Linker and linked fusion polypeptides

• US 5,990,275 A
• Filed: 09/10/1997
• Issued: 11/23/1999
• Est. Priority Date: 11/20/1992
• Status: Expired due to Term

• Current Assignee: Enzon Pharmaceuticals Inc. (Icahn Associates Holding LLC)
• Original Assignee: Enzon Pharmaceuticals Inc. (Icahn Associates Holding LLC)
• Inventors: Filpula, David R., Whitlow, Marc D.
• Primary Examiner(s): Hutzell, Paula K.
• Assistant Examiner(s): UNGAR, SUSAN NMN
• Application Number:
  US08/926,789
• Time in Patent Office: 804 Days
• Field of Search: 530/387.3, 530/326, 530/324, 530/350, 530/391.1, 530/391.5, 530/402, 536/23.1
• US Class Current: 530/324
• CPC Class Codes: C07K 14/70503 Immunoglobulin superfamily
• CPC Class Codes: C07K 16/18 against material from animals or humans
• CPC Class Codes: C07K 16/3046 Stomach, Intestines
• CPC Class Codes: C07K 2317/31 multispecific
• CPC Class Codes: C07K 2317/622 Single chain antibody (scFv)
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C12N 15/62 DNA sequences coding for fusion proteins
• CPC Class Codes: Y10S 930/31 Linker sequence

Abstract

The invention is directed to a novel peptide linker useful for connecting polypeptide constituents into a novel linked fusion polypeptide. The peptide linker of the invention provides greater stability and is less susceptible to aggregation than previously known peptide linkers. The peptide linker of the invention may be up to about 50 amino acids in length and contains at least one occurrence of a charged amino acid followed by a proline. When used for making a single chain Fv (sFv), the peptide linker is preferably from 18 to about 30 amino acids in length. A preferred embodiment of the peptide linker of the invention comprises the sequence:

GSTSGSGXPGSGEGSTKG (SEQ. ID NO 1),

where X is a charged amino acid, preferably lysine or arginine. Methods of making linked fusion polypeptides using the peptide linker of the invention are claimed.

Claims

1. A linked fusion polypeptide comprising a first polypeptide and a second polypeptide connected by a peptide linker, wherein said peptide linker is 18 to 50 amino acid residues long, said peptide linker comprises one or more occurrences of a sequence XP wherein X is a charged amino acid, and said peptide linker comprises the sequence GSTSGSGXPGSGEGSTKG (SEQ. ID No. 1), said sequence positioned within said peptide linker so as to inhibit proteolysis of said linker by either subtilisin or trypsin.

2. The linked fusion polypeptide of claim 1 wherein said first and second polypeptides are not from the same single chain protein or from the same chain of a multi-chain protein.

3. The linked fusion polypeptide of claim 2 wherein said first and second polypeptides are from different proteins.

4. The linked fusion polypeptide of claim 3 wherein said first and second polypeptides are from members of the immunoglobulin superfamily.

5. The linked fusion polypeptide of claim 4 wherein said first and second polypeptides are from immunoglobulins.

6. The linked fusion polypeptide of claim 5 wherein said linked fusion polypeptide is a mixed sFv.

7. The linked fusion polypeptide of claim 1 wherein said first and second polypeptides are from the same multi-chain protein.

8. The linked fusion polypeptide of claim 7 wherein said multi-chain protein is a member of the immunoglobulin superfamily.

9. The linked fusion polypeptide of claim 8 wherein said multi-chain protein is a T cell receptor.

10. The linked fusion polypeptide of claim 8 wherein said multi-chain protein is an immunoglobulin.

11. The linked fusion polypeptide of claim 10 wherein said first polypeptide comprises the binding portion of the variable region of the heavy chain of said immunoglobulin and said second polypeptide comprises the binding portion of the variable region of the light chain of said immunoglobulin.

12. The linked fusion polypeptide of claim 1 wherein said peptide linker comprises about 18 to about 30 amino acids.

13. The linked fusion polypeptide of claim 12 wherein said sequence XP occurs at positions 8 and 9 from the amino terminus of said peptide linker.

14. The linked fusion polypeptide of claim 1 wherein said charged amino acid is a positively-charged amino acid.

15. The linked fusion polypeptide of claim 14 wherein said charged amino acid is lysine or arginine.

31. The linked fusion polypeptide of claim 1 wherein said first polypeptide is 4-4-20 V_L and said second polypeptide is CC49 V_H.

32. The linked fusion polypeptide of claim 1 wherein said first polypeptide is CC49 V_L and said second polypeptide is 4-4-20 V_H.

88. The linked fusion polypeptide of claim 10 wherein said first polypeptide comprises the binding portion of the variable region of the light chain of said immunoglobulin and said second polypeptide comprises the binding portion of the variable region of the heavy chain of said immunoglobulin.

92. The linked fusion polypeptide of claim 1 wherein said first polypeptide is CC49 V_L and said second polypeptide is CC49 V_H.

93. The linked fusion polypeptide of claim 1 wherein said first polypeptide is A33 V_L and said second polypeptide is A33 V_H.

16. A peptide linker comprising a single amino acid chain of 14 to about 30 amino acids, said amino acid chain comprising the sequence:

GSTSGSGXPGSGEGSTKG (SEQ. ID No.

     1)

wherein X is a charged amino acid.

17. The peptide linker of claim 16 wherein said charged amino acid is a positively charged amino acid.

18. The peptide linker of claim 17 wherein said charged amino acid is lysine or arginine.

19. A method of making a linked fusion polypeptide from a multi-chain protein, said method comprising:

(a) providing a first polypeptide corresponding to a first chain, or subfragment thereof, of said multi-chain protein;

(b) providing a second polypeptide corresponding to a second chain, or subfragment thereof, of said multi-chain protein;

(c) connecting said first polypeptide and said second polypeptide to opposite ends of a peptide linker to form said linked fusion polypeptide, said peptide linker comprising one or more occurrences of the sequence XP, wherein X is a charged amino acid and said peptide linker comprises at least one sequence selected from the group of sequences consisting of sequences represented by GSTSGSGXPGSGEGSTKG (SEQ. ID No.

     1), GSTSGSGKPGSGEGSTKG (SEQ. ID No.

     10). GSTSGKPSEGKG (amino acid nos. 113-124 of SEQ. ID No.

     12). and GSTSGXPSEGKG (SEQ. ID No.

     25), said sequence is positioned within said peptide linker so as to inhibit proteolysis of said linker by either subtilisin or trypsin; and

(d) recovering said linked fusion polypeptide.

20. The method of claim 19 wherein said multi-chain protein is a member of the immunoglobulin superfamily.

21. The method of claim 20 wherein said multi-chain protein is a T cell receptor.

22. The method of claim 20 wherein said multi-chain protein is an immunoglobulin.

23. The method of claim 22 wherein said first polypeptide comprises the binding portion of the variable region of said immunoglobulin light chain and said second polypeptide comprises the binding portion of the variable region of said immunoglobulin heavy chain.

100. The method of claim 22 wherein said first polypeptide comprises the binding portion of a variable region of said immunoglobulin heavy chain and said second polypeptide comprises a binding portion of the variable region of said immunoglobulin light chain.

101. The method of claim 22 wherein said first polypeptide comprises the binding portion of a variable region of said immunoglobulin light chain and said second polypeptide comprises a binding portion of the variable region of said immunoglobulin heavy chain.

102. The method of claim 19 wherein said linked fusion polypeptide is a mixed sFV.

24. A method of making a linked fusion polypeptide from two different proteins, said method comprising:

(a) providing a first polypeptide corresponding to either a single chain protein or a chain of a multi-chain protein, or a subfragment thereof;

(b) providing a second polypeptide corresponding to either a single chain protein or a chain of a multi-chain protein different from that of said first polypeptide, or a subfragment thereof;

(c) connecting said first polypeptide and said second polypeptide to opposite ends of a peptide linker to form said linked fusion polypeptide, said peptide linker comprising one or more occurrences of the sequence XP, wherein X is a charged amino acid and said peptide linker comprises at least one sequence selected from the group of sequences consisting of sequences represented by GSTSGSGXPGSGEGSTKG (SEQ. ID No.

     1), GSTSGSGKPGSGEGSTKG (SEQ. ID No.

     10) GSTSGKPSEGKG (amino acid nos. 113-124 of SEQ. ID No.

     12) and GSTSCGXPSEGKG (SEQ. ID No.

     25), said sequence is positioned within said peptide linker so as to inhibit proteolysis of said linker by either subtilisin or trypsin,

(d) recovering said linked fusion polypeptide.

25. The method of claim 24 wherein said proteins are members of the immunoglobulin superfamily.

26. The method of claim 25 wherein said proteins are immunoglobulins.

27. The method of claim 25 wherein said linked fusion polypeptide is a mixed sFV.

98. The method of claim 26 wherein said first polypeptide comprises the binding portion of the variable region of said immunoglobulin light chain and said second polypeptide comprises the binding portion of the variable region of said immunoglobulin heavy chain.

99. The method of claim 26 wherein said first polypeptide comprises a binding portion of the variable region of said immunoglobulin heavy chain and said second polypeptide comprises a binding portion of the variable region of said immunoglobulin light chain.

28. A linked fusion polypeptide comprising a first polypeptide and a second polypeptide connected by a peptide linker, wherein said peptide linker is 18 to 50 amino acid residues long, said peptide linker comprises one or more occurrences of a sequence XP wherein X is a charged amino acid, and said peptide linker comprises the sequence represented by GSTSGSGKPGSGEGSTKG (SEQ. ID No. 10), wherein said sequence is positioned within said peptide linker so as to inhibit proteolysis of said linker by either subtilisin or trypsin.

29. The linked fusion polypeptide of claim 28 wherein said first polypeptide is CC49 V_L and said second polypeptide is CC49 V_H.

30. The linked fusion polypeptide of claim 28 wherein said first polypeptide is A33 V_L and said second polypeptide is A33 V_H.

35. The linked fusion polypeptide of claim 28 wherein said first polypeptide is 4-4-20 V_L and said second polypeptide is CC49 V_H.

36. The linked fusion polypeptide of claim 28 wherein said first polypeptide is CC49 V_L and said second polypeptide is 4-4-20 V_H.

37. The linked fusion polypeptide of claim 28 wherein said first and second polypeptides are not from the same single chain protein or from the same chain of a multi-chain protein.

38. The linked fusion polypeptide of claim 37 wherein said first and second polypeptides are from different proteins.

39. The linked fusion polypeptide of claim 38 wherein said first and second polypeptides are from members of the immunoglobulin superfamily.

40. The linked fusion polypeptide of claim 39 wherein said first and second polypeptides are from immunoglobulins.

41. The linked fusion polypeptide of claim 40 wherein said linked fusion polypeptide is a sFv.

42. The linked fusion polypeptide of claim 28 wherein said first and second polypeptides are from the same multi-chain protein.

43. The linked fusion polypeptide of claim 42 wherein said multi-chain protein is a member of the immunoglobulin superfamily.

44. The linked fusion polypeptide of claim 43 wherein said multi-chain protein is a T cell receptor.

45. The linked fusion polypeptide of claim 43 wherein said multi-chain protein is an immunoglobulin.

46. The linked fusion polypeptide of claim 45 wherein said first polypeptide comprises the binding portion of the variable region of the heavy chain of said immunoglobulin and said second polypeptide comprises the binding portion of the variable region of the light chain of said immunoglobulin.

47. The linked fusion polypeptide of claim 28 wherein said peptide linker comprises about 18 to about 30 amino acids.

48. The linked fusion polypeptide of claim 28 wherein said sequence XP occurs at positions 8 and 9 from the amino terminus of said peptide linkers.

49. The linked fusion polypeptide of claim 28 wherein said charged amino acid is a positively-charged amino acid.

50. The linked fusion polypeptide of claim 49 wherein said charged amino acid is lysine or arginine.

89. The linked fusion polypeptide of claim 45 wherein said first polypeptide comprises the binding portion of the variable region of the light chain of said immunoglobulin and said second polypeptide comprises the binding portion of the variable region of the heavy chain of said immunoglobulin.

33. A peptide linker comprising the amino acid sequence GSTSGSGXPGSGEGSTKG (SEQ. ID No. 1) wherein X is a charged amino acid and wherein said linker is 18 to 50 amino acid residues long.

34. A linked fusion polypeptide comprising a first polypeptide and a second polypeptide connected by a peptide linker, wherein said first and second polypeptides are derived from the same multi-chain protein, said multi-chain protein being a member of the immunoglobulin superfamily;

and said peptide linker comprising one or more occurrences of a sequence XP, wherein X is a charged amino acid and said peptide linker sequence comprises at least one sequence selected from the group of sequences consisting of sequences represented by GSTSGSGXPGSGEGSTKG (SEQ. ID No.

     1), GSTSGSGKPGSGEGSTKG (SEQ. ID No.

     10), GSTSGKPSEGKG (amino acid nos. 113-124 of SEQ. ID No.

     12), and GSTSGXPSEGKG (SEQ. ID No.

     25), said peptide linker sequence being positioned within said peptide linker so as to inhibit proteolysis of said linker by either subtilisin or trypsin.

51. A linked fusion polypeptide comprising a first polypeptide and a second polypeptide connected by a peptide linker, wherein said peptide linker is 12 to 50 amino acid residues long, said peptide linker comprises one or more occurrences of a sequence XP wherein X is a charged amino acid, and said peptide linker comprises the sequence represented by GSTSGKPSEGKG (amino acid nos. 113-124 of SEQ. ID No. 12), wherein said sequence is positioned within said peptide linker so as to inhibit proteolysis of said linker by at least subtilisin or trypsin.

52. The linked fusion polypeptide of claim 51 wherein said first polypeptide is 4-4-20 V_L and said second polypeptide is CC49 V_H.

53. The linked fusion polypeptide of claim 51 wherein said first polypeptide is CC49 V_L and said second polypeptide is 4-4-20 V_H.

54. The linked fusion polypeptide of claim 51 wherein said first and second polypeptides are not from the same single chain protein or from the same chain of a multi-chain protein.

55. The linked fusion polypeptide of claim 54 wherein said first and second polypeptides are from different proteins.

56. The linked fusion polypeptide of claim 55 wherein said first and second polypeptides are members of the immunoglobulin superfamily.

57. The linked fusion polypeptide of claim 56 wherein said first and second polypeptides are from immunoglobulins.

58. The linked fusion polypeptide of claim 57 wherein said linked fusion polypeptide is a sFv.

59. The linked fusion polypeptide of claim 51 wherein said first and second polypeptides are from the same multi-chain protein.

60. The linked fusion polypeptide of claim 59 wherein said multi-chain protein is a member of the immunoglobulin superfamily.

61. The linked fusion polypeptide of claim 60 wherein said multi-chain protein is a T cell receptor.

62. The linked fusion polypeptide of claim 60 wherein said multi-chain protein is an immunoglobulin.

63. The linked fusion polypeptide of claim 62 wherein said first polypeptide comprises the binding portion of the variable region of the heavy chain of said immunoglobulin and said second polypeptide comprises the binding portion of the variable region of the light chain of said immunoglobulin.

64. The linked fusion polypeptide of claim 51 wherein said peptide linker comprises about 12 to about 30 amino acids.

65. The linked fusion polypeptide of claim 51 wherein said sequence XP occurs at positions 6 and 7 from the amino terminus of said peptide linker.

66. The linked fusion polypeptide of claim 51 wherein said charged amino acid is a positively-charged amino acid.

67. The linked fusion polypeptide of claim 51 wherein said charged amino acid is lysine or arginine.

90. The linked fusion polypeptide of claim 62 wherein said first polypeptide comprises the binding portion of the variable region of the light chain of said immunoglobulin and said second polypeptide comprises the binding portion of the variable region of the heavy chain of said immunoglobulin.

96. The linked fusion polypeptide of claim 51 wherein said first polypeptide is CC49 V_L and said second polypeptide is CC49 V_H.

97. The linked fusion polypeptide of claim 51 wherein said first polypeptide is A33 V_L and said second polypeptide is A33 V_H.

68. A linked fusion polypeptide comprising a first polypeptide and a second polypeptide connected by a peptide linker, wherein said peptide linker is 12 to 50 amino acid residues long, said peptide linker comprises one or more occurrences of the sequence XP wherein X is a charged amino acid, and said peptide linker comprises the sequence represented by GSTSGXPSEGKG (SEQ. ID NO 25), wherein said sequence is positioned within said peptide linker so as to inhibit proteolysis of said linker by either subtilisin or trypsin.

69. The linked fusion polypeptide of claim 68 wherein said first polypeptide is 4-4-20 V_L and said second polypeptide is CC49 V_H.

70. The linked fusion polypeptide of claim 68 wherein said first polypeptide is CC49 V_L and said second polypeptide is 4-4-20 V_H.

71. The linked fusion polypeptide of claim 68 wherein said first and second polypeptides are not from the same single chain protein or from the same chain of a multi-chain protein.

72. The linked fusion polypeptide of claim 71 wherein said first and second polypeptides are from different proteins.

73. The linked fusion polypeptide of claim 72 wherein said first and second polypeptides are from members of the immunoglobulin superfamily.

74. The linked fusion polypeptide of claim 73 wherein said first and second polypeptides are from immunoglobulins.

75. The linked fusion polypeptide of claim 74 wherein said linked fusion polypeptide is a sFv.

76. The linked fusion polypeptide of claim 68 wherein said first and second polypeptides are from the same multi-chain protein.

77. The linked fusion polypeptide of claim 76 wherein said multi-chain protein is a member of the immunoglobulin superfamily.

78. The linked fusion polypeptide of claim 77 wherein said multi-chain protein is a T cell receptor.

79. The linked fusion polypeptide of claim 77 wherein said multi-chain protein is an immunoglobulin.

80. The linked fusion polypeptide of claim 79 wherein said first polypeptide comprises the binding portion of the variable region of the heavy chain of said immunoglobulin and said second polypeptide comprises the binding portion of the variable region of the light chain of said immunoglobulin.

81. The linked fusion polypeptide of claim 68 wherein said peptide linker comprises about 12 to about 30 amino acids.

82. The linked fusion polypeptide of claim 68 wherein said sequence XP occurs at positions 6 and 7 from the amino terminus of said peptide linker.

83. The linked fusion polypeptide of claim 68 wherein said charged amino acid is a positively-charged amino acid.

84. The linked fusion polypeptide of claim 83 wherein said charged amino acid is lysine or arginine.

91. The linked fusion polypeptide of claim 79 wherein said first polypeptide comprises the binding portion of the variable region of the light chain of said immunoglobulin and said second polypeptide comprises the binding portion of the variable region of the heavy chain of said immunoglobulin.

94. The linked fusion polypeptide of claim 68 wherein said first polypeptide is CC49 V_L and said second polypeptide is CC49 V_H.

95. The linked fusion polypeptide of claim 68 wherein said first polypeptide is A33 V_L and said second polypeptide is A33 V_H.

85. A peptide linker comprising the sequence represented by GSTSGSGKPGSGEGSTKG (SEQ. ID No. 10) wherein said linker is 18 to 50 amino acid residues long.

86. A polypeptide linker comprising the sequence represented by GSTSGKPSEGKG (amino acid nos. 113-124 of SEQ. ID No. 12) wherein said linker is 12 to 50 amino acid residues long.

87. A peptide linker comprising the sequence represented by GSTSGXPSEGKG (SEQ. ID NO 25) wherein X is a charged amino acid and wherein said linker is 12 to 50 amino acid residues long.