ZA200608909B

ZA200608909B - O-linked glycoforms of polypeptides and method to manufacture them

Info

Publication number: ZA200608909B
Application number: ZA200608909A
Authority: ZA
Inventors: Klausen Niels Kristian; Rasmussen Daniel
Original assignee: Novo Nordisk Healthcare Ag
Priority date: 2004-05-04
Filing date: 2006-10-26
Publication date: 2007-07-25
Also published as: CN101023180B; CN101023180A

Description

6841 WO . E

O-LINKED GLYCOFORMS OF POLYPEPTIDES

FIELD OF THE INVENTION

The present invention relates to compositions comprising glycoproteins having altered patterns of O-linked glycosylation, in particular Factor VII, Factor IX and other blood clot- ting factors.

BACKGROUND OF THE INVENTION

The biological activity of many glycoproteins is highly dependent upon the pres- ence or absence of particular oligosaccharide structures attached to the glycoprotein. The glycosylation pattern of a therapeutic glycoprotein can affect numerous aspects of the therapeutic efficacy, such as, e.g, solubility, resistance to proteolytic attack, thermal in- activation, immunogenicity, half-life, bioactivity, bioavailability, and stability.

Glycosylation is a complex post-transitional modification that is cell dependent.

Following translation, proteins are transported into the endoplasmic reticulum (ER), gly- cosylated and sent to the Golgi for further processing and subsequent targeting and/or secretion. During glycosylation, either N-linked or O-linked glycoproteins are formed.

Serum proteins involved in coagulation or fibrinolysis, including, e.g., Factor VII and Factor IX are proving to be useful therapeutic agents to treat a variety of pathologi- cal conditions. Accordingly, there is an increasing need for formulations comprising these proteins that are pharmaceutically acceptable and exhibit a uniform and predetermined clinical efficacy.

Because of the many disadvantages of using human plasma as a source of pharmaceutical products, it is preferred to produce these proteins in recombinant Sys- tems. The clotting proteins, however, are subject to a variety of co- and post- translational modifications, including, e.g., asparagine-linked (N-linked) glycosylation: serine- or threonine-linked (O-linked) glycosylation: and y-carboxylation of glu residues.

These modifications may be qualitatively or quantitatively different when heterologous cells are used as hosts for large-scale production of the proteins. In particular, produc- tion in heterologous cells often results in a different array of glycoforms, which identical polypeptides are having different covalently linked oligosaccharide structures.

In different systems, variations in the oligosaccharide structure of therapeutic proteins have been linked to, inter alia, changes in immunogenicity and in vivo clearance.

Thus, there is a need in the art for compositions and methods that provide glycoprotein preparations, particularly preparations comprising recombinant Factor IX or recombinant

5807-WO human Factor VII or modified Factor VII or Factor Vll-related polypeptides that contain predetermined glycoform patterns.

SUMMARY OF THE INVENTION

The present invention relates to preparations comprising polypeptides that ex- hibit predetermined serine or threonine-linked glycoform patterns. The preparations are at least about 80% homogenous in respect of the attached glycans or oligosaccharide chains, preferably at least about 90%, at least about 95%, or at least about 98% ho- mologous.

As used herein, a glycoform pattern refers to the distribution within the prepara- tion of oligosaccharide chains having varying structures that are covalently linked to a serine or threonine residue located in an EGF-like domain in the amino acid backbone of the polypeptide.

In one aspect, the invention provides a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2-Pro-Cys motif and wherein said serine/threonine forms part of a

Glc-O-Ser/Thr covalent bond, said preparation containing a substantially uniform ser- ine/threonine-linked glycosylation pattern.

In one embodiment of the invention, the glycosylation pattern is at least 80% uniform, preferably at least 85%, at least 90%, at least 95%, or at least 98% uniform.

In one embodiment, the serine/threonine-linked glycans are Xyl-Xyl-Glc-; in another, the glycans are Xyl-Glc-; in yet another, the glycans are Glc-.

In different embodiments the glycoproteins are selected from the group of: Fac- tor VII polypeptides, Factor VIII-related polypeptides, Factor IX polypeptides, Factor X polypeptides, Factor XII polypeptides, and protein Z polypeptides. In a preferred em- bodiment, the glycoprotein is selected from the group of: Human Factor VII, Factor VII sequence variants, human Factor IX, and Factor IX sequence variants. In one embodi- ment, the glycoprotein is a Factor VII variant wherein the ratio between the activity of the Factor VII-variant and the activity of native human factor VIia (wild-type FVIla) is at least about 1.25 when tested in the "In Vitro Hydrolysis Assay" as described in the pre- sent description, preferably at least about 2.0, or at least about 4.0.

In another aspect the invention provides methods for making preparations of glycoproteins containing Cys-X1-Ser/Thr-X2-Pro-Cys motifs and wherein said ser- ine/threonine forms part of a Glc-O-Ser/Thr covalent bond, said preparations containing a substantially uniform serine/threonine-linked glycosylation pattern. The methods are

3865 WO . " useful for remodelling or altering the glycosylation pattern present on a glycoprotein upon its initial expression.

More particular, the present invention provide a general enzymatic methodology for the modification of glycans (in particular O-linked glycans) of glycoproteins, in order to improve or enhance their pharmaceutically properties. One method involves treatment of the glycoprotein with xylosidases in order to remove any terminal xylose residues; other methods includes attachment of xylose residues to the exposed glucose or xylose residues on the glycoprotein by treatment with xylosyltransferases; a third method in- cludes attachment of glucose residues to serine and/or threonine amino acid residues in the polypeptide backbone thereby creating a glycosylated polypeptide.

BRIEF DESCRIPTION OF THE DRAWINGS

Fig. 1 shows the serine 52 glycosylation of wt-Factor VII.

Fig. 2 shows an O-glycosylation mapping of Factor VII.

Fig. 3 shows a reaction scheme for the making of a preparation of glycoproteins exhibit- ing a predetermined serine/threonine-linked glycosylation.

Fig. 4 shows a chromatogram from first HIC cycle showing fractions “A” and “B".

Fig. 5 shows a chromatogram obtained by reloading fraction “A” onto the HIC column;

Glc-O-Ser52-FVII was identified in the peak fraction, fraction 10.

Fig. 6 shows a chromatogram obtained by reloading fraction “B” onto the HIC column:

Xyl-Xyl-Glc-O-Ser52-FVII was identified in the peak fraction, fraction 15.

Fig. 7A shows a tryptic peptide map of the peak fraction, fraction 10; the arrow indicates the Glc-O-Ser52 O-glycopeptide.

Fig. 7B shows a tryptic peptide map of the peak fraction, fraction 15; the arrow indicates the Xyl-Xyl-Glc-O-Ser52 O-glycopeptide.

Fig. 8A shows a total mass analysis of the peak fraction, fraction 10; the arrow indicates the Glc-O-Ser52-rFVIla O-glycoform.

Fig. 8B shows a total mass analysis of the peak fraction, fraction 15; the arrow indicates the Xyl-Xyl-Glc-O-rfFVIla O-glycoform.

DETAILED DESCRIPTION

The following abbreviations are used herein:

Glc = glucosyl

Xyl = xylosyl su 0 Larpelscesos

Ser = serine (one letter code: S)

Thr = threonine (one letter code: T)

Pro = proline (one letter code: P)

Cys = cysteine (one letter code: C)

FVII = Factor VII

FVila = activated (two-chain) Factor VII

FIX = Factor IX

FIXa = activated (two-chain) Factor IX

As used herein, a "glycoform pattern” (or “glycosylation pattern”) refers to the distribution within the preparation of oligosaccharide chains having varying structures that are covalently linked to a serine or threonine residue located in the amino acid back- bone of the polypeptide. “Homogeneity” refers to the structural consistency across a population of poly- peptides with conjugated glycans. Thus, a glycoprotein preparation is said to be about 100% homologous if all contained glycoprotein molecules contain identical glycans at- tached to the relevant glycosylation site. For example, a preparation of Factor VII poly- peptides is said to be at least 90% homologous if at least 90% of the Factor VII polypep- tide molecules contain the glycan of interest attached to serine 52 (e.g., Xyl-Xyl-Glc-O-

Ser52). “Substantially uniform glycoform” or “substantially uniform glycosylation” or “substantially uniform glycosylation pattern”, when referring to a glycopeptide species, refers to the percentage of acceptor moieties, i.e., serine or threonine residues, that are glycosylated by the glycan of interest. For example, in the case of Factor VII, a substan- tially uniform glycosylation patterns exists if substantially all (as defined below) of the serine residues in position 52 are glycosylated with the glycan of interest. It is under- stood by one skilled in the art that the starting material may contain glycosylated serine and/or threonine residues that are glycosylated with a species having the same structure as the glycan of interest. Thus, the calculated percent glycosylation includes ser- ine/threonine residues that are glycosylated with the glycan of interest according to the invention, as well as those serine/threonine residues already glycosylated with the glycan of interest in the starting material.

The term “substantially” is intended to mean that at least about 80%, such as at least about 90%, at least about 95%, or at least about 98% of the serine/threonine resi- dues in the glycoprotein is glycosylated with a predetermined, specific glycan or glycan of

£881-WC

Interest. The glycosylation pattern is typically determined by one or more methods known to those skilled in the art, such as, e.g., tryptic digestion followed by high per- formance liquid chromatography (HPLC), liquid-chromatography-mass spectrometry (LC-

MS), matrix assisted laser desorption mass time of flight spectrometry (MALDITOF), cap- 5 illary electrophoresis, and the like.

The term “acceptor moiety” is intended to encompass the group or moiety to which a desired oligo- or mono-saccharide group is transferred such as, without limita- tion, the serine/threonine residue located within a Cys-X1-Ser/Thr-X2-Pro-Cys motif, a

Glc-residue covalently linked to such a serine/threonine residue, or a Xyi-residue cova- lently linked to a Glc-residue or a Xyl-residue in a Glc-O-Ser/Thr or Xyl-Glc-O-Ser/Thr moiety, respectively.

The term “saccharide donor moiety” is intended to encompass an activated sac- charide donor molecule (e.g., a desired oligo- or mono-saccharide structure such as, for example, a xylosyl-xylosyl-donor, xylosyi-donor, or glycosyl-donor) having a leaving group (e.g., xylose-UDP or glucose-UDP) suitable for the donor moiety acting as a sub- strate for the relevant catalysing enzyme (e.g. glycosyltransferase, xylosidase or xylosyl- transferase).

Oligosaccharides are considered to have a reducing and a non-reducing end, whether or not the saccharide at the reducing end is in fact a reducing sugar. In accor- dance with accepted nomenclature, oligosaccharides are depicted herein with the non- reducing end on the left and the reducing end on the right (e.g., Xyl-Xyl-Glc-0O-Ser)

EGF domain-containing polypeptides

The term ” EGF domain-containing polypeptides” is intended to encompass pep- tides, oligopeptides and polypeptides containing one or more epidermal growth factor (EGF)-like domain(s). EGF domains or repeats are small motifs with about 40 amino ac- ids defined by 6 conserved cysteines forming three disulfide bonds. EGF domain- containing polypeptides all contain a consensus sequence for O-glucose modification:

Cys1-X1-Ser/Thr-X2-Pro-Cys2 (i.e., a Cys1-X1-Ser-X2-Pro-Cys2 or a Cys1-X1-Thr-X2-

Pro-Cys2 consensus sequence) where Cysl and Cys2 are the first and second conserved cysteines of the EGF repeat and X1 and X2 independently is any amino acid.

The term “glycoprotein” is intended to encompass EGF domain-containing potly- peptides containing one or more glycans attached to one or more serine/threonine amino

5851-WO acid residues of the EGF-domain located in the back bone amino acid sequence of the polypeptide.

As used herein, the term “glycan” or, interchangeable, “sugar chain”, “oligosac- charide chain” or “oligosaccharide moiety” refers to the entire oligosaccharide structure that is covalently linked to a single serine/threonine residue. The glycan may comprise one or more saccharide units; examples of glycans include, e.g., Glc-, Xyl-Glc-, and Xyi-

Xyl-Glc-.

The term “O-glycosylation site” is intended to indicate the glycosylation site at serine/threonine (i.e., Ser or Thr) located within the motif Cysl-X1-Ser/Thr-X2-Pro-Cys2 where Cysl and Cys2 are the first and second conserved cysteines of the EGF repeat and

X1 and X2 independently is any amino acid. These include the glycosylation site at posi- tion Ser-52 (S52) of human wt-FVII and the corresponding residues in homologous poly- peptides such as, without limitation, FVII sequence variants and FIX polypeptides. The term “corresponding residues” is intended to indicate the Ser or Thr amino acid residue corresponding to the Ser52 residue of wild-type Factor Vii (see Fig.1) when the se- quences are aligned. Amino acid sequence homology/identity is conveniently determined from aligned sequences, using a suitable computer program for sequence alignment, such as, e.g., the ClustalW program, version 1.8, 1999 (Thompson et al., 1994, Nucleic

Acid Research, 22: 4673-4680). For example, the wt-factor VII Ser52-residue corre- sponds to the Ser53-residue of wt-Factor IX. It is further to be understood that polypep- tide variants may be created containing non-naturally occurring Cys-X1-Ser/Thr-X2-Pro-

Cys motifs and thereby containing non-naturally occurring O-glycosylation sites that can be glycosylated in accordance with the present invention. In one embodiment of the in- vention, the O-glycosylation site is a serine-glycosylation site and the motif is Cys1-X1-

Ser-X2-Pro-Cys2. In another embodiment, the O-glycosylation site is a threonine- glycosylation site and the motif is Cys1-X1-Thr-X2-Pro-Cys2.

The term “terminal glucose” is intended to encompass glucose residues linked as the terminal sugar residue in a glycan, or oligosaccharide chain, i.e., the terminal sugar of each antenna is glucose. The term “terminal xylose” is intended to encompass xylose residues linked as the terminal sugar residue in a glycan, or oligosaccharide chain.

Enzymes

Protein O-glycosyitransferase may be prepared as described, e.g., in Shao et al. (Glycobiology 12(11): 763-770 (2002)).

B8Y1-WO

The alpha-xylosidase enzymes may be prepared, e.g., as described by Monroe et al. (Plant Physiology and Biochemistry 41:877-885 (2003)).

The enzyme, UDP-D-xylose: -D-glucoside a-1,3-D-xylosyltransferase can be pre- pared from HepG2 cells as described by Omichi et al. (Eur. J. Biochem. 245:143-146 (1997)).

The enzyme, UDP-D-xylose: «-D-xyloside al,3-xylosyltransferase can be prepared from HepG2 cells as described by Minamida et al. ((J.Biochem. (Tokyo) 120: 1002-1006 (1996).

UDP-beta-D-glucose is commercially available from, e.g., Sigma (Sigma U4625)

UDP-D-xylose is commercially available from, e.g., Sigma (Sigma U5875)

Glycoproteins

The motif: Cys-X1-Ser/Thr-X2-Pro-Cys appears to be primarily found in epidermal growth factor (EGF) domains of multi-modular proteins such as coagulation and fibri- nolytic factors. The motif is a consensus sequence for O-glucose modification whereby a serine-glucose (Glc-O-Ser) or threonine-glucose (Glc-O-Thr) bond is formed. Coagulation factors VII, IX, X and XII as well as plasma Protein Z, Fibrillin and thrombospondin have all been shown to contain the Cys-X1-Ser/Thr-X2-Pro-Cys consensus sequence. Of these, Factors VII and IX and Protein Z have been described to contain the consensus sequence Cys-X1-Ser-X2-Pro-Cys.

The thrombospondins are a family of extracellular proteins that participate in cell-to-cell and cell-to-matrix communication. The proteins are secreted from platelets.

They regulate cellular phenotype during tissue genesis and repair.

Protein Z is a vitamin k-dependent plasma protein whose structure is similar to that of Factors VII, IX and X. In contrast to these proteins, however, Protein Z is not the zymogen of a serine protease because it lacks the His and Ser residues of the catalytic triad. Like Proteins C and S, Protein Z participates in limiting the coagulation response, believably by assisting in inhibition of activated Factor X (FXa).

Factor X (Stuart Prower Factor) is a vitamin K-dependent serine protease which participates in the blood clotting process by participating in activation of prothrombin into thrombin.

HIG T-WO . "

Factor XII (Hageman factor) is a blood coagulation factor activated by contact with the sub-endothelial surface of an injured vessel. Along with prekallikrein, it serves as the contact factor that initiates the intrinsic pathway of blood coagulation. Kallikrein activates factor XII to Xlla.

Factor IX (Christmas factor) is a vitamin K-dependent serine protease which par- ticipates in the blood clotting process by participating in activation of FX into FXa.

Factor VII (proconvertin) is a vitamin K-dependent serine protease which partici- pates in the blood clotting process by participating in activation of prothrombin into thrombin. FVII is activated into FVIla by contact with exposed tissue factor (TF) at sites of injury of the vessel wall.

Factor VII polypeptides and Factor VIII-related polypeptides

As used herein, the terms “Factor VII polypeptide ” or “FVII polypeptide” means any protein comprising the amino acid sequence 1-406 of wild-type human Factor VIla (i.e., a polypeptide having Lhe amino acid sequence disclosed in U.S. Patent No. 4,784,950), variants thereof as well as Factor VII-related polypeptides, Factor VII deriva- tives and Factor VII conjugates. This includes FVII variants, Factor VII-related polypep- tides, Factor VII derivatives and Factor VII conjugates exhibiting substantially the same or improved biological activity relative to wild-type human Factor Vila.

The term “Factor VII” is intended to encompass Factor VII polypeptides in their uncleaved (zymogen) form, as well as those that have been proteolytically processed to yield their respective bioactive forms, which may be designated Factor VIIa. Typically,

Factor VII is cleaved between residues 152 and 153 to yield Factor VIIa. Such variants of

Factor VII may exhibit different properties relative to human Factor VII, including stabil- ity, phospholipid binding, altered specific activity, and the like.

As used herein, "wild type human FVIla"” is a polypeptide having the amino acid sequence disclosed in U.S. Patent No. 4,784,950.

As used herein, "Factor VII-related polypeptides” encompasses polypeptides, in- cluding variants, in which the Factor VIIa biological activity has been substantially modi- fied, such as reduced, relative to the activity of wild-type Factor Vila. These polypeptides include, without limitation, Factor VII or Factor Vila into which specific amino acid se- quence alterations have been introduced that modify or disrupt the bioactivity of the polypeptide.

The term “Factor VII derivative” as used herein, is intended to designate a FVII polypeptide exhibiting substantially the same or improved biological activity relative to wild-type Factor VII, in which one or more of the amino acids of the parent peptide have

§891-WO . i been genetically and/or chemically and/or enzymatically modified, e.g. by alkylation, gly- cosylation, PEGylation, acylation, ester formation or amide formation or the like. This in- cludes but is not limited to PEGylated human Factor VIla, cysteine-PEGylated human Fac- tor Vila and variants thereof. Non-limiting examples of Factor VII derivatives includes GlycoPegylated FVII derivatives as disclosed in WO 03/31464 and US Patent applications

US 20040043446, US 20040063911, US 20040142856, US 20040137557, and US 20040132640 (Neose Technologies, Inc.); FVII conjugates as disclosed in WO 01/04287,

US patent application 20030165996, WO 01/58935, WO 03/93465 (Maxygen ApS) and

WO 02/02764, US patent application 20030211094 (University of Minnesota).

The term “improved biological activity” refers to FVII polypeptides with i) substan- tially the same or increased proteolytic activity compared to recombinant wild type hu- man Factor VIIa or ii) to FVII polypeptides with substantially the same or increased TF binding activity compared to recombinant wiid type human Factor Vila or iii) to FVII polypeptides with substantially the same or increased half life in blood plasma compared to recombinant wild type human Factor VIla.The term "PEGylated human Factor VIIa" means human Factor Vila, having a PEG moiecule conjugated to a human Factor Vila polypeptide. It is to be understood, that the PEG molecule may be attached to any part of the Factor VIIa polypeptide including any amino acid residue or carbohydrate moiety of the Factor VIla polypeptide. The term "cysteine-PEGylated human Factor VIIa” means

Factor VIla having a PEG molecule conjugated to a sulfhydryl group of a cysteine intro- duced in human Factor Vila.

Non-limiting examples of Factor VII variants having substantially the same or in- creased proteolytic activity compared to recombinant wild type human Factor Vila in- clude S52A-FVIIa, S60A-FVIIa ( Lino et al., Arch. Biochem. Biophys. 352: 182-192, 1998); FVIla variants exhibiting increased proteolytic stability as disclosed in U.S. Patent

No. 5,580,560; Factor VIIa that has been proteolytically cleaved between residues 290 and 291 or between residues 315 and 316 (Mollerup et al., Biotechnol. Bioeng. 48:501- 505, 1995); oxidized forms of Factor Vila (Kornfelt et al., Arch. Biochem. Biophys. 363:43-54, 1999); FVII variants as disclosed in PCT/DK02/00189 (corresponding to WO 02/077218); and FVII variants exhibiting increased proteolytic stability as disclosed in

WO 02/38162 (Scripps Research Institute); FVII variants having a modified Gla-domain and exhibiting an enhanced membrane binding as disclosed in WO 99/20767, US patents

US 6017882 and US 6747003, US patent application 20030100506 (University of Minne- sota) and WO 00/66753, US patent applications US 20010018414, US 2004220106, and

US 200131005, US patents US 6762286 and US 6693075 (University of Minnesota); and

FVII variants as disclosed in WO 01/58935, US patent US 6806063, US patent application 20030096338 (Maxygen ApS), WO 03/93465 (Maxygen ApS), WO 04/029091 (Maxygen

CoO WO . 0

ApS), WO 04/083361 (Maxygen ApS), and WO 04/111242 {(Maxygen ApS), as well as in

WO 04/108763 (Canadian Blood Services).

Non-limiting examples of FVII variants having increased biological activity com- pared to wild-type FVIla include FVII variants as disclosed in WO 01/83725, WO 02/22776, WO 02/077218, PCT/DK02/00635 (corresponding to WO 03/027147), Danish patent application PA 2002 01423 (corresponding to WO 04/029090), Danish patent ap- plication PA 2001 01627 (corresponding to WO 03/027147); WO 02/38162 (Scripps Re- search Institute); and FVIIa variants with enhanced activity as disclosed in JP 2001061479 (Chemo-Sero-Therapeutic Res Inst.).

Examples of variants of factor VII include, without limitation, L305V-FVII,

L305V/M306D/D309S-FVII, L30SI-FVII, L305T-FVII, F374P-FVII, V158T/M298Q-FVII,

V158D/E296V/M298Q-FVII, K337A-FVII, M298Q-FVII, V158D/M298Q-FVI],

L305V/K337A-FVII, V158D/E296V/M298Q/L305V-FV1], V158D/E296V/M298Q/K337A-

FVII, V158D/E296V/M298Q/L305V/K337A-FVII, K157A-FVII, E296V-FVII, E296V/M298Q-

FVII, V158D/E296V-FVII, V158D/M298K-FVII, and S336G-FVII, L305V/K337A-FVII,

L305V/V158D-FVII, L305V/E296V-FVII, L305V/M298Q-FVIi, L305V/V158T-FVII,

L305V/K337A/V158T-FVII, L305V/K337A/M298Q-FVII, L305V/K337A/E296V-FVII,

L305V/K337A/V158D-FVII, L305V/V158D/M298Q-FVII, L305V/V158D/E296V-FVII,

L305V/V158T/M298Q-FVII, L305V/V158T/E296V-FVII, L305V/E296V/M298Q-FVII,

L305V/V158D/E296V/M298Q-FVII, L305V/V158T/E296V/M298Q-FVII,

L305V/V158T/K337A/M298Q-FVII, L305V/V158T/E296V/K337A-FVII,

L305V/V158D/K337A/M298Q-FVII, L305V/V158D/E296V/K337A-FVI],

L305V/V158D/E296V/M298Q/K337A-FVII, L305V/V158T/E296V/M298Q/K337A-FVII,

S314E/K316H-FVII, S314E/K316Q-FVII, S314E/L305V-FVII, S314E/K337A-FVII, 5314E/V158D-FVII, S314E/E296V-FVII, S314E/M298Q-FVII, S314E/V158T-FVII,

K316H/L305V-FVII, K316H/K337A-FVII, K316H/V158D-FVII, K316H/E296V-FVII,

K316H/M298Q-FVII, K316H/V158T-FVII, K316Q/L305V-FVII, K316Q/K337A-FVII,

K316Q/V158D-FVII, K316Q/E296V-FVII, K316Q/M298Q-FVII, K316Q/V158T-FVI],

S314E/L305V/K337A-FVII, S314E/L305V/V158D-FVII, S314E/L305V/E296V-FVII, 5314E/L305V/M298Q-FVII, S314E/L305V/V158T-FVII, S314E/L305V/K337A/V158T-FVII,

S314E/L305V/K337A/M298Q-FVII, S314E/L305V/K337A/E296V-FVI],

S314E/L305V/K337A/V158D-FVII, S314E/L305V/V158D/M298Q-FVII,

S314E/L305V/V158D/E296V-FVII, S314E/L305V/V158T/M298Q-FVII, N

S314E/L305V/V158T/E296V-FVII, S314E/L305V/E296V/M298Q-FVII,

S314E/L305V/V158D/E296V/M298Q-FVII, S314E/L305V/V158T/E296V/M298Q-FVII,

S314E/L305V/V158T/K337A/M298Q-FVII, S314E/L305V/V158T/E296V/K337A-FVI],

S314E/L305V/V158D/K337A/M298Q-FVI1, S314E/L305V/V158D/E296V/K337A-FVII,

0BLT-WO . " 11

S314E/L305V/V158D/E296V/M298Q/K337A-FVII,

S314E/L305V/V158T/E296V/M298Q/K337A-FVII, K316H/L305V/K337A-FVII,

K316H/L305V/V158D-FVII, K316H/L305V/E296V-FVII, K316H/L305V/M298Q-FVII,

K316H/L305V/V158T-FVII, K316H/L305V/K337A/V158T-FVII,

K316H/L305V/K337A/M298Q-FVII, K316H/L305V/K337A/E296V-FVII,

K316H/L305V/K337A/V158D-FVII, K316H/L305V/V158D/M298Q-FVII,

K316H/L305V/V158D/E296V-FVII, K316H/L305V/V158T/M298Q-FVII,

K316H/L305V/V158T/E296V-FVII, K316H/1.305V/E296V/M298Q-FVII,

K316H/L305V/V158D/E296V/M298Q-FVII, K316H/L305V/V158T/E296V/M298Q-FVII,

K316H/L305V/V158T/K337A/M298Q-FVII, K316H/L305V/V158T/E296V/K337A-FVII,

K316H/L305V/V158D/K337A/M298Q-FVII, K316H/L305V/V158D/E296V/K337A -FVII,

K316H/L305V/V158D/E296V/M298Q/K337A-FVII,

K316H/L305V/V158T/E296V/M298Q/K337A-FVII, K316Q/L305V/K337A-FVII,

K316Q/L305V/V158D-FVII, K316Q/L305V/E296V-FVII, K316Q/L305V/M298Q-FVII,

K316Q/L305V/V158T-FVII, K316Q/L305V/K337A/V158T-FVII,

K316Q/L305V/K337A/M298Q-FVI1I, K316Q/L305V/K337A/E296V-FVII,

K316Q/L305V/K337A/V158D-FVII, K316Q/L305V/V158D/M298Q-FVII,

K316Q/L305V/V158D/E296V-FVII, K316Q/L305V/V158T/M298Q-FVII,

K316Q/L305V/V158T/E296V-FVII, K316Q/L305V/E296V/M298Q-FVII,

K316Q/L305V/V158D/E296V/M298Q-FVII, K316Q/L305V/V158T/E296V/M298Q-FVII,

K316Q/L305V/V158T/K337A/M298Q-FVII, K316Q/L305V/V158T/E296V/K337A-FVII,

K316Q/L305V/V158D/K337A/M298Q-FVII, K316Q/L305V/V158D/E296V/K337A -FVII,

K316Q/L305V/V158D/E296V/M298Q/K337A-FVII,

K316Q/L305V/V158T/E296V/M298Q/K337A-FVII, F374Y/K337A-FVII, F374Y/V158D-FVII,

F374Y/E296V-FVII, F374Y/M298Q-FVII, F374Y/V158T-FVII, F374Y/S314E-FVII,

F374Y/L305V-FVII, F374Y/L305V/K337A-FVII, F374Y/L305V/V158D-FVII,

F374Y/L305V/E296V-FVII, F374Y/L305V/M298Q-FVII, F374Y/1.305V/V158T-FVII,

F374Y/L305V/S314E-FVII, F374Y/K337A/S314E-FVII, F374Y/K337A/V158T-FVII,

F374Y/K337A/M298Q-FVII, F374Y/K337A/E296V-FVII, F374Y/K337A/V158D-FVII,

F374Y/V158D/S314E-FVII, F374Y/V158D/M298Q-FVII, F374Y/V158D/E296V-FVII,

F374Y/V158T/S314E-FVII, F374Y/V158T/M298Q-FVlI, F374Y/V158T/E296V-FVII,

F374Y/E296V/S314E-FVII, F374Y/S314E/M298Q-FVII, F374Y/E296V/M298Q-FVII,

F374Y/L305V/K337A/V158D-FVII, F374Y/L305V/K337A/E296V-FVII,

F374Y/L305V/K337A/M298Q-FVII, F374Y/L305V/K337A/V158T-FVII,

F374Y/L305V/K337A/S314E-FVII, F374Y/L305V/V158D/E296V-FVII,

F374Y/L305V/V158D/M298Q-FVII, F374Y/L305V/V158D/S314E-FVII,

F374Y/L305V/E296V/M298Q-FVII, F374Y/L305V/E296V/V158T-FVII,

689 1-W0) a. Tne - oo C8909

F374Y/L305V/E296V/S314E-FVII, F374Y/L305V/M298Q/V158T-FVII,

F374Y/L305V/M298Q/S314E-FVII, F374Y/L305V/V158T/S314E-FVII,

F374Y/K337A/S314E/V158T-FVII, F374Y/K337A/S314E/M298Q-FVII,

F374Y/K337A/S314E/E296V-FVI]I, F374Y/K337A/S314E/V158D-FVII, F374Y/K337A/V158T/M298Q-FVII, F374Y/K337A/V158T/E296V-FVII,

F374Y/K337A/M298Q/E296V-FVII, F374Y/K337A/M298Q/V158D-FVII,

F374Y/K337A/E296V/V158D-FVI], F374Y/V158D/S314E/M298Q-FVII,

F374Y/V158D/S314E/E296V-FVII, F374Y/V158D/M298Q/E296V-FVII,

F374Y/V158T/S314E/E296V-FVI], F374Y/V158T/S314E/M298Q-FVII,

F374Y/V158T/M298Q/E296V-FVII, F374Y/E296V/S314E/M298Q-FVI],

F374Y/L305V/M298Q/K337A/S314E-FVII, F374Y/L305V/E296V/K337A/S314E-FVII,

F374Y/E296V/M298Q/K337A/S314E-FVII, F374Y/L305V/E296V/M298Q/K337A FVII,

F374Y/L305V/E296V/M298Q/S314E-FVII, F374Y/V158D/E296V/M298Q/K337A-FVII,

F374Y/V158D/E296V/M298Q/S314E-FVII, F374Y/L305V/V158D/K337A/S314E-FVII,

F374Y/V158D/M298Q/K337A/S314E-FVII, F374Y/V158D/E296V/K337A/S314E-FVII,

F374Y/L305V/V158D/E296V/M298Q-FVII, F374Y/L305V/V158D/M298Q/K337A-FVII,

F374Y/L305V/V158D/E296V/K337A-FVII, F374Y/L305V/V158D/M298Q/S314E-FVII,

F374Y/L305V/V158D/E296V/S314E-FVII, F374Y/V158T/E296V/M298Q/K337A-FVI],

F374Y/V158T/E296V/M298Q/S314E-FVII, F374Y/L305V/V158T/K337A/S314E-FVII,

F374Y/V158T/M298Q/K337A/S314E-FVII, F374Y/V158T/E296V/K337A/S314E-FVI],

F374Y/L305V/V158T/E296V/M298Q-FVII, F374Y/L305V/V158T/M298Q/K337A-FVII,

F374Y/L305V/V158T/E296V/K337A-FVII, F374Y/L305V/V158T/M298Q/S314E-FVII,

F374Y/L305V/V158T/E296V/S314E-FVII, F374Y/E296V/M298Q/K337A/V158T/S314E-

FVII, F374Y/V158D/E296V/M298Q/K337A/S314E-FVII, F374Y/L305V/V158D/E296V/M298Q/S314E-FVII,

F374Y/L305V/E296V/M298Q/V158T/S314E-FVII,

F374Y/L305V/E296V/M298Q/K337A/V158T-FVII,

F374Y/L305V/E296V/K337A/V158T/S314E-FVII,

F374Y/L305V/M298Q/K337A/V158T/S314E-FVII, F374Y/L305V/V158D/E296V/M298Q/K337A-FVII,

F374Y/L305V/V158D/E296V/K337A/S314E-FVII,

F374Y/L305V/V158D/M298Q/K337A/S314E-FVII,

F374Y/L305V/E296V/M298Q/K337A/V158T/S314E-FVII,

F374Y/L305V/V158D/E296V/M298Q/K337A/S314E-FVII, S52A-Factor VII, S60A-Factor

VII; R152E-Factor VII, S344A-Factor VII, TI06N-FVII, K143N/N145T-FVI], V253N-FVII,

R290N/A292T-FVII, G291N-FVII, R315N/V317T-FVII, K143N/N145T/R315N/V317T-FVII; and FVII having substitutions, additions or deletions in the amino acid sequence from

GEG WO

233Thr to 240Asn; FVII having substitutions, additions or deletions in the amino acid se- quence from 304Arg to 329Cys; and FVII having substitutions, additions or deletions in the amino acid sequence from 153lle to 223Arg.

Factor VII variants having substantially the same or improved biological activity relative to wild-type Factor Vila encompass those that exhibit at least about 25%, such as, e.g., at least about 50%, at least about 75%, at least about 90%, at least about 120, at least about 130, or at least about 150% of the specific activity of wild-type Factor Vila that has been produced in the same cell type, when tested in one or more of a clotting assay, proteolysis assay, or TF binding assay as described above. Factor VII variants having substantially reduced biological activity relative to wild-type Factor Vila are those that exhibit less than about 25%, preferably less than about 10%, more preferably less than about 5% and most preferably less than about 1% of the specific activity of wild- type Factor Vila that has been produced in the same cell type when tested in one or more of a clotting assay, proteolysis assay, or TF binding assay as described below. Fac- tor VII variants having a substantially modified biological activity relative to wild-type

Factor VII include, without limitation, Factor VII variants that exhibit TF-independent

Factor X proteolytic activity and those that bind TF but do not cleave Factor X.

The biological activity of Factor VIIa in blood clotting derives from its ability to (i) bind to tissue factor (TF) and (ii) catalyze the proteolytic cleavage of Factor IX or Factor

X to produce activated Factor IX or X (Factor IXa or Xa, respectively). For purposes of the invention, Factor Vila biological activity may be quantified by measuring the ability of a preparation to promote blood clotting using Factor VII-deficient plasma and throm- boplastin, as described, e.g., in U.S. Patent No. 5,997,864. In this assay, biological ac- tivity is expressed as the reduction in clotting time relative to a control sample and is converted to "Factor VII units” by comparison with a pooled human serum standard con- taining 1 unit/mi Factor VII activity. Alternatively, Factor Vila biological activity may be quantified by (i) measuring the ability of Factor Vila to produce of Factor Xa in a system comprising TF embedded in a lipid membrane and Factor X. (Persson et al., J. Biol.

Chem. 272:19919-19924, 1997); (ii) measuring Factor X hydrolysis in an aqueous Sys- tem (see, "General Methods” below); (iii) measuring its physical binding to TF using an instrument based on surface plasmon resonance (Persson, FEBS Letts. 413:359-363, 1997) (iv) measuring hydrolysis of a synthetic substrate (see, “General Methods" below); and (v) measuring generation of thrombin in a TF-independent in vitro system (see, “General Methods” below).

£351. WO

Factor IX polypeptides and Factor IX-related polypeptides

The present invention encompasses factor IX polypeptides, such as, e.g., those having the amino acid sequence disclosed in, e.g., Jaye et al., Nucleic Acids Res. 11:

S 2325-2335, 1983. (wild-type human factor IX).

In practicing the present invention, any factor IX polypeptide may be used that is effective in preventing or treating bleeding. This includes factor IX polypeptides de- rived from blood or plasma, or produced by recombinant means.

As used herein, “factor IX polypeptide” encompasses, without limitation, factor

IX, as well as factor IX-related polypeptides. The term “factor IX” is intended to encom- pass, without limitation, polypeptides having the amino acid sequence as described in

Jaye et al., Nucleic Acids Res. 1983 (see above) (wild-type human factor IX), as well as wild-type Factor IX derived from other species, such as, e.g., bovine, porcine, canine, murine, and salmon Factor IX. It further encompasses natural allelic variations of Factor

IX that may exist and occur from one individual to another. Also, degree and location of glycosylation or other post-transiation modifications may vary depending on the chosen host cells and the nature of the host cellular environment. The term “Factor IX" is also intended to encompass Factor IX polypeptides in their uncleaved (zymogen) form, as well as those that have been proteolytically processed to yield their respective bioactive forms, which may be designated Factor IXa. "Factor IX-related polypeptides” include, without limitation, factor IX polypep- tides that have either been chemically modified relative to human factor IX and/or con- tain one or more amino acid sequence alterations relative to human factor IX (i.e., factor

IX variants), and/or contain truncated amino acid sequences relative to human factor IX (i.e. factor IX fragments). Such factor IX-related polypeptides may exhibit different properties relative to human factor IX, including stability, phospholipid binding, altered specific activity, and the like.

The term “factor IX-related polypeptides” are intended to encompass such poly- peptides in their uncieaved (zymogen) form, as well as those that have been proteolyti- cally processed to yield their respective bioactive forms, which may be designated “factor

IXa-related polypeptides” or “activated factor IX-related polypeptides”.

As used herein, “factor IX-related polypeptides” encompasses, without limitation, polypeptides exhibiting substantially the same or improved biological activity relative to wild-type human factor IX, as well as polypeptides, in which the factor IX biological activ- ity has been substantially modified or reduced relative to the activity of wild-type human factor IX. These polypeptides include, without limitation, factor IX or factor IXa that has

BLT WG “oe . Co 009u8 been chemically modified and factor IX variants into which specific amine acid sequence alterations have been introduced that modify or disrupt the bioactivity of the polypeptide.

It further encompasses polypeptides with a slightly modified amino acid se- quence, for instance, polypeptides having a modified N-terminal end including N-terminal amino acid deletions or additions, and/or polypeptides that have been chemically modi- fied relative to human factor IX.

Factor IX-related polypeptides, including variants of factor IX, whether exhibiting substantially the same or better bioactivity than wild-type factor IX, or, alternatively, ex- hibiting substantially modified or reduced bioactivity relative to wild-type factor IX, in- clude, without limitation, polypeptides having an amino acid sequence that differs from the sequence of wild-type factor IX by insertion, deletion, or substitution of one or more amino acids.

Factor IX-related polypeptides, including variants, encompass those that exhibit at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 110%, at least about 120%, and at least about 130%, of the specific activity of wild-type factor IX that has been produced in the same cell type, when tested in the factor IX activity assay as described in the present specifica- tion.

Factor IX-related polypeptides, including variants, having substantially the same or improved biological activity relative to wild-type factor IX encompass those that ex- hibit at least about 25%, preferably at least about 50%, more preferably at feast about 75%, more preferably at least about 100%, more preferably at least about 110%, more preferably at least about 120%, and most preferably at least about 130% of the specific biological activity of wild-type human factor IX that has been produced in the same cell type when tested in one or more of the specific factor IX activity assays as described. For purposes of the invention, factor IX biological activity may be quantified as described later in the present description (see “General Methods").

Factor IX-related polypeptides, including variants, having substantially reduced biological activity relative to wild-type factor IX are those that exhibit less than about 25%, preferably less than about 10%, more preferably less than about 5% and most preferably less than about 1% of the specific activity of wild-type factor IX that has been produced in the same cell type when tested in one or more of the specific factor IX activ- ity assays as described above.

Non-limiting examples of factor IX polypeptides include plasma-derived human factor IX as described, e.g., in Chandra et al., Biochem. Biophys. Acta 1973, 328:456;

5891-WO

Andersson et al., Thromb.Res. 1975, 7:451; Suomela et a!., Eur. J. Biochem. 1676, 71:145.

Suitable assays for testing for factor IX activity, and thereby providing means for selecting suitable factor IX variants for use in the present invention, can be performed as simple in vitro tests as described, for example, in Wagenvoord et al., Haemostasis 1990;20(5):276-88. Factor IX biological activity may also be quantified by measuring the ability of a preparation to correct the clotting time of factor IX-deficient plasma, e.g., as described in Nilsson et al., 1959.(Nilsson IM, Blombaeck M, Thilen A, von Francken I.,

Carriers of haemophilia A - A laboratory study, Acta Med Scan 1959; 165:357). In this assay, biological activity is expressed as units/ml plasma (1 unit corresponds to the amount of FIX present in normal pooled plasma.

In some embodiments of the invention, the factor IX are factor IX-related poly- peptides wherein the ratio between the activity of said factor IX polypeptide and the ac- tivity of native human factor IX (wild-type factor IX) is at least about 1.25 when tested in the " chromogenic assay” (see below); in other embodiments, the ratio is at least about 2.0; in further embodiments, the ratio is at least about 4.0.

O-linked Glycosylation

In practicing the present invention, the pattern of oligosaccharides may be de- termined using any method known in the art, including, without limitation: high- performance liquid chromatography (HPLC); capillary electrophoresis (CE); nuclear mag- netic resonance (NMR); mass spectrometry (MS) using ionization techniques such as fast-atom bombardment, electrospray, or matrix-assisted laser desorption (MALDI); gas chromatography (GC); and treatment with exoglycosidases in conjunction with anion- exchange (AIE)-HPLC, size-exclusion chromatography (SEC), or MS. See, e.g., Weber et al., Anal. Biochem. 225:135 (1995); Klausen et al., J. Chromatog. 718:195 (1995);

Morris et al., in Mass Spectrometry of Biological Materials, McEwen et al., eds., Marcel

Dekker, (1990), pp 137-167; Conboy et al., Biol. Mass Spectrom. 21:397, 1992; Hel- lerqvist, Meth. Enzymol. 193:554 (1990); Sutton et al., Anal. Biohcem. 318:34 (1994);

Harvey et al., Organic Mass Spectrometry 29:752 (1994).

The relative content of O-glycoforms can be determined, for example, by tryptic peptide mapping. In short, the glycoprotein is digested with trypsin and the polypeptides containing the O-glycosylation site are separated according to the glycan structure by

RP-HPLC chromatography, mass spectrometry or another suitable analytical separation technique. If necessary in order to obtaining a suitable separation, the glycoprotein can prior to the digestion with trypsin be reduced and alkylated and the polypeptide chain

8RC1-WO containing the O-glycosylation site is purified by, e.g. RP-HPLC chromatography. Then the purified polypeptide is subjected to tryptic digestion followed by analysis as described above.

S) Methods for producing glycoprotein preparations having a predetermined pattern of O- linked oligosaccharides

The origin of the acceptor glycoprotein is not a critical aspect of the invention.

Typically, the glycoprotein will be expressed in a cultured prokaryote cell or eukaryote cell such as a mammalian, yeast insect, fungal or plant cell. The protein, however, may also be isolated from a natural source such as plasma, serum or blood. The glycoprotein can either be a full length protein or a fragment.

The invention provides compositions that include glycoprotein species that have a substantially uniform glycosylation pattern. The methods are useful for remodelling or altering the glycosylation pattern present on a glycoprotein upon its initial expression.

Thus, the methods of the invention provide a practical means for large-scale preparation of glycoforms having pre-selected or pre-determined uniform derivatization patterns. The methods are particularly well suited for modification of therapeutic peptides, including but not limited to, glycoproteins that are incompletely glycosylated during production in cell culture cells or transgenic animals. However, the preparations and compositions of the invention may also be prepared by purification of natural sources, such as plasma, serum or blood, or cell culture fluids and isolating the desired glycoforms therefrom.

The polypeptides to be re-modelled in accordance with the invention are typically prepared by cell culture processes. Suitable host cells include, without limitation, human cells expressing an endogenous gene such as, e.g., a Factor VII, IX, X, or XII gene or a protein Z gene. In these cells, the endogenous gene may be intact or may have been modified /n situ, or a sequence outside the endogenous gene may have been modified in situ to alter the expression of the endogenous glycoprotein gene. Any human cell capa- ble of expressing an endogenous glycoprotein gene may be used. Other, included host cells are heterologous host cells programmed to express a glycoprotein such as, e.g., human Factor VII or IX or X or XII from a recombinant gene. The host cells may be ver- tebrate, insect, or fungal cells. Preferably, the cells are mammalian cells capable of the entire spectrum of mammalian N-linked glycosylation; O-linked glycosylation; and v- carboxylation. See, e.g., U.S. Patent Nos. 4,784,950. Preferred mammalian cell lines include the CHO (ATCC CCL 61), COS-1 (ATCC CRL 1650), baby hamster kidney (BHK) and HEK293 (ATCC CRL 1573; Graham et al., J. Gen. Virol. 36:59-72, 1977) cell lines. A

ART WO preferred BHK cell line is the tk ts13 BHK cell line {Waechter and Baserga,

Proc. Natl.Acad. Sci. USA 79:1106-1110, 1982), hereinafter referred to as BHK 570 cells.

The BHK 570 cell line is available from the American Type Culture Collection, 12301 Park- lawn Dr., Rockville, MD 20852, under ATCC accession number CRL 10314. A tk ts13

BHK cell line is also available from the ATCC under accession number CRL 1632. In addi- tion, a number of other cell lines may be used, including Rat Hep I (Rat hepatoma; ATCC

CRL 1600), Rat Hep II (Rat hepatoma; ATCC CRL 1548), TCMK (ATCC CCL 139), Human lung (ATCC HB 8065), NCTC 1469 (ATCC CCL 9.1) and DUKX cells (CHO cell line) (Ur- laub and Chasin, Proc. Natl. Acad. Sci. USA 77:4216-4220, 1980). (DUKX cells also re- ferred to as CXB11 cells), and DG44 (CHO cell line) (Cell, 33:405, 1983, and Somatic Cell and Molecular Genetics 12:555, 1986). Also useful are 3T3 cells, Namalwa cells, myelo- mas and fusions of myelomas with other cells. Suitable host cells include BHK 21 cells that have been adapted to grow in the absence of serum and have been programmed to express Factor VII. The cells may be mutant or recombinant cells that express a qualita- tively or quantitatively different spectrum of glycosylation enzymes (such as, e.g., glyco- syl transferases and/or glycosidases) than the cell type from which they were derived.

The cells may also be programmed to express other heterologous peptides or proteins, including, e.g., truncated forms of Factor VII. The host cells may also be CHO cells that have been programmed to co-express both the Factor VII polypeptide of interest (i.e.,

Factor VII or a Factor-VII-related polypeptide) and another heterologous peptide or poly- peptide such as, e.g., a modifying enzyme or a Factor VII fragment.

Methods: The present invention encompasses methods for producing a prepara- tion comprising a predetermined serine/threonine-linked glycoform pattern as described above and, in further embodiments, methods for optimizing the glycoform distribution of a glycoprotein (see Figure 3). The individual process steps described can be applied in different combinations in order to obtain the desired glycoform pattern. Non-limiting ex- amples are given below.

In one aspect, these methods are carried out by the steps of: (a) obtaining a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2-

Pro-Cys motif and wherein said serine/threonine forms part of a Glc-O-Ser/Thr covalent bond from a cell in which it is prepared; e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (b) contacting the glycoprotein preparation with an activated donor of the de- sired mono- or oligosaccharide moiety and an enzyme suitable for transferring the de- sired mono- or oligo-saccharide group under conditions appropriate for transferring the

5891-W 0) mono- or oligo-saccharide group from the donor moiety to the acceptor moiety, thereby producing the glycopeptide having an altered glycosylation pattern.

In another aspect, these methods are carried out by the steps of: (aa) obtaining a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2-

Pro-Cys motif and wherein said serine/threonine forms part of a Glc-O-Ser/Thr covalent bond from a cell in which it is prepared; e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (bb) contacting the glycoprotein preparation with an enzyme suitable for remov- ing the terminal mono- or oligo-saccharide group under conditions appropriate for re- moving said mono- or oligo-saccharide group, thereby producing the glycopeptide having an altered glycosylation pattern.

In one embodiment, the methods comprise a combination of steps (b) and (bb).

In one embodiment the methods further comprise a step of isolating the glycoprotein having an altered glycosylation pattern.

In one embodiment, the methods comprise a further step of:

Analyzing the structure of the oligosaccharides linked to the polypeptides to de- termine a glycoform pattern, and, optionally, repeating steps (b) and/or (bb) until a de- sired glycoform pattern is achieved.

These methods may further comprise the step of subjecting preparations having predetermined glycoform patterns to at least one test of bioactivity (including, e.qg., clot- ting, Factor X proteolysis, or TF binding) or other functionality (such as, e.g., pharma- cokinetic profile or stability), and correlating particular glycoform patterns with particular bioactivity or functionality profiles in order to identify a desired glycoform pattern.

In one embodiment, the desired glycoform pattern is a substantially uniform g/u- cose-O-serine/threonine glycosylation: In this embodiment, wherein the initially obtained glycoprotein contains terminal xylose the method (METHOD B) comprises the steps of: (a) obtaining a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2-

Pro-Cys motif and wherein said serine/threonine forms part of a Gic-O-Ser/Thr covalent bond from a cell in which it is prepared; e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source;

5801-WO (b) contacting the preparation obtained in step (a) with a xylosidase under con- ditions appropriate for removing xylose residues from the glycoprotein, thereby produc- ing the glycoprotein having an altered glycosylation pattern.

In one embodiment, the method further includes the step of isolating the glyco- protein prepared in step b having a Glc-O-Ser/Thr glycosylation.

In one embodiment, the method further includes the step of analysing the struc- ture of the oligosaccharides linked to the polypeptides to determine a glycoform pattern, and, optionally, repeating step (b) until the desired glycoform pattern is achieved.

In another embodiment for making a desired glycoforms pattern in the form of a substantially uniform glucose-O-serine/threonine glycosylation, the method (METHOD C) comprises the steps of: (a) obtaining a preparation of a polypeptide containing a Cys-X1-Ser/Thr-X2-

Pro-Cys motif, e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (b) contacting the preparation obtained in step (a) with a O-glucosyltransferase and an activated glucose donor under conditions appropriate for transferring a glucose residue from the glucose donor moiety to the serine/threonine acceptor moiety, thereby producing the polypeptide having an altered glycosylation pattern.

In one embodiment, the desired glycoform pattern is a substantially uniform xy- lose-glucose-O-serine/threonine glycosylation: In this embodiment, the method (METHOD Al) comprises the steps of: (a) obtaining a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2-

Pro-Cys motif and wherein said serine/threonine forms part of a Glc-O-Ser/Thr covalent bond; e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (b) contacting the preparation obtained in step (a) with UDP-D-xylose: B-D- glucoside «-1,3-D-xylosyltransferase and an activated xylosyl donor under condi- tions appropriate for transferring a xylose residue from the Xylose donor moiety to

58G1-WO the acceptor moiety, thereby producing the glycopeptide having an altered glycosy- lation pattern.

In one embodiment, the method further includes the step of isolating the glyco- protein prepared in step b having a Xyl-Glc-O-Ser/Thr glycosylation.

In one embodiment, the method further includes the step of removing terminal xylose-residues by subjecting the preparation obtained in step (a) to METHOD B prior to step (b).

In one embodiment, the desired glycoform pattern is a substantially uniform xy- lose-xylose-glucose-O-serine/threonine glycosylation: 1n this embodiment, the method (METHOD A2) comprises the steps of: (a) obtaining a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2-

Pro-Cys motif and wherein said serine/threonine forms part of a Glc-O-Ser/Thr covalent bond; e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (b) contacting the preparation obtained in step (a) with UDP-D-xylose: p-D- glucoside «-1,3-D-xylosyltransferase and an activated xylosyl donor under condi- tions appropriate for transferring a xylose residue from the xylose donor moiety to the acceptor moiety, thereby producing the glycopeptide having an altered glycosy- lation pattern. (c) contacting the preparation obtained in step (b) with UDP-D-xylose: «-D- xyloside «-1,3-xylosyltransferase and an activated xylosyl donor under conditions appropriate for transferring a xylose residue from the xylose donor moiety to the acceptor moiety, thereby producing the glycopeptide having an altered glycosylation pattern.

In one embodiment, the method further includes the step of isolating the preparation obtained in step (b) prior to subjecting the preparation to step (c).

In one embodiment, the method further includes the step of isolating the glyco- protein prepared in step (c) having a Xyl-Xyl-Glc-O-Ser/Thr glycosylation.

In one embodiment, the method further includes the step of analysing the struc- ture of the oligosaccharides linked to the polypeptides to determine a glycoform pattern, and, optionally, repeating step (b) and/or step (c) until the desired glycoform pattern is achieved.

5561-WO

In different embodiments, the glycoprotein exhibits substantially uniform Xyl-

Xyl-Glc-O-Ser glycosylation, Xyl-Glc-O-Ser glycosylation, and Glc-O-Ser glycosylation;

Ser being the serine of the contained Cys-X1-Ser-X2-Pro-Cys motif (X1 and X2 inde- pendently being any amino acid residue). In other, different embodiments, the glycopro- tein exhibits substantially uniform Xyl-Xyl-Glc-O-Thr glycosylation, Xyl-Glc-O-Thr glyco- sylation, and Glc-O-Thr glycosylation; Thr being the threonine of the contained Cys-X1-

Thr-X2-Pro-Cys motif (X1 and X2 independently being any amino acid residue).

In different embodiments, the polypeptides are selected from the list of: Factor

VII polypeptides, Factor VlI-related polypeptides, Factor IX polypeptides, Factor IX- related polypeptides, Factor X polypeptides, and Factor X-related polypeptides.

In preferred embodiments, the glycoprotein preparation is selected from the list of:

Factor VII polypeptides exhibiting substantially uniform Xyl-Xyl-Glc-O-Ser52 glycosyla- tion,

Factor VII polypeptides exhibiting substantially uniform Xyl-Glc-O-Ser52 glycosylation

Factor VII polypeptides exhibiting substantially uniform Glc-O-Ser52 glycosylation

Factor VII-related polypeptides exhibiting substantially uniform Xyl-Xyl-Glc-O-Ser52 gly- cosylation

Factor VII-related polypeptides exhibiting substantially uniform Xyl-Glc-O-Ser52 glycosy- lation

Factor Vil-related polypeptides exhibiting substantially uniform Glc-O-Ser52 glycosylation

Factor VII variants exhibiting substantially uniform Xyl-Xyl-Glc-O-Ser52 glycosylation

Factor VII variants exhibiting substantially uniform Xyl-Glc-O-Ser52 glycosylation

Factor VII variants exhibiting substantially uniform Glc-O-SerS2 glycosylation

Factor IX polypeptides exhibiting substantially uniform Xyl-Xyl-Glc-O-Ser53 glycosylation

Factor IX polypeptides exhibiting substantially uniform Xyl-Glc-O-Ser53 glycosylation

Factor IX polypeptides exhibiting substantially uniform Glc-O-Ser53 glycosylation

Factor IX-related polypeptides exhibiting substantially uniform Xyl-Xyl-Glc-O-Ser53 gly- cosylation

Factor IX-related polypeptides exhibiting substantially uniform Xyl-Glc-O-Ser53 glycosy- lation

Factor IX-related polypeptides exhibiting substantially uniform Glc-O-Ser53 glycosylation

6691-WO . »

Factor IX variants exhibiting substantially uniform Xyl-Xyl-Glc-0O-SerS3 glycosylation

Factor IX variants exhibiting substantially uniform Xyl-Glc-O-Ser53 glycosylation

Factor IX variants exhibiting substantially uniform Glc-0O-Ser53 glycosylation

It is to be understood that oligosaccharides such as Xyl-Xyl- may also be trans- ferred to the acceptor Glc-O-Ser/Thr moiety by using a suitable transferring enzyme and an activated Xyl-Xy!- donor.

Chromatographic method: The present invention also encompasses hydrophobic interaction chromatographic methods for producing a preparation comprising a prede- termined serine/threonine-linked glycoform pattern as described above, and for purifying a O-glycosylated polypeptide having a desired glycoform pattern from a composition comprising said polypeptide and polypeptides having unwanted glycoform patterns.

In one aspect, the method comprises the following steps: (a) obtaining a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2-

Pro-Cys motif and wherein said serine/threonine forms part of a Glc-O-Ser/Thr covalent bond from a cell in which it is prepared; e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (b) binding the glycoprotein to an hydrophic interaction material using using a solution comprising water, optionally a salt component, and optionally a buffer, (c) optionally washing the hydrophobic interaction material using a solution comprising water, optionally a salt component, and optionally a buffer so as to elute con- taminants from the hydrophobic interaction material; (d) washing the hydrophobic interaction material using a solution comprising an organic modifier, water, optionally a salt component, and optionally a buffer, at a linear or step gradient or isocratically in salt component so as to separate glycoproteins having a desired glycoform patter from glycoproteins not having the desired glycoform from the hydrophobic interaction material; (e) collecting the fraction containing the glycoproteins having the desired glyco- form pattern.

In one embodiment, the above-described methods further includes the step of repeating steps (a) to e) by subjecting the preparation obtained in step (e) to steps (a) to (e). This further step may be repeated more than once if deemed necessary.

5801. WO

It is to be understood that the preparations according to the invention may also be prepared by a process comprising a combination of purification steps whereby glyco- protein species having the desired glycosylation are captured from the cell culture liquid or natural source of origin and the above-described enzymatic methods.

The above-described methods may further comprise the step of subjecting preparations having predetermined glycoform patterns to at least one test of bioactivity (including, e.g., clotting, Factor X proteolysis, or TF binding) or other functionality (such as, e.g., pharmacokinetic profile or stability), and correlating particular glycoform pat- terns with particular bioactivity or functionality profiles in order to identify a desired gly- coform pattern.’

Further enzymatic treatments may be used in connection with the above meth- ods to modify the oligosaccharide pattern of N- or O-linked glycans of a preparation; such treatments include, without limitation, treatment with one or more of sialidase (neuraminidase), galactosidase, fucosidase; galactosyl transferase, fucosyl transferase, and/or sialyltransferase, in a sequence and under conditions that achieve a desired modi- fication in the distribution of oligosaccharide chains having particular terminal structures.

Glycosyl transferases are commercially available from Calbiochem (La Jolla, CA) and gly- cosidases are commercially available from Glyko, Inc., (Novato, CA).

Glycoprotein preparations

As used herein, a “glycoprotein preparation” refers to a plurality of glycoforms that have been separated from the cell in which they were synthesized. The glycoprotein preparation include inactivated forms, activated forms, functionally related polypeptides such as, e.g., variants and chemically modified forms, that have been separated from the cell in which they were synthesized.

For example, as used herein, a “Factor VII preparation” refers to a plurality of

Factor VII polypeptides, Factor VIIa polypeptides, or Factor ViI-related polypeptides, in- cluding variants and chemically modified forms, that have been separated from the cell in which they were synthesized or isolated from a natural source. Likewise, a “Factor IX preparation” refers to a plurality of Factor IX polypeptides, Factor IXa polypeptides, or

Factor IX-related polypeptides, including variants or chemically modified forms, that have been separated from the cell in which they were synthesized or isolated from a natural source (e.g., plasma, serum, blood).

Separation of polypeptides from their cell of origin may be achieved by any method known in the art, including, without limitation, removal of cell culture medium

5810 —- - UN BN 99 ‘ . RR ~ Ch containing the desired product from an adherent cell culture; centrifugation or filtration to remove non-adherent cells; and the like.

Optionally, the polypeptides may be further purified. Purification may be achieved using any method known in the art, including, without limitation, affinity chromatogra-

Phy, such as, e.g., on an anti-Factor VII or anti-Factor 1X antibody column (see, e.g.,

Wakabayashi et al., J. Biol. Chem. 261:11097, 1986; and Thim et al., Biochem. 27:7785, 1988); hydrophobic interaction chromatography; ion-exchange chromatography; size ex- clusion chromatography; electrophoretic procedures (e.g., preparative isoelectric focus- ing (IEF), differential solubility (e.g., ammonium sulfate precipitation), or extraction and the like. See, generally, Scopes, Protein Purification, Springer-Verlag, New York, 1982; and Protein Purification, J.-C. Janson and Lars Ryden, editors, VCH Publishers, New York, 1989. Following purification, the preparation preferably contains less than about 10% by weight, more preferably less than about 5% and most preferably less than about 1%, of non-related proteins derived from the host cell.

Factor VII and Factor VliI-related polypeptides, Factor IX and Factor IX-related polypeptides, or Factor X and Factor X-related polypeptides, respectively, may be acti- vated by proteolytic cleavage, using Factor XlIIa or other proteases having trypsin-like specificity, such as, e.g., Factor IXa, kallikrein, Factor Xa, and thrombin. See, e.g., Os- terud et al., Biochem. 11:2853 (1972); Thomas, U.S. Patent No. 4,456,591; and Hedner et al., J. Clin. Invest. 71:1836 (1983). Alternatively, Factor VII, IX or X, respectively, may be activated by passing it through an ion-exchange chromatography column, such as Mono

Q® (Pharmacia) or the like. The resulting activated polypeptide, e.g., Factor VII, may then be formulated and administered as described below.

Functional properties of glycoprotein preparations

The preparations of glycoproteins having predetermined oligosaccharide patterns according to the invention (including Factor VII polypeptides, Factor ViI-related polypep- tides, Factor IX polypeptides and Factor IX-related polypeptides) exhibit improved func- tional properties relative to reference preparations. The improved functional properties may include, without limitation, a) physical properties such as, e.g., storage stability; b) pharmacokinetic properties such as, e.g., bioavailability and half-life; c) immunogenicity in humans, and d) biological activity, such as, e.qg., clotting activity.

A reference preparation refers to a preparation comprising a polypeptide that is identical to that contained in the preparation of the invention to which it is being com- pared (such as, e.g., wild-type Factor VII or wild-type Factor IX or a particular variant or

58G1-WO chemically modified form) except for exhibiting a different pattern of serine/threonine- linked glycosylation.

Storage stability of a glycoprotein (e.g., Factor VII) preparation may be assessed by measuring (a) the time required for 20% of the bioactivity of a preparation to decay when stored as a dry powder at 25°C and/or (b) the time required for a doubling in the proportion of (e.g., Factor Vila) aggregates of said glycoprotein in the preparation.

In some embodiments, the preparations of the invention exhibit an increase of at least about 30%, preferably at least about 60% and more preferably at least about 100%, in the time required for 20% of the bioactivity to decay relative to the time re- quired for the same phenomenon in a reference preparation, when both preparations are stored as dry powders at 25°C. Bioactivity measurements may be performed using any of a clotting assay, proteolysis assay, TF-binding assay, or TF-independent thrombin generation assay.

In some embodiments, the preparations of the invention exhibit an increase of at least about 30%, preferably at least about 60%, and more preferably at least about 100%, in the time required for doubling of aggregates relative to a reference prepara- tion, when both preparations are stored as dry powders at 25°C. The contents of aggre- gates may be determined according to methods known to the skilled person, such as, e.g., gel permeation HPLC methods. For example, the content of Factor VII aggregates is determined by gel permeation HPLC on a Protein Pak 300 SW column (7.5 x 300 mm) (Waters, 80013) as follows. The column is equilibrated with Eluent A (0.2 M ammonium sulfate, 5 % isopropanol, pH adjusted to 2.5 with phosphoric acid, and thereafter pH is adjusted to 7.0 with triethylamine), after which 25 1g of sample is applied to the column.

Elution is with Eluent A at a flow rate of 0.5 mi/min for 30 min, and detection is achieved by measuring absorbance at 215 nm. The content of aggregates is calculated as the peak area of the Factor VII aggregates/total area of Factor VII peaks (monomer and ag- gregates). “Bioavailability” refers to the proportion of an administered dose of a (e.g., Fac- tor VII or Factor VlI-related) glycoprotein preparation that can be detected in plasma at predetermined times after administration. Typically, bioavailability is measured in test animals by administering a dose of between about 25-250 ng/kg of the preparation; ob- taining plasma samples at predetermined times after administration; and determining the content of (e.g., Factor VII or Factor VII-related ) glycosylated polypeptides in the sam- ples using one or more of a clotting assay (or any bioassay), an immunoassay, or an equivalent. The data are typically displayed graphically as polypeptide [e.g., Factor VII] v. time and the bioavailability is expressed as the area under the curve (AUC). Relative

68G1-WO bioavailability of a test preparation refers to the ratio between the AUC of the test prepa- ration and that of the reference preparation.

In some embodiments, the preparations of the present invention exhibit a rela- tive bioavailability of at least about 110%, preferably at least about 120%, more pref- erably at least about 130% and most preferably at least about 140% of the bioavailabil- ity of a reference preparation. The bioavailability may be measured in any mammalian species, preferably dogs, and the predetermined times used for calculating AUC may en- compass different increments from 10 min- 8 h. “Half-life” refers to the time required for the plasma concentration of (e.qg.,

Factor VII polypeptides of Factor VII-related polypeptides) the glycoprotein to de- crease from a particular value to half of that value. Half-life may be determined us- ing the same procedure as for bioavailability. In some embodiments, the prepara- tions of the present invention exhibit an increase in half-life of at least about 0.25 h, preferably at least about 0.5 h, more preferably at least about 1 h, and most pref- erably at least about 2 h, relative to the half-life of a reference preparation. “Immunogenicity” of a preparation refers to the ability of the preparation, when administered to a human, to elicit a deteterious immune response, whether humoral, cel- lular, or both. Factor Vila polypeptides and Factor Vlla-related polypeptides are not known to elicit detectable immune responses in humans. Nonetheless, in any human sub-population, there may exist individuals who exhibit sensitivity to particular adminis- tered proteins. Immunogenicity may be measured by quantifying the presence of anti-

Factor VII antibodies and/or Factor VII-responsive T-cells in a sensitive individual, using conventional methods known in the art. In some embodiments, the preparations of the present invention exhibit a decrease in immunogenicity in a sensitive individual of at least about 10%, preferably at least about 25%, more preferably at least about 40% and most preferably at least about 50%, relative to the immunogenicity for that individual of a reference preparation.

Pharmaceutical compositions and Methods of Use

The preparations of the present invention may be used to treat any syndrome responsive to the relevant glycoprotein. Factor VII-, FIX and FX-responsive syndromes, respectively, include syndromes such as, e.g., bleeding disorders, including, without limitation, those caused by clotting factor deficiencies (e.g., haemophilia A and B or deficiency of coagulation factors XI or VII); by thrombocytopenia or von Willebrand's disease, or by clotting factor inhibitors, or excessive bleeding from any cause. The preparations may also be administered to patients in association with surgery or other trauma or to patients receiving anticoagulant therapy.

6841-WC

Preparations comprising Factor ViI-related polypeptides according to the inven- tion, which have substantially reduced bioactivity relative to wild-type Factor VII, may be used as anticoagulants, such as, e.g., in patients undergoing angioplasty or other surgi- cal procedures that may increase the risk of thrombosis or occlusion of blood vessels as occurs, e.g., in restenosis. Other medical indications for which anticoagulants are pre- scribed include, without limitation, deep vein thrombosis, pulmonary embolism, stroke, disseminated intravascular coagulation (DIC), fibrin deposition in lungs and kidneys asso- ciated with gram-negative endotoxemia, myocardial infarction; Acute Respiratory Dis- tress Syndrome (ARDS), Systemic Inflammatory Response Syndrome (SIRS), Hemolytic

Uremic Syndrome (HUS), MOF, and TTP.

Pharmaceutical compositions comprising the Factor VII and Factor VIi-related preparations according to the present are primarily intended for parenteral administration for prophylactic and/or therapeutic treatment. Preferably, the pharmaceutical compositions are administered parenterally, i.e., intravenously, subcutaneously, or intramuscularly. They may be administered by continuous or pulsatile infusion.

Pharmaceutical compositions or formulations comprise a preparation according to the invention in combination with, preferably dissolved in, a pharmaceutically acceptable carrier, preferably an aqueous carrier or diluent. A variety of aqueous carriers may be used, such as water, buffered water, 0.4% saline, 0.3% glycine and the like.

The preparations of the invention can also be formulated into liposome preparations for delivery or targeting to the sites of injury. Liposome preparations are generally described in, e.g., U.S. Patents Nos. 4,837,028, 4,501,728, and 4,975,282. The compositions may be sterilised by conventional, well-known sterilisation techniques. The resulting aqueous solutions may be packaged for use or filtered under aseptic conditions and lyophilised, the lyophilised preparation being combined with a sterile aqueous solution prior to administration.

The compositions may contain pharmaceutically acceptable auxiliary substances or adjuvants, including, without limitation, pH adjusting and buffering agents and/or tonicity adjusting agents, such as, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, etc.

The concentration of Factor VII or Factor VII-related polypeptides in these formulations can vary widely, i.e., from less than about 0.5% by weight, usually at or at least about 1% by weight to as much as 15 or 20% by weight and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.

Thus, a typical pharmaceutical composition for intravenous infusion could be made up to contain 250 ml of sterile Ringer's solution and 10 mg of the preparation.

5891-WQ

Actual methods for preparing parenterally administrable compositions will be known or apparent to those skilled in the art and are described in more detail in, for example,

Remington's Pharmaceutical Sciences, 18th ed., Mack Publishing Company, Easton, PA (1990).

The compositions containing the preparations of the present invention can be administered for prophylactic and/or therapeutic treatments. In therapeutic applications, compositions are administered to a subject already suffering from a disease, as described above, in an amount sufficient to cure, alleviate or partially arrest the disease and its complications. An amount adequate to accomplish this is defined as "therapeutically effective amount". Effective amounts for each purpose will depend on the severity of the disease or injury as well as the weight and general state of the subject. In general, however, the effective amount will range from about 0.05 mg up to about 500 mg of the preparation per day for a 70 kg subject, with dosages of from about 1.0 mg to about 200 mg of the preparation per day being more commonly used. It will be understood that determining an appropriate dosage may be achieved using routine experimentation, by constructing a matrix of values and testing different points in the matrix.

Local delivery of the preparations of the present invention, such as, for example, topical application, may be carried out, e.g., by means of a spray, perfusion, double balloon catheters, stents, incorporated into vascular grafts or stents, hydrogels used to coat balloon catheters, or other well established methods. In any event, the pharmaceutical compositions should provide a quantity of the preparation sufficient to effectively treat the subject.

The pharmaceutical compositions of the invention may further comprise other bioactive agents, such as, e.qg., non-Factor ViI-related coagulants or anticoagulants.

EXPERIMENTALS

General methods a-xylosidase assay

The a-xylosidase assays are conducted in an appropriate buffer, e.g. 50 mM so- dium acetate, pH 4.5, containing a suitable substrate, e.g. the O-glycopeptides that can be obtained from the O-glycopeptide map of the relevant glycoprotein (e.g., rFVIla). The

8801-WO reaction is stopped after an appropriate time that can be determined experimentally, by e.g. addition of trifluoroacetic acid, and the assay mixtures are analysed by HPLC. a-xylosyltransferase assay

RS) The «-xylosyltransferase assays are conducted in an appropriate buffer, e.g. 10 mM Hepes, pH 7.2, 0.1% Triton X-100, 0.5 mM UDP-Xylose (Sigma U5875), containing a suitable substrate, e.g. the O-glycopeptides that can be obtained from the O- glycopeptide map of the relevant glycoprotein (e.g., rfFVIla) or the pyridyl-aminated oli- gosaccharides prepared as described in Minamida et al. (Minamida et.al., Detection of

UDP-D-xylose: u-D-xyloside «1-3xylosyltransferase activity in human hepatoma cell tine

HepG2. J. Biochem. 120 1002-1006, 1996). The reaction is stopped after an appropriate time, that can be determined experimentally, by e.g. addition of trifluoroacetic acid, and the assay mixtures are analysed by HPLC.

The u-xylosidase and u-xylosyltransferase assays are optimized for time and, op- tionally for temperature and pH.

O-glucosyltransferase assay.

The O-glucosyltransferase assays are conducted, e.g., as described by Shao et al. (Glycobiology 12(11) 763-770 2002).

Factor VII assays

A suitable assay for testing for factor VIIa activity and thereby selecting suitable factor Vila variants can be performed as a simple preliminary in vitro test. The assay is also suitable for selecting suitable factor Vila variants.

In Vitro Hydrolysis Assay

Native (wild-type) factor Vila and factor V1la variant (both hereafter referred to as “factor VIIa”) may be assayed for specific activities. They may also be assayed in par- allel to directly compare their specific activities. The assay is carried out in a microtiter plate (MaxiSorp, Nunc, Denmark). The chromogenic substrate D-Ile-Pro-Arg-p- nitroanilide (5-2288, Chromogenix, Sweden), final concentration 1 mM, is added to factor

Vila (final concentration 100 nM) in 50 mM Hepes, pH 7.4, containing 0.1 M NaCl, 5 mM

CaCl; and 1 mg/ml bovine serum albumin. The absorbance at 405 nm is measured con- tinuously in a SpectraMax™ 340 plate reader (Molecular Devices, USA). The absorbance developed during a 20-minute incubation, after subtraction of the absorbance in a blank

5891-WO well containing no enzyme, is used to calculate the ratio between the activities of variant and wild-type factor Vila:

Ratio = (Aus .m factor Vila variant)/ (Aas om factor Vila wild-type).

Based thereon, factor Vila variants with an activity comparable to or higher than native factor Vila may be identified, such as, for example, variants where the ratio be- tween the activity of the variant and the activity of native factor VII (wild-type FVII) is around, versus above 1.0.

The activity of factor Vila or factor Vila variants may also be measured using a physiological substrate such as factor X, suitably at a concentration of 100-1000 nM, where the factor Xa generated is measured after the addition of a suitable chromogenic substrate (eg. S-2765). In addition, the activity assay may be run at physiological tem- perature.

In Vitro Proteolysis Assay

Native (wild-type) Factor VIia and Factor VIIa variant (both hereafter referred to as "Factor VIIa”) are assayed in parallel to directly compare their specific activities. The assay is carried out in a microtiter plate (MaxiSorp, Nunc, Denmark). Factor VIIa (10 nM) and Factor X (0.8 microM) in 100 microL 50 mM Hepes, pH 7.4, containing 0.1 M NaCl, 5 mM CaCl2 and 1 mg/mi bovine serum albumin, are incubated for 15 min. Factor X cleav- age is then stopped by the addition of 50 microl 50 mM Hepes, pH 7.4, containing 0.1 M

NaCl, 20 mM EDTA and 1 mg/ml bovine serum albumin. The amount of Factor Xa gener- ated is measured by addition of the chromogenic substrate Z-D-Arg-Gly-Arg-p- nitroanilide (S-2765, Chromogenix, Sweden), final concentration 0.5 mM. The absorb- ance at 405 nm is measured continuously in a SpectraMax™ 340 plate reader (Molecular

Devices, USA). The absorbance developed during 10 minutes, after subtraction of the ab- sorbance in a blank well containing no FVIla, is used to calculate the ratio between the proteolytic activities of variant and wild-type Factor Vila:

Ratio = (A405 nm Factor Vila variant)/(A405 nm Factor Vila wild-type).

Based thereon, factor VIla variants with an activity comparable to or higher than native factor Vila may be identified, such as, for example, variants where the ratio be- tween the activity of the variant and the activity of native factor VII (wild-type FVII) is around 1, versus above 1.0.

Thrombin generation assay:

ERO

The ability of factor VII or factor ViI-related polypeptides (e.g., variants) to gen- erate thrombin can be measured in an assay comprising all relevant coagulation factors and inhibitors at physiological concentrations and activated platelets (as described on p. 543 in Monroe et al. (1997) Brit. J. Haematol. 99, 542-547 which is hereby incorporated as reference).

Clot assays. 1st generation assay

The activity of the Factor VII polypeptides may also be measured using a one- stage clot assay essentially as described in WO 92/15686 or US 5,997,864. Briefly, the sample to be tested is diluted in 50 mM Tris (pH 7.5), 0.1% BSA and 100 nL is incubated with 100 ul of Factor VII deficient plasma and 200 nk of thromboplastin C containing 10 mM Ca2+. Clotting times are measured and compared to a standard curve using a refer- ence standard or a pool of citrated normal human plasma in serial dilution. 2nd generation assay:

Essentially the same, except that recombinant human tissue factor is used instead for thromboplastin C.

Factor IX assay

Test for factor IX activity:

Suitable assays for testing for factor IX activity, and thereby providing means for selecting suitable factor IX variants for use in the present invention, can be performed as simple in vitro tests as described, for example, in Wagenvoord et al., Haemostasis 1990;20(5):276-88

Factor IX biological activity may also be quantified by measuring the ability of a preparation to correct the clotting time of factor IX-deficient plasma, e.g., as described in

Nilsson et al., 1959.(Nilsson IM, Blombaeck M, Thilen A, von Francken 1., Carriers of haemophilia A - A laboratory study, Acta Med Scan 1959; 165:357). In this assay, biological activity is expressed as units/ml plasma (1 unit corresponds to the amount of

FIX present in normal pooled plasma.

Examples

084 WwO

The following examples are intended as non-timiting illustrations of the present invention.

Example 1

Preparation of «-xylosidase by extraction and purification

The enzyme, u-xylosidase, can be prepared from various sources, e.g. from plant material as described by Monroe et al. (Plant Physiology and Biochemistry 41:877-885 i (2003)). For example, plant tissues from e.g. Arabidopsis thaliana are ground in a mortar and pestle with quartz sand in two volumes of Buffer A (40 mM Hepes, pH 7.0, 1 M

NaCl), and the filtered extract is centrifuged at 15000 x g for 15 min. Ammonium sulfate is added to for example 80% saturation. Precipated proteins are collected by centrifuga- tion at 15000 x g for 15 min and redissolved in Buffer A. The a-xylosidase is purified by chromatography, for example on a Concanavalin A-Sepharose column, on an anion- exchange column and/or on other chromatographic columns known for the skilled per- son. Fractions are collected during elution and the fractions containing the u-Xylosidase enzyme are identified by use of the u-xylosidase assay.

Example 2

Preparation of a-xylosidase by cloning and expression in E. coli and purification

Genes encoding a-xylosidases, which can hydrolyse alpha xylosidic bonds, have been cloned and characterized previously and genes showing significant homology to characterized u-xylosidases have been annotated in the genomes from several prokary- otic and eukaryotic organisms. The gene sequences are available in databases such as

SWISS-PROT or NCBI and can be amplified by PCR from genomic DNA from the respec- tive organisms. Several candidates were chosen for cloning and expression in E. coli after searching protein databases for the presence of a-xylosidase proteins. The following can- didate genes were selected on the basis of already existing annotation in databases (A), previous published characterization(P) or based on homology analysis to known «- xylosidases(H): gene tm0308 (Thermotoga maritima: A); gene bt3085 (2139 bp) and gene bt3659(2475 bp) (Bacteroides thetaiotaomicron: A); gene bf0551 (2238 bp) and gene bf1247 (2538 bp) (Bacteroides fragilis: A); gene bl02681(2310 bp)( Bacillus licheni- formis: H); gene bh1905 (2328 bp)(Bacillus halodurans: H), gene xylS (2196 bp)(Sulfolobus solfataricus: P); gene yicl (2319 bp) (Escherichia coli: P)

5861-WO (x te

Strategy for cloning and expression of -xylosidases in E. col

The SignalP software (Bendtsen,].D.et al. .]. Mol. Biol., 340:783-795, 2004) is used to evaluate whether a signal peptide is potentially present in the N-terminal of the cafididate enzymes. BF0O551, BF1247, BT3085, BT3659 are presumably secreted as indi- cated by a strong prediction of a signalpeptidase I cleavage site. A methionine codon en- coding a start-methionine is included in front of the first amino acid following the pre- dicted cleavage site.

Purified genomic DNA from Bacteroides thetaiotaomicron (ATCC 29148D), Bacter- oides fragilis (ATCC 25285D), Bacillus haludurans(ATCC 21591D&BAA-125D), Sulfolobus solfataricus (ATCC 35092D), Thermotoga maritima (ATCC 43589D) is obtained from

American Type Culture Collection. In case of E. coli (strain K-12 derivative) and Bacillus licheniformis (ATCC 28450), genomic DNA is prepared from bacterial cells cultivated overnight in LB medium using the DNeasy tissue kit (Qiagen) according to the manufac- tures instructions.

Forward and reverse primers for PCR amplification are designed with an extension in the 5" -ends comprising the restriction enzyme cleavage sites Ndel(or Xbal) and Xmal, respectively. PCR is performed using the following conditions:1) 95°C for 3 min: denatu- ration, 2) 94°C for 30 sec: denaturation, 3) 55°C or 60 °C for 30 sec: annealing, 4) 72°C for 2 min: elongation. Step 2-4 is repeated for 15 cycles. PCR products are separated on 1% ethidium bromide agarose gels and bands showing the correct predicted sizes are excised from the gels and purified using the GFX DNA purification kit (Amersham Phar- macia). Purified PCR products are cloned into the PCR2.1TOPO vector according to the instructions of the manufacturer (Invitrogen). Clones showing the correct restriction en- zyme cleavage profile are sequenced to evaluate the DNA sequence. The insert repre- senting the a-xylosidase genes are released from the PCR2.1TOPO vector using the rele- vant restriction enzymes. A pET11a E. coli expression vector (Novagen) containing a

Ndel (and Xbal) and a Xmal site is cleaved with relevant restriction enzymes and the vector part is purified as described for the PCR products. Vector and inserts are ligated together using the Rapid Ligation Kit (Roche) according to the manufacturer's instruc- tions.

Ligation products are transformed into E.coli TOP10 (Invitrogen) cells by means of chemical transformation or heat shock methods known to the skilled persons. Cells are plated on LB/ampecillin(Amp)-medium culture plates overnight. Single colonies are se- lected from plates and grown overnight in LB/Amp medium. Purified PET plasmids from each colony are screened for the presence of correct inserts using restriction cleavage enzymes and evaluation of sizes of released inserts.

6891-WG o .

E. Coli Rosetta DE3 (Novagen) is transformed with pET plasmids containing the u-

Xylosidase genes and plated on chloramphinicol(Cam)/Amp LB plates. Cells from over- night plates are resuspended in liquid Cam/Amp LB medium and diluted to ODgno = 0.1.

Cells in liquid medium are propagated until OD¢uo = 0.4-0.8. Cells are then equilibrated to a temperature of 18°C for 30 min. and protein induction is induced with 0.5 mM IPTG o/n at 18 °C. Cells are harvested and pellets are re-suspended in a buffer (e.g., 25mM

Tris HCI pH 7 or 10 mM potassium phosphate buffer pH 7) to a cell density corresponding to ODgoe=~10. Cells are sonicated on ice for 3-7 times 15-30 sec with interruptions of 30 sec on ice. Cell debris is removed by centrifugation and supernatants are assayed for ac- tivity.

Assay for «-xylosidase activity

Supernatants resulting from sonication are evaluated on p-nitrophenyl «-D xy- lopyranoside (Sigma) for presence of a-xylosidase activity. Crude enzyme is incubated with 5 mM p-nitrophenyl «-D xylopyranoside at 37°C for 1-2 hours in a buffer (e.qg., 10mM potassium buffer pH 7 or a 25 mM Tris HCI pH 7 buffer). Crude enzymes are also assayed on a fragment of human FVII comprising the Xyl-Xyl-Glc-O-Ser52 glycosylation (peptide fragment consisting of amino acid residues 39-62 of FVII) to evaluate whether the enzyme can cleave the alpha- 1,3 xylosidic bonds. The incubation with peptide is per- formed for 3 hours or overnight at 37°C. Peptide samples incubated with or without «- xylosidase are then evaluated by MALDI MS directly after incubation to evaluate whether the enzyme can remove zero, one or two xylose sugars from the glycopeptide.

Purification of «-xylosidases

A partial purification of the expressed «-xylosidase is performed prior to incuba- tion with rfFVII. Supernatants (from approximately 20-50 ml cell culture) obtained after cell disruption in a suitable buffer (eg. a 10mM phosphate buffer pH 7). In case of en- zymes coming from thermopbhiles (eg. tm0308, BH1905, XylS), supernatants are also heated at 50-70°C for 30 min, cooled on ice for 10 min and precipitate is removed by centrifugation for 15 min at 15.000 G in order to remove thermo-labile E. coli contami- nants..

The supernatants are sterile filtrated and applied to a 1 ml DEAE FF column (Am- ersham Pharmacia). The purification is performed with the AKTA explorer (Amersham

Pharmacia) FPLC with the following buffers: Buffer A: 25 mM sodium phosphate pH 7,

Buffer B: 25 mM sodium phosphate pH 7 and 1 M NaCl. After the application is loaded, un- bound sample is washed out with buffer A for 5 CV. A gradient from 0-100% buffer B is used for 20 CV during which the target protein is eluted in fractions. After purification, frac-

BHYT-WO tions comprising the main peak in the resulting chromatogram are assayed by incubation on p-nitrophenyl «-D xylopyranoside or by SDS PAGE. The fractions containing the «- xylosidase activity are diluted in a 20 mM Tris HC] pH 7, 2 mM CaCl, buffer and concen- trated on Vivaspin 20 50.000 MWCO columns (Vivascience) by centrifugation at 2900 rpm,

O-glycoforms of rFVIia with exclusively glucose at serine 52

The O-glycoforms of rFVila with exclusively glucose at serine 52 are obtained by incubation of rFVIIa in an appropriate buffer, e.g. glycylglycine or 20 mM Tris HCI pH 7.0, 2 mM CacCl,, with purified «-xylosidase for an appropriate time, that can be determined experimentally. Mass spectra visualizing the deglycosylation are obtained by analysing rFVII «-xylosidase incubations ESI-MS (Q-STAR).

The resulting glycan-remodeled rFVIla is purified from the u-xylosidase enzyme by for example anion-exchange chromatography or gel filtration or suitable combinations.

The purity of the prepared O-glycoform of rFVIia is verified by the O-glycopeptide map of rfViia.

Example 3

Preparation of a-xylosidase by cloning and expression of T. maritima putative a- xylosidase gene (tm0308) in E. coli and purification

The above strategy (see Example 2) was followed all the way to a conclusion for tm0308. The T. maritima putative u-xylosidase gene (tm0308) was PCR amplified and cloned into a E. coli pET11a vector. Soluble tm0308 could be obtained after expression in an E. coli Rosetta (DE3) expression strain and evaluation of a crude TM0308 prepara- tion on a p-nitrophenyl «-D xylopyranoside, clearly indicated a-xylosidase activity. The «- xylosidase was partly purified using DEAE FF chromatography followed by up- concentration by ultra filtration. The partly purified enzyme was incubated with FVII in a 25 mM Tris pH 7, 2 mM CaCl, buffer at different enzyme/FVII ratios for 3 hours at 50°C or overnight at 37°C. Controls with identical compositions of o-xylosidase and rFVII, to which synthetic substrate was added, showed that the enzyme was active under these conditions and it was possible to visualize FVII with and without xylosidase treatment on

SDS-gels and by ESI-MS. However, no significant removal of the xylose sugars linked to Glc-O-Ser52 could be detected in this first experiment. In contrast, removal of xylose from a purified reduced and alkylated FVIIa peptide comprising Xyl-Xyl-Glc-0-Ser52 was observed.

58G1-WO

Example 4

Preparation of «-xylosidase by cloning and expression in E. coli

The following constructs have been cloned into the PET expression vectors in ac- cordance with the strategy described in Example 2: Gene bl02681(2310 bp)( Bacillus licheniformis: H); gene bl1905 (2328 bp) (Bacillus halodurans: H), gene xylIS (2196 bp) (Sulfolobus solfataricus: P); gene yicl (2319 bp) (Escherichia coli: P).

The constructs will be expressed in Rosetta, isolated, purified, and evaluated for «-

Xylosidase activity in accordance with the above-described strategy.

Each «-xylosidase will be incubated with rFViia in an appropriate buffer, e.g. glycylgly- cine or 20 mM Tris HCI pH 7.0, 2 mM CaCl,, for an appropriate time that can be deter- mined experimentally and MS Spectra visualizing the deglycosylation will be obtained by analysing rFVII u-xylosidase incubations ESI-LC-MS (Q-STAR).

The resulting glycan-remodeled rFVIIa will be purified from the a-xylosidase en- zyme by for example anion-exchange chromatography or gel filtration or suitable combi- nations thereof. The purity of the prepared O-glycoform of rFVIla is verified by the O- glycopeptide map of rFVIia.

Example 5

Preparation of truncated a-xylosidase by cloning and expression in E. coli

The crystal structure of Yicl was recently solved. Thus, cloning of a truncated «- xylosidase enzyme representing an active, catalytical domain of the Yicl protein (or other similar a-xylosidases) may be possible and is being planned, since a smaller en- zyme, if active, may better access the Xyl-Xyl-Glc-O-Ser52 present in native rFVIla. A domain comprising the active site in the enzyme is predicted from the structure. Gene sequence encoding this part of the Yicl sequence is prepared from the already existing

Yicl pET11a plasmid for an example by PCR amplification of relevant areas of the Yic] gene, The primers used for PCR will have extensions with restriction enzyme sites that can be used for ligation of the truncated Yicl gene into the pET11la vector. The truncated enzyme will after expression and purification be evaluated for its potential for deglycosy- lation of rFVIla as described above.

5841.WQ

Example 6

Preparation of rFVIia with exclusively xylose-glucose at serine 52 or exclusively xylose- xylose-glucose at serine 52 by a-xylosyltransferase treatment

Preparation of «-xylosyltransferase

The enzyme, UDP-D-xylose: p-D-glucoside a-1,3-D-xylosyltransferase, can be prepared from HepG2 cells as described by Omichi et al. (1997). In short, HepG2 cells are grown in a medium supplemented with 10% fetal calf serum. The microsomal fraction is prepared by homogenisation of the cells followed by centrifugation. The «- xylosyltransferase enzyme is purified by chromatography, for example on an anion- exchange column and/or on other chromatographic columns known for the skilled per- son. Fractions are collected during elution and the fractions containing the «- xylosyltransferase enzyme are identified by use of the «-xylosyltransferase assay.

The enzyme, UDP-D-xylose: a-D-xyloside al,3-xylosyltransferase, can be pre- pared from HepG2 cells as described by Minamida et al. (1996). In short, HepG2 cells are grown in a medium supplemented 10% fetal calf serum. The microsomal fraction is pre- pared by homogenisation of the cells followed by centrifugation. The a-xylosyltransferase enzyme is purified by chromatography, for example on an anion-exchange column and/or on other chromatographic columns known for the skilled person. Fractions are collected during elution and the fractions containing the a-Xylosyltransferase enzyme are identified by use of the a-xylosyltransferase assay. a-xylosyltransferase assay

The u-xylosyltransferase assays are conducted in an appropriate buffer, e.g. 10 mM Hepes, pH 7.2, 0.1% Triton X-100, 0.5 mM UDP-Xylose (Sigma U5875), containing a suitable substrate, e.g. the O-glycopeptides that can be obtained from the O- glycopeptide map of rFVIla or the pyridylaminated oligosaccharides prepared as de- scribed in Minamida et al. (Minamida et.al., Detection of UDP-D-xylose: a-D-xyloside «1- 3xylosyltransferase activity in human hepatoma cell line HepG2. J. Biochem. 120 1002- 1006, 1996). The reaction is stopped after an appropriate time, that can be determined experimentally, by e.g. addition of trifluoroacetic acid, and the assay mixtures are ana- lysed by HPLC.

O-glycoforms of rfVIla with exclusively xylose-glucose- at serine 52

A8G1TWD)

The O-glycoforms of rFVIla with exclusively xylose-glucose at serine 52 are ob- tained by (1) treatment of rFVIla with xylosidase as described above, (2) purification of the xylosidase treated rFVIla from the xylosidase by for example anion-exchange chro- matography, and (3) by incubation of xylosidase-treated rfFVIla in an appropriate buffer, e.g. glycylglycine, pH 7.0, 10 mM calcium chloride, with purified UDP-D-xylose: $-D- glucoside «-1,3-D-xylosyltransferase and UDP-D-xylose for an appropriate time, that can be determined experimentally. The resulting glyco-remodelled rFVIla is purified from the

UDP-D-xylose: 3-D-glucoside u-1,3-D-xylosyltransferase enzyme by for example anion- exchange chromatography. The purity of the prepared O-glycoform of rFVIla is verified by the O-glycopeptide map of rFVIia.

O-glycoforms of rFVIla with exclusively xylose-xylose-glucose- at serine 52

The O-glycoforms of with xylose-xylose-glucose at serine 52 are obtained by (1) treatment of rFVIIa with xylosidase as described above, (2) purification of the xylosidase treated rFVIla from the xylosidase by for example anion-exchange chromatography, (3) further treatment with UDP-D-xylose: B-D-glucoside o-1,3-D-xylosyltransferase and UDP-

D-xylose as described above, and (4) by incubation of the product in an appropriate buffer, e.g. glycylglycine, pH 7.0, 10 mM calcium chloride, with purified UDP-D-xylose: «-

D-xyloside al,3-xylosyltransferase and UDP-D-xylose for an appropriate time, that can be determined experimentally. The resulting glyco-remodelled rFVIia is purified from the

UDP-D-xylose: a-D-xyloside «1,3-xylosyltransferase enzyme by for example anion- exchange chromatography. The purity of the prepared O-glycoform of rFVila is verified by the O-glycopeptide map of rFVila.

Example 7

Analysis of O-glycoform pattern of rFVIia

Tryptic peptide mapping of the rFVIIa light chain

The relative content of the O-glycoforms of rFVIla is determined by tryptic peptide map- ping of the rFVlIa light chain. The rFVIla is reduced and alkylated and the rFVIla light chain is purified on a RP-HPLC column eluted with an acetonitrile gradient in wa- ter: trifluoroacetic acid. The purified rFVIla light chain is buffer-exchanged to Tris buffer, pH 7.5 and digested with trypsin. The tryptic digest of the rFVila light chain is analysed on a RP-HPLC column (for example Nucleosil C18, 5 ii, 300 &, 4.0 x 250 mm, Macherey-

Nagel 720065) eluted with an acetonitrile gradient (0%-45% acetonitrile in 100 min) in

83G1-WO water: trifluoroacetic acid (see Figure 2). Flow is 1.0 ml/min and detection is UV at 215 nm,

The peaks containing the O-glycopeptides of rFVIia are eluted after approx. 60-65 min where the 1st and the 3rd peak contain O-glycopeptides with a xylose-xylose-glucose- linked to serine 52, and the 2nd and 4th peak contain O-glycopeptides with a glucose linked to serine 52.

Similarly, the 1st and the 2nd peak contain O-glycopeptides with a tetrasaccharide linked to serine 60, and the 3rd and the 4th peak contain O-glycopeptides with a fucose linked to serine 60.

Tryptic peptide mapping of rFVIia

The O-glycoform pattern can be analysed by tryptic peptide mapping of rFVIla.The rFVila is buffer-exchanged to Tris buffer, pH 7.5, and digested with trypsin. The tryptic digest of the rFVIla is analysed on a RP-HPLC column (for example Nucleosil C18, 5 py, 300 A, 4.0 x 250 mm, Macherey-Nagel 720065) eluted with an acetonitrile gradient (0%-45% ace- tonitrile in 100 min) in water: trifluoroacetic acid. Flow is 1.0 ml/min and detection is UV at 215 nm.

The peaks containing the O-glycopeptides of rFVIIa are eluted after approx. 67-70 min where the 1st peak contains O-glycopeptides with a xylose-xylose-glucose linked to ser- ine 52, and the 2nd peak contains O-glycopeptides with a glucose linked to serine 52.

Total mass analysis of rFVIila

The O-glycoform pattern can be analysed by total mass analysis of rFVIIa. The rFVIla is desalted on a Millipore ZipTip C4 column equilibrated with 1 % formic acid and eluted with 3 % formic acid in 90 % methanol. The eluted sample is analysed by the nanospray technique on a Qstar XL mass spectrometer.

The major peak at approximately 50500 Da represents rFVIia O-glycoforms with a glu- cose linked to serine 52 and the major peak at approximately 50800 Da represents rEVIla O-glycoforms with a xylose-xylose-glucose linked to serine 52.

Example 8

Purification of Glc-O-Ser52-FVII and Xyl-Xyl-Glc-O-Ser52-FVI]

6841 WO

Glc-O-ser52-FVII and Xyl-Xyl-Glc-O-Ser52-FVII was purified using two cycles of hydrophobic interaction chromatography (HIC). The column (1.0 ¢cm in inner diameter x 7.0 cm length = 5.5 ml column volume (CV)) packed with Toso Haas TSK-Gel phenyl 5

PW, was equilibrated with S CV 10 mM histidine, 10 mM CaCl2, 2.0 M NH4-acetate, pH 6.0. The column was loaded with approximately 2.5 mg of FVII pr. ml resin. To the load solution 2.0 M NH4-acetate and 10 mM CaCl2 was added prior to load. The column was washed with 5 CV 10 mM histidine, 10 mM CaCl2, 2.0 M NH4-acetate, pH 6.0. Elution was performed using a 20 CV linear gradient from 10 mM histidine, 10 mM CacCl2, 2.0 M

NH4-acetate, pH 6.0 to 10 mM histidine, 10 mM CaCl2, pH 6.0. The purification was per- formed at a flow rate of 6 CV/h and at a temperature of 5°C. Fractions were collected during elution.

The FVII eluted in two overlapping major peaks (see Figure 4: Chromatogram from first HIC cycle). Fractions containing the first peak were pooled (fraction “A”, Figure 4) and further purified by a second cycle of HIC, using the same chromatographic proce- dure as for the first HIC cycle (see Figure 5: Chromatogram obtained by reloading frac- tion "A" onto the HIC column). Fractions containing the second major peak (fraction “8”,

Figure 4) were pooled as well and further purified by a second cycle of HIC, using the same chromatographic procedure as for the first HIC cycle (see Figure 6: Chromatogram obtained by reloading fraction “B” onto the HIC column),

Purified Glc-O-Ser52-FVII was identified in the peak fraction, fraction 10 (Figure 5), obtained by reloading fraction “A” onto the second HIC step. Purified Xyl-Xyl-Glc-O-

Ser52-FVII was identified in the peak fraction, fraction 15 (Figure 6), obtained by reload- ing fraction "B” onto the second HIC step. The identification was obtained by tryptic pep- tide mapping of rFVIla as described in Example 7 (Figure 7A and 78) and by total mass analysis of rFVIla as described in Example 7 (Figure 8A and 8B). Both analyses showed a high content of Glc-O-Ser52-rFVIla and a low content of Xyl-Xyl-Glc-O-Ser52-rFVila in the peak fraction, Fraction 10, and a low content of Glc-O-Ser52-rFVila and a high con- tent of Xyl-Xyl-Glc-O-Ser52-rFVIIa in the peak fraction, Fraction 15. A quantitation of the content of the O-glycoforms in the two peak fractions could not be obtained due to rela- tively low rFVIIa content in the fractions (Figure 7A and 7B: Tryptic peptide mapping:

Other peptide fragments of rFVIla co-eluted with or eluted close to the O-glycopeptides, and the content of O-glycopeptides in low amounts could therefore not be determined.) (Figure 8A and 8B: Total mass analysis: Other O- and/or N-glycoforms of rFVIla, for ex- ample N-glycoforms of rFVIla lacking one N-acetylneuraminic acid, appeared in the mass

B8YT-WO spectra, and the content of O-glycoforms of rFVIla in low amounts could therefore not be determined).

The specific activities of the peak fractions obtained from the HIC (Table 1) were determined by the 1st generation clotting assay. It was found that the Glc-O-Ser52- rkVIila O-glycoform had a low specific activity while the Xyi-Xyi-Gic-0-Ser52-rfFvila O- glycoform had a high specific activity.

Table 1. Specific activities determined using the 1st generation clotting assay for the peak fractions obtained from HIC. The content of rFVIiia was determined by HPLC.

Sample Specific activity

PS5002-014 Frak. 10 44 1U/ug

Example 9

Purification by hydrophobic interaction chromatography

Highly purified Glc-O-Ser52-rFVila preparations and highly purified Xyl-Xy!-Glc-

O-Ser52-rFVIla preparations can be obtained by repeated purification on the hydrophobic interaction chromatography as described above. Highly purified Glc-O-Ser52-rFVIla and

Xyl-Xyl-Glc-O-Ser52-rFVIla preparations with higher rFVIla content can be obtained by increasing the amount of starting material for the hydrophobic interaction chromatogra- phy performed as described above. The content of each O-glycoform of rFViIa in the highly purified preparations with higher rFVIla content can be quantitated by tryptic pep- tide mapping of the rFVIla light chain as described in Example 7. The specific activities of the highly purified preparations can be determined by the 1st generation clotting assay as above. a

Claims

£841-W0 CLAIMS

1. A preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2-Pro-Cys motif and wherein said serine/threonine forms part of a Glc-O-Ser/Thr covalent bond, wherein the preparation contains a substantially uniform serine/threonine-linked glycosylation pattern.

2. A preparation according to claim 1, wherein the glycosylation pattern is at least 80% uniform, preferably at least 85%, at least 90%, at least 95%, or at least 98% uniform.

3. A preparation according to claim 1 or claim 2, wherein the serine/threonine-linked glycan is Xyl-Xyl-Glc-.

4. A preparation according to claim 1 or claim 2, wherein the serine/threonine- linked glycan is Xyl-Glc-.

5. A preparation according to claim 1 or claim 2, wherein the serine/threonine- linked glycan is Glc-.

6. A preparation according to any one of claims 1 to 5, wherein the glycoprotein is se- lected from the group of: Factor VII polypeptides, Factor VII-related polypeptides, Factor IX polypeptides, Factor X polypeptides, Factor XII polypeptides, and protein Z polypep- tides.

7. A preparation according to claim 6, wherein the glycoprotein is human Factor VII.

8. A preparation according to claim 6, wherein the glycoprotein is a variant of Factor VII and wherein the ratio between the activity of the Factor VII-variant and the activity of native human factor VIla (wild-type FVIIa) is at least about 1.25 when tested in the "In Vitro Hydrolysis Assay" or in the “In vitro Proteolysis Assay”, both as described in the present description, preferably at least about 2.0, or at least about 4.0.

9. A preparation according to claim 6, wherein the glycoprotein is selected from the group of: human Factor IX, Factor IX sequence variants.

BECT-WO

10. A method for making a preparation as described in claims 1 tc 9, wherein the serine/threonine-linked glycan is -Glc; the method comprising the steps of: (a) obtaining a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2- Pro-Cys motif and wherein said serine/threonine forms part of a Glc-O-Ser/Thr covalent bond from a cell in which it is prepared; e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (b) contacting the preparation obtained in step (a) with a a-xylosidase under conditions appropriate for removing xylose residues from the glycoprotein, thereby pro- ducing the glycoprotein having an altered glycosylation pattern.

11. A method according to claim 10, further including the step of isolating the glycopro- tein prepared in step b having a glucose-O-serine/threonine glycosylation.

12. A method according to any one of claims 10-11, wherein the glycosylation is a serine glycosylation.

13. A method according to any one of claims 10 to 12, further including the step of ana- tysing the structure of the oligosaccharides linked to the polypeptides to determine a gly- coform pattern, and, optionally, repeating step (b) until the desired glycoform pattern is achieved.

14. A method for making a preparation as described in claims 1 to 9, wherein the serine/threonine-linked glycan is Glc; the method comprising the steps of: (a) obtaining a preparation of a polypeptide containing a Cys-X1-Ser/Thr-X2- Pro-Cys motif, e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (b) contacting the preparation obtained in step (a) with a O-glucosyltransferase and an activated glucose donor under conditions appropriate for transferring a glucose residue from the glucose donor moiety to the serine/threonine acceptor moiety, thereby producing the polypeptide having an altered glycosylation pattern.

15. A method according to claim 14, further including the step of isolating the glycopro- tein prepared in step b having a glucose-O-serine/threonine glycosylation.

16. A method according to any one of claims 14-15, wherein the glycosylation is a serine glycosylation.

5891-WO

17. A method according to any one of claims 14 to 16, further including the step of ana- lysing the structure of the oligosaccharides linked to the polypeptides to determine a gly- coform pattern, and, optionally, repeating step (b) until the desired glycoform pattern is achieved.

18. A method for making a preparation as described in claims 1 to 9, wherein the serine/threonine-linked glycan is Xyl-Glc-: the method comprising the steps of: (a) obtaining a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2- Pro-Cys motif and wherein said serine/threonine forms part of a Glc-0O-Ser/Thr covalent bond; e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (b) contacting the preparation obtained in step (a) with UDP-D-xylose: j3-D- glucoside «-1,3-D-xylosyltransferase and an activated xylosyl donor under condi- tions appropriate for transferring a xylose residue from the xylose donor moiety to the acceptor moiety, thereby producing the glycopeptide having an altered glycosy- lation pattern.

19. A method according to claim 18, further including the step of isolating the glycopro- tein prepared in step b having a xylose-glucose-O-serine/threonine glycosylation.

20. A method according to any one of claims 18-19, wherein the glycosylation is a serine glycosylation.

21. A method according to any one of claims 18 to 20, further including the step of ana- lysing the structure of the oligosaccharides linked to the polypeptides to determine a gly- coform pattern, and, optionally, repeating step (b) until the desired glycoform pattern is achieved.

22. A method according to any one of claims 18 to 21, further including the step of re- moving terminal xylose-residues by subjecting the preparation obtained in step (a) to the method described in claims 10-13 prior to step (b).

23. A method for making a preparation as described in claims 1 to 9, wherein the serine/threonine-linked glycan is Xyl-Xyl-Glc-; the method comprising the steps of: (a) obtaining a preparation of a glycoprotein containing a Cys-X1-Ser/Thr-X2- Pro-Cys motif and wherein said serine/threonine forms part of a Glc-O-Ser/Thr covalent

389 1-Q)

, . bond; e.g., from an engineered cell (cell culture) or by isolating the glycoprotein from a natural source; (b) contacting the preparation obtained in step (a) with UDP-D-xylose: p-D- glucoside «-1,3-D-xylosyltransferase and an activated xylosyl donor under condi- tions appropriate for transferring a xylose residue from the xylose donor moiety to the acceptor moiety, thereby producing the glycopeptide having an altered glycosy- lation pattern. (c) contacting the preparation obtained in step (b) with UDP-D-xylose: «-D- xyloside «-1,3-xylosyltransferase and an activated xylosyl donor under conditions appropriate for transferring a xylose residue from the xylose donor moiety to the acceptor moiety, thereby producing the glycopeptide having an altered glycosylation pattern.

24. A method according to claim 23, further including the step of isolating the preparation obtained in step (b) prior to subjecting the preparation to step (c).

25. A method according to any one of claims 23 to 24, further including the step of iso- tating the glycoprotein prepared in step (c¢) having a xylose-xylose-glucose-0O- serine/threonine glycosylation.

26. A method according to any one of claims 23-25, wherein the glycosylation is a serine glycosylation.

27. A method according to any one of claims 23 to 26, further including the step of ana- lysing the structure of the oligosaccharides linked to the polypeptides to determine a gly- coform pattern, and, optionally, repeating step (b) and/or step (c) until the desired gly- coform pattern is achieved.

28. A method according to any one of claims 23 to 27, further including the step of re- moving terminal xylose-residues by subjecting the preparation obtained in step (a) to the method described in claims 10-13 prior to step (b). Novo Nordisk A/S