Single-Chain Multivalent Binding Proteins with Effector Function

• US 20090175867A1
• Filed: 03/03/2008
• Published: 07/09/2009
• Est. Priority Date: 06/12/2006
• Status: Abandoned Application

• Current Assignee: Emergent Product Development Seattle, LLC
• Original Assignee: Trubion Pharmaceuticals Inc.
• Inventors: Ledbetter, Jeffrey A., Brady, William, Hayden-Ledbetter, Martha S., Thompson, Peter A.
• Application Number:
  US12/041,590
• Publication Number:
  US 20090175867A1
• Time in Patent Office: Days
• US Class Current: 424/135.100
• 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: A61P 1/04 for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
• CPC Class Codes: A61P 11/06 Antiasthmatics
• CPC Class Codes: A61P 17/06 Antipsoriatics
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 25/04 Centrally acting analgesics, e.g. opioids
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 3/10 for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 31/22 for herpes viruses
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/00 Drugs for immunological or allergic disorders
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 37/06 Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07K 16/18 against material from animals or humans
• CPC Class Codes: C07K 16/28 against receptors, cell surface antigens or cell surface determinants
• 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 16/2818 : against CD28 or CD152
• CPC Class Codes: C07K 16/2827 : against B7 molecules, e.g. CD80, CD86
• CPC Class Codes: C07K 16/2833 : against MHC-molecules, e.g. HLA-molecules
• CPC Class Codes: C07K 16/2851 : against the lectin superfamily, e.g. CD23, CD72
• CPC Class Codes: C07K 16/2875 : against the NGF/TNF superfamily, e.g. CD70, CD95L, CD153, CD154 against NGF C07K16/22, against TNF C07K16/241
• CPC Class Codes: C07K 16/2878 : against the NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
• CPC Class Codes: C07K 16/2887 : against CD20
• CPC Class Codes: C07K 16/2896 : against molecules with a "CD"-designation, not provided for elsewhere
• CPC Class Codes: C07K 16/30 : from tumour cells
• CPC Class Codes: C07K 16/46 : Hybrid immunoglobulins hybrids of an immunoglobulin with a peptide not being an immunoglobulin C07K19/00
• CPC Class Codes: C07K 16/468 : Immunoglobulins having two or more different antigen binding sites, e.g. multifunctional antibodies
• 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 2317/34 : 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 2317/52 : Constant or Fc region; Isotype
• CPC Class Codes: C07K 2317/53 : Hinge
• CPC Class Codes: C07K 2317/622 : Single chain antibody (scFv)
• CPC Class Codes: C07K 2317/64 : comprising a combination of variable region and constant region components
• CPC Class Codes: C07K 2317/732 : Antibody-dependent cellular cytotoxicity [ADCC]
• CPC Class Codes: C07K 2317/734 : Complement-dependent cytotoxicity [CDC]
• CPC Class Codes: C07K 2319/30 : Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto

Abstract

Multivalent binding peptides, including bi-specific binding peptides, having immunoglobulin effector function are provided, along with encoding nucleic acids, vectors and host cells as well as methods for making such peptides and methods for using such peptides to treat or prevent a variety of diseases, disorders or conditions, as well as to ameliorate at least one symptom associated with such a disease, disorder or condition.

Claims

1. A multivalent single-chain binding protein with effector function comprising

a. a first binding domain derived from an immunoglobulin or immunoglobulin-like molecule;

b. a constant sub-region providing an effector function, the immunoglobulin constant sub-region located C-terminal to the first binding domain;

c. a scorpion linker located C-terminal to the constant sub-region; and

d. a second binding domain derived from an immunoglobulin or immunoglobulin-like molecule located C-terminal to the constant sub-region;

thereby localizing the constant sub-region between the first binding domain and the second binding domain.

2. The protein according to claim 1 wherein at least one of the first binding domain and the second binding domain comprises a variable light region derived from a first immunoglobulin and a variable heavy region derived from a second immunoglobulin.

3. The protein according to claim 1 wherein at least one of the first binding domain and the second binding domain comprises a variable light region and a variable heavy region derived from the same immunoglobulin.

4. The protein according to claim 1 wherein the first binding domain and the second binding domain recognize the same molecular target.

5. The protein according to claim 1 wherein the first binding domain and the second binding domain recognize the same epitope.

6. The protein according to claim 1 wherein the first binding domain and the second binding domain recognize different molecular targets on the same eukaryotic cell, prokaryotic cell, virus, carrier, or object.

7. The protein according to claim 1 wherein the first binding domain and the second binding domain recognize molecular targets associated with physically distinct eukaryotic cells, prokaryotic cells, viruses, carriers or objects.

8. The protein according to claim 1 wherein at least one of the first binding domain and the second binding domain recognize at least one molecular target not associated with a eukaryotic cell, prokaryotic cell, virus, carrier or object.

9. The protein according to claim 1 wherein the first binding domain, the second binding domain and the constant sub-region are each derived from a human immunoglobulin.

10. The protein according to claim 1 wherein at least one of the first binding domain and the second binding domain recognizes a target on a cancer cell.

11. The protein according to claim 9 wherein at least one of the first binding domain and the second binding domain recognizes a target selected from the group consisting of a tumor antigen, a B-cell target, a TNF receptor superfamily member, a Hedgehog family member, a receptor tyrosine kinase, a proteoglycan-related molecule, a TGF-beta superfamily member, a Wnt-related molecule, a receptor ligand, a T-cell target, a Dendritic cell target, an NK cell target, a monocyte/macrophage cell target and an angiogenesis target.

12. The protein according to claim 10 wherein the cancer cell is a transformed hematopoietic cell.

13. The protein according to claim 12 wherein at least one of the first binding domain and the second binding domain recognizes a target selected from the group consisting of a B-cell target, a T-cell target, a dendritic cell target, a myeloid cell target, or an NK-cell target.

14. The protein according to claim 12 wherein at least one of the first binding domain and the second binding domain recognizes a target selected from the group consisting of CD5, CD10, CD11c, CD15, CD19, CD20, CD21, CD22, CD23, CD25, CD27, CD30, CD38, CD45, CD70, CD72, CD79a, CD79b, CD80, CD86, CD103, IRTA1, IRTA2, IRTA3, IRTA4, IRTA5, B-B2, B-B8, a MHC Class II peptide, and B-cell antigen receptor.

15. The protein according to claim 1 comprising a sequence selected from the group consisting of SEQ ID NOS:

2, 4, 6, 103, 105, 107, 109, 333, and 334.

16. The protein according to claim 1 wherein the constant sub-region recognizes an effector cell F_C receptor.

17. The protein according to claim 1 wherein the constant sub-region recognizes an effector cell surface protein selected from the group consisting of CD16, CD32a, CD32b, CD64, CD89, Fcε

R1, FcRn, and pIgR.

18. The protein according to claim 1 wherein the constant sub-region comprises a C_H2 domain and a C_H3 domain.

19. The protein according to claim 18, wherein the C_H3 domain is truncated and comprises a C-terminal sequence selected from the group consisting of SEQ ID NOS:

366, 367, 368, 369, 370 and 371.

20. The protein according to claim 1, wherein the scorpion linker is derived from an interdomain region of an immunoglobulin superfamily member.

21. The protein according to claim 1, wherein the scorpion linker is derived from an an immunoglobulin hinge.

22. The protein according to claim 21, wherein the scorpion linker has a reduced, but non-zero, number of cysteines relative to the hinge from which the scorpion linker is derived, and wherein one cysteine corresponds to the N-terminal hinge cysteine of the immunoglobulin hinge.

23. The protein according to claim 22 wherein the scorpion linker is derived from an IgG1 hinge region and wherein the linker comprises 1 or 2 cysteines, further wherein the linker retains the cysteine corresponding to an N-terminal hinge cysteine of the IgG1 hinge region.

24. The protein according to claim 1, wherein the scorpion linker is derived from the stalk region of a C-type lectin.

25. The protein according to claim 1, wherein the scorpion linker comprises a sequence selected from the group consisting of SEQ ID NOS:

373, 374, 375, 376, 377, 380 and 381.

26. The protein according to claim 1 further comprising an N-terminal proximal linker of at least about 5 amino acids attached to the constant sub-region and attached to the first binding domain, thereby localizing the linker between the constant sub-region and the first binding domain.

27. The protein according to claim 1 in which the binding affinity of at least one of the first binding domain and the second binding domain is about 10⁻

6M to 10<sup>−

9</sup> M.

28. The protein according to claim 1, wherein the effector function is selected from the group consisting of antibody-dependent cell-mediated cytotoxicity (ADCC) complement-dependent cytotoxicity (CDC), antibody-dependent cellular phagocytosis (ADCP) and F_CR binding.

29. The protein according to claim 1, wherein the in vivo half-life of the protein is at least 28 hours in a human.

30. A pharmaceutical composition comprising the protein according to claim 1 and a pharmaceutically acceptable adjuvant, carrier or excipient.

31. A nucleic acid encoding a protein according to claim 1.

32. A vector comprising a nucleic acid according to claim 31.

33. A host cell comprising a vector according to claim 32.

34. A method of producing the protein according to claim 1 comprising:

a. introducing a nucleic acid encoding the protein according to claim 1 into a host cell; and

b. incubating the host cell under conditions suitable for expression of the protein, thereby expressing the protein.

35. The method according to claim 34 further comprising isolating the protein.

36. A method of producing a nucleic acid encoding the protein according to claim 1 comprising:

a. covalently linking the 3′

end of a polynucleotide encoding a first binding domain derived from an immunoglobulin variable region to the 5′

end of a polynucleotide encoding a constant sub-region;

b. covalently linking the 5′

end of a polynucleotide encoding a scorpion linker to the 3′

end of the polynucleotide encoding the constant sub-region; and

c. covalently linking the 5′

end of a polynucleotide encoding a second binding domain derived from an immunoglobulin variable region to the 3′

end of the polynucleotide encoding the scorpion linker,

thereby generating a nucleic acid encoding a multivalent binding protein with effector function.

37. The method according to claim 36 wherein the polynucleotide encoding a first binding domain comprises a sequence selected from the group consisting of SEQ ID NO:

1 (anti-CD20 variable region), SEQ ID NO;

3 (anti-CD28 variable region, oriented V_L-V_H) and SEQ ID NO;

5 (anti-CD28 variable region, oriented V_H-V_L).

38. The method according to claim 36, further comprising a linker polynucleotide inserted between the polynucleotide encoding a first binding domain and the polynucleotide encoding a constant sub-region, the linker polynucleotide encoding a peptide linker of at least 5 amino acids.

39. The method according to claim 36, further comprising a linker polynucleotide inserted between the polynucleotide encoding a constant sub-region and the polynucleotide encoding a second binding domain, the linker polynucleotide encoding a peptide linker of at least 5 amino acids.

40. A method of inducing damage to a target cell comprising contacting a target cell with a therapeutically effective amount of a protein according to claim 1.

41. The method according to claim 40 wherein the target cell is contacted in vivo by administration of the protein to an organism in need.

42. A method of treating a cell proliferation disorder comprising administering a therapeutically effective amount of a protein according to claim 1 to an organism in need.

44. The method according to claim 43 wherein the protein is administered by in vivo expression of a nucleic acid encoding the protein according to claim 1.

46. A method of ameliorating a symptom associated with a disorder selected from the group consisting of a cancer, an autoimmune disorder, an infectious disease and inflammation comprising administering a therapeutically effective amount of a protein according to claim 1 to an organism in need.

47. The method according to claim 46, wherein the symptom is selected from the group consisting of pain, heat, swelling and joint stiffness.

48. A method of treating an infection associated with an infectious agent comprising administering a therapeutically effective amount of the protein according to claim 1 to a patient in need, wherein the protein comprises a binding domain that specifically binds a target molecule of the infectious agent.

49. A method of ameliorating a symptom of an infection associated with an infectious agent comprising administering an effective amount of the protein according to claim 1 to a patient in need, wherein the protein comprises a binding domain that specifically binds a target molecule of the infectious agent.

50. A method of reducing the risk of infection attributable to an infectious agent comprising administering a prophylactically effective amount of the protein according to claim 1 to a patient at risk of developing the infection, wherein the protein comprises a binding domain that specifically binds a target molecule of the infectious agent.

51. A kit comprising the protein according to claim 1 and a set of instructions for administering the protein to treat a cell proliferation disorder or to ameliorate a symptom of the cell proliferation disorder.

52. The multivalent single-chain binding protein according to claim 1 wherein at least one of the first binding domain and the second binding domain specifically binds an antigen selected from the group consisting of CD19, CD20, CD21, CD22, CD23, CD30, CD37, CD40, CD70, CD72, CD79a, CD79b, CD80, CD81, CD86, and a major histocompatibility complex class II peptide.

53. The protein according to claim 52 wherein one of the first binding domain and the second binding domain specifically binds CD20.

54. The protein according to claim 53 wherein the other binding domain specifically binds an antigen selected from the group consisting of CD19, CD20, CD21, CD22, CD23, CD30, CD37, CD40, CD70, CD72, CD79a, CD79b, CD80, CD81, CD86, and a major histocompatibility complex class II peptide.

55. The protein according to claim 52 wherein one of the first binding domain and the second binding domain specifically binds CD79b.

56. The protein according to claim 55 wherein the other binding domain specifically binds an antigen selected from the group consisting of CD19, CD20, CD21, CD22, CD23, CD30, CD37, CD40, CD70, CD72, CD79a, CD79b, CD80, CD81, CD86, and a major histocompatibility complex class II peptide.

57. The protein according to claim 52 wherein one of the first binding domain and the second binding domain specifically binds a major histocompatibility complex class II peptide.

58. The protein according to claim 57 wherein the other binding domain specifically binds an antigen selected from the group consisting of CD19, CD20, CD21, CD22, CD23, CD30, CD37, CD40, CD70, CD72, CD79a, CD79b, CD80, CD81, CD86, and a major histocompatibility complex class II peptide.

59. The protein according to claim 52 wherein one of the first binding domain and the second binding domain specifically binds CD22.

60. The protein according to claim 59 wherein the other binding domain specifically binds an antigen selected from the group consisting of CD19, CD20, CD21, CD22, CD23, CD30, CD37, CD40, CD70, CD72, CD79a, CD79b, CD80, CD81, CD86 and a major histocompatibility complex class II peptide.

61. The protein according to claim 52 wherein the protein has at least an additive effect on a target cell behavior relative to the sum of the effects of each of the binding domains, and wherein the protein comprises a binding domain pair specifically recognizing a pair of antigens selected from the group consisting of CD20-CD19, CD20-CD21, CD20-CD22, CD20-CD23, CD20-CD30, CD20-CD37, CD20-CD40, CD20-CD70, CD20-CD79a, CD20-CD79b, CD20-CD80, CD20-CD81, CD20-CD86, CD79b-CD19, CD79b-CD23, CD79b-CD30, CD79b-CD37, CD79b-CD72, CD79b-CD81, CD79b-major histocompatibility complex class II (CL II), CL II-CD19, CL II-CD30, CL II-CD37, CL II-CD72, CL II-CD79a, CL II-CD81, CD19-CD37, CD19-CD79a, CD37-CD79a, CD81-CD37, and CD81-CD72.

62. The protein according to claim 52 wherein the protein has a synergistic effect on a target cell behavior relative to the sum of the effects of each of the binding domains, and wherein the protein comprises a binding domain pair specifically recognizing a pair of antigens selected from the group consisting of CD20-CD19, CD20-CD21, CD20-CD22, CD20-CD79a, CD20-CD79b, CD20-CD81, CD79b-CD37, major histocompatibility complex class II (CL II)-CD19, CL II-CD30, CL II-CD37, and CL II-CD72.

63. The protein according to claim 52 wherein the protein has an inhibitory effect on a target cell behavior relative to the sum of the effects of each of the binding domains, and wherein the protein comprises a binding domain pair specifically recognizing a pair of antigens selected from the group consisting of CD22-CD19, CD22-CD21, CD22-CD23, CD22-CD30, CD22-CD37, CD22-CD40, CD22-CD70, CD22-CD72, CD22-CD79a, CD22-CD79b, and CD22-major histocompatibility complex class II (CL II).

64. A method of identifying at least one of the binding domains of the multivalent binding molecule according to claim 1 comprising:

(a) linking an antibody specifically recognizing a first antigen and an antibody specifically recognizing a second antigen;

(b) contacting a target comprising at least one of the antigens with the composition of step (a); and

(c) measuring an activity of the target, wherein the activity is used to identify at least one of the binding domains of the multivalent binding molecule.

65. The method according to claim 64 wherein the target is a diseased cell.

66. The method according to claim 40 wherein the multivalent single-chain binding protein induces a synergistic amount of damage to the target cell compared to the sum of the damage induced by a first antibody comprising the first binding domain but not the second binding domain and a second antibody comprising the second binding domain but not the first binding domain.

67. The method according to claim 66 wherein the multivalent single-chain binding protein comprises a binding domain pair specifically recognizing a pair of antigens selected from the group consisting of CD20-CD40, CD20-CD79a, CD20-CD79b, CD20-CD81, CD79b-CD37, CD79b-CD81, major histocompatibility complex class II (CL II)-CD37, CL II-CD72 and CL II-CD79b.

68. The method according to claim 40 wherein the multivalent single-chain binding protein induces at least an additive amount of damage to the target cell compared to the sum of the damage induced by a first antibody comprising the first binding domain but not the second binding domain and a second antibody comprising the second binding domain but not the first binding domain.

69. The method according to claim 68 wherein the multivalent single-chain binding protein comprises a binding domain pair specifically recognizing a pair of antigens selected from the group consisting of CD20-CD19, CD20-CD21, CD20-CD22, CD20-CD23, CD20-CD30, CD20-CD37, CD20-CD40, CD20-CD70, CD20-CD79a, CD20-CD79b, CD20-CD80, CD20-CD81, CD20-CD86, CD79b-CD19, CD79b-CD23, CD79b-CD30, CD79b-CD37, CD79b-CD72, CD79b-CD81, CD79b-major histocompatibility complex class II (CL II), CL II-CD19, CL II-CD30, CL II-CD37, CL II-CD72, CL II-CD79a, CL II-CD81, CD19-CD37, CD19-CD79a, CD37-CD79a, CD81-CD37, and CD81-CD72.

70. The method according to claim 40 wherein the multivalent single-chain binding protein induces an inhibited amount of damage to the target cell compared to the sum of the damage induced by a first antibody comprising the first binding domain but not the second binding domain and a second antibody comprising the second binding domain but not the first binding domain.

71. The method according to claim 70 wherein the multivalent single-chain binding protein comprises a binding domain pair specifically recognizing a pair of antigens selected from the group consisting of CD22-CD19, CD22-CD21, CD22-CD23, CD22-CD30, CD22-CD37, CD22-CD40, CD22-CD70, CD22-CD72, CD22-CD79a, CD22-CD79b, and CD22-major histocompatibility complex class II (CL II).

72. The method according to claim 40 further comprising a plurality of multivalent single-chain binding proteins.

73. The method according to claim 72 wherein a binding domain of a first multivalent single-chain binding protein and a binding domain of a second multivalent single-chain binding protein induce a synergistic amount of damage to the target cell.

74. The method according to claim 72 wherein a binding domain of a first multivalent single-chain binding protein and a binding domain of a second multivalent single-chain binding protein induce at least an additive amount of damage to the target cell.

75. The method according to claim 72 wherein a binding domain of a first multivalent single-chain binding protein and a binding domain of a second multivalent single-chain binding protein induce an inhibited amount of damage to the target cell.

76. A composition comprising a plurality of multivalent single-chain binding proteins according to claim 1.

77. The composition according to claim 76 wherein a binding domain of a first multivalent single-chain binding protein and a binding domain of a second multivalent single-chain binding protein are capable of inducing a synergistic amount of damage to a target cell.

78. The composition according to claim 76 wherein a binding domain of a first multivalent single-chain binding protein and a binding domain of a second multivalent single-chain binding protein are capable of inducing an additive amount of damage to a target cell.

79. The composition according to claim 76 wherein a binding domain of a first multivalent single-chain binding protein and a binding domain of a second multivalent single-chain binding protein are capable of inducing an inhibited amount of damage to a target cell.

80. A pharmaceutical composition comprising the composition according to claim 76 and a pharmaceutically acceptable carrier, diluent or excipient.

81. A kit comprising the composition according to claim 76 and a set of instructions for administering the composition to damage a target cell.

43. A method of treating a disorder selected from the group consisting of a cancer, an autoimmune disorder, an infectious disease and inflammation.

45. The method according to claim 43 wherein the protein is administered by a route selected from the group consisting of intravenous injection, intraarterial injection, intramuscular injection, subcutaneous injection, intraperitoneal injection and direct tissue injection.