acid sequence of SEQ ID NO;

72;

(c) HVR-H3 comprising the amino acid sequence of SEQ ID NO;

73;

(e) HVR-L2 comprising the amino acid sequence of SEQ ID NO;

75; and

(f) HVR-L3 comprising the amino acid sequence of SEQ ID NO;

76.

16. The anti-CLL-1 antibody of claim 14, wherein the CD3 binding domain comprises (a) HVR-H1 comprising the amino acid sequence of SEQ ID NO:

77;

(b) HVR-H2 comprising the amino acid sequence of SEQ ID NO;

78;

(c) HVR-H3 comprising the amino acid sequence of SEQ ID NO;

79; and

(e) HVR-L2 comprising the amino acid sequence of SEQ ID NO;

80.

17. The anti-CLL-1 antibody of claim 16, wherein the CD3 binding domain comprises (f) HVR-L3 comprising the amino acid sequence of SEQ ID NO:

81.

18. The anti-CLL-1 antibody of claim 16, wherein the CD3 binding domain comprises (f) HVR-L3 comprising the amino acid sequence of SEQ ID NO:

76.

19. The anti-CLL-1 antibody of claim 14, the antibody comprises a CD3 binding domain comprising:

a) a heavy chain variable region comprising the sequence of SEQ ID NO;

82 and a light chain variable region comprising the sequence of SEQ ID NO;

83;

b) a heavy chain variable region comprising the sequence of SEQ ID NO;

84 and a light chain variable region comprising the sequence of SEQ ID NO;

85;

or

c) a heavy chain variable region comprising the sequence of SEQ ID NO;

84 and a light chain variable region comprising the sequence of SEQ ID NO;

93.

20. The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody is a monoclonal, human, humanized, or chimeric antibody.

21. The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody is an IgG antibody.

22. The anti-CLL-1 antibody of claim 1, wherein the antibody is a bispecific antibody.

23. The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody is an antibody fragment that binds CLL-1 and CD3.

24. The anti-CLL-1 antibody of claim 23, wherein the anti-CLL-1 antibody fragment is a Fab, Fab′

-SH, Fv, scFv, and/or (Fab′

)₂ fragment.

25. The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody is a full-length antibody.

26. The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody comprises an aglycosylation site mutation.

27. The anti-CLL-1 antibody of claim 26, wherein the aglycosylation site mutation is a substitution mutation.

28. The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody comprises reduced effector function.

29. The anti-CLL-1 antibody of claim 1, wherein the anti-CLL-1 antibody comprises a substitution mutation is at amino acid residue N297, L234, L235, D265, and/or P329G according to EU numbering.

30. The anti-CLL-1 antibody of claim 29, wherein the substitution mutation is selected from the group consisting of N297G, N297A, L234A, L235A, D265A, and P329G according to EU numbering.

31. The anti-CLL-1 antibody of claim 29, wherein the antibody comprises an N297G substitution mutation at amino acid residue 297 according to EU numbering.

32. The anti-CLL-1 antibody of claim 1, wherein (a) the CD3 binding domain comprises a Fc domain, wherein the Fc domain comprises T366S, L368A, Y407V, and N297G substitution mutations according EU numbering and (b) the CLL-1 binding domain comprises a Fc domain, wherein the Fc domain comprises T366W and N297G substitution mutations according EU numbering.

33. An isolated nucleic acid encoding the anti-CLL-1 antibody of claim 1.

34. A vector comprising the isolated nucleic acid of claim 33.

35. A host cell comprising the vector of claim 34.

36. A method of producing the anti-CLL-1 antibody of claim 1, the method comprising culturing the host cell of claim 35 in a culture medium.

37. A pharmaceutical composition comprising the anti-CLL-1 antibody of claim 1.

38. A method of treating or delaying the progression of a cell proliferative disorder or an autoimmune disorder in a subject in need thereof, the method comprising administering to the subject the anti-CLL-1 antibody of claim 1.

39. A method of enhancing immune function in a subject having a cell proliferative disorder or an autoimmune disorder, the method comprising administering to the subject an effective amount of the anti-CLL-1 antibody of claim 1.

40. The method of claim 38, wherein the cell proliferative disorder is a cancer.

41. The method of claim 40, wherein the cell proliferative disorder is AML, CML, and/or MDS.

42. The method of claim 38, further comprising administering to the subject daunorubicin and/or cytarabine.

43. The method of claim 38, further comprising administering to the subject a glucocorticoid (such as dexamethasone).

44. The method of claim 38, further comprising administering to the subject a PD-1 axis binding antagonist (such as an anti-PD-L1 antibody).

45. The method of claim 44, wherein the PD-1 axis binding antagonist is an anti-PD-L1 antibody.

46. The method of claim 45, wherein the anti-PD-L1 antibody comprises:

(a) the HVR-H1 sequence is GFTFSDSWIH (SEQ ID NO;

99);

(b) the HVR-H2 sequence is AWISPYGGSTYYADSVKG (SEQ ID NO;

100);

(c) the HVR-H3 sequence is RHWPGGFDY (SEQ ID NO;

98);

(d) the HVR-L1 sequence is RASQDVSTAVA (SEQ ID NO;

104);

(e) the HVR-L2 sequence is SASFLYS, (SEQ ID NO;

105); and

(f) the HVR-L3 sequence is QQYLYHPAT (SEQ ID NO;

106).

47. The method of claim 45, wherein the anti-PD-L1 antibody comprises the heavy chain variable region of SEQ ID NO:

94 and the light chain variable region of SEQ ID NO;

95.

48. The method of claim 45, wherein the anti-PD-L1 antibody is MPDL3280A.