Main > SURGERY > Wound > Healing > PDGF-BB Dimer Recombinant

Product USA. C

PATENT ASSIGNEE'S COUNTRY USA
UPDATE 07.00
PATENT NUMBER This data is not available for free
PATENT GRANT DATE 04.07.00
PATENT TITLE Therapeutic uses of resolved intact or clipped native-sequence PDGF-BB dimers

PATENT ABSTRACT Methods for improving purification and quantification of platelet derived growth factor (PDGF) proteins having structural heterogeneity are provided. Preparation of substantially pure isoforms of these proteins is achieved using TSK sulfopropyl cation exchange chromatography and reverse phase high performance liquid chromatography. A reverse charged capillary zone electrophoresis method enables quantification of substantially pure isoforms of these proteins resulting from endoproteolytic post-translational modifications. Compositions of the invention are substantially purified isoforms of secreted PDGF proteins having structural heterogeneity, more particularly purified intact, single-clipped, and double-clipped isoforms of recombinant PDGF-BB. Pharmaceutical compositions comprising at least one of these substantially purified recombinant PDGF isoforms and methods for their use in promoting wound healing are also provided.

PATENT INVENTORS This data is not available for free
PATENT ASSIGNEE This data is not available for free
PATENT FILE DATE 12.12.97
PATENT REFERENCES CITED Cook et al., "Purification and Analysis of Proteinase-Resistant Mutants of Recombinant Platelet-Derived Growth Factor-BB Exhibiting Improved Biological Activity," The Biochemical Journal, vol. 281, 1 (Jan. 1992), pp. 56-65.
Oefner et al., "Crystal Structure of Human Platelet-Derived Growth Factor BB," EMBO Journal, vol. 11 (1992) pp. 3921-3926.

PATENT PARENT CASE TEXT This data is not available for free
PATENT CLAIMS What is claimed is:

1. A composition comprising purified, biologically active recombinant PDGF (rPDGF)-BB dimers,

wherein at least about 80% of the PDGF-BB dimers are intact isoforms, single-clipped isoforms, or a mixture thereof;

and wherein the rPDGF-B polypeptides in the dimers are native-sequence or variant PDGF-B polypeptides, provided that the rPDGF-B polypeptides are not proteinase-resistant mutant PDGF-B polypeptides.

2. A composition according to claim 1, wherein the rPDGF-B polypeptides exhibit at least about 80% identity to native-sequence PDGF-B polypeptides.

3. A composition comprising purified, biologically active recombinant PDGF (rPDGF)-BB dimers,

wherein at least about 80% of the PDGF-BB dimers are intact isoforms, single-clipped isoforms, or a mixture thereof;

and wherein the rPDGF-B polypeptides in the dimers are native-sequence or variant PDGF-B polypeptides that exhibit at least about 95% identity to native-sequence PDGF-B polypeptides, provided that the rPDGF-B polypeptides are not proteinase-resistant mutant PDGF-B polypeptides.

4. A composition according to claim 3, wherein the rPDGF-B polypeptides are native-sequence PDGF-B polypeptides.

5. A composition according to claim 4, wherein the rPDGF-B polypeptides have the amino acid sequences of human PDGF-B polypeptides.

6. A composition according to claim 3, wherein about 80% to about 95% of the rPDGF-BB dimers are intact isoforms.

7. A composition according to claim 3, wherein at least about 80% of the rPDGF-BB dimers are single-clipped isoforms.

8. A composition according to claim 3, wherein the rPDGF-B polypeptides are the products of a yeast cell expression system.

9. A composition according to claim 8, wherein the yeast cell is a Saccharomyces cell.

10. A composition according to claim 9, wherein the rPDGF-B polypeptides have the amino acid sequences of human PDGF-B polypeptides.

11. A composition according to claim 10, wherein about 80% to about 95% of the rPDGF-BB dimers are intact isoforms.

12. A composition according to claim 10, wherein at least about 80% of the rPDGF-BB dimers are single-clipped isoforms.

13. A composition according to claim 1, wherein the composition is suitable for pharmaceutical use.

14. A composition according to claim 2, wherein the composition is suitable for pharmaceutical use.

15. A composition according to claim 3, wherein the composition is suitable for pharmaceutical use.

16. A composition according to claim 4, wherein the composition is suitable for pharmaceutical use.

17. A composition according to claim 5, wherein the composition is suitable for pharmaceutical use.

18. A composition according to claim 6, wherein the composition is suitable for pharmaceutical use.

19. A composition according to claim 7, wherein the composition is suitable for pharmaceutical use.

20. A composition according to claim 8, wherein the composition is suitable for pharmaceutical use.

21. A composition according to claim 9, wherein the composition is suitable for pharmaceutical use.

22. A composition according to claim 10, wherein the composition is suitable for pharmaceutical use.

23. A composition according to claim 11, wherein the composition is suitable for pharmaceutical use.

24. A composition according to claim 12, wherein the composition is suitable for pharmaceutical use.

25. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 13.

26. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 14.

27. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 15.

28. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 16.

29. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 17.

30. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 18.

31. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 19.

32. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 20.

33. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 21.

34. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 22.

35. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 23.

36. A method for treating a wound comprising administering to a subject having the wound a therapeutically effective amount of a composition according to claim 24.

37. A method according to claim 25, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

38. A method according to claim 26, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

39. A method according to claim 27, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

40. A method according to claim 28, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

41. A method according to claim 29, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

42. A method according to claim 30, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

43. A method according to claim 31, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

44. A method according to claim 32, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

45. A method according to claim 33, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

46. A method according to claim 34, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

47. A method according to claim 35, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.

48. A method according to claim 36, wherein the wound is a laceration, a burn, an ulcer, a surgical wound, a bone injury, an epithelial wound, or an endothelial wound.
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PATENT DESCRIPTION FIELD OF THE INVENTION

The present invention relates to the field of protein analysis and separation, particularly to preparations of purified isoforms of heterologous proteins having structural heterogeneity.

BACKGROUND

Platelet-derived growth factor (PDGF), the primary mitogen in serum for mesenchymal-derived cells, is stored in platelet alpha-granules. Injury to blood vessels activates the release of PDGF from these granules in the vicinity of the injured vessels. This mitogen acts as a potent chemoattractant for fibroblasts and smooth muscle cells, as well as monocytes and neutrophils. The mitogenic activity of the localized PDGF results in proliferation of these cells at the site of injury, contributing to the process of wound repair.

Purified native platelet-derived growth factor (PDGF), a glycoprotein of about 30,000 daltons, is composed of two disulfide-linked polypeptide chains. Two forms of these chains, designated A and B, have been identified. The native protein occurs as the homodimer AA or BB or the heterodimer AB, or a mixture thereof. A partial amino acid sequence for the PDGF-A chain has been identified (Johnsson et al. (1984) EMBO J. 3:921-928) and cDNAs encoding two forms of PDGF A-chain precursors have been described (U.S. Pat. No. 5,219,759). The mature A-chain consists of a 104 amino acid polypeptide that is derived by proteolytic processing of a 211 amino acid precursor polypeptide. The cDNA encoding the PDGF-B chain has also been described (Nature (1985) 316:748-750). The mature B-chain consists of a 109 amino acid polypeptide that is derived by proteolytic processing of a 241 amino acid precursor polypeptide. The mature A and B chains of PDGF show sequence identity of 51%, with the eight cysteine residues being conserved in each of the chains (Johnsson et al. (1984) EMBO J. 3:921-928).

In addition to proteolytic processing of the precursor polypeptides into mature PDGF-A and PDGF-B chains, recombinant PDGF (rPDGF) produced in a yeast host undergoes further post-translational processing that results in a secreted mature protein having considerable structural heterogeneity. This is true for the heterodimer rPDGF-AB, and more particularly for the homodimer rPDGF-BB.

When expressed in a yeast host for production of a bulk drug substance, PDGF undergoes endoproteolytic cleavage, or so-called clipping, of the B-chain between the Arg-32 and Thr-33 residues, resulting in a bulk drug substance having a mixture of unclipped or so-called intact rPDGF and clipped rPDGF that has been cleaved in the B-chain between the Arg-32 and Thr-33 residues. In the case of rPDGF-BB, one or both of the B-chains may be clipped, resulting in single-clipped or double-clipped rPDGF-BB, respectively. Other post-translational modifications of interest to the present invention include exoproteolytic removal of C-terminal amino acids, or so-called truncation, which may remove Arg-32 from clipped B-chains and/or Thr-109 from intact and clipped B-chains. These post-translational modifications lead to a number of structural forms, or so-called isoforms, of rPDGF-BB present in the secreted product. Methods of the present invention are directed to separation and purification of the intact, single-clipped, and double-clipped isoforms of rPDGF, more particularly rPDGF-BB.

The three dimeric forms of PDGF exhibit different binding affinities for the two known PDGF receptor gene products, .alpha. and .beta.. The beta receptor recognizes PDGF B chain and is dimerized in the presence of PDGF-BB. The alpha receptor recognizes PDGF B and A chains and can be dimerized by PDGF-BB, PDGF-AA, and PDGF-AB (see, for example, Abboud et al (1994) J. Cell. Phys. 158:140-150). The amino acid residue region of PDGF-BB involved in binding or activation of the receptor has been narrowed down to residues Ile25-Phe37 (Giese et al. (1990) Mol. Cell. Biol. 10:5496-5501). These residues include the Arg-32/Thr-33 site cleaved by endoproteolytic processing during production of PDGF-BB by a yeast host

Proteinase-resistant mutants of recombinant PDGF-BB exhibiting improved biological activity have been identified (Cook et al. (1992) Biochem. J. 281:57-65; see also European Patent Application No. 0 547 064 B1). These mutants prevent endoproteolytic cleavage of the B-chains at Arg-32. Thus elimination of endoproteolytic cleavage in this region apparently leads to increased biological activity of the PDGF-BB produced in a yeast host during the fermentation process. This increase in biological activity is presumably associated with an increase in the relative amount of unclipped, or so-called intact, PDGF-BB and a decrease in the relative amount of clipped PDGF-BB in the recombinant PDGF-BB product Similarly, endoproteolytic cleavage in this region of either or both of the B-chains within a rPDGF-BB protein would be expected to yield a bulk drug substance having different biological activity than found for a bulk drug substance consisting solely of the intact rPDGF-BB.

Prior to the present invention, methods commonly used in the art to purify recombinantly produced PDGF have not distinguished between the various isoforms of PDGF resulting from post-translational processing, including endoproteolytic cleavage of the PDGF-B chain between Arg-32 and Thr-33. Prior art teaches that structural isoforms resulting from post-translational endoproteolytic cleavage could have varying degrees of biological activity, and hence can effect the overall biological activity of bulk drug substance produced by fermentation.

Methods are needed to separate and quantify the structural isoforms of recombinantly produced PDGF such that their biological activities can be compared. These methods would be useful in preparing bulk drug substances consisting of pure isoforms.

SUMMARY OF THE INVENTION

Methods for improving purification and quantification of platelet derived growth factor (PDGF) proteins having structural heterogeneity are provided. Preparation of substantially pure isoforms of these proteins is achieved using TSK sulfopropyl cation exchange chromatography and reverse phase high performance liquid chromatography. These methods are particularly useful for separating isoforms that result from post-translational endoproteolytic processing of secreted recombinant PDGF (rPDGF), more particularly rPDGF-BB. A reverse charge capillary zone electrophoresis method of the invention is useful for quantifying endoproteolytic post-translational modifications.

Compositions of the invention are substantially purified isoforms of secreted PDGF proteins having structural heterogeneity, more particularly purified intact, single-clipped, and double-clipped isoforms of PDGF-BB. Pharmaceutical compositions comprising at least one of these substantially purified PDGF isoforms and methods for their use in promoting wound healing are also provided.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic representation of intact isoforms of rhPDGF-BB (group A) with or without truncation of Thr-109. Single lines represent B chains; paired lines represent rhPDGF-BB.

FIG. 2 is a schematic representation of single-clipped isoforms of rhPDGF-BB with or without truncation of Arg-32 and Thr-109. Paired lines represent single-clipped rhPDGF-BB. The clip in one of the B chains is represented by a break in the line. Isoforms of single-clipped species are separated into groups B and C based on the difference in the overall charge of the protein. Truncation of Arg-32 at the clip site (group C) produces a more acidic isoform, while truncation only of Thr-109 (group B) does not alter the molecular charge.

FIG. 3 is a schematic representation of double-clipped isoforms of rhPDGF-BB with or without truncation of Arg-32 and Thr-109. Paired broken lines represent double-clipped rhPDGF-BB. The clip in each of the B chains is represented by a break in each line. The double-clipped isoform is separated into groups D, E, and F based on the difference in the overall charge of the protein. Truncation of the Arg-32 at one of the clip sites (group E) makes the isoform more acidic, while truncation of Arg-32 at both of the clip sites (group F) removes two basic amino acid residues. Truncation only of Thr-109 (group D) does not alter the molecular charge, similar to single-clipped species (group B).

FIG. 4 is a high temperature reverse phase (RP) HPLC profile of rhPDGF-BB using a linear gradient elution. Double-clipped and truncated double-clipped isoforms (A), single-clipped and truncated single-clipped isoforms (B), and intact and truncated intact isoforms (C) of rhPDGF-BB are resolved as three groups of several peaks.

FIG. 5 is a high temperature RP HPLC profile of rhPDGF-BB using a step gradient elution. Double-clipped and truncated double-clipped isoforms (A), single-clipped and truncated single-clipped isoforms (B), intact and truncated intact isoforms (C), and a dimer/dimer (D) of rhPDGF-BB are resolved as individual peaks.

FIGS. 6A-B are an electropherogram of reverse charge capillary zone electrophoresis (RC CZE) of carboxypeptidase B treated PDGF-BB 6B in comparison to non-treated rhPDGF-BB 6A. Letters correspond to the groups identified in FIGS. 1-3.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is directed to compositions having PDGF activity that are useful as therapeutic agents in the treatment of wounds. More specifically, these compositions comprise at least one biologically active, substantially purified isoform of a recombinant PDGF (rPDGF) protein. By "recombinant" is intended the protein is produced as a heterologous or foreign protein in the cells of a host organism stably transformed with a nucleotide sequence encoding the foreign PDGF protein of interest.

Methods of the invention provide for the separation of biologically active isoforms of rPDGF from a bulk drug substance comprising a mixture of these isoforms. The methods are particularly useful for separating isoforms that result from post-translational endoproteolytic processing of secreted rPDGF, more particularly rPDGF-BB. Once separated, isoforms can be substantially purified and incorporated into a pharmaceutical composition for use in treatment of wounds.

An isoform of a rPDGF protein is "biologically active" when it has the capability of performing one or more biological functions or a set of activities normally attributed to PDGF in a biological context These biological activities include inducing chemotaxis and/or mitogenesis of responsive cell types following the binding of PDGF to a specific cell surface receptor. Other biological activities of PDGF may include, but are not limited to phospholipase activation, increased phosphotidylinositol turnover and prostaglandin metabolism, stimulation of both collagen and collagenase synthesis by responsive cells, indirect proliferative response of cells lacking PDGF receptors, and potent vasoconstrictor activity. Biological activity can be determined using any number of assays available in the art for PDGF, including but not limited to the mitogenic assay described herein.

By "substantially purified isoform" is intended at least about 80%, preferably at least about 90%, more preferably at least about 95% of the composition comprising rPDGF is the isoform of interest. Substantially purified isoforms of a protein are obtained using methods of the present invention that provide for separation of the isoform of interest from a cell culture comprising a mixture of rPDGF isoforms. By "separation of the isoform of interest" is intended removal of any undesirable isoforms or other components in the cell culture such that the remaining isoform is substantially purified.

The rPDGF protein whose isoforms are separated using methods of the present invention will be a biologically active dimeric form, more particularly the homodimer rPDGF-AA and PDGF-BB or the heterodimer rPDGF-AB, as well as any substantially homologous and functionally equivalent variants thereof. By "variant" is intended a protein derived from the native protein by deletion or addition of one or more amino acids to the N-terminal or C-terminal end of the native protein; deletion or addition of one or more amino acids at one or more sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Conservative substitutions that preserve the general charge, hydrophobicity/hydrophilicity, and/or steric bulk of the amino acid substituted may be preferred. Such substitutions may be made, for example, between the members of the following groups: GlyAla, ValIleLeu, AspGlu, LysArg, AsnGln, and PheTrpTyr. Other substitutions may be made to eliminate nonessential amino acid residues, such as to alter a glycosylation site, a phosphorylation site, an acetylation site, or to alter the folding pattern by altering the position of a cysteine residue that is not necessary for function. Methods for such manipulations are generally known in the art.

For example, amino acid sequence variants of the PDGF protein of interest can be prepared by mutations in the DNA sequence encoding the native PDGF protein. Methods for mutagenesis and nucleotide sequence alterations are well known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods Enzymol. 154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds. (1983) Techniques in Molecular Biology (MacMillan Publishing Company, New York) and the references cited therein; herein incorporated by reference. Such variants will continue to possess the desired biological activity. Obviously, the mutations that will be made in the DNA encoding the variant PDGF protein must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure. See EP Patent Application Publication No. 75,444.

Thus rPDGF proteins whose isoforms are separated using methods of the present invention include the naturally occurring PDGF proteins as well as variants thereof. These variants will be substantially homologous and functionally equivalent to their native PDGF protein. A variant of a native PDGF protein is "substantially homologous" to the native protein when at least about 80%, more preferably at least about 90%, and most preferably at least about 95% of its amino acid sequence is identical to the amino acid sequence of the native PDGF protein. Variants may differ by about 1, 2, 3, or 4 amino acids. By "functionally equivalent" is intended that the sequence of the variant defines a chain that produces a protein having substantially the same biological activity as the native protein of interest. Such functionally equivalent variants that comprise substantial sequence variations are also encompassed by the invention. Thus a functionally equivalent variant of the native protein will have a sufficient biological activity to be therapeutically useful. by "therapeutically useful" is intended effective in achieving a therapeutic goal, as, for example, healing a wound.

Methods are available in the art for determining functional equivalence. Biological activity can be measured using assays specifically designed for measuring activity of the native protein. Additionally, antibodies raised against the biologically active native protein can be tested for their ability to bind to the functionally equivalent analog, where effective binding is indicative of a protein having a conformation similar to that of the native protein.

Methods of the present invention provide for improved separation and purification of isoforms of rPDGF proteins, more particularly those isoforms resulting from post-translational endoproteolytic processing of rPDGF. The rPDGF whose isoforms are separated may be the homodimer PDGF-BB or the heterodimer PDGF-AB. In one preferred embodiment, the isoforms of recombinant human PDGF (rhPDGF) protein are separated and purified using methods of the invention.

The nucleotide sequence encoding the rPDGF protein whose isoforms are separated using methods of the present invention may be a genomic, cDNA, or synthetic DNA sequence. The genes encoding the native forms of PDGF have been sequenced, and various analogs are well known in the art. Expression of PDGF homodimers and heterodimers is described in, for example, U.S. Pat. Nos. 4,766,073; 4,769,328; 4,801,542; 4,845,075; 4,849,407; 5,045,633; 5,128,321; and 5,187,263; herein incorporated by reference. Based on the known amino acid sequences for the A- and B-chain polypeptides, synthetic nucleotide sequences encoding PDGF A-chain and B-chain polypeptides may be made in vitro using methods available in the art. See particularly Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, N.Y.). Where the recombinant PDGF protein of interest is the heterodimer rhPDGF-AB, the nucleotide sequences encoding the hybrid precursor polypeptides comprising the A- and B-chain polypeptides may be assembled as part of one expression cassette or assembled into separate expression cassettes for cotransformation of a host cell.

The nucleotide sequence encoding a recombinant PDGF protein of interest can be expressed in a suitable expression system for subsequent separation and purification of isoforms of interest according to methods of the present invention. Methods are available in the art for expressing heterologous proteins, more particularly for expressing recombinant PDGF homodimers and heterodimers in bacteria (see, for example, Hoppe et al. (1990) Eur. J. Biochem 187:207-214; Fretto et al. (1993) J. Biol. Chem. 268:3625-3631), yeast (Kelly et al. (1984) EMBO J. 4:3399-3405; Ostman et al. (1989) Growth Factors 1:271-281), and mammalian cells (see, for example, Ostman et al. (1988) J. Biol. Chem. 263:16202-16208). See also EP 177,957; U.S. Pat. No. 5,219,759; and the copending patent application filed concurrently herewith entitled "Improved Expression of Heterologous Proteins in Yeast," Ser. No. 08/989,251; herein incorporated by reference. Methods of the present invention may be practiced with rPDGF produced in any host system where post-translational endoproteolytic processing leads to a secreted rPDGF product comprising a mixture of isoforms.

Problems with post-translational proteolytic processing and generation of isoforms are frequently encountered in rPDGF produced in a yeast host By "yeast" is intended ascosporogenous yeasts (Endomycetales), basidiosporogenous yeasts, and yeast belonging to the Fungi Imperfecti (Blastomycetes). The ascosporogenous yeasts are divided into two families, Spermophthoraceae and Saccharomycetaceae. The later is comprised of four subfamilies, Schizosaccharomycoideae (e.g., genus Schizosaccharomyces), Nadsonioideae, Lipomycoideae, and Saccharomycoideae (e.g., genera Pichia, Kluyveromyces, and Saccharomyces). The basidiosporogenous yeasts include the genera Leucosporidium, Rhodosporidium, Sporidiobolus, Filobasidium, and Filobasidiella. Yeast belonging to the Fungi Imperfecti are divided into two families, Sporobolomycetaceae (e.g., genera Sporobolomyces, Bullera) and Cryptococcaceae (e.g., genus Candida). Of particular interest to the present invention are species within the genera Pichia, Kluyveromyces, Saccharomyces, Schizosaccharomyces, and Candida. Of particular interest are the Saccharomyces species S. cerevisiae, S. carlsbergensis, S. diastaticus, S. douglasii, S. kluyveri, S. norbensis, and S. oviformis. Species of particular interest in the genus Kluyveromyces include K. lactis. Since the classification of yeast may change in the future, for the purposes of this invention, yeast shall be defined as described in Skinner el al., eds. (1980) Biology and Activities of Yeast (Soc. App. Bacteriol. Symp. Series No. 9). In addition to the foregoing, those of ordinary skill in the art are presumably familiar with the biology of yeast and the manipulation of yeast genetics. See, for example, Bacila et al., eds. (1978) Biochemistry and Genetics of Yeast; Rose and Harrison, eds. (1987) The Yeasts (2.sup.nd ed.); Strathern et al., eds. (1981) The Molecular Biology of the Yeast Saccharomyces; herein incorporated by reference.

The selection of suitable yeast and other microorganism hosts for expression of heterologous proteins is within the skill of the art. When selecting yeast hosts for expression, suitable hosts may include those shown to have, inter alia, good secretion capacity, low proteolytic activity, and overall robustness. Yeast and other microorganisms are generally available from a variety of sources, including the Yeast Genetic Stock Center, Department of Biophysics and Medical Physics, University of California, Berkeley, Calif.; and the American Type Culture Collection, Rockville, Md.

Methods for expression of rPDGF in a yeast host are available in the art. One such method comprises transforming a yeast host cell with a plasmid expression vector comprising a nucleotide sequence encoding human PDGF-BB. This method is briefly described in Example 1 herein and is described in detail in the copending patent application filed concurrently herewith entitled "Improved Expression of Heterologous Proteins in Yeast," Ser. No. 08/989,251, herein incorporated by reference.

When expressed in a yeast host, rPDGF is secreted as a complex mixture of structural isoforms that result from post-translational processing of the protein during the fermentation production process. Post-translational processing is particularly prevalent in expression of rPDGF-BB. These structural isoforms have varying degrees of biological activity, as demonstrated using standard assays for PDGF activity. Methods of the invention are directed to separation of these structural isoforms such that a final pharmaceutical composition comprising substantially purified isoforms of the greatest biological activity can be prepared. These methods are useful for separating isoforms of rPDGF-AB, and more particularly isoforms of rPDGF-BB.

Recombinant PDGF-BB produced in a yeast host cell is secreted as a fully folded, biologically active homodimeric protein consisting of two highly twisted antiparallel pairs of B chains (Oefner et al. (1992) EMBO J. 11"3921-3926). Each B chain comprises 109 amino acid residues. During fermentation to produce a bulk drug substance, several post-translational modifications occur to the secreted rPDGF-BB. This results in a bulk drug substance comprising rPDGF protein having considerable structural heterogeneity. Such modifications include, but are not limited to endoproteolytic digestion between residues Arg-32 and Thr-33 (referred to as "clipping") and exoproteolytic removal of C-terminal amino acids (referred to as "truncation") at Arg-32 and Thr-109, glycosylation of Ser and/or Thr residues, and oxidation of methionine. These post-translational modifications lead to a number of structural forms, or so-called isoforms, of rPDGF-BB present in the secreted product. The structural heterogeneity of the rPDGF-BB yeast product is further complicated by the presence of a rigid Pro-Pro bond at residues 41 and 42. The rotation of this rigid bond is further hindered by its proximity to a disulfide bond and the bulky side chain of Trp-40. This rotational hindrance leads to the formation of stable cis-trans isomers of rPDGF-BB at room temperature. Although numerous potential isoforms exist when considering the multiple combinations of post-translational modifications and Pro-Pro isomerization, isoforms resulting from post-translational clipping and truncation are of primary interest to the present invention.

Post-translational endoproteolytic processing or clipping between Arg-32 and Thr-33 leads to three different and distinct basic isoforms of rPDGF-BB: intact, single-clipped, and double-clipped. By "intact" is intended both B chains remain intact and are not endoproteolytically cleaved. By "single-clipped" is intended one B chain is intact and one B chain is endoproteolytically cleaved between Arg-32 and Thr-33. By "double-clipped" is intended both B chains are endoproteolytically cleaved between Arg-32 and Thr-33. Each respective isoform may be additionally modified by C-terminal truncation of Arg-32 or Thr-109, producing a known number of derived structural species for any given basic isoform. Thus, for the intact isoform, C-terminal truncation may occur only at residue 109, leading to three different structural species of that isoform. For the single-clipped isoform, C-terminal truncation of both residues 32 and 109 can produce eight different structural species of that isoform. For the double-clipped isoform, ten structural species of that isoform are possible. All together, the post-translational processes of clipping followed by C-terminal truncation of Arg-32 or Thr-109 residues leads to a complex mixture of twenty-one possible structural isoforms of rPDGF-BB in the bulk drug substance, as illustrated schematically in FIGS. 1-3.

Methods of the invention are directed to separation of the basic isoforms designated as intact, single-clipped, and double-clipped isomers of rPDGF-BB, each of which comprises a known number of derived structural species resulting from truncation of the Arg-32 or Thr-109 residues. It has been determined that the intact isoform has 100% mitogenic activity, the single-clipped isoform has 120% mitogenic activity, and the double-clipped isoform has 20% mitogenic activity. The reference sample exhibits 50% activity. Accordingly, utilizing the methods of the invention compositions can be obtained having having at least about 20% greater, preferably at least about 50% greater, more preferably at least about 100% greater PDGF activity than the unpurified cell culture. Thus, for purposes of preparing pharmaceutical rPDGF-BB compositions having use as a therapeutic agent for treatment of wounds, it is clearly desirable to separate these isoforms such that the pharmaceutical compositions comprise intact and/or single-clipped isoforms of rPDGF-BB. Methods of the invention enable preparation of such pharmaceutical compositions by providing for separation of the intact and single-clipped isoforms from the double-clipped isoform of rPDGF-BB of the bulk drug substance produced by fermentation.

Methods of the invention utilize ion exchange enrichment, reverse phase high pressure liquid chromatography, and reverse charge capillary zone electrophoresis. The first of these methods is directed at separation of intact, single-clipped, and double-clipped isomers of rPDGF, particularly rPDGF-BB, where separation is to a degree of purification appropriate for therapeutic use of the rPDGF. Hence, this method is appropriate for separation of these isomers for use in production of a pharmaceutical composition comprising substantially purified intact, single-clipped, or intact and single-clipped rPDGF, particularly rPDGF-BB. The second and third methods, while providing a means for separation of the intact, single-clipped, and double-clipped isomers, are primarily useful for analytical means, as described below.

The intact and single-clipped isoforms of rPDGF-BB can be separated by ion-exchange enrichment from the double-clipped isoform to a degree of purification appropriate for therapeutic use of rPDGF-BB. A bulk drug comprising biologically active rPDGF-BB can be enriched in substantially purified intact and single-clipped rPDGF-BB isoforms by separating these isoforms from the double-clipped isoform using cation exchange chromatography and a TSK sulfopropyl column (TSK SP). The bulk drug substance produced by fermentation, which comprises all three of the isoforms, is run on the column, and the desired isoforms are eluted with NaCl solution. The double-clipped isoform elutes in the earlier fractions, followed by the single-clipped and intact isoforms. Removal of the eluted fraction comprising the double-clipped isoform allows for subsequent collection of fractions eluting the single-clipped and intact isoforms. These fractions can be used separately, or together, to produce a composition comprising the isolated intact isoform, single-clipped isoform, or a mixture of the intact and single-clipped isoforms of rPDGF-BB.

Reverse phase high pressure liquid chromatography (RP HPLC) is a method useful for separating certain isoforms of a dimeric protein preparation having multiple isoforms, where at least one isoform has two different faces. By "face" is intended a term used in the context of RP HPLC, where each polypeptide chain of a dimeric protein is a "face" of the molecule. For homodimers, like PDGF-BB, where the two chains are identical and have no modifications that make one face different than the other, the molecule has but one face. However, where the molecule has, as in the case of rPDGF-BB, a chain that is endoproteolytically cleaved on one of the chains, thus making a single-clipped isoform, the dimer resulting has two faces: the face of the unclipped chain and the face of the clipped chain. A heterodimer naturally has two faces. For example, in the case of the rPDGF-AB heterodimer, the A chain is one face and the B chain is another.

For the purposes of the present invention, RP HPLC conducted at high temperature is used to separate the intact, single-clipped, and double-clipped isoforms of rPDGF-BB. In accordance with the present invention, the RP HPLC method is conducted at a temperature between about 75.degree. C. at a minimum and about 90.degree. C. at a maximum, and more preferably the temperature is about 85.degree. C., for separation of rPDGF-BB isoforms. The RP HPLC method of the invention can further include using a combination isocratic/step gradient of acetonitrile.

Prior to the present application of high temperature RP HPLC to analyze and separate isoforms of rPDGF-BB, it had been noted by researchers producing PDGF-BB in E. coli and analyzing it by RP HPLC that at least 4 peaks were routinely observed in the resulting chromatograms (see Watson and Kenney (1992) J. Chromatography 606:165-170). It was established that these peaks were due to differences in exposed hydrophobicity caused by a Pro-Pro sequence at residue 41 and 42 (Watson and Kenney (1992) J. Chromatogr. 606:165-170) and thus measured pro-pro conformers. Furthermore, rPDGF-BB expressed in the yeast Saccharomyces cerevisae exhibits multiple conformers that produce broad and heterogenous chromatographic profiles when analyzed with RP HPLC at various ambient and subambient temperatures, as disclosed in Example 3 below. Analysis and separation of rPDGF-BB by RP HPLC at these temperatures is complicated by Pro-Pro isomerizations within the molecule. Additionally, absorptive chromatography cannot simultaneously resolve clipping and truncation to opposing faces of the homodimeric protein under these conditions.

When conducted at high temperature in accordance with the present invention, RP HPLC analysis accelerates the equilibrium of Pro-Pro isomerization as well as accelerating the rate of desorption. As a result, the phenomena of multiple Pro-Pro conformers is not observed. Thus, the number of isoforms potentially resolved can be reduced to the twenty-one structures described earlier as intact, single-clipped, and double-clipped isoforms and their exoproteolyzed species. Furthermore, when RP HPLC analysis is carried out at about 85 C, the heterogeneity resulting from the post-translational modifications due to clipping and truncation occurring on both faces of the dimeric molecule can be resolved.

A combination isocratic/step gradient can also be employed in addition to the high temperature to improve separation of the isoforms, thus greatly simplifying the chromatographic profile. Using the high temperature RP HPLC method with the isocratic/step gradient provides for separation of the isoforms of rPDGF-BB predominantly on the basis of clipping, facilitating analysis and separation of intact, single-clipped, and double-clipped isoforms of rPDGF-BB. Methods for conducting an isocratic/step gradient are available in the art.

Quantities of the intact, single-clipped, and double-clipped isoforms of rPDGF-BB can be separated from a bulk drug substance comprising a mixture of rPDGF isoforms using the RP HPLC method at high temperature and an isocratic/step gradient of acetonitrile in accordance with the present invention. These isoforms can be purified from the acetonitrile and TFA solvent and buffer components. Purification is achieved using standard means for removing proteins from such solvents. For example, dialysis using small tubes, or for larger amounts using continuous flow dialysis fibers, can be conducted to yield a product suitable for use as a therapeutic agent.

The purified rPDGF-BB isoforms obtained in accordance with this method of the invention are useful for conducting biological activity assays to determine relative biological activity of the purified isoforms. In the case of rPDGF-BB, a mitogenic assay to determine the biological activity of a bulk drug substance comprising at least one isoform of rPDGF-BB can be conducted as described in Example 5 disclosed herein.

While the high temperature RP HPLC method of the present invention is useful for separating quantities of isoforms of rPDGF-BB sufficient to analyze biological activity of individual isoforms, the method is not suitable for routine analysis and quantification of the intact and clipped isoforms in a bulk drug substance. The third method of the invention, reverse charge capillary zone electrophoresis (RC CZE) was developed to provide for such quantification and routine analysis.

The reverse charge CZE of the present invention was originally developed to monitor charge heterogeneity since the extremely high isoelectric point (pI=10.5) of the rPDGF-BB molecule precluded the use of conventional isoelectric focusing (IEF) analysis. However, the use of hand cast very high pI IEF gels may be possible.

Separation by RC CZE is based on charge/size ratio. Thus, with respect to the rPDGF-BB of the present invention, truncation of the basic residue Arg-32 has a greater effect on RC CZE assay selectivity than truncation of the neutral amino acid residue Thr-109. Since truncation of the Thr-109 residue does not appreciably alter the charge or size of the protein, there is no separation between the three possible categories of isoforms within the intact isoform. The baseline separation observed between the intact isoform and the single-clipped isoform may be due to an increase in hydrodynamic size of the single-clipped isoform, which may occur through partial denaturation of the secondary structure. Within the single-clipped isoform, the separation of the two species (one without the C-terminal truncation of Arg-32 and the other with that truncation) is due to the decrease in charge of the species of isoform resulting from C-terminal truncation of Arg-32. Within the double-clipped isoforms, three isoforms can be distinguished; the separation of them may be due to the charge difference resulting from either a single or a double C-terminal truncation of Arg-32.

The RC CZE method described thus far is unable to distinguish between, and thus separate, single-clipped isoforms that have the Arg-32 truncation and double-clipped isoforms that do not have the Arg-32 truncation. In order to separate these two isoform categories, and in order to quantify the intact, single-clipped, and double-clipped isoforms, the RC CZE method of the present invention further comprises treating the bulk drug substance comprising the various rPDGF-BB isoforms with carboxypeptidase B prior to analysis. This enzyme is specific for the basic amino acids arginine and lysine located at the carboxy terminus. Enzyme treatment converts single-clipped isoforms not having an Arg-32 truncation to single-clipped isoforms having the Arg-32 truncation, and converts double-clipped isoforms having no, or only one, Arg-32 truncation to isoforms having two Arg-32 truncations. Thus, the treatment of PDGF-BB bulk drug substance with carboxypeptidase B simplifies the RC CZE electropherogram and allows quantification of the three isoforms of rPDGF-BB as defined by the clipping between Arg-32 and Thr-33 (the isoforms referred to as intact, single-clipped, and double-clipped).

The RC CZE method of analysis of PDGF-BB, as modified in the present invention to isolate intact, single-clipped, and double-clipped by use of carboxypeptidase B, is useful, in a quality control context, for analysis of a bulk drug substance comprising the rPDGF-BB isoforms described herein. The advantage of use of RC CZE for analyzing PDGF-BB in a quality control context is the ease and precision achieved by this method, which makes the method an appropriate method for such routine activities of analysis as required in quality control of bulk drug substances.

Thus the methods of the invention are useful in analyzing and separating intact, single-clipped, and double-clipped isoforms of rPDGF-BB. Following separation of the desired intact, single-clipped, or mixture of intact and single-clipped isoforms of rPDGF-BB, contaminating buffer or other impurities can be removed where necessary to produce compositions comprising substantially purified isoforms of interest. These compositions can be prepared for use as a therapeutic agent as described below. By "therapeutic agent" is intended an agent that accomplishes a therapeutic goal, as for example, healing a wound.

Compositions comprising the substantially purified intact, single-clipped, or a mixture of intact and single-clipped isoforms of rPDGF-BB are useful as therapeutic agents in the treatment of wounds, particularly those wounds that are normally repaired in response to the release of the native PDGF.

The release of PDGF in vivo acts as a chemotactic agent to attract monocytes, fibroblasts, and smooth muscle cells to the site of injury, and to initiate cell replication for the purposes of wound repair. This growth factor has been shown to promote healing of incision wounds in rats and healing in regions of the body such as chambers or subcutaneous spaces. Thus PDGF has application in healing such wounds as ulcers, burns, and skin grafts. In addition, PDGF can be used to heal wounds resulting from damaged connective tissue, the repair of which requires fibroblast proliferation and collagen deposition. In addition, where wound healing is retarded by any number of factors including, but not limited to advanced age, diabetes, cancer, and treatment with anti-inflammatory drugs or anticoagulants, PDGF can be used to promote normal wound healing in mammals in situations that would otherwise delay wound healing.

The usefulness of platelet-derived growth factor as a therapeutic agent for full and partial thickness burn repair has also been described by Danilenko et al. (1995) Am. J. Pathol. 147:1261-1277. In this manner, recombinant PDGF-BB induces marked extracellular matrix and granulation tissue production such that the bum defects are repaired.

In the context of diabetes, a condition with the complication of delayed wound healing, it has been postulated that refractory diabetic wounds are the result of deficiencies in growth factors and/or cytokines that are important for the healing process. Some preliminary studies have shown that application of certain growth factors or cytokines can facilitate wound healing, as described in Doxey et al. (1995) Life Sciences 57(11):111-23. In this study, PDGF of wounded diabetic rats was produced at low levels compared to control animals. These rats had a delayed production of PDGF in cells surrounding the wounds that occurred many days after the wound was incurred, possibly explaining the delay in wound healing in the diabetic animals. Thus, there is a potential application for administration of PDGF-BB to diabetics to induce and normalize wound healing.

Mechanisms of action of PDGF-BB and the other PDGF dimers, including PDGF-AA and PDGF-AB, are discussed generally in Lepisto et al. (1995) Biochem. Biophys. Res. Comm. 209(2):393-9. The dimers PDGF-AA and PDGF-BB down-regulate both the steady-state levels of pro-alpha 1 (I), and pro alpha 1 (III) collagen chain mRNAs and the production of collagen, both in a dose-dependent manner.

Additionally, compositions comprising PDGF can facilitate the healing of injured or depleted bones by promoting growth of the connective tissue, growth of the bone and cementum, and by stimulation of protein and collagen synthesis in the region of the injured bone, especially as in the case, for example, of periodontal disease (see WO 88/03409).

Compositions comprising PDGF can provide fast, effective healing for such wounds as, for example, bedsores, lacerations, and burns, as described in WO 91/15231 and U.S. Pat. No. 5,019,559, wherein PDGF in a composition with insulin-like growth factor (IGF) promotes an increase in new connective tissue and an increase in the growth of epithelial tissue.

Compositions comprising PDGF can be administered in a gel formulation, and such a formulation is suitable for topical administration to promote wound healing in conditions such as ulcers, superficial wounds and lacerations, abrasions, surgical wounds, burns, and bone defects, as described in WO 93/08825.

For use as a therapeutic agent for the treatment of wounds, compositions comprising the intact, single-clipped, or a mixture of intact and single-clipped isoforms of PDGF-BB described herein can be administered topically with an appropriate pharmaceutically acceptable carrier or in a substantially purified preparation of protein such that it is free from impurities and elements that would interfere with a therapeutic use. Such preparations that are free of toxic, antigenic, inflammatory, or other deleterious substances and that are at least about 80% pure are considered appropriate. The concentration of the protein can be from about 1 to about 25 .mu./ml of total volume, or can be in a range as broad as about 1 ng/ml to about 50 ug/ml depending on the therapeutic use for the rPDGF-BB. A therapeutically effective amount sufficient to accelerate the rate of appearance and increase the number of new fibroblasts in the wound space and to stimulate DNA synthesis in and collagen deposition by those fibroblasts will be in the range of about 1 to about 5 milliliters of the preparation, depending on the characteristics of the wound.

A pharmaceutical composition comprising substantially purified intact or single-clipped isoforms of rPDGF-BB or a mixture of such isoforms and an appropriate pharmaceutically acceptable carrier can be formulated for administration as a therapeutic agent for the treatment of wounds. Pharmaceutically acceptable carriers may be large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, and inactive viruses in particles. Such carriers are well known to those of ordinary skill in the art. Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. Pharmaceutically acceptable carriers in therapeutic compositions may contain liquids such as water, saline, glycerol, and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.

The method for formulating a pharmaceutical composition is generally known in the art. A thorough discussion of formulation and selection of pharmaceutically acceptable carriers, stabilizers, and isomolytes can be found in Remington's Pharmaceutical Sciences, 18.sup.th edition (Mack Pub. Co., Eaton, Penn., 1990).

Typically, the therapeutic pharmaceutical compositions are prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. Liposomes are included within the definition of a pharmaceutically acceptable carrier. Some liposome compositions are described in U.S. Pat. No. 5,422,120; WO 95/13796; WO 94/23697; WO 91/14445; and EP 524,968 B1.

Administration of the PDGF-BB therapeutic pharmaceutical composition can be by any means and to any location of the body of the animal being treated as is appropriate for the wound being treated. Thus, the PDGF-BB can be administered, for example, parenterally or topically. Parenteral administration can include subcutaneous, intravenous, intra-arterial, intramuscular, or direct injection into a region or organ of the body.

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