THROMBIN CLEAVABLE LINKER WITH XTEN AND ITS USES THEREOF

• US 20160251408A1
• Filed: 06/27/2014
• Published: 09/01/2016
• Est. Priority Date: 06/28/2013
• Status: Abandoned Application

• Current Assignee: Bioverativ Therapeutics Inc. (Sanofi )
• Original Assignee: Biogen MA Inc. (Biogen, Inc.)
• Inventors: CHHABRA, Ekta Seth, KULMAN, John, LIU, Tongyao
• Application Number:
  US14/894,108
• Publication Number:
  US 20160251408A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61K 38/37 Factors VIII
• CPC Class Codes: A61K 48/00 Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• CPC Class Codes: A61P 1/00 Drugs for disorders of the alimentary tract or the digestive system
• CPC Class Codes: A61P 1/02 Stomatological preparations, e.g. drugs for caries, aphtae, periodontitis
• CPC Class Codes: A61P 17/02 for treating wounds, ulcers, burns, scars, keloids, or the like
• CPC Class Codes: A61P 19/00 Drugs for skeletal disorders
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 19/08 for bone diseases, e.g. rachitism, Paget's disease
• CPC Class Codes: A61P 21/00 Drugs for disorders of the muscular or neuromuscular system
• CPC Class Codes: A61P 25/00 Drugs for disorders of the nervous system
• CPC Class Codes: A61P 7/04 Antihaemorrhagics; Procoagulants; Haemostatic agents; Antifibrinolytic agents
• CPC Class Codes: C07K 14/755 Factors VIII , e.g. factor VIII C (AHF), factor VIII Ag (VWF)
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• 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
• CPC Class Codes: C07K 2319/35 containing a fusion for enhanced stability/folding during expression, e.g. fusions with chaperones or thioredoxin
• CPC Class Codes: C07K 2319/50 containing protease site
• CPC Class Codes: C07K 2319/70 containing domain for protein-protein interaction
• CPC Class Codes: C07K 2319/90 containing a motif for post-translational modification

Abstract

The present invention provides a chimeric molecule comprising a VWF protein fused to a heterologous moiety via a VWF linker. The invention provides an efficient VWF linker that can be cleaved in the presence of thrombin. The chimeric molecule can further comprise a polypeptide chain comprising a FVIII protein and a second heterologous moiety, wherein the chain comprising the VWF protein and the chain comprising the FVIII protein are associated with each other. The invention also includes nucleotides, vectors, host cells, methods of using the chimeric proteins.

Claims

1. A chimeric molecule comprising a von Willebrand Factor (VWF) protein, a heterologous moiety (H1), an extended recombinant polypeptide (XTEN) sequence, and a VWF linker connecting the VWF protein with the heterologous moiety, wherein the VWF linker comprises a polypeptide selected from:

i. an a2 region from Factor VIII (FVIII);

ii. an a1 region from FVIII;

iii. an a3 region from FVIII;

iv. a thrombin cleavage site which comprises X-V-P-R (SEQ ID NO;

     3) and a PAR1 exosite interaction motif, wherein X is an aliphatic amino acid;

or

v. any combination thereof, and

wherein the XTEN sequence is connected to the VWF protein, the heterologous moiety (H1), the VWF linker, or any combination thereof.

2. The chimeric molecule of claim 1, wherein the XTEN sequence connects the VWF protein with the VWF linker or the VWF linker with the heterologous moiety.

3. The chimeric molecule of claim 1, further comprising a second polypeptide chain which comprises a FVIII protein, wherein the first polypeptide chain comprising the VWF protein and the second polypeptide chain are associated with each other.

4. The chimeric molecule of claim 3, wherein the FVIII protein further comprises an additional XTEN sequence.

6. The chimeric molecule of claim 3, wherein the second polypeptide chain further comprises a second heterologous moiety (H2).

12. The chimeric molecule of claim 1, wherein the XTEN sequence comprises about 42 amino acids, about 72 amino acids, about 108 amino acids, about 144 amino acids, about 180 amino acids, about 216 amino acids, about 252 amino acids, about 288 amino acids, about 324 amino acids, about 360 amino acids, about 396 amino acids, about 432 amino acids, about 468 amino acids, about 504 amino acids, about 540 amino acids, about 576 amino acids, about 612 amino acids, about 624 amino acids, about 648 amino acids, about 684 amino acids, about 720 amino acids, about 756 amino acids, about 792 amino acids, about 828 amino acids, about 836 amino acids, about 864 amino acids, about 875 amino acids, about 912 amino acids, about 923 amino acids, about 948 amino acids, about 1044 amino acids, about 1140 amino acids, about 1236 amino acids, about 1318 amino acids, about 1332 amino acids, about 1428 amino acids, about 1524 amino acids, about 1620 amino acids, about 1716 amino acids, about 1812 amino acids, about 1908 amino acids, or about 2004 amino acids.

13. The chimeric molecule of claim 1, wherein the XTEN sequence is selected from AE42, AE72, AE864, AE576, AE288, AE144, AG864, AG576, AG288, AG144, SEQ ID NO:

39;

SEQ ID NO;

40;

SEQ ID NO;

47;

SEQ ID NO;

45;

SEQ ID NO;

44;

SEQ ID NO;

41;

SEQ ID NO;

48;

SEQ ID NO;

46, SEQ ID NO;

44, and SEQ ID NO;

42.

18. The chimeric molecule of claim 1, wherein:

(i) the VWF linker comprises the a2 region which comprises an amino acid sequence at least about 80%, about 85%, about 90%, about 95%, or 100% identical to Glu720 to Arg740 corresponding to full-length FVIII, wherein the a2 region is capable of being cleaved by thrombin;

(ii) the VWF linker comprises the a1 region which comprises an amino acid sequence at least about 80%, at least about 85%, at least about 90%, at least about 95%, or 100% identical to Met337 to Arg372 corresponding to full-length FVIII, wherein the a1 region is capable of being cleaved by thrombin;

(ii) the VWF linker comprises the a3 region which comprises an amino acid sequence at least about 80%, about 85%, about 90%, about 95%, or 100% identical to Glu1649 to Arg1689 corresponding to full-length FVIII, wherein the a3 region is capable of being cleaved by thrombin;

(iv) the VWF linker comprises the thrombin cleavage site which comprises X-V-P-R (SEQ ID NO;

     3) and the PAR1 exosite interaction motif and wherein the PAR1 exosite interaction motif comprises S-F-L-L-R-N(SEQ ID NO;

     7);

or

(v) any combination thereof.

19. The chimeric molecule of claim 18, wherein:

(i) the a2 region comprises SEQ ID NO;

4;

(ii) the a1 region comprises SEQ ID NO;

5;

(iii) the a3 region comprises SEQ ID NO;

6;

or

(iv) any combination thereof.

25. The chimeric molecule of claim 1, wherein the PAR1 exosite interaction motif further comprises a sequence selected from the group consisting of P, P-N, P-N-D, P-N-D-K (SEQ ID NO:

8), P-N-D-K-Y (SEQ ID NO;

     9), P-N-D-K-Y-E (SEQ ID NO;

     10), P-N-D-K-Y-E-P (SEQ ID NO;

     11), P-N-D-K-Y-E-P-F (SEQ ID NO;

     12), P-N-D-K-Y-E-P-F-W (SEQ ID NO;

     13), P-N-D-K-Y-E-P-F-W-E (SEQ ID NO;

     14), P-N-D-K-Y-E-P-F-W-E-D (SEQ ID NO;

     20), P-N-D-K-Y-E-P-F-W-E-D-E (SEQ ID NO;

     21), P-N-D-K-Y-E-P-F-W-E-D-E-E (SEQ ID NO;

     22), P-N-D-K-Y-E-P-F-W-E-D-E-E-S(SEQ ID NO;

     23), and any combination thereof.

30. The chimeric molecule of claim 1, wherein the VWF linker further comprises one or more amino acids, wherein the one or more amino acids comprise GlyGly or a Gly/Ser peptide.

36. The chimeric molecule of claim 1, wherein the VWF protein comprises the D′

domain and D3 domain of VWF, wherein the D′

domain and D3 domain are capable of binding to a FVIII protein.

44. The chimeric molecule of claim 36, wherein the VWF protein consists essentially of or consists of:

(1) the D′ and

D3 domains of VWF or fragments thereof;

(2) the D1, D′

, and D3 domains of VWF or fragments thereof;

(3) the D2, D′

, and D3 domains of VWF or fragments thereof;

(4) the D1, D2, D′

, and D3 domains of VWF or fragments thereof;

or (5) the D1, D2, D′

, D3, and A1 domains of VWF or fragments thereof.

46. The chimeric molecule of claim 1, wherein the VWF protein is pegylated, glycosylated, hesylated, or polysialylated.

48. The chimeric molecule of claim 1, wherein the heterologous moiety (H1) comprises an immunoglobulin constant region or a portion thereof, albumin, albumin-binding polypeptide, PAS, the C-terminal peptide (CTP) of the β

subunit of human chorionic gonadotropin, polyethylene glycol (PEG), hydroxyethyl starch (HES), albumin-binding small molecules, or any combinations thereof, or wherein the heterologous moiety (H1) comprises a clearance receptor, or fragment thereof, wherein the clearance receptor blocks binding of a FVIII protein to FVIII clearance receptors.

49. The chimeric molecule of claim 48, wherein the immunoglobulin constant region or a portion thereof comprises an FcRn binding partner.

53. The chimeric molecule of claim 6, wherein the second heterologous moiety (H2) comprises an immunoglobulin constant region or a portion thereof, albumin, albumin-binding polypeptide, PAS, the C-terminal peptide (CTP) of the β

subunit of human chorionic gonadotropin, polyethylene glycol (PEG), hydroxyethyl starch (HES), albumin-binding small molecules, or any combinations thereof.

57. The chimeric molecule of claim 6, wherein the second heterologous moiety comprises an FcRn binding partner.

62. The chimeric molecule of claim 6, wherein the first heterologous moiety is an FcRn binding partner and the second heterologous moiety is an FcRn binding partner.

68. The chimeric molecule of claim 6, comprising a formula selected from the group consisting of:

(a) V-L1-X1-H1;

H2-L2-X2-C;

(b) V-X1-L1-H1;

H2-L2-X2-C;

(c) V-L1-X1-H1;

H2-X2-L2-C;

(d) V-X1-L1-H1;

H2-X2-L2-C;

(e) V-L1-X1-H1;

H2-L2-C(X2);

(f) V-X1-L1-H1;

H2-L2-C(X2);

(g) C-X2-L2-H2;

H1-X1-L1-V;

(h) C-X2-L2-H2;

H1-L1-X1-V;

(i) C-L2-X2-H2;

H1-L1-X1-V;

(j) C-L2-X2-H2;

H1-L1-X1-V;

(k) C(X2)-L2-H2;

H1-X1-L1-V;

or

(l) C(X2)-L2-H2;

H1-L1-X1-V;

wherein V is the VWF protein;

L1 is the VWF linker;

L2 is an optional FVIII linker;

H1 is the first heterologous moiety;

H2 is the second heterologous moiety;

C is the FVIII protein;

C(X2) is the FVIII protein fused to the XTEN sequence, wherein the XTEN sequence is inserted between two FVIII amino acids adjacent to each other;

(-) is a peptide bond or one or more amino acids; and

(;

) is a covalent bond between the H1 and the H2.

84. A polynucleotide or a set of polynucleotides encoding the chimeric molecule of claim 1 or a complementary sequence thereof.

86. A vector or a set of vectors comprising the polynucleotide or the set of polynucleotides of claim 84 and one or more promoter operably linked to the polynucleotide or the set of polynucleotides.

88. A host cell comprising the polynucleotide or the set of the polynucleotides of claim 86.

91. A pharmaceutical composition comprising the chimeric molecule of claim 1 and a pharmaceutically acceptable carrier.

94. A method of reducing a frequency or degree of or preventing an occurrence of a bleeding episode in a subject in need thereof comprising administering an effective amount of the chimeric molecule of claim 1.

98. A method of making a chimeric molecule, comprising transfecting one or more host cell with the polynucleotide or the set of polynucleotides of claim 84 and expressing the chimeric molecule in the host cell.

5. (canceled)

7. A chimeric molecule comprising a first polypeptide chain which comprises a VWF protein, a heterologous moiety (H1), and a VWF linker connecting the VWF protein and the heterologous moiety (H1) and a second polypeptide chain comprising a FVIII protein and an XTEN sequence, wherein the VWF linker in the first polypeptide chain comprises:

i. an a2 region from FVIII;

ii. an a1 region from FVIII;

iii. an a3 region from FVIII;

iv. a thrombin cleavage site which comprises X-V-P-R (SEQ ID NO;

     3) and a PAR1 exosite interaction motif, wherein X is an aliphatic amino acid;

or

v. any combination thereof,

and wherein the first polypeptide chain and the second polypeptide chain are associated with each other.

8-11. -11. (canceled)

14-17. -17. (canceled)

20-24. -24. (canceled)

26-29. -29. (canceled)

31-35. -35. (canceled)

37-43. -43. (canceled)

45. (canceled)

47. (canceled)

50-52. -52. (canceled)

54-56. -56. (canceled)

58-61. -61. (canceled)

63-67. -67. (canceled)

69-83. -83. (canceled)

85. (canceled)

87. (canceled)

89-90. -90. (canceled)

92-93. -93. (canceled)

95-97. -97. (canceled)

99. (canceled)

100. A method of improving FVIII activity of a chimeric FVIII protein comprising a VWF protein, a heterologous moiety (H1), and a VWF linker connecting the VWF protein and the heterologous moiety (H1) and a second polypeptide chain comprising a FVIII protein and an XTEN sequence, wherein the VWF linker in the first polypeptide chain comprises:

vi. an a2 region from FVIII;

vii. an a1 region from FVIII;

viii. an a3 region from FVIII;

ix. a thrombin cleavage site which comprises X-V-P-R (SEQ ID NO;

     3) and a PAR1 exosite interaction motif, wherein X is an aliphatic amino acid;

or

x. any combination thereof.

101-111. -111. (canceled)