Coagulation factor IX compositions and methods of making and using same

• US 9,376,672 B2
• Filed: 05/12/2015
• Issued: 06/28/2016
• Est. Priority Date: 08/24/2009
• Status: Active Grant

• Current Assignee: Amunix Pharmaceuticals, Inc. (Sanofi )
• Original Assignee: Amunix Operating Inc.
• Inventors: Schellenberger, Volker, Stemmer, Willem P., Geething, Nathan C., To, Wayne, Silverman, Joshua, Wang, Chia-wei, Spink, Benjamin
• Primary Examiner(s): Alstrum Acevedo, James H
• Assistant Examiner(s): Beane, Randall L
• Application Number:
  US14/710,077
• Publication Number:
  US 20150344862A1
• Time in Patent Office: 413 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: A61P 7/02 Antithrombotic agents; Anticoagulants; Platelet aggregation inhibitors
• CPC Class Codes: A61P 7/04 Antihaemorrhagics; Procoagulants; Haemostatic agents; Antifibrinolytic agents
• CPC Class Codes: C07K 14/001 by chemical synthesis
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C07K 2319/31 fusions, other than Fc, for prolonged plasma life, e.g. albumin
• CPC Class Codes: C07K 2319/50 containing protease site
• CPC Class Codes: C12N 15/70 Vectors or expression systems specially adapted for E. coli
• CPC Class Codes: C12N 9/6437 Coagulation factor VIIa (3.4.21.21)
• CPC Class Codes: C12N 9/644 Coagulation factor IXa (3.4.21.22)
• CPC Class Codes: C12Y 304/21022 Coagulation factor IXa (3.4.21.22)

Abstract

The present invention relates to compositions comprising factor IX coagulation factors linked to extended recombinant polypeptide (XTEN), isolated nucleic acids encoding the compositions and vectors and host cells containing the same, and methods of making and using such compositions in treatment of coagulation factor-related diseases, disorders, and conditions.

Claims

1. A factor IX fusion protein comprising a factor IX polypeptide and an extended recombinant polypeptide (XTEN), said XTEN comprising an amino acid sequence having at least 90% sequence identity to a sequence selected from SEQ ID NOs:

35, 36, 37, 38, 43, 44, 45, and 46, wherein the XTEN is characterized in that;

(a) the sum of glycine (G), alanine (A), serine (S), threonine (T), glutamate (E) and proline (P) residues constitutes more than 80% of the total amino acid residues of the XTEN; and

(b) the XTEN is non-repetitive such that (i) the XTEN contains no three contiguous amino acids that are identical unless the amino acids are serine, or (ii) at least 80% of the XTEN comprises non-overlapping sequence motifs, each of the sequence motifs comprising about 9 to about 14 amino acid residues, wherein any two contiguous amino acid residues do not occur more than twice in each of the sequence motifs.

2. The factor IX fusion protein of claim 1, wherein the XTEN comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO 36.

3. The factor IX fusion protein of claim 1, wherein said XTEN comprises the amino acid sequence set forth in SEQ ID NO:

36.

4. The factor IX fusion protein of claim 1, wherein the XTEN comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO:

37.

5. The factor IX fusion protein of claim 1, wherein said XTEN comprises the amino acid sequence set forth in SEQ ID NO:

37.

6. The factor IX fusion protein of claim 1, wherein said factor IX polypeptide is linked at its C-terminus to the XTEN.

7. The factor IX fusion protein of claim 1 that is configured according to formula VII:

(Gla)-(XTEN)_u-(EGF1)-(XTEN)_v-(EGF2)-(AP1)-(XTEN)_w-(AP2)-(XTEN)_x-(Pro)-(s)_y-(XTEN)_z 

 

VII

wherein independently for each occurrence,

(a) Gla is a Gla domain of the factor IX polypeptide;

(b) EGF1 is an EGF1 domain of the factor IX polypeptide;

(c) EGF2 is an EFG2 domain of the factor IX polypeptide;

(d) AP1 is a portion of an activator peptide domain of the factor IX polypeptide;

(e) AP2 is a portion of an activator peptide domain of the factor IX polypeptide that includes at least a first cleavage sequence;

(f) PRO is a protease domain of the factor IX polypeptide;

(g) S is a spacer sequence having between 1 to about 50 amino acid residues that can optionally include a cleavage sequence;

(h) XTEN is the extended recombinant polypeptide;

(i) u is either 0 or 1;

(j) v is either 0 or 1;

(k) x is either 0 or 1;

(1) y is either 0 or 1; and

(m) z is either 0 or 1, with the proviso that u+v+x+y+z≧

1.

8. The factor IX fusion protein of claim 1, which comprises more than one XTEN.

9. The factor IX fusion protein of claim 1, wherein said XTEN is incorporated between any two adjacent domains contained in said factor IX, wherein said two adjacent domains are selected from the group consisting of Gla, EGF1, EGF2, AP, and peptidase S1 (Pro).

10. The factor IX fusion protein of claim 1, wherein the XTEN comprises an amino acid sequence having at least 90% sequence identity to a sequence selected from SEQ ID NOs:

225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 341, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, and 489.

11. The factor IX fusion protein of claim 10, wherein the XTEN comprises an amino acid sequence having at least 95% sequence identity to a sequence selected from SEQ ID NOs:

225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 341, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, and 489.

12. The factor IX fusion protein of claim 11, wherein the XTEN comprises an amino acid sequence selected from SEQ ID NOs:

225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 249, 251, 253, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 283, 285, 287, 289, 291, 293, 295, 297, 341, 403, 405, 407, 409, 411, 413, 415, 417, 419, 421, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 453, 455, 457, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, 485, 487, and 489.

13. The factor IX fusion protein of claim 12, wherein the XTEN comprises an amino acid sequence selected from SEQ ID NOs:

225, 229, 231, 239, 243, 249, 255, 257, 265, and 283.

14. The factor IX fusion protein of claim 13, wherein the fusion protein comprises SEQ ID NO:

229.

15. The factor IX fusion protein of claim 1, wherein the XTEN comprises an amino acid sequence having at least 90% sequence identity to a sequence selected from SEQ ID NOs:

61, 62, 63, 65, 66, 69, 71, 73, 74, 75, 76, 77, 78, 79, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, and 556.

16. The factor IX fusion protein of claim 15, wherein the XTEN comprises an amino acid sequence having at least 95% sequence identity to a sequence selected from SEQ ID NOs:

61, 62, 63, 65, 66, 69, 71, 73, 74, 75, 76, 77, 78, 79, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, and 556.

17. The factor IX fusion protein of claim 16, wherein the XTEN comprises an amino acid sequence selected from SEQ ID NOs:

61, 62, 63, 65, 66, 69, 71, 73, 74, 75, 76, 77, 78, 79, 492, 494, 496, 498, 500, 502, 504, 506 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, and 556.

18. The factor IX fusion protein of claim 17, wherein the XTEN comprises SEQ ID NO:

63 or 65.

19. The factor IX fusion protein of claim 1, wherein the fusion protein comprises an amino acid sequence having at least 90% sequence identity to a sequence selected from SEQ ID NOs:

602, 604, 606, 608, 612, 614, 616, and 618.

20. The factor IX fusion protein of claim 19, wherein the fusion protein comprises an amino acid sequence having at least 95% sequence identity to a sequence selected from SEQ ID NOs:

602, 604, 606, 608, 612, 614, 616, and 618.

21. The factor IX fusion protein of claim 20, wherein the fusion protein comprises an amino acid sequence selected from SEQ ID NOs:

602, 604, 606, 608, 612, 614, 616, and 618.

22. A polynucleotide encoding the factor IX fusion protein of claim 1.

23. A vector comprising the polynucleotide of claim 22.

24. A host cell comprising the polynucleotide of claim 22.

25. A method of producing a FIX fusion protein comprising culturing the host cell of claim 24 under suitable condition, wherein the FIX fusion protein is expressed.

26. A pharmaceutical composition comprising the factor IX fusion protein of claim 1.

27. A pharmaceutical composition comprising the polynucleotide of claim 22.