Heterodimer Binding Proteins and Uses Thereof

• US 20130129723A1
• Filed: 12/29/2010
• Published: 05/23/2013
• Est. Priority Date: 12/29/2009
• Status: Abandoned Application

• Current Assignee: Emergent Product Development Seattle, LLC
• Original Assignee: Emergent Product Development Seattle, LLC
• Inventors: Blankenship, John W., Tan, Philip
• Application Number:
  US13/519,727
• Publication Number:
  US 20130129723A1
• Time in Patent Office: Days
• US Class Current: 424/134.1
• CPC Class Codes: C07K 14/5428 IL-10
• CPC Class Codes: C07K 14/70532 B7 molecules, e.g. CD80, CD86
• CPC Class Codes: C07K 16/248 IL-6
• 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 16/2863 against receptors for growth factors, growth regulators
• CPC Class Codes: C07K 16/2887 against CD20
• CPC Class Codes: C07K 16/44 against material not provided for elsewhere , e.g. haptens, metals, DNA, RNA, amino acids
• CPC Class Codes: C07K 16/468 Immunoglobulins having two or more different antigen binding sites, e.g. multifunctional antibodies
• CPC Class Codes: C07K 2317/35 Valency
• CPC Class Codes: C07K 2317/524 CH2 domain
• 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 2317/71 Decreased effector function due to an Fc-modification
• CPC Class Codes: C07K 2317/73 Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
• CPC Class Codes: C07K 2317/74 Inducing cell proliferation

Abstract

The present disclosure provides polypeptide heterodimers formed between two different single chain fusion polypeptides via natural heterodimerization of an immunoglobulin CH1 region and an immunoglobulin light chain constant region (CL). The polypeptide heterodimer comprises two or more binding domains that specifically bind one or more targets (e.g., a receptor). In addition, both chains of the heterodimer further comprise an Fc region portion. The present disclosure also provides nucleic acids, vectors, host cells and methods for making polypeptide heterodimers as well as methods for using such polypeptide heterodimers, such as in directing T cell activation, inhibiting solid malignancy growth, and treating autoimmune or inflammatory conditions.

Claims

1. A polypeptide heterodimer, comprising:

(a) a first single chain polypeptide (SCP-I) comprising from one to four binding domains that specifically bind from one to four targets, a hinge (H-I), an immunoglobulin heterodimerization domain (HD-I), and an Fc region portion (FRP-I); and

(b) a second single chain polypeptide (SCP-II) comprising from zero to four binding domains that specifically bind from zero to four targets, a hinge (H-II), an immunoglobulin heterodimerization domain (HD-II), and an Fc region portion (FRP-II);

wherein

(i) the immunoglobulin heterodimerization domain of the first single chain polypeptide (HD-I) and the immunoglobulin heterodimerization domain of the second single chain polypeptide (HD-II) preferentially associate with each other to form a polypeptide heterodimer comprised of the first single chain polypeptide (SCP-I) and the second single chain polypeptide (SCP-II), and

(1) the immunoglobulin heterodimerization domain of the first single chain polypeptide (HD-I) comprises a first immunoglobulin CHI region, and the immunoglobulin heterodimerization domain of the second single chain polypeptide (HD-II) comprises a first immunoglobulin CL region, or

(2) the immunoglobulin heterodimerization domain of the first single chain polypeptide (HD-I) comprises a first immunoglobulin CL region, and the immunoglobulin heterodimerization domain of the second single chain polypeptide (HD-II) comprises a first immunoglobulin CHI region; and

(ii) the Fc region portion of the first single chain polypeptide (FCP-I) and the Fc region portion of the second single chain polypeptide (FCP-II) each comprise an immunoglobulin CH2 and CH3 domain of IgG1, IgG2, IgG3, IgG4, IgA1, IgA2, IgD, or any combination thereof;

an immunoglobulin CH3 domain of IgG1, IgG2, IgG3, IgG4, IgA1, IgA2, IgD, IgE, IgM, or any combination thereof;

or an immunoglobulin CH3 and CH4 domain of IgE, IgM, or a combination thereof,

provided that the polypeptide heterodimer comprises at least two binding domains that specifically bind at least two different targets.

2. The polypeptide heterodimer of claim 1, wherein the binding domains are single chain Fv (scFv) polypeptides.

3. The polypeptide heterodimer of claim 1, wherein the polypeptide heterodimer comprises two binding domains (BD1 and BD2), three binding domains (BD1, BD2 and BD3), four binding domains (BD1, BD2, BD3 and BD4), or five to eight binding domains.

16. The polypeptide heterodimer of claim 1, wherein at least one of the binding domains is an agonist of IL-10, HLA-G, HGF, IL-35, PD-1, BTLA, TNFR1, TNFR2, DR4, DR5, TWEAKR, or FAS.

17. The polypeptide heterodimer of claim 1, wherein at least one binding domain specifically binds a TCR complex or a component thereof, and at least another binding domain specifically binds to PSMA, CD79b, CD19, HLA-DR, CD20, RON, c-Met, or CEACAM-6.

18. The polypeptide heterodimer of claim 1, wherein at least one binding domain specifically binds to CD28, and at least another binding domain specifically binds to or is an antagonist of, CD79b, hyperIL-6, PDL2, monoIL-10, CD86, LIGHT, GITRL, CD40, PDL1, HVEM, or LTBR.

19. The polypeptide heterodimer of claim 1, wherein at least one binding domain specifically binds to CD28, and at least another binding domain is an agonist of IL-10, HLA-G, HGF, IL-35, PD-1, or BTLA.

20. The polypeptide heterodimer of claim 1, wherein the immunoglobulin heterodimerization domain of the first single chain polypeptide (HD-I) comprises the first immunoglobulin CHI region and the immunoglobulin heterodimerization domain of the second single chain polypeptide (HD-II) comprises the first immunoglobulin CL region.

23. The polypeptide heterodimer of claim 20 wherein the first single chain polypeptide further comprises a second CHI region and the second single chain polypeptide further comprises a second CL region, and wherein the second CHI region of the first single chain polypeptide and the second CL region of the second single chain polypeptide associate with each other in the polypeptide heterodimer.

27. The polypeptide heterodimer of claim 1, wherein the immunoglobulin heterodimerization domain of the first single chain polypeptide (HD-I) comprises a first immunoglobulin CL region, and the immunoglobulin heterodimerization domain of the second single chain polypeptide (HD-II) comprises a first immunoglobulin CHI region.

30. The polypeptide heterodimer of claim 27 wherein the first single chain polypeptide further comprises a second CL region and the second single chain polypeptide further comprises a second CHI region, and wherein the second CL region of the first single chain polypeptide and the second CHI region of the second single chain polypeptide associate with each other in the polypeptide heterodimer.

41. The polypeptide heterodimer of claim 1, wherein the first CL region is a Cκ

region or a Cλ

region.

43. The polypeptide heterodimer of claim 23, wherein the second CL region is a Cκ

region or a Cλ

region.

45. The polypeptide heterodimer of claim 41, wherein the Cκ

region is a wild type human immunoglobulin Cκ

region.

46. The polypeptide heterodimer of claim 41, wherein the Cκ

region is an altered human immunoglobulin Cκ

region with one or more amino acids of a wild type human Cκ

region substituted at N29, N30, Q52, V55, T56, S68, or T70.

48. The polypeptide heterodimer of claim 41, wherein the CHI region is an altered human immunoglobulin CHI region comprising an amino acid substitution by which Val (V) at position 68 is substituted by Lys (K), Arg (R) or His (H), and wherein the Cκ

region is an altered human immunoglobulin Cκ

region comprising an amino acid substitution by which Leu (L) at position 27 is substituted by Asp (D) or Glu (E).

49. The polypeptide heterodimer of claim 41, wherein the CHI region is an altered human immunoglobulin CHI region comprising an amino acid substitution by which Val (V) at position 68 is changed to Asp (D) or Glu (E), and wherein the Cκ

region is an altered human immunoglobulin Cκ

region comprising an amino acid substitution by which Leu (L) at position 27 is changed to Lys (K), Arg (R) or His (H).

53. The polypeptide heterodimer of claim 1, wherein the first CHI region is an altered human immunoglobulin CHI region with the cysteine of a wild type human immunoglobulin CHI region that is involved in forming a disulfide bond with a wild type human immunoglobulin CL region deleted or substituted.

57. The polypeptide heterodimer of claim 53, wherein the first CHI region is a polypeptide comprising SEQ ID NO:

114, 844 or 845.

58. The polypeptide heterodimer of claim 41, wherein the Cκ

region is selected from any one of the polypeptides comprising SEQ IL NOS;

141-178, 202, and 838-843.

59. The polypeptide heterodimer of claim 41, wherein the Cλ

region is a polypeptide comprising SEQ ID NO;

140.

60. The polypeptide heterodimer of claim 1, wherein the Fc region portion of the first single chain polypeptide (FRP-I) and the Fc region portion of the second single chain polypeptide (FRP-II) each comprise an immunoglobulin CH2 domain of an immunoglobulin CH3 domain.

66. The polypeptide heterodimer of claim 1, wherein the Fc region portion of the first single chain polypeptide (FRP-I) and the Fc region portion of the second single chain polypeptide (FRP-II) each comprise an immunoglobulin CH2 domain and an immunoglobulin CH3 domain.

75. The polypeptide heterodimer of claim 1, wherein the hinge of both the first and second single chain polypeptides is an immunoglobulin hinge region.

79. The polypeptide heterodimer of claim 75, wherein the hinge region is

(a) amino terminal to the Fc region portion,

(b) disposed between the binding domain and the immunoglobulin heterodimerization domain,

(c) disposed between the immunoglobulin heterodimerization domain and the Fc region portion, or

(d) at the amino terminus of the first or second single chain polypeptide.

84. The polypeptide heterodimer of claim 1, wherein the hinges of the first and second single chain polypeptides are different.

88. The heterodimer of claim 1, wherein the first and second single chain polypeptides comprise SEQ ID NOS:

SEQ ID NOS;

2 and 4, SEQ ID NOS;

6 and 8, SEQ ID NOS;

10 and 12, SEQ ID NOS;

14 and 16, SEQ ID NOS;

18 and 20, SEQ ID NOS;

20 and 22, SEQ ID NOS;

20 and 24, SEQ ID NOS;

30 and 32, SEQ ID NOS;

29 and 31, SEQ ID NOS;

29 and 32, SEQ ID NOS;

30 and 72, SEQ ID NOS;

53 and 72, SEQ ID NOS;

54 and 72, SEQ ID NOS;

55 and 72, SEQ ID NOS;

70 and 72, SEQ ID NOS;

71 and 72, SEQ ID NOS;

63 and 56, SEQ ID NOS;

64 and 57, SEQ ID NOS;

65 and 60, SEQ ID NOS;

66 and 58, SEQ ID NOS;

67 and 59, SEQ ID NOS;

68 and 61, SEQ ID NOS;

69 and 62, SEQ ID NOS;

54 and 811, SEQ ID NOS;

54 and 812, SEQ ID NOS;

54 and 813, SEQ ID NOS;

814 and 818, SEQ ID NOS;

815 and 818, SEQ ID NOS;

816 and 818, SEQ ID NOS;

817 and 818, SEQ ID NOS;

814 and 820, SEQ ID NOS;

814 and 821, SEQ ID NOS;

54 and 819, SEQ ID NOS;

814 and 826, SEQ ID NOS;

814 and 822, SEQ ID NOS;

814 and 823, SEQ ID NOS;

814 and 824, SEQ ID NOS;

859 and 862, SEQ ID NOS;

860 and 863, SEQ ID NOS;

861 and 864, SEQ ID NOS;

874 and 825, SEQ ID NOS;

875 and 879, SEQ ID NOS;

876 and 880, SEQ ID NO;

877 and 881, or SEQ ID NOS;

878 and 882.

89. A composition comprising a polypeptide heterodimer of claim 1 and a pharmaceutically acceptable excipient.

90. An expression vector capable of expressing the polypeptide heterodimer of claim 1, comprising a first polynucleotide encoding the first single chain polypeptide and a second polynucleotide encoding the second single chain polypeptide.

91. A host cell comprising the expression vector of claim 90.

92. A host cell comprising first and second expression vectors capable of expressing the first and second single chain polypeptides, respectively, of the polypeptide heterodimer of claim 1.

93. A method for making a polypeptide heterodimer, comprising

(a) culturing the host cell of claim 91 under conditions suitable to express first and second single chain polypeptides, and

(b) optionally isolating or purifying the heterodimers formed from the first and second single chain polypeptides from the culture.

94. A method for directing T cell activation, comprising administering to a patient in need thereof an effective amount of a polypeptide heterodimer according to claim 1, wherein the polypeptide heterodimer comprises a binding domain that specifically binds TCRα

, TCRβ

, CD3γ

, CD3ε

, CD3β

or a combination thereof, and a second binding domain that specifically binds a different target.

95. A method for inhibiting growth, metastasis or metastatic growth of a malignancy, comprising administering to a patient in need thereof an effective amount of a polypeptide heterodimer according to claim 1, wherein the polypeptide heterodimer comprises a binding domain that specifically binds TCRα

, TCRβ

, CD3γ

, CD3ε

, CD3ε

, c-Met, or Ron.

96. A method for treating an autoimmune or inflammatory condition, comprising administering to a patient in need thereof an effective amount of a polypeptide heterodimer according to claim 1, wherein the polypeptide heterodimer comprises a binding domain that specifically binds TCRα

, TCRβ

, CD3γ

, CD3ε

, CDR or CD28.

97. A method for treating a B-cell associated disorder or disease comprising administering to a patient in need thereof an effective amount of a polypeptide heterodimer according to claim 1, wherein the polypeptide heterodimer comprises a binding domain that specifically binds TCRα

, TCRβ

, CD3γ

, CD3ε

, CD3β

, and a second binding domain that specifically binds to CD19, CD20, CD79b or HLA-DR.

4-15. -15. (canceled)

21. (canceled)

22. (canceled)

24-26. -26. (canceled)

28. (canceled)

29. (canceled)

31-40. -40. (canceled)

42. (canceled)

44. (canceled)

47. (canceled)

50-52. -52. (canceled)

54-56. -56. (canceled)

61-65. -65. (canceled)

67-74. -74. (canceled)

76-78. -78. (canceled)

80-83. -83. (canceled)

85-87. -87. (canceled)

98-101. -101. (canceled)