# Patent

## Title
Modified vitamin K dependent polypeptides

## Abstract

The present invention relates to modified cDNA sequences coding for vitamin K-dependent polypeptides, in particular human Factor VII, human Factor VIIa, human Factor IX and human protein C and their derivatives with improved stability and extended plasma half life, recombinant expression vectors containing such cDNA sequences, host cells transformed with such recombinant expression vectors, recombinant polypeptides and derivatives which do have biological activities of the unmodified wild type protein but having improved stability and processes for the manufacture of such recombinant proteins and their derivatives. The invention also covers a transfer vector for use in human gene therapy, which comprises such modified DNA sequences.

## Background
This application is the U.S. National Stage of International Application No. PCT/EP2005/008678, filed Aug. 10, 2005, and also claims priority to European Application No.04019485.4, filed Aug. 17, 2004, both of which are incorporated herein by reference.
FIELD OF THE INVENTION
The present invention relates to modified cDNA sequences coding for vitamin K-dependent polypeptides, in particular human Factor VII, human Factor VIIa, human Factor IX and human protein C and their derivatives with improved stability and extended plasma half-life, recombinant expression vectors containing such cDNA sequences, host cells transformed with such recombinant expression vectors, recombinant polypeptides and derivatives which do have biological activities of the unmodified wild type protein but having improved stability and processes for the manufacture of such recombinant proteins and their derivatives. The invention also covers a transfer vector for use in human gene therapy, which comprises such modified DNA sequences.
BACKGROUND OF THE INVENTION
Vitamin K-dependent proteins are used to treat certain types of hemophilia. Classic hemophilia or hemophilia A is an inherited bleeding disorder. It results from a chromosome X-linked deficiency of blood coagulation Factor VIII, and affects almost exclusively males with an incidence between one and two individuals per 10.000. The X-chromosome defect is transmitted by female carriers who are not themselves hemophiliacs. The clinical manifestation of hemophilia A is an increased bleeding tendency. Before treatment with Factor VII concentrates was introduced the mean life span for a person with severe hemophilia was less than 20 years. The use of concentrates of Factor VIII from plasma and later on that of recombinant forms of FVIII has considerably improved the situation for the hemophilia patients increasing the mean life span extensively, giving most of them the possibility to live a more or less normal life. Hemophilia B being 5 times less prevalent than hemophilia A is caused by non-functional or missing FIX and is treated with FIX concentrates from plasma or a recombinant form of FIX. In both hemophilia A and in hemophilia B the most serious medical problem in treating the disease is the generation of alloantibodies against the replacement factors. Up to 30% of all hemophilia A patients develop antibodies to FVIII. Antibodies to FIX occur to a lesser extent but with more severe consequences, as they are less susceptible to immune tolerance induction therapy.
The current model of coagulation states that the physiological trigger of coagulation is the formation of a complex between tissue factor (TF) and Factor VIIa (FVIIa) on the surface of TF expressing cells which are normally located outside the vasculature. This leads to the activation of FIX and FX ultimately generating some thrombin. In a positive feedback loop thrombin activates FVIII and FIX, the so-called “intrinsic” arm of the blood coagulation cascade, thus amplifying the generation of FXa, which is necessary for the generation of the full thrombin burst to achieve complete hemostasis. It was shown that by administering supraphysiological concentrations of FVIIa hemostasis is achieved bypassing the need for FVIIa and FIXa. The cloning of the cDNA for FVII (U.S. Pat. No. 4,784,950) made it possible to develop a recombinant replacement of that plasma derived coagulation factor. This FVIIa was successfully administered for the first time in 1988 to a patient with a high titer of inhibitory antibodies to FVIII. Ever since the number of indications of FVIIa has grown steadily showing a potential to become a universal hemostatic agent (Erhardtsen, 2002).
FVII is a single-chain glycoprotein with a molecular weight of 50 kDa, which is secreted by liver cells into the blood stream as an inactive zymogen of 406 amino acids. It contains 10 γ-carboxy-glutamic acid residues (positions 6, 7, 14, 16, 19, 20, 25, 26, 29, and 35) localized in the Gla-domain of the protein. The Gla residues require vitamin K for their biosynthesis. Located C-terminal to the Gla domain are two epidermal growth factor domains followed by a trypsin-type serine protease domain. Further posttranslational modifications of FVII encompass hydroxylation (Asp 63), N-(Asn145 and Asn322) as well as O-type glycosylation (Ser52 and Ser60).
FVII is converted to its active form FVIIa by proteolysis of the single peptide bond at Arg152-Ile153 leading to the formation of two polypeptide chains, a N-terminal light chain (17 kDa) and a C-terminal heavy chain (28 kDa) which are held together by one disulfide bridge. In contrast to other vitamin K-dependent polypeptides no activation peptide which is cleaved off during activation has been described for FVII. The Arg152-Ile153 cleavage site corresponds by homology comparison to the C-terminal activation cleavage site of other vitamin K-dependent polypeptides. However as Arg144 might also constitute a protease cleavage site it cannot be excluded that FVII in contrast to current thinking possesses an activation peptide of 8 amino acids between Arg144 and Arg152.
Essential for attaining the active conformation of FVIIa is the formation of a salt bridge after activation cleavage between Ile153 and Asp343. Activation of FVII can be achieved in vitro by FXa, FXIIa, FIXa, FVIIa, FSAP and thrombin. Mollerup et al. (Biotechnol. Bioeng. (1995) 48: 501-505) reported that some cleavage also occurs in the heavy chain at Arg290 and or Arg315.
FVII is present in plasma in a concentration of 500 ng/ml. 1%, e.g. 5 ng/ml of FVII is present as FVIIa. Plasma half-life of FVII was found to be about 4 hours and that of FVIa about 2 hours. Although the half-life of FVIIa of 2 hours is comparatively long for an activated coagulation factor, which is, otherwise more in the order of minutes due to the irreversible inhibition by Serpins like antithrombin III, this nevertheless constitutes a severe drawback for the therapeutic use of FVIIa, as it leads to the need of multiple i.v. injections or continuous infusion to achieve hemostasis resulting in very high cost of treatment and inconvenience for the patient. As on the other hand FVIIa has the potential to be used as a universal hemostatic agent there is a high medical need to develop forms of FVIIa which have a longer functional half-life.
Several attempts have been made to modify FVII:
Nicolaisen et al. (WO 88/10295, Jun. 25, 1987) suggest that by deleting or modifying the following amino acids FVII will be stabilized against proteolytic degradation: Lys32, Lys38, Lys143, Arg290, Arg315, Lys316, Lys341, Arg392, Arg 396, Arg 402, Ile42 and Tyr44.
Nicolaison (U.S. Pat. No. 5,580,560, Nov. 13, 1989) extends WO 88/10295 to include also mutations or deletions in Arg304, Phe278 and Tyr332 to render FVII/FVIIa less susceptible to proteolysis.
Bharadwaj et al. (JBC (1996), 48 pp. 30685-30691) expressed the FVII mutant Phe328Ser that failed to activate FX and showed no detectable amidolytic activity. Dickinson et al. (PNAS (1996) 93, 14379-14384) proposed FVIIa variants in which Lys157, Val158, Glu296, Met298, Asp334, Ser336 or Lys337 have been replaced by Ala.
Nelsestuen (WO 99/29767 Oct. 23, 1997) modified the Gla domain by introducing point mutations in a way to enhance its affinity to phospholipid membranes thereby resulting into a modified FVIIa with enhanced specific activity. Proposed point mutations are at Pro10, Gly11, Arg28 and Lys32.
Nelsestuen (WO 00/66753, Apr. 29, 1999) modified the Gla domain by introducing point mutations in a way to enhance its affinity to phospholipid membranes thereby resulting into a modified FVIIa with enhanced specific activity. Proposed point mutations are at 5, 9, 11, 12, 29, 33, 34, 35 and/or 36.
Kornfelt et al. (Archiv. Biochem. and Biophys., 363, pp 43-54) showed that the oxidation of Met298 and Met306 leads to a 30% higher dissociation rate of FVIIa-ox from TF and a 20% lower FX activation as compared to wild type FVIIa.
Kemball-Cook et al. (JBC (1998), 14 pp. 8516-8521) expressed the FVII mutant Gln100Arg and showed that it had no detectable clotting activity though having amidolytic activity comparable to wild type FVIIa and speculate that this might be due to impaired association with TF.
Iino et al. Arch. Biochem. Biophys. (1998) 352:182-192 showed that mutating the O-glycosylation sites Ser-52 and Ser-60 decreases the coagulatory activity of FVIIa possibly interfering with the interaction with TF.
Ruf et al. (Biochemistry (1999) 16, pp. 1957-66) showed that the mutation Arg36Ala leads to decreased rate of FX activation.
Iwanaga et al. (Thromb. Haemost. (supplement August 1999), 466 abstract 1474) refer to a FVII variant in which residues 316-320 are deleted or residues 311-322 are replaced with the corresponding residues from trypsin.
Soeiima Kenji et al. (JP2001061479, Aug. 24, 1999) created a modified FVIIa with enhanced specific activity by cleaving the disulfide group between Cys159 and Cys164 or by substituting, adding or deleting at least a part of the loop structure from Thr233 to Asp244 or by substituting, adding, or deleting at least a part of the intervening sequence between Arg304 and Cys329.
Pedersen et al. (US 2003/0096338 Feb. 11, 2000) claim conjugates of FVII and FVIIa with non-polypeptidic moieties including also sugars with the aim to prolong FVIIa half-life. The claims also encompass the introduction of novel N- and/or O-type glycosylation sites or the introduction of novel combined with the removal of a preexisting N- and/or O-type glycosylation sites to obtain in vivo glycoconjugates.
Persson and Olsen (US 2003/0170863, May 3, 2000) taught modified FVIIa in which Leu305 or Phe374 have been replaced by another amino acid. At most 20 amino acids in the protease domain (153-406) have been replaced in combination with the above mentioned mutations. Other modified FVII molecules are disclosed which have optionally other amino acids replaced in positions 274, 300-304 and 306-312 in combination with Leu305 and Phe374. These modifications have the effect that FVIIa will spontaneously attain a more active conformation that normally has to be induced by TF.
Persson and Olsen (US 2003/0104978 and 2003/0100740, Sep. 29, 2000) further taught other modified FVIIa molecules with point mutations other than Ala substitutions at positions Lys157, Lys337, Asp334, Ser336, Val158, Glu296 and Met298.
Pingel and Klausen (US 2002/0151471 and US 2002/0137673, Oct. 2, 2000) claim a preparation comprising a plurality of FVII or related polypeptides, which comprise certain ratios of different N-type glycosylations.
Ruf et al. (WO 02/38162, Nov. 9, 2000) claimed FVII/FVIIa variants with the modifications Met298Gln, Glu296Ile and Val158Asn or combinations thereof leading to a higher amidolytic activity in the absence of TF and a higher affinity to TF. The factor was further modified to increase its stability in modifying the trypsin-like cleavage sites at Lys32, Lys38, Arg290, Arg304, Arg315 and Lys341 and the chymotrypsin-like sites at Ile42, Tyr44, Phe278 and Tyr332.
Persson (WO 02/077218, Mar. 22, 2001) teaches FVII/FVIIa mutants in which amino acids 247-260, 393-405 and Pro406 are mutated, more specifically R396, Q250 and Pro406, preferably an amino acid to which a chemical group can be attached with the goal of increasing the half life of FVII/FVIIa. This can be combined with mutations which increase the activity of FVII/FVIIa at K157, V158, E296, M298, L305, D334, S336, K337 and F374.
Persson and Olsen (US 2003/0100075, Sep. 27, 2001) teach that Leu305 is located at the end of an α-Helix found in the TF complexed form of FVIIa, which is believed to be important for the activity. In free FVIIa this helix is distorted and thus possibly unstable. Replacing Leu305 with other amino acids leads according to this invention to variants which attain the active conformation which otherwise is induced by TF. The amino acids Lys157, Lys337, Asp334, Ser336, Val 158, Glu296 and Met298 are located in areas which affect the formation of the salt bridge between Ile153 and Asp343. Replacing these amino acids leads according to this invention to the facilitation of the insertion of the N-terminus of the protease e.g. the generation of the salt bridge essential for activity.
Persson and Olsen (US 2003/0130191, Nov. 2, 2001) teach further modified FVII/VIIa mutants with increased specific activity which are substituted with other amino acids in positions: 313-329, 364, 366, 373 and 376 as well as in positions 330-339.
Haaning et al. (WO 03/093465, Apr. 30, 2002) extend the teaching of Nelsestuen (modification of the Gla Domain to enhance phospholipid binding), namely a substitution at Pro10 preferably Gln, Lys32 preferably Glu, Asp33 preferably a hydrophobic amino acid preferably Phe, Ala34 preferably a negatively charged amino acid preferably Glu and an insertion of an amino acid after Ala3 preferably Tyr with the introduction of further N-glycosylation sites.
Foncuberta et al. (WO 2004/011675, Jul. 25, 2002) describe naturally occurring allelic variants of FVII which could theoretically lead to higher expression levels and improved function of FVIIa. No data for such improved properties are shown. Two variants out of 49 were found in exons and lead to a substitution of amino acids: A294V and R353Q.
Persson and Olsen (WO 2004/029090, Sep. 25, 2002) showed that mutating Phe374 in combination with some other amino acids leads to an increase of TF independent activity of FVIIa. namely L305V, S314E, K337A and F374Y led to an increase of the TF amidolytic activity.
Haaning et al. (WO 2004/029091, Sep. 30, 2002) modified FVII at L39, I42, S43, K62, L65, F71, E82 and F275 in the TF binding site of FVII/FVIIa increasing the affinity to TF.
Andersen et al. (WO 2004/083361, Mar. 20, 2003) modified FVII/FVIIa in positions 196 (D196N/K), 237 (G237L or insertions GM GAAA or GAAA) and 341 (K341N/Q) to increase affinity to TF.
Blaichman et al. (WO 2004/108763, Jun. 5, 2003) modified FVII/FVIIa within the EGF domain based on an analysis of differences between the human and rabbit EGF domain as rabbit Factor VIIa has higher affinity to human TF as human Factor VIIa. Mutants in position 53, 62, 74, 75 and 83 are claimed and shown to have higher affinity to human TF and increased hemostatic potential.
Haaning et al (WO 2004/111242, Jun. 19, 2003) modified FVII/FVIIa at: positions 4, 10, 28, 32, 33, 34, 36, 74, 77, 116 preferably A3Y, P10Q, R28F, K32E, D33F, A34L, R36E, K38E, P74S, E77A, E116D. The R36E mutation causes reduced binding to TF and reduced thrombin generation in TF-dependent assays while maintaining in PL-dependent assays the same activity.
Johansen et al. (WO 2005/032581, Oct. 7, 2003) Teaches hybrid molecules consisting of a lipid membrane binding domain coupled to a Factor VII activity domain optionally coupled to a bulking agent, preferentially to PEG.
Maun et al. Protein Sci. (2005) 14:1171-80 introduced new disulfide bonds to lock the FVII conformation into an active TF*FVIIa-like state. Kinetic analysis of amidolytic activity revealed that all Factor VIIa variants alone had increased specific activity compared to wild type, the largest being for variants 136:160 and 138:160 with substrate S-2765, having 670- and 330-fold increases, respectively. Factor VIIa disulfide-locked variants no longer required TF as a co-factor for maximal activity in amidolytic assays. In the presence of soluble TF, activity was enhanced 20- and 12-fold for variants 136:160 and 138:160, respectively, compared to wild type.
DETAILED DESCRIPTION OF THE INVENTION
It is an object of the present invention to provide modified vitamin K-dependent polypeptides, e.g. modified FVII and modified FVIIa, with a longer functional half-life.
FVII is related to other Gla domain proteins like FIX, FX, protein C, protein Z, prothrombin, GAS6 and protein S. More closely related are FVII, FIX, FX and protein C in which the N-terminal Gla domain is followed by two epidermal growth factor (EGF) domains followed by the trypsin-type serine protease domain. Protein Z has a similar structure but an inactive protease domain. In prothrombin the Gla domain is followed by two kringle domains instead the two EGF domains then followed by the trypsin-type protease domain. In GAS6 and protein S the Gla domain is followed by 4 EGF domains and then by two laminin-G domains instead of the protease domain.
Striking is the large difference in plasma half life of these closely related plasma proteins:















FVII
2-4 hours



Protein C:
6-8 hours



FIX:
18-30 hours



FX:
20-42 hours



Protein S:
24-58 hours



Prothrombin:
41-72 hours









A particular closely related subgroup of these proteins comprises FVII, FIX, FX and protein C.
In FIG. 1 the homology between FVII, protein C, FIX and FX of human origin and of other species is compared. The molecules are highly conserved, the most striking difference being within the activation domain. For FVII no activation peptide has been described. However, during activation FVII might in addition to cleavage at Arg152 also be cleaved at Arg144, then resulting in the release of a putative activation peptide of 8 amino acids containing a conserved N-glycosylation site.
Surprisingly the length of the activation peptides and posttranslational modifications of the activation peptides correlate with increased half-life:










TABLE 1







Length of human
N-glycosylation sites



Plasma half-
activation
within activation



life
peptide
peptide







FVII
2-4 hours
No activation
1 in putative 8 amino




peptide (or putative
acid activation




8 amino acid
peptide




activation peptide)



Protein
6-8 hours
11 amino acids
0


C





FIX
18-30 hours
35 amino acids
2


FX
20-42 hours
52 amino acids
2









The invention therefore relates to a method for preparing a modified vitamin K-dependent polypeptide, comprising modifying the activation peptide of a first vitamin K-dependent polypeptide such that the modified vitamin K-dependent polypeptide has an increased half-life compared to the first vitamin K-dependent polypeptide in which the activation peptide has not been modified.
The invention further relates to a method for preparing such a modified vitamin K-dependent polypeptide, comprising modifying the activation peptide of a first vitamin K-dependent polypeptide by adding at least part of an activation peptide of a second vitamin K-dependent polypeptide or by replacing at least part of an activation peptide of a first vitamin K-dependent polypeptide with at least part of an activation peptide of a second vitamin K-dependent polypeptide.
Vitamin K-dependent polypeptides are a group of proteins that need vitamin K in their biosynthetic pathways to carboxylate the side chains of glutamic acid residues of their protein precursors. Vitamin K-dependent polypeptides include, but are not limited to, Factor VII, Factor VIIa, Factor IX, Factor IXa, Factor X, Factor Xa, Factor II (Prothrombin), Protein C, activated Protein C, Protein S, activated Protein S, GAS6, activated GAS6, Protein Z, activated Protein Z, and the like. Furthermore, useful vitamin K-dependent polypeptides can be wild-type or can contain mutations. Degree and location of glycosylation or other post-translation modifications may vary depending on the chosen host cells and the nature of the host cellular environment. When referring to specific amino acid sequences, posttranslational modifications of such sequences are encompassed in this application.
“Factor VII/VIIa” as used in this application means a product consisting of either the nonactivated form (factor VII) or the activated form (factor VIIa) or mixtures thereof. “Factor VII/VIIa” within the above definition includes proteins that have the amino acid sequence of native human factor VII/VIIa. It also includes proteins with a slightly modified amino acid sequence, for instance, a modified N-terminal end including N-terminal amino acid deletions or additions so long as those proteins substantially retain the activity of factor VIIa. “Factor VII” within the above definition also includes natural allelic variations that may exist and occur from one individual to another. “Factor VII” within the above definition further includes variants of FVII/FVIIa. Such variants differ in one or more amino acid residues from the wild type sequence. Examples of such differences may include truncation of the N- and/or C-terminus by one or more amino acid residues (e.g. 1 to 10 amino acid residues), or addition of one or more extra residues at the N- and/or C-terminus, e.g. addition of a methionine residue at the N-terminus, as well as conservative amino acid substitutions, i.e. substitutions performed within groups of amino acids with similar characteristics, e.g. (1) small amino acids, (2) acidic amino acids, (3) polar amino acids, (4) basic amino acids, (5) hydrophobic amino acids, and (6) aromatic amino acids. Examples of such conservative substitutions are shown in the following table.











TABLE 2







(1)
Alanine
Glycine




(2)
Aspartic acid
Glutamic acid




(3)
Asparagine
Glutamine
Serine
Threonine


(4)
Arginine
Histidine
Lysine



(5)
Isoleucine
Leucine
Methionine
Valine


(6)
Phenylalanine
Tyrosine
Tryptophane









The amino acid sequences of various vitamin K-dependent polypeptides and the cDNA sequences encoding them are shown in the sequence listing:










TABLE 3







SEQ ID NO: of





amino acid



Vitamin K-

sequence
SEQ ID NO: of


dependent
SEQ ID NO: of
encoded by
mature


polypeptide
cDNA sequence
cDNA
polypeptide


















human Factor VII
1
2
3


human Protein C
4
5
6


human Factor IX
7
8
9


human Factor X
10
11
12


human Prothrombin
13
14
15









The first vitamin K-dependent polypeptide is preferably selected from the group consisting of Factor VII, Factor VIIa, Factor IX, Factor IXa, Protein C and activated Protein C. More preferably, the first vitamin K-dependent polypeptide is selected from the group consisting of human Factor VII, human Factor VIIa, human Factor IX, human Factor IXa, human Protein C and human activated Protein C. Most preferably, the first vitamin K-dependent polypeptide is human Factor VII or human Factor VIIa. In a specific embodiment, the first vitamin K-dependent polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 3, 6 and 9.
The second vitamin K-dependent polypeptide is different from the first vitamin K-dependent polypeptide. Accordingly, the modified vitamin K-dependent polypeptide obtainable by the process of the invention comprises at least part of an activation peptide not naturally occurring in the first vitamin K-dependent polypeptide.
The second vitamin K-dependent polypeptide has a longer plasma half life than the first vitamin K-dependent polypeptide. In another embodiment, the length of the activation peptide of the second vitamin K-dependent polypeptide is greater than the length of the activation peptide of the first vitamin K-dependent polypeptide. Preferably, the second vitamin K-dependent polypeptide is selected from the group consisting of Factor IX, Factor X and Prothrombin. More preferably, the second vitamin K-dependent polypeptide is selected from the group consisting of human Factor IX, human Factor X and human Prothrombin. In a specific embodiment, the second vitamin K-dependent polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs:9, 12 and 15.
The part of the activation peptide of the activation peptide of the second vitamin K-dependent polypeptide, which is added, preferably consists of at least 8, more preferably of at least 12, even more preferably of at least 15 contiguous amino acids in the amino acid sequence of the activation peptide of the second vitamin K-dependent polypeptide.
In another embodiment the part of the activation peptide of the second vitamin K-dependent polypeptide, which is added, may consist of at least 0.15·N contiguous amino acids in the amino acid sequence of the activation peptide of the second vitamin K-dependent polypeptide, wherein N is the total number of amino acids of the activation peptide of the second vitamin K-dependent polypeptide. Preferably, the part of the activation peptide of the second vitamin K-dependent polypeptide consists of at least 0.5·N, more preferably of at least 0.75·N, more preferably of at least 0.9·N, most preferably of at least 0.95·N contiguous amino acids in the amino acid sequence of the activation peptide of the second vitamin K-dependent polypeptide.
In another embodiment, the part of the activation peptide of the second vitamin K-dependent polypeptide, which is added, consists of at least (N-x) contiguous amino acids in the amino acid sequence of the activation peptide of the second vitamin K-dependent polypeptide, wherein N is the total number of amino acids of the activation peptide of the second vitamin K-dependent polypeptide and wherein x may be 7, preferably x is 5, more preferably x is 4, more preferably x is 3, even more preferably x is 2.
It is also possible that the part of the activation peptide of the second vitamin K-dependent polypeptide, which is added, consists of a central part of the activation peptide, i.e. it does not comprise the very C-terminal amino acid or the very N-terminal amino acid of the activation peptide.
Most preferably, the complete activation peptide of the second vitamin K-dependent polypeptide is added to the amino acid sequence of the first vitamin K-dependent polypeptide while retaining the specificity of activation of the first vitamin K-dependent polypeptide. Alternatively, a variant of the complete activation peptide of the second vitamin K-dependent polypeptide may be added to the amino acid sequence of the first vitamin K-dependent polypeptide. Variants include activation peptides in which 1 to 10, preferably 1 to 7, more preferably 1 to 5, most preferably 1 to 3 amino acids have been added, deleted and/or substituted.
If only the half-life of the zymogen shall be prolonged N- and C-terminal activation cleavage sites of the first vitamin K-dependent polypeptide are preferably retained in the variant activation peptides. If also the half-life of the activated form of the vitamin K-dependent polypeptide shall be prolonged either an N- or C-terminal activation cleavage site of the first vitamin K-dependent polypeptide shall be deleted. Preferably, the N-terminal activation cleavage site is deleted. If the half-life of FVIIa shall be prolonged preferentially N-terminal activation cleavage sites shall be deleted whereas preferentially C-terminal activation cleavage sites shall be retained.
The following table summarizes the sequences of activation peptides from several vitamin K-dependent polypeptides.









TABLE 4





vitamin K-

SEQ ID NO: 


dependent
amino acid sequence of
of activation


polypeptide
activation peptide
peptide







human Factor
NASKPQGR (putative)
16


VII
(aa 145-152 of SEQ ID NO: 3)



 


human Protein
TEDQEDQVDPR
17


C
(aa 159-169 of SEQ ID NO: 6)



 


human Factor
AETVFPDVDYVNSTEAETILDNITQSTQSFNDFTR
18


IX
(aa 146-180 of SEQ ID NO: 9)



 


human Factor
SVAQATSSSGEAPDSITWKPYDAADLDPTE
19


X
NPFDLLDFNQTQPERGDNNLTR




(aa 143-194 of SEQ ID NO: 12)



 


human
TATSEYQTFFNPRTFGSGEADCGLRPLFEKKSLE
20


Prothrombin
DKTERELLESYIDGR




(aa 272-320 of SEQ ID NO: 15)









The term “activation peptide” as used herein includes known activation peptides and putative activation peptides such as that in Factor VII.
By way of non-limiting example, any one of the following amino acid sequences can be added to the amino acid sequence of SEQ ID NO:3 or 6
aa 1 to 35 of SEQ ID NO:18;
aa 1 to 34 of SEQ ID NO:18;
aa 1 to 33 of SEQ ID NO:18;
[ . . . ]
aa 1 to 8 of SEQ ID NO:18;
aa 1 to 7 of SEQ ID NO:18;
aa 1 to 6 of SEQ ID NO:18;
aa 1 to 5 of SEQ ID NO:18;
aa 2 to 35 of SEQ ID NO:18;
aa 2 to 34 of SEQ ID NO:18;
aa 2 to 33 of SEQ ID NO:18;
[ . . . ]
aa 2 to 9 of SEQ ID NO:18;
aa 2 to 8 of SEQ ID NO:18;
aa 2 to 7 of SEQ ID NO:18;
aa 2 to 6 of SEQ ID NO:18;
aa 3 to 35 of SEQ ID NO:18;
aa 3 to 34 of SEQ ID NO:18;
aa 3 to 33 of SEQ ID NO:18;
[ . . . ]
aa 3 to 10 of SEQ ID NO:18;
aa 3 to 9 of SEQ ID NO:18;
aa 3 to 8 of SEQ ID NO:18;
aa 3 to 7 of SEQ ID NO:18;
and so forth.
By way of non-limiting example, any one of the following amino acid sequences can be added to the amino acid sequence of SEQ ID NO:3, 6 or 9
aa 1 to 52 of SEQ ID NO:19;
aa 1 to 51 of SEQ ID NO:19;
aa 1 to 50 of SEQ ID NO:19;
[ . . . ]
aa 1 to 8 of SEQ ID NO:19;
aa 1 to 7 of SEQ ID NO:19;
aa 1 to 6 of SEQ ID NO:19;
aa 1 to 5 of SEQ ID NO:19;
aa 2 to 52 of SEQ ID NO:19;
aa 2 to 51 of SEQ ID NO:19;
aa 2 to 50 of SEQ ID NO:19;
[ . . . ]
aa 2 to 9 of SEQ ID NO:19;
aa 2 to 8 of SEQ ID NO:19;
aa 2 to 7 of SEQ ID NO:19;
aa 2 to 6 of SEQ ID NO:19;
aa 3 to 52 of SEQ ID NO:19;
aa 3 to 51 of SEQ ID NO:19;
aa 3 to 50 of SEQ ID NO:19;
[ . . . ]
aa 3 to 10 of SEQ ID NO:19;
aa 3 to 9 of SEQ ID NO:19;
aa 3 to 8 of SEQ ID NO:19;
aa 3 to 7 of SEQ ID NO:19;
and so forth.
The part of or the complete activation peptide of the second vitamin K-dependent polypeptide is inserted in the vicinity of the activation peptide region of the first vitamin K-dependent polypeptide. It may be inserted between two amino acids of the first vitamin K-dependent polypeptide without deleting amino acids of the first vitamin K-dependent polypeptide. For example, in case of FVII being the first vitamin K-dependent polypeptide, the part of or the complete activation peptide of the second vitamin K-dependent polypeptide may be inserted between amino acids 144 and 145, between amino acids 145 and 146, between amino acids 146 and 147, between amino acids 147 and 148, between amino acids 148 and 149, between amino acids 149 and 150, between amino acids 150 and 151, between amino acids 151 and 152 or between amino acids 152 and 153, wherein the numbering refers to SEQ ID NO:3. Preferably, the part of or the complete activation peptide of the second vitamin K-dependent polypeptide is inserted between amino acids 144 and 145, wherein the numbering refers to SEQ ID NO:3. Preferably, the C-terminal cleavage site and the specificity of activation of the first vitamin K-dependent polypeptide is preserved by the insertion. The N-terminal cleavage site may be deleted by the insertion.
In another aspect, the part of or the complete activation peptide of the second vitamin K-dependent polypeptide replaces a stretch of amino acids in the first vitamin K-dependent polypeptide. For example, in case of FVII being the first vitamin K-dependent polypeptide, the part of or the complete activation peptide of the second vitamin K-dependent polypeptide may replace amino acids 140 to 152 of SEQ ID NO:3. Preferably, the C-terminal cleavage site and the specificity of activation of the first vitamin K-dependent polypeptide is preserved by the replacement. The N-terminal cleavage site may be deleted by the replacement.
The N-terminal cleavage site may be deleted by replacing certain amino acids of the first vitamin K-dependent polypeptide with the part of or the complete activation peptide of the second vitamin K-dependent polypeptide. Accordingly, the part of or the complete activation peptide of the second vitamin K-dependent polypeptide may replace any one of the following amino acid sequences of SEQ ID NO:3:
aa 140 to 145;
aa 141 to 145;
aa 142 to 145;
aa 143 to 145;
aa 144 to 145;
aa 145;
aa 140 to 144;
aa 141 to 144;
aa 142 to 144;
aa 143 to 144; or
aa 144.
In another embodiment, the proteolytic cleavage sites in the first vitamin K-dependent polypeptide, which are N-terminal and C-terminal to the activation peptide region are retained during the modification. Thus the specificity of activation of the first vitamin K-dependent polypeptide is retained.
In another embodiment if the plasma half-life of the zymogen shall be prolonged the N-terminal and C-terminal activation cleavage sites of the second vitamin K-dependent polypeptide replace those of the first vitamin K-dependent polypeptide or an N-terminal activation cleavage site can be retained from the first vitamin K-dependent polypeptide and a C-terminal activation cleavage site can be retained from the second vitamin K-dependent polypeptide or vice versa. If the plasma half-life of the activated vitamin K-dependent polypeptide shall be stabilized either an N-terminal or a C-terminal activation cleavage site shall be deleted. In case of a stabilized FVIIa variant the activation peptide must be retained with the N-terminal light chain. This implies that the C-terminal activation cleavage site must be retained whereas an N-terminal activation cleavage site transferred from a vitamin K-dependent polypeptide must be deleted. Also it might be necessary to delete the hypothetical activation peptide cleavage site at Arg144.
The modification may further comprise in addition to the insertion of the activation peptide of a second vitamin K-dependent polypeptide or a variant thereof the concomitant deletion of at least part of the activation peptide of the first vitamin K-dependent polypeptide while preferentially retaining the specificity of activation of the first vitamin K-dependent polypeptide. The part to be deleted may consist of at least 2, preferably at least 4, more preferably at least 6, even more preferably at least 8 contiguous amino acids of the activation peptide of the first vitamin K-dependent polypeptide.
In another embodiment the part of the activation peptide of the first vitamin K-dependent polypeptide, which is deleted, may consist of at least 0.15·N contiguous amino acids in the amino acid sequence of the activation peptide of the first vitamin K-dependent polypeptide, wherein N is the total number of amino acids of the activation peptide of the first vitamin K-dependent polypeptide. Preferably, the part of the activation peptide of the first vitamin K-dependent polypeptide consists of at least 0.5·N, more preferably of at least 0.75·N, more preferably of at least 0.9·N, most preferably of at least 0.95·N contiguous amino acids in the amino acid sequence of the activation peptide of the first vitamin K-dependent polypeptide.
In another embodiment, the part of the activation peptide of the first vitamin K-dependent polypeptide, which is deleted, consists of at least (N-x) contiguous amino acids in the amino acid sequence of the activation peptide of the first vitamin K-dependent polypeptide, wherein N is the total number of amino acids of the activation peptide of the first vitamin K-dependent polypeptide, wherein x may be 7, preferably x is 5, more preferably x is 4, more preferably x is 3, even more preferably x is 2.
It is also possible that the part of the activation peptide of the first vitamin K-dependent polypeptide, which is deleted, consists of a central part of the activation peptide, i.e. it does not comprise the very C-terminal amino acid or the very N-terminal amino acid of the activation peptide.
In a specific embodiment, the complete activation peptide of the first vitamin K-dependent polypeptide is deleted.
Usually, the modification comprises replacing at least part of the activation peptide of the first vitamin K-dependent polypeptide with at least part of the activation peptide of the second vitamin K-dependent polypeptide. The preferred embodiments of the parts of the activation peptide of the first vitamin K-dependent polypeptide and of the activation peptide of the second vitamin K-dependent polypeptide correspond to those described above.
In a particular embodiment, the complete activation peptide of the first vitamin K-dependent polypeptide is replaced with the complete activation peptide of the second vitamin K-dependent polypeptide or with a variant of the complete activation peptide of the second vitamin K-dependent polypeptide while retaining the amino acids necessary to retain the specificity of activation of the first vitamin K-dependent polypeptide.
By way of non-limiting example the invention encompasses the introduction of activation peptide sequences from animal vitamin K-dependent polypeptides (some of which are shown in FIG. 1), such as murine, canine, bovine, porcine or rodent prothrombin factors, as well as combinations thereof.
By way of non-limiting example the invention encompasses the introduction of the activation peptide of FIX or FX into the vicinity of the activation site of FVII, as well as replacing the activation peptide of protein C by that of FIX or FX, as well as replacing the activation peptide of FIX by that of FX. By way of illustrating the breadth of this aspect of the invention with the preferred FVII molecule the half life of FVII is increased by simply replacing the putative activation peptide of 8 amino acids completely by one of the activation peptides taken from protein C, FIX or FX or by creating a hybrid activation peptide by adding the activation peptides taken from protein C, FIX or FX to, from one amino terminus proximal amino acid up to the complete putative FVII activation peptide.
Another aspect of the invention is the variation of the post translational modification of these transferred activation peptides, as by way of non-limiting example the removal of N-glycosylation sites in the transferred activation peptides or alternatively the removal of the N-glycosylation site in the putative activation peptide of FVII between Arg144 and Arg152, can lead to less asialoprotein-receptor mediated clearance of the coagulation factor. In one embodiment of the invention, the modification therefore comprises modifying sites of posttranslational modification within the activation peptide. Preferably, the modification comprises removing at least one N-glycosylation site within the activation peptide.
Another aspect of the invention is the prolongation of plasma half-life by the transfer of analogues of the activation peptides of longer-lived vitamin K-dependent proteins. An analogue in its widest sense is an insert having longer than 8 continuous amino acids or conservative substitutions of these amino acids of the activation peptide of a longer lived wild-type vitamin K-dependent protein while preserving its N- and its C-terminal activation cleavage sites if the half-life of the zymogen of the first vitamin K-dependent polypeptide shall be prolonged or while preserving either its N- or its C-terminal activation cleavage site if also the half-life of the activated vitamin K-dependent polypeptide shall be prolonged.
Conservative amino acid substitutions are substitutions performed within groups of amino acids with similar characteristics, e.g. (1) small amino acids, (2) acidic amino acids, (3) polar amino acids, (4) basic amino acids, (5) hydrophobic amino acids and (6) aromatic amino acids. Examples of such conservative substitutions are shown in table 2.
Another aspect of the invention is a method for increasing the stability of a vitamin K-dependent polypeptide, comprising modifying its activation peptide. Yet another aspect of the invention is a method for increasing the functional half life or plasma half-life of a vitamin K-dependent polypeptide, comprising modifying its activation peptide. These methods may comprise the same steps as the method for producing a modified vitamin K-dependent polypeptide described above.
The invention further relates to a modified vitamin K-dependent polypeptide obtainable by a process of the invention. The modified vitamin K-dependent polypeptide may comprise a modified activation peptide, wherein the modified vitamin K-dependent polypeptide has an increased half-life compared to the vitamin K-dependent polypeptide in which the activation peptide has not been modified.
Another aspect of the invention is a modified vitamin K-dependent polypeptide comprising a modified activation peptide, said modified activation peptide comprising at least part of an activation peptide of a different vitamin K-dependent polypeptide. Alternatively, the modified vitamin K-dependent polypeptide may comprise an analogue or a variant of an activation peptide of a different vitamin K-dependent polypeptide. Analogues and variants are molecules as defined supra.
Preferably, the vitamin K-dependent polypeptide is a first vitamin K-dependent polypeptide as defined supra. The “different vitamin K-dependent polypeptide” is a second vitamin K-dependent polypeptide as defined supra. The preferred embodiments of the modified vitamin K-dependent polypeptide of the invention correspond to the preferred embodiments described hereinbefore with respect to the method of the invention.
In another embodiment, the modified vitamin K-dependent polypeptide of the invention exhibits an increased functional half-life compared to the non-modified form and/or to the wild type form of the vitamin K-dependent polypeptide. The functional half-life can be determined in vitro as shown in Lindley et al. (Pharmacokinetics and pharmacodynamics of recombinant Factor VIIa, Clin. Pharmacol Ther. 1994 55:638-648)
The functional half life is usually increased by at least 50%, preferably by at least 100%, more preferably by at least 200%, even more preferably by at least 500% compared to the non-modified form and/or to the wild type form of the vitamin K-dependent polypeptide.
The functional half life of the wild type form of human Factor VII is approximately 4 hours. The functional half life of the modified Factor VII molecule of the invention is usually at least about 6 hours, preferably at least about 10 hours, more preferably at least about 15 hours, most preferably at least about 24 hours.
The functional half life of the wild type form of human Factor VIIa is approximately 2 hours. The functional half life of the modified Factor VIIa molecule of the invention is usually at least about 3 hours, preferably at least about 5 hours, more preferably at least about 8 hours, most preferably at least about 12 hours.
Generally, the modified vitamin K-dependent polypeptide has an increased stability compared to the non-modified form and/or compared to the wild type form of the vitamin K-dependent polypeptide. An increase in stability of the modified Factor VII molecules can for example be measured as previously described by functional assays
The modified vitamin K-dependent polypeptide of the invention usually has substantially the same activity as the corresponding wild type form and/or non-modified form of the vitamin K-dependent polypeptide. A “substantially the same” activity means at least about 10%, preferably about 50%, more preferably at least about 75%, most preferably at least about 100% of the activity of the corresponding wild type form and/or non-modified form of the vitamin K-dependent polypeptide. The activity of Factor VII/VIIa is the ability to convert the substrate Factor X to the active Factor Xa. The activity of a Factor VII/VIIa polypeptide may be measured with the assays described in Shaw et al., 1998, PNAS, Vol. 95, pp. 4229-4234 or as in Gabriel et al. 2004, Sem. Hematol. Vol 41, Suppl. 1 pp 20-24.
The invention further relates to a polynucleotide encoding a modified vitamin K-dependent polypeptide as described in this application. The term “polynucleotide(s)” generally refers to any polyribonucleotide or polydeoxyribonucleotide that may be unmodified RNA or DNA or modified RNA or DNA. The polynucleotide may be single- or double-stranded DNA, single or double-stranded RNA. As used herein, the term “polynucleotide(s)” also includes DNAs or RNAs that comprise one or more modified bases and/or unusual bases, such as inosine. It will be appreciated that a variety of modifications may be made to DNA and RNA that serve many useful purposes known to those of skill in the art. The term “polynucleotide(s)” as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including, for example, simple and complex cells.
The skilled person will understand that, due to the degeneracy of the genetic code, a given polypeptide can be encoded by different polynucleotides. These “variants” are encompassed by this invention.
Preferably, the polynucleotide of the invention is an isolated polynucleotide. The term “isolated” polynucleotide refers to a polynucleotide that is substantially free from other nucleic acid sequences, such as and not limited to other chromosomal and extrachromosomal DNA and RNA. Isolated polynucleotides may be purified from a host cell. Conventional nucleic acid purification methods known to skilled artisans may be used to obtain isolated polynucleotides. The term also includes recombinant polynucleotides and chemically synthesized polynucleotides.
Yet another aspect of the invention is a plasmid or vector comprising a polynucleotide according to the invention. Preferably, the plasmid or vector is an expression vector. In a particular embodiment, the vector is a transfer vector for use in human gene therapy.
Still another aspect of the invention is a host cell comprising a polynucleotide of the invention or a plasmid or vector of the invention.
The host cells of the invention may be employed in a method of producing a modified vitamin K-dependent polypeptide, which is part of this invention. The method comprises:

    
    
        (a) culturing host cells of the invention under conditions such that the modified vitamin K-dependent polypeptide is expressed; and
        (b) optionally recovering the modified vitamin K-dependent polypeptide from the host cells or from the culture medium.
    
    


Expression of the Proposed Variants:
The production of recombinant proteins at high levels in suitable host cells, requires the assembly of the above-mentioned modified cDNAs into efficient transcriptional units together with suitable regulatory elements in a recombinant expression vector, that can be propagated in various expression systems according to methods known to those skilled in the art. Efficient transcriptional regulatory elements could be derived from viruses having animal cells as their natural hosts or from the chromosomal DNA of animal cells. Preferably, promoter-enhancer combinations derived from the Simian Virus 40, adenovirus, BK polyoma virus, human cytomegalovirus, or the long terminal repeat of Rous sarcoma virus, or promoter-enhancer combinations including strongly constitutively transcribed genes in animal cells like beta-actin or GRP78 can be used. In order to achieve stable high levels of mRNA transcribed from the cDNAs, the transcriptional unit should contain in its 3′-proximal part a DNA region encoding a transcriptional termination-polyadenylation sequence. Preferably, this sequence is derived from the Simian Virus 40 early transcriptional region, the rabbit beta-globin gene, or the human tissue plasminogen activator gene.
The cDNAs are then integrated into the genome of a suitable host cell line for expression of the hybrid, modified Gla domain proteins, preferably FIX, FX, protein C most preferred Factor VII proteins. Preferably this cell line should be an animal cell-line of vertebrate origin in order to ensure correct folding, Gla-domain synthesis, disulfide bond formation, asparagine-linked glycosylation, O-linked glycosylation, and other post-translational modifications as well as secretion into the cultivation medium. Examples of other post-translational modifications are tyrosine O-sulfation, hydroxylation and proteolytic processing of the nascent polypeptide chain. Examples of cell lines that can be use are monkey COS-cells, mouse L-cells, mouse C127-cells, hamster BHK-21 cells, human embryonic kidney 293 cells, and preferentially hamster CHO-cells.
The recombinant expression vector encoding the corresponding cDNAs can be introduced into an animal cell line in several different ways. For instance, recombinant expression vectors can be created from vectors based on different animal viruses. Examples of these are vectors based on baculovirus, vaccinia virus, adenovirus, and preferably bovine papilloma virus.
The transcription units encoding the corresponding DNA's can also be introduced into animal cells together with another recombinant gene which may function as a dominant selectable marker in these cells in order to facilitate the isolation of specific cell clones which have integrated the recombinant DNA into their genome. Examples of this type of dominant selectable marker genes are Tn5 amino glycoside phosphotransferase, conferring resistance to geneticin (G418), hygromycin phosphotransferase, conferring resistance to hygromycin, and puromycin acetyl transferase, conferring resistance to puromycin. The recombinant expression vector encoding such a selectable marker can reside either on the same vector as the one encoding the cDNA of the desired protein, or it can be encoded on a separate vector which is simultaneously introduced and integrated to the genome of the host cell, frequently resulting in a tight physical linkage between the different transcription units.
Other types of selectable marker genes which can be used together with the cDNA of the desired protein are based on various transcription units encoding dihydrofolate reductase (dhfr). After introduction of this type of gene into cells lacking endogenous dhfr-activity, preferentially CHO-cells (DUKX-B11, DG-44) it will enable these to grow in media lacking nucleosides. An example of such a medium is Ham's F12 without hypoxanthine, thymidin, and glycine. These dhfr-genes can be introduced together with the coagulation factor cDNA transcriptional units into CHO-cells of the above type, either linked on the same vector or on different vectors, thus creating dhfr-positive cell lines producing recombinant protein.
If the above cell lines are grown in the presence of the cytotoxic dhfr-inhibitor methotrexate, new cell lines resistant to methotrexate will emerge. These cell lines may produce recombinant protein at an increased rate due to the amplified number of linked dhfr and the desired protein's transcriptional units. When propagating these cell lines in increasing concentrations of methotrexate (1-10000 nM), new cell lines can be obtained which produce the desired protein at very high rate.
The above cell lines producing the desired protein can be grown on a large scale, either in suspension culture or on various solid supports. Examples of these supports are micro carriers based on dextran or collagen matrices, or solid supports in the form of hollow fibres or various ceramic materials. When grown in cell suspension culture or on micro carriers the culture of the above cell lines can be performed either as a bath culture or as a perfusion culture with continuous production of conditioned medium over extended periods of time. Thus, according to the present invention, the above cell lines are well suited for the development of an industrial process for the production of the desired recombinant proteins
The recombinant protein, which accumulates in the medium of secreting cells of the above types, can be concentrated and purified by a variety of biochemical and chromatographic methods, including methods utilizing differences in size, charge, hydrophobicity, solubility, specific affinity, etc. between the desired protein and other substances in the cell cultivation medium.
An example of such purification is the adsorption of the recombinant protein to a monoclonal antibody which is immobilised on a solid support. After desorption, the protein can be further purified by a variety of chromatographic techniques based on the above properties.
It is preferred to purify the modified vitamin K-dependent polypeptide of the present invention to >80% purity, more preferably >95% purity, and particularly preferred is a pharmaceutically pure state that is greater than 99.9% pure with respect to contaminating macromolecules, particularly other proteins and nucleic acids, and free of infectious and pyrogenic agents. Preferably, an isolated or purified modified vitamin K-dependent polypeptide of the invention is substantially free of other polypeptides.
The recombinant proteins described in this invention can be formulated into pharmaceutical preparations for therapeutic use. The purified proteins may be dissolved in conventional physiologically compatible aqueous buffer solutions to which there may be added, optionally, pharmaceutical excipients to provide pharmaceutical preparations.
The various products of the invention are useful as medicaments. Accordingly, the invention relates to a pharmaceutical composition comprising a modified vitamin K-dependent polypeptide as described herein, a polynucleotide of the invention, or a plasmid or vector of the invention.
The modified DNA's of this invention may also be integrated into a transfer vector for use in the human gene therapy.
Another aspect of the invention is the use of a modified vitamin K-dependent polypeptide as described herein, of a polynucleotide of the invention, of a plasmid or vector of the invention, or of a host cell of the invention for the manufacture of a medicament for the treatment or prevention of a blood coagulation disorder. Blood coagulation disorders include but are not limited to hemophilia A. Preferably, the treatment comprises human gene therapy.
The invention also concerns a method of treating an individual suffering from a blood coagulation disorder such as hemophilia A. The method comprises administering to said individual an efficient amount of the modified vitamin K-dependent polypeptide as described herein. In another embodiment, the method comprises administering to the individual an efficient amount of the polynucleotide of the invention or of a plasmid or vector of the invention. Alternatively, the method may comprise administering to the individual an efficient amount of the host cells of the invention described herein.



DESCRIPTION OF THE DRAWINGS
FIG. 1: Homology comparison between FVII, protein C, FIX and FX of human origin and of other species. FIG. 1 discloses SEQ ID NOS 54-69, respectively, in order of appearance.
FIG. 2: Pharmacokinetics of FVII variants with inserted activation peptides from long lived vitamin-K dependent polypeptides



EXAMPLES
The present invention will be further described more in detail in the following examples thereof. This description of specific embodiments of the invention will be made in conjunction with the appended figures.
Example 1
Insertion of the Factor IX Activation Peptide Sequence into the Factor VII Coding Sequence
In this example the majority of the FIX activation peptide is inserted into the respective location in the FVII cDNA while preserving the FVII activation site. First, FVII cDNA, inserted into cloning vector pIRESpuro3 (Becton Dickinson; plasmid designated pFVII-538 wt) was prepared for insertion of foreign activation peptide sequences by introduction of a restriction site, NheI, between amino acids Ala146 and Ser147 (numbering refers to SEQ ID NO:3). Site directed mutagenesis was performed with a commercially available mutagenesis kit (e.g. Stratagene QuickChange SiteDirected Mutagenesis Kit) according to the manufacturer's instructions. Primers used for mutagenesis are listed below; mutagenic bases are indicated in bold letters.









forward primer







(SEQ ID NO: 21)









5′CCTATTCTAGAAAAAAGAAATGCTAGCAAACCCCAAGGCCG3′


 



reverse primer







(SEQ ID NO: 22)









5′CGGCCTTGGGGTTTGCTAGCATTTCTTTTTTCTAGAATAGG3′






The resulting plasmid was designated pFVII-NheI186.
Second, amino acids 165 to 194 of the FIX activation peptide (numbering refers to SEQ ID NO:9) were amplified on a FIX cDNA construct by polymerase chain reaction using the following primers.









forward primer







(SEQ ID NO: 23)









5′GTGGCTAGCGCTGAGACTGTTTTTCCTG3′


 



reverse primer







(SEQ ID NO: 24)









5′CACGCTAGCTTGGGTGCTTTGAGTGATG3′






Both primers added a NheI restriction site (underlined). The amplification product was digested with NheI and cloned into the NheI digested pFVII-NheI186 described above.
After verification of the correct orientation by DNA sequencing two rounds of mutagenesis were performed to backmutate the NheI sites into the natural FVII/FIX sequences. The mutagenic primers are indicated below:
Primers to Backmutate the NheI Site at the 5′-End of the FIX Insert:







forward primer


(SEQ ID NO: 25)


5′CTAGAAAAAAGAAATGCTCGTGCTGAGACTGTTTTTCCTGATGTGG3′


 


reverse primer


(SEQ ID NO: 26)


5′CCACATCAGGAAAAACAGTCTCAGCACGAGCATTTCTTTTTTCTAG3′






Primers to Backmutate the NheI Site at the 3′-End of the FIX Insert:







forward primer


(SEQ ID NO: 27)


5′CATCACTCAAAGCACCCAATCAAGCAAACCCCAAGGCCGAATTG3′


 


reverse primer


(SEQ ID NO: 28)


5′CAATTCGGCCTTGGGGTTTGCTTGATTGGGTGCTTTGAGTGATG3′






The resulting expression plasmid was designated pFVII-552. The resulting mature FVII/FIX chimeric protein sequence (SEQ ID NO:29) is given below, the inserted FIX activation peptide sequence being underlined.









1
ANAFLEELRP GSLERECKEE QCSFEEAREI FKDAERTKLF WISYSDGDQC 



 


51
ASSPCQNGGS CKDQLQSYIC FCLPAFEGRN CETHKDDQLI CVNENGGCEQ


 


101
YCSDHTGTKR SCRCHEGYSL LADGVSCTPT VEYPCGKIPI LEKRNARAET


 


151
VFPDVDYVNS TEAETILDNI TQSTQSSKPQ GRIVGGKVCP KGECPWQVLL


 


201
LVNGAQLCGG TLINTIWVVS AAHCFDKIKN WRNLIAVLGE HDLSEHDGDE


 


251
QSRRVAQVII PSTYVPGTTN HDIALLRLHQ PVVLTDHVVP LCLPERTFSE


 


301
RTLAFVRFSL VSGWGQLLDR GATALELMVL NVPRLMTQDC LQQSRKVGDS


 


351
PNITEYMFCA GYSDGSKDSC KGDSGGPHAT HYRGTWYLTG IVSWGQGCAT


 


401
VGHFGVYTRV SQYIEWLQKL MRSEPRPGVL LRAPFP 436 






Depending on which cDNA sequences are being used for cloning, the chimeric protein may also contain polymorphisms of FVII and FIX like the FIX activation peptide RAEAVFPDVDYVNSTEAETILDNITQSTQS (SEQ ID NO:30) polymorphism.
Based on plasmid pFVII-552 another expression plasmid was constructed with different transition sequences between the FVII cDNA and the FIX activation peptide sequences. For that two rounds of mutagenesis were applied to pFVII-552 as described above. The first round deleted amino acids 145 to 147 of SEQ ID NO:29 and used the following primers:









forward primer



(SEQ ID NO: 42)



5′CTATTCTAGAAAAAAGAGCTGAGACTGTTTTTCCTGATG3′



 



reverse primer



(SEQ ID NO: 43)



5′CATCAGGAAAAACAGTCTCAGCTCTTTTTTCTAGAATAG3′






The second round of mutagenesis inserted 4 amino acids between amino acids 176 and 177 of SEQ ID NO:29 and used the following primers:









forward primer







(SEQ ID NO: 44)









5′CAAAGCACCCAATCAAAGCGGAATGCTAGCAAACCCCAAGG3′


 



reverse primer







(SEQ ID NO: 45)









5′CCTTGGGGTTTGCTAGCATTCCGCTTTGATTGGGTGCTTTG3′






The resulting plasmid was called pFVII-681. The resulting mature FVII/FIX chimeric protein sequence (SEQ ID NO:46) is given below, the inserted FIX activation peptide sequence being underlined.









1
ANAFLEELRP GSLERECKEE QCSFEEAREI FKDAERTKLF WISYSDGDQC



 


51
ASSPCQNGGS CKDQLQSYIC FCLPAFEGRN CETHKDDQLI CVNENGGCEQ


 


101
YCSDHTGTKR SCRCHEGYSL LADGVSCTPT VEYPCGKIPI LEKRAETVFP


 


151
DVDYVNSTEA ETILDNITQS TQSKRNASKP QGRIVGGKVC PKGECPWQVL


 


201
LLVNGAQLCG GTLINTIWVV SAAHCFDKIK NWRNLIAVLG EHDLSEHDGD


 


251
EQSRRVAQVI IPSTYVPGTT NHDIALLRLH QPVVLTDHVV PLCLPERTFS


 


301
ERTLAFVRFS LVSGWGQLLD RGATALELMV LNVPRLMTQD CLQQSRKVGD


 


351
SPNITEYMFC AGYSDGSKDS CKGDSGGPHA THYRGTWYLT GIVSWGQGCA


 


401
TVGHFGVYTR VSQYIEWLQK LMRSEPRPGV LLRAPFP  437






Example 2
Insertion of the Factor X Activation Peptide Sequence into the Factor VII Coding Sequence
The FX activation peptide was amplified by PCR on a cloned FX cDNA using the following primers, attaching an NheI restriction site (underlined).









forward primer







(SEQ ID NO: 47)









5′GTGGCTAGCCAGGCCACCAGCAGCAG3′


 



reverse primer







(SEQ ID NO: 48)









5′GCGGCTAGCATTCCGCTTCTCAGGCTGCGTCTGGTTG3′






The PCR fragment containing the FX activation peptide was then digested with NheI and ligated into NheI digested plasmid pFVII-NheI186 (example 1). In 2 subsequent rounds of site-directed mutagenesis as described supra the transition between the FVII cDNA sequence and the FX activation peptide was corrected.
First Round of Mutagenesis was Performed with the Following Oligonucleotides:







forward primer


(SEQ ID NO: 49)


5′CCTATTCTAGAAAAAAGAAATGCCCAGGCCACCAGCAGCAGCGG3′


 


reverse primer


(SEQ ID NO: 50)


5′CCGCTGCTGCTGGTGGCCTGGGCATTTCTTTTTTCTAGAATAGG3′






Second Round of Mutagenesis was Performed with the Following Oligonucleotides:







forward primer


(SEQ ID NO: 51)


5′CCTATTCTAGAAAAAAGCGTGGCCCAGGCCACCAGCAGCAGCGGGG3′


 


reverse primer


(SEQ ID NO: 52)


5′CCCCGCTGCTGCTGGTGGCCTGGGCCACGCTTTTTTCTAGAATAGG3′






The resulting plasmid was called pFVII-611. The resulting mature FVII/FX chimeric protein sequence (SEQ ID NO:53) is given below, the inserted FX activation peptide sequence being underlined.









1
ANAFLEELRP GSLERECKEE QCSFEEAREI FKDAERTKLF WISYSDGDQC



 


51
ASSPCQNGGS CKDQLQSYIC FCLPAFEGRN CETHKDDQLI CVNENGGCEQ


 


101
YCSDHTGTKR SCRCHEGYSL LADGVSCTPT VEYPCGKIPI LEKSVAQATS


 


151
SSGEAPDSIT WKPYDAADLD PTENPFDLLD FNQTQPEKRN ASKPQGRIVG


 


201
GKVCPKGECP WQVLLLVNGA QLCGGTLINT IWVVSAAHCF DKIKNWRNLI


 


251
AVLGEHDLSE HDGDEQSRRV AQVIIPSTYV PGTTNHDIAL LRLHQPVVLT


 


301
DHVVPLCLPE RTFSERTLAF VRFSLVSGWG QLLDRGATAL ELMVLNVPRL


 


351
MTQDCLQQSR KVGDSPNITE YMFCAGYSDG SKDSCKGDSG GPHATHYRGT


 


401
WYLTGIVSWG QGCATVGHFG VYTRVSQYIE WLQKLMRSEP RPGVLLRAPF


 


451
P  452






Example 3
Insertion of the Factor X Activation Peptide Sequence into the Factor IX Coding Sequence
In this example the FX activation peptide is inserted into the respective location in the FIX cDNA preserving the FIX activation site.
First, FIX cDNA in cloning vector pIRESpuro3 (Becton Dickinson) was prepared for insertion of foreign activation peptide sequences by introduction of two restriction sites: an XbaI site between amino acids Ser161 and Lys162 and a PinAI site between Thr192 and Gln193 (numbering refers to SEQ ID NO:9). Site directed mutagenesis was performed with a commercially available mutagenesis kit (e.g. Stratagene QuickChange SiteDirected Mutagenesis Kit) according to the manufacturer's instructions. Primers used for mutagenesis are listed below; mutagenic bases are indicated in bold letters.
Mutagenic Primers for Introduction of XbaI Site:







forward primer


(SEQ ID NO: 31)


5′GAAGAGTTTCTGTTTCACAAACTTCTAGACTCACCCGTGCTGAGAC3′


 


reverse primer


(SEQ ID NO: 32)


5′GTCTCAGCACGGGTGAGTCTAGAAGTTTGTGAAACAGAAACTCTTC3′






Mutagenic Primers for Introduction of PinAI Site:







forward primer


(SEQ ID NO: 33)


5′GGATAACATCACTCAAAGCACCGGTTCATTTAATGACTTCACTCGGGT


 


TG3′


 


reverse primer


(SEQ ID NO: 34)


5′CAACCCGAGTGAAGTCATTAAATGAACCGGTGCTTTGAGTGATGTTAT


 


CC3′






Second, amino acids 159 to 213 of the FX activation peptide (numbering refers to SEQ ID NO:12) were amplified by polymerase chain reaction using following primers adding a 5′-terminal XbaI and a 3′-terminal PinAI site (underlined).








forward primer



5′GTGTCTAGAAGGAAGAGGTCAGTGGCCC3′
(SEQ ID NO: 35)


 


reverse primer



5′CACACCGGTGAGGTTGTTGTCGCCC3′
(SEQ ID NO: 36)






The amplification product was digested with XbaI and PinAI and cloned into the XbaI and PinAI digested FIX cDNA modified as described above. Two rounds of mutagenesis were subsequently performed to backmutate the XbaI and PinAI sites into the natural FIX and FX sequences. The mutagenic primers are indicated below:
Primers to Backmutate the XbaI Site at the 5′-End of the FX Insert:









forward primer







(SEQ ID NO: 37)









5′GAGTTTCTGTTTCACAAACTTCTCGCAGGAAGAGGTCAGTGG3′


 



reverse primer







(SEQ ID NO: 38)









5′CCACTGACCTCTTCCTGCGAGAAGTTTGTGAAACAGAAACTC3′






Primers to Backmutate the PinAI Site at the 3′-End of the FX Insert:







forward primer


(SEQ ID NO: 39)


5′GCGACAACAACCTCACCCAATCATTTAATGACTTCACTCGGGTTG3′


 


reverse primer


(SEQ ID NO: 40)


5′CAACCCGAGTGAAGTCATTAAATGATTGGGTGAGGTTGTTGTCGC3′






The resulting mature FIX/FX chimeric protein sequence (SEQ ID NO:41) is given below, the inserted FX activation peptide sequence being underlined.









1
YNSGKLEEFV QGNLERECME EKCSFEEARE VFENTERTTE FWKQYVDGDQ



 


51
CESNPCLNGG SCKDDINSYE CWCPFGFEGK NCELDVTCNI KNGRCEQFCK


 


101
NSADNKVVCS CTEGYRLAEN QKSCEPAVPF PCGRVSVSQT SRRKRSVAQA


 


151
TSSSGEAPDS ITWKPYDAAD LDPTENPFDL LDFNQTQPER GDNNLTQSFN


 


201
DFTRVVGGED AKPGQFPWQV VLNGKVDAFC GGSIVNEKWI VTAAHCVETG


 


251
VKITVVAGEH NIEETEHTEQ KRNVIRIIPH HNYNAAINKY NHDIALLELD


 


301
EPLVLNSYVT PICIADKEYT NIFLKFGSGY VSGWGRVFHK GRSALVLQYL


 


351
RVPLVDRATC LRSTKFTIYN NMFCAGFHEG GRDSCQGDSG GPHVTEVEGT


 


401
SFLTGIISWG EECAMKGKYG IYTKVSRYVN WIKEKTKLT  439






Example 4
Transfection and Expression of Modified FVII and FIX Proteins
Expression plasmids were grown up in E. coli TOP10 (Invitrogen) and purified using standard protocols (Qiagen). HEK 293 cells (Invitrogen) were transfected using the Lipofectamine 2000 reagent (Invitrogen) and grown up in serum-free medium (Invitrogen 293 Express) in the presence of 50 ng/ml Vitamin K3 and 4 μg/ml Puromycin. Transfected cell populations were spread through T-flasks into roller bottles from which supernatant was harvested for purification.
Example 5
Purification of Modified FVII Proteins
FVII proteins were purified as described in patent EP 0770625. Briefly, soluble tissue factor was covalently coupled to sepharose beads by bromine cyanide. FVII containing cell culture supernatant was loaded in a 10 mM calcium buffer. Unbound proteins were washed away with the same buffer. Elution of bound FVII proteins was performed with a 100 mM sodium citrate buffer.
Example 6
Determination of FVII Activity and Antigen
FVII antigen was determined by an ELISA whose performance is known to those skilled in the art. Briefly, microplates were incubated with 120 μL per well of the capture antibody (sheep anti human FVII IgG, Cedarlane CL20030AP, diluted 1:1000 in Buffer A [Sigma C3041]) overnight at ambient temperature. After washing plates three times with buffer B (Sigma P3563), each well was incubated with 200 μL buffer C (Sigma P3688) for one hour at ambient temperature. After another three wash steps with buffer B, serial dilutions of the test sample in buffer B as well as serial dilutions of standard human plasma (Dade Behring; 50-0.5 mU/mL) in buffer B (volumes per well: 100 μL) were incubated for two hours at ambient temperature. After three wash steps with buffer B, 100 μL of a 1:5000 dilution in buffer B of the detection antibody (sheep anti human FVII IgG, Cedarlane CL20030K, peroxidase labelled) were added to each well and incubated for another two hours at ambient temperature. After three wash steps with buffer B, 100 μL of substrate solution (TMB, Dade Behring, OUVF) were added per well and incubated for 30 minutes at ambient temperature in the dark. Addition of 100 μL undiluted stop solution (Dade Behring, OSFA) prepared the samples for reading in a suitable microplate reader at 450 nm wavelength. Concentrations of test samples were then calculated using the standard curve with standard human plasma as reference.
Example 7
Pharmacokinetics of Modified FVII Proteins
Wild-type and modified FVII proteins were administered intravenously to narcotised CD/Lewis rats (6 rats per substance) with a dose of 100 μg/kg body weight. Blood samples were drawn from 3 rats at 5, 30, 60, 120 and 480 minutes and from the other 3 rats at 15, 45, 90 and 240 minutes after application of the test substances from the arteria carotis. FVII antigen content was subsequently quantified by an ELISA assay specific for human factor VII (see above). The mean FVII antigen concentrations for each group are shown in FIG. 2. Table 5 summarizes the calculated half-lifes for the alpha and beta phases of elimination, whereby alpha phase was defined from 5 to 30 min and beta phase from 30 min to the last time point with concentrations above the limit of detection of the antigen assay. Calculations were done according to the formula T1/2=ln 2/k, whereby k is the slope of the regression line.


















half life






extension



half-life
half-life
beta phase
(beta phase)



alpha phase
beta phase
calculated
compared to FVII


construct
[min]
[min]
from
wild-type



















pFVII-538wt
10
29
30-90 min 



pFVII-552
20
128
30-480 min
4.4 fold


pFVII-611
19
102
30-240 min
3.5 fold


pFVII-681
22
178
30-480 min
6.1 fold









The data clearly show that replacement of the native putative FVII activation peptide by an activation peptide from longer-lived prothrombin factors significantly extended the proteins' in vivo half-lifes compared to the wild-type FVII protein.

## Claims

1. A modified human Factor VII, human Factor Vila, or human Factor IX polypeptide having a lengthened activation domain amino acid sequence as compared to a corresponding unmodified, native human Factor VII, human Factor Vila, or human Factor IX, the modified polypeptide comprising
(a) a human Factor VII, human Factor Vila, or human Factor IX polypeptide wherein all or a portion of an activation domain from human Factor IX, human Factor X, or human Prothrombin is inserted into the native activation domain of the human Factor VII, human Factor Vila, or human Factor IX polypeptide, such that the modified polypeptide has a lengthened activation domain amino acid sequence; or
(b) a human Factor VII, human Factor Vila, or human Factor IX polypeptide wherein all or a portion of the native activation domain is removed and all or a portion of an activation domain from human Factor IX, human Factor X, or human Prothrombin is inserted, such that the modified polypeptide has a lengthened activation domain amino acid sequence;
wherein the modified human Factor VII, human Factor Vila, or human Factor IX polypeptide is modified only in the activation domain and has an increased half-life as compared to the unmodified, native human Factor VII, human Factor Vila, or human Factor IX.

2. The modified polypeptide of claim 1, wherein the modified polypeptide does not contain an N-glycosylation site within its activation peptide.

3. The modified polypeptide of claim 1, wherein the half-life of the modified polypeptide is increased by at least 50%, as compared to the corresponding unmodified polypeptide.

4. The modified polypeptide of claim 1, wherein the modified polypeptide has increased stability in an in vitro functional assay, as compared to the corresponding unmodified polypeptide.

5. The modified polypeptide of claim 1, wherein the modified polypeptide has coagulant activity, as measured in an in vitro coagulation assay.

6. The modified polypeptide of claim 1, wherein: (i) the activation peptide of the modified polypeptide is capable of being cleaved off during activation, and/or (ii) the zymogen form of the modified polypeptide has an increased half-life as compared to the zymogen form of the corresponding unmodified polypeptide.

7. The modified polypeptide of claim 1, wherein: (i) the activation peptide of the modified polypeptide is not capable of being cleaved off during activation, and/or (ii) the activated form of the modified polypeptide has an increased half-life as compared to the activated form of the corresponding unmodified polypeptide.

8. The modified polypeptide of claim 1, comprising an activation domain from human Factor IX, human Factor X, or human Prothrombin in which 1 to 7 amino acids have been added, deleted, and/or substituted.

9. The modified polypeptide of claim 1, comprising an activation domain from human Factor IX, human Factor X, or human Prothrombin in which 1 to 5 amino acids have been added, deleted, and/or substituted.

10. The modified polypeptide of claim 1, comprising an activation domain from human Factor IX, human Factor X, or human Prothrombin in which 1 to 3 amino acids have been added, deleted, and/or substituted.

11. The modified polypeptide of claim 1, wherein the activation domain of the modified polypeptide comprises side chains with glutamic acid residues that can be carboxylated.

12. The modified polypeptide of claim 1, wherein at least 2 contiguous amino acids have been deleted from the native activation peptide.

13. The modified polypeptide of claim 1, wherein at least 4 contiguous amino acids have been deleted from the native activation peptide.

14. The modified polypeptide of claim 1, wherein at least 6 contiguous amino acids have been deleted from the native activation peptide.

15. The modified polypeptide of claim 1, wherein at least 8 contiguous amino acids have been deleted from the native activation peptide.

16. The modified polypeptide of claim 1, wherein at least 8 contiguous amino acids from the activation peptide of human Factor IX, human Factor X, or human Prothrombin have been inserted into the native activation peptide.

17. The modified polypeptide of claim 1, wherein at least 12 contiguous amino acids from the activation peptide of human Factor IX, human Factor X, or human Prothrombin have been inserted into the native activation peptide.

18. The modified polypeptide of claim 1, wherein at least 15 contiguous amino acids from the activation peptide of human Factor IX, human Factor X, or human Prothrombin have been inserted into the native activation peptide.

19. A pharmaceutical composition comprising the modified polypeptide of claim 1.