Anticoagulant Analogues of the Tissue Factor Extrinsic Pathway Inhibitor (EPI) With Reduced Affinity for Heparin

The present invention relates to new protein analogues of the Extrinsic Pathway Inhibitor (EPI; also known as Tissue Factor Pathway Inhibitor, TFPI, or Lipoprotein-Associated Pathway Inhibitor, LACI). The invention also features a method of making the analogues and therapeutic preparations containing them.

Blood coagulation is a complex process involving many activating and inactivating coagulation factors. Anticoagulant proteins are known to be important for regulation of the coagulation process (see B. Lammle and J. Griffin (Clinics in Haematology 14 (1985), 281-342) and anticoagulants are thus important in the treatment of a variety of diseases, e.g. thrombosis, myocardial infarction, disseminated intravascular coagulation etc.

Thus heparin is used clinically to increase the activity of antithrombin III and heparin cofactor II. Antithrombin III is used for the inhibition of factor Xa and thrombin. Hirudin is used for the inhibition of thrombin and protein C may be used for the inhibition of factor V and factor VIII.

Anticoagulant proteins may also be used in the treatment of cancer. Thus, antistatin has been shown to have anti-metastatic properties (J. H. Han et al., Gene 75 (1989), 47-57). Also heparin and warfarin have been shown to possess antimetastatic properties (G. J. Gasic et al., Int. Rev. Exp. Pathol. 29 (1985), 173-209).

Coagulation can be initiated through the extrinsic pathway by the exposure of tissue factor (TF) to the circulating blood (Y. Nemerson, Blood 71 (1988), 1-8). Tissue factor is a protein cofactor for factor VII/VIIa and binding of tissue factor enhances the enzymatic activity of factor VIIa (FVIIa) towards its substrates factor IX and factor X. Placenta anticoagulant protein is able to inhibit tissue factor activity, probably by interfering with TF/FVIIa-phospholipid interaction (S. Kondo et al., Thromb. Res. 48 (1987), 449-459).

Recently a new anticoagulant protein, the extrinsic pathway inhibitor (EPI) has been isolated (Broze et al., Proc. Natl. Acad. Sci. 84 (1987), 1886-1890).

On a molar basis EPI has been shown to be a potent inhibitor of TF/FVIIa induced coagulation (R. A. Gramzinski et al., Blood 73 (1989), 983-989). EPI binds and inhibits factor Xa (FXa) and the complex between EPI and FXa inhibits TF/FVIIa (Rapaport, Blood 73 (1989), 359-365). EPI is especially interesting as an anticoagulant/antimetastatic agent as many tumor cells express TF activity (T. Sakai et al., J. Biol. Chem. 264 (1989), 9980-9988) and because EPI shows anti-Xa activity like antistatin.

EPI has been recovered by Broze et al. (supra) from HepG2 hepatoma cells (Broze EP A 300988) and the gene for the protein has been cloned (Broze EP A 318451). A schematic diagram over the secondary structure of EPI is shown in FIG. 1 and the amino acid sequence of EPI is shown in FIG. 2 where the N-terminal amino acid Asp is given the number 1. The protein consists of 276 amino acid residues and has in addition to three inhibitor domains of the Kunitz type three potential glycosylation sites at position Asn117, Asn167 and Asn229. The molecular weight shows that some of these sites are glycosylated. Furthermore, it has been shown that the second Kunitz domain binds FXa while the first Kunitz domain binds FVIIa/TF (Girard et al., Nature 338 (1989), 518-520). EPI has also been isolated from HeLa cells (PCT/DK90/00016) and it was shown that HeLa EPI binds heparin.

Heparin binding is an important factor for the pharmacokinetics of substances for injection. It has been shown that platelet factor 4 (M. Prosdomi et al., Thromb. Res. 39 (1985), 541-547) and aprotinin with one Kunitz domain (Arzneimittelforschung, 33 (4) 479-94, 1983) has a short half life probably due to the heparin binding properties. Lowering of the heparin binding capacity of an anticoagulant would therefore seem to be advantageous. Furthermore, it might be advantageous to use a smaller molecule than EPI for the medical treatment.

It has according to the present invention surprisingly been found that certain EPI analogues retain the EPI activity as well as anti Xa activity although parts of the molecule has been deleted. Furthermore, these analogues show a much lower affinity for heparin than full length EPI, making them more useful as therapeutic agents than the native molecule. The EPI analogues will furthermore have a longer half life as compared with native EPI which will further reduce the amount of active ingredients for the medical treatment.

In its first aspect the present invention is related to novel EPI analogues wherein one or more of the amino acid residues of native EPI have been deleted.

In its second aspect the present invention is related to a new group of EPI analogues having EPI activity but with no or low heparin binding capacity under physiological conditions (pH, ionic strength).

In the present context the term "low heparin binding capacity" is intended to mean a binding capacity of about 50%, more preferably of about 25% and most prefereably less than about 10% of that of native EPI at physiological pH and ionic strength.

The preferred group of the novel EPI analogues can be characterized as being devoid of the heparin binding domain cf native EPI or having a non-functional heparin binding domain by having deleted one or more of the amino acid residues in said domain resulting in loss or a substantial lowering of the heparin binding capacity. The same effect may also be obtained by substituting one or more of the amino acid residues in the heparin binding domain with another amino acid residue.

To retain the EPI activity the analogues according to the present invention should at least contain the N-terminal sequence including the first and second Kunitz domain. Thus, the EPI analogues according to the present invention should at least contain the amino acid sequence from amino acid number 25 to amino acid number 148 of native EPI (see FIG. 1 and 2).

It has been shown by the inventors hereof that the heparin binding capacity is lost when the sequence from amino acid residue number 162 to amino acid residue number 275 is deleted from the EPI molecule. It is therefore concluded that the heparin binding domain is situated in this part of the EPI molecule. It is assumed that the heparin binding domain comprises at least a region from Arg246 to Lys265 near the C-terminal end of the EPI molecule being rich in positively charged amino acid residues.

Preferred EPI analogues according to the present invention are such in which one or more amino acid residues have been deleted in the native EPI molecule from amino acid residue Glu148 to the C-terminal Met276.

More specifically, one or more amino acid residues in the sequence from Arg246 to Lys275 have been deleted.

Examples of EPI analogues according to the present invention are:

In addition to the described deletions in the EPI molecule, certain amino acid residues of native EPI may also be replaced by another naturally occurring amino acid residue. The EPI analogues may also advantageously contain a Ser residue as the N-terminal residue. This is necessary if a signal sequence is used requiring an N-terminal Ser in the mature protein as a recognition site for cleavage. Thus, the N-terminal in the EPI molecule may be replaced by a Ser or an additional Ser may be inserted adjacent to the original N-terminal residue. Also the potential glycosylation sites at Asn167 and Asn238 may be substituted by another amino acid residue to avoid glycosylation.

It has not previously been shown that glycosylation sites are dispensable for EPI activity. Neither has it been shown that large fragments of the EPI protein are dispensable for EPI activity, i.e. for FXa dependent inhibition of TF/FVIIa. It has previously been shown that a single amino acid in EPI can be replaced by another amino acid residue (Arg199-->Leu199), (Girard et al., Nature 338 (1989), 518-520) without affecting the activity. However, such a change does not significantly change the structure of the protein. In contrast hereto the deletions according to the present invention give rise to new molecules with other properties than the native molecule, as illustrated by the changed affinity for heparin.

The present EPI-analogues may be produced by well-known recombinant DNA technology.

The gene for the native EPI has been cloned and sequenced (Wun et al., J. Biol. Chem. 263 (1988), 6001-6004). DNA-sequences encoding the desired EPI-analogue may be contructed by altering EPI cDNA by site-directed mutagenesis using synthetic oligonucleotides encoding the desired amino acid sequence for homologous recombination in accordance with well-known procedures.

The DNA sequence encoding the EPI analogue of the invention may also be prepared synthetically by established standard methods, e.g. the phosphoamidite method described by S. L. Beaucage and M. H. Caruthers, Tetrahedron Letters 22, 1981, pp. 1859-1869, or the method described by Matthes et al., EMBO Journal 3, 1984, pp. 801-805. According to the phosphoamidite method, oligonucleotides are synthesized, e.g. in an automatic DNA synthesizer, purified, annealed, ligated and cloned in suitable vectors.

In a further aspect, the present invention relates to a recombinant expression vector which comprises a DNA sequence encoding the EPI analogue of the invention. The expression vector may be any vector which may conveniently be subjected to recombinant DNA procedures, and the choice of vector will often depend on the host cell into which it is to be introduced. Thus, the vector may be an autonomously replicating vector, i.e. a vector which exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g. a plasmid. Alternatively, the vector may be one which, when introduced into a host cell, is integrated into the host cell genome and replicated together with the chromosome(s) into which it has been integrated.

In the vector, the DNA sequence encoding the EPI analogue of the invention should be operably connected to a suitable promoter sequence. The promoter may be any DNA sequence which shows transcriptional activity in the host cell of choice and may be derived from genes encoding proteins either homologous or heterologous to the host cell. Examples of suitable promoters for directing the transcription of the DNA encoding the EPI analogue of the invention in mammalian cells are the SV 40 promoter (Subramani et al., Mol.Cell Biol. 1, 1981, pp. 854-864), the MT-1 (metallothionein gene) promoter (Palmiter et al., Science 222, 1983, pp. 809-814), the adenovirus 2 major late promoter or the CMV (cytomegalovirus IE1) promoter (Henninghausen et al., EMBO J. 5 (1986), 1367-71) Suitable promoters for use in yeast host cells include promoters from yeast glycolytic genes (Hitzeman et al., J.Biol.Chem. 255, 1980, pp. 12073-12080; Alber and Kawasaki, J.Mol.Appl.Gen. 1, 1982, pp. 419-434) or alcohol dehydrogenase genes (Young et al., in Genetic Engineering of Microorganisms for Chemicals (Hollaender et al., eds.), Plenum Press, New York, 1982), or the PTI1 (U.S. Pat. No. 4,599,311) or ADH2-4c (Russell et al., Nature 304, 1983, pp. 652-654) promoters. Suitable promoters for use in filamentous fungus host cells are, for instance, the ADH3 promoter (McKnight et al., The EMBO J. 4, 1985, pp. 2093-2099) or the tipA promoter.

To ensure secretion a suitable signal sequence is inserted at the 5' of the DNA sequence encoding the EPI analogue. A suitable signal sequence is the t-PA signal sequence (Friezner et al., J.Biol.Chem. 261 (1986), 6972-85).

The DNA sequence encoding the EPI analogue of the invention should also be operably connected to a suitable terminator, such as the human growth hormone terminator (Palmiter et al., op. cit.) or (for fungal hosts) the TPII (Alber and Kawasaki, op. cit.) or ADH3 (McKnight et al., op. cit.) promoters. The vector may further comprise elements such as polyadenylation signals (e.g. from SV 40 or the adenovirus 5 Elb region), transcriptional enhancer sequences (e.g. the SV 40 enhancer) and translational enhancer sequences (e.g. the ones encoding adenovirus VA RNAs).

The recombinant expression vector of the invention may further comprise a DNA sequence enabling the vector to replicate in the host cell in question. An example of such a sequence (when the host cell is a mammalian cell) is the SV 40 origin of replication. The vector may also comprise a selectable marker, e.g. a gene the product of which complements a defect in the host cell, such as the gene coding for dihydrofolate reductase (DHFR) or one which confers resistance to a drug, e.g. neomycin, hygromycin or methotrexate.

The procedures used to ligate the DNA sequences coding for the EPI analogue of the invention, the promoter and the terminator, respectively, and to insert them into suitable vectors containing the information necessary for replication, are well known to persons skilled in the art (cf., for instance, Sambrook et al., op. cit.).

In a further aspect, the present invention relates to a cell which contains the recombinant expression vector described above. The host cell may be any cell which is capable of producing the EPI analogue and is preferably a eukaryotic cell, in particular a mammalian cell. Examples of suitable mammalian cell lines are the COS (ATCC CRL 1650 and 1651), BHK (ATCC CRL 1632, ATCC CCL 10) or CHO (ATCC CCL 61) cell lines. Methods of transfecting mammalian cells and expressing DNA sequences introduced in the cells are described in e.g. Kaufman and Sharp, J.Mol.Biol. 159, 1982, pp. 601-621; Southern and Berg, J.Mol.Appl.Genet. 1, 1982, pp. 327-341; Loyter et al., Proc.Natl.Acad.Sci. USA 79, 1982, pp. 422-426; Wigler et al., Cell 14, 1978, p. 725; Corsaro and Pearson, Somatic Cell Genetics 7, 1981, p. 603, Graham and van der Eb, Virology 52, 1973, p. 456; and Neuman et al., EMBO J. 1, 1982, pp. 841- 845.

Alternatively, fungal cells (including yeast cells) may be used as host cells of the invention. Examples of suitable yeast cells include cells of Saccharomyces spp. or Schizosaccharomyces spp., in particular strains of Saccharomyces cerevisiae. Examples of other fungal cells are cells of filamentous fungi, e.g. Aspergillus spp. or Neurospora spp., in particular strains of Aspergillus oryzae or Aspergillus niger. The use of Aspergillus spp. for the expression of proteins is described in, e.g., EP 272,277.

In a still further aspect the present invention relates to a process for producing an EPI analogue according to the invention, which comprises culturing a cell as described above in a suitable nutrient medium under conditions which are conductive to the expression of the EPI analogue, and recovering the polypeptide from the culture. The medium used to culture the cells may be any conventional medium suitable for growing mammalian cells, such as a serum-containing or serum-free medium containing appropriate supplements. Suitable media are available from commercial suppliers or may be prepared according to published recipes (e.g. in catalogues of the American Type Culture Collection).

The EPI analogue will preferably be secreted to the growth medium and may be recovered from the medium by conventional procedures including separating the host cells from the medium by centrifugation or filtration, precipitating the proteinaceous components of the supernatant or filtrate by means of a salt, e.g. ammonium sulphate, followed by purification by a variety of chromatographic procedures, e.g. ion exchange chromatography, affinity chromatography, or the like.

The novel EPI analogues may be used for the treatment of patients having coagulation disorders or cancer.

Accordingly the invention is also related to a pharmaceutical preparation for the treatment of patients having coagulation disorders or cancer containing an EPI analogue in a suitable amount together with suitable adjuvants and additions.

The pharmaceutical preparations may be in a buffered aqueous solution with appropriate stabilizers and preservatives. The solution may be heat treated and may be contained in ampoules or in carpoules for injection pens. Alternatively the stabilized solution may be freeze dried and contained in ampoules or in two chamber injection systems with freeze dried substance in one chamber and solvent in the other chamber.

The present invention is further described with reference to the drawings in which

FIG. 1 shows the amino acid sequence and the two dimensional structure of EPI,

FIG. 2 shows the amino acid sequence of native EPI (SEQ ID NO: 1),

FIG. 3 shows plasmid pJR77 containing the t-PA signal, the human cytomegalovirus IEI gene promoter and the human growth hormone gene polyadenylation signal,

FIG. 4 shows pCMVEPIhGH containing the EPI gene,

FIG. 5 shows plasmid pEPlb1 containing a DNA sequence encoding Ser-(Thr88- Thr161)-EPI,

FIG. 6 shows plasmid PEPlab containing a DNA sequence encoding Ser-(Glu15- Thr161)-EPI,

FIG. 7 shows the DNA and amin acid sequence for Ser-(Thr88-Thr161)-EPI preceded by the t-PA signal sequence (SEQ ID NOs: 2 and 3),

FIGS. 8A and 8B together show the DNA, and amino acid sequence for the Ser-(Glu15 - Thr161)-EPI preceded by the t-PA signal sequence (SEQ ID NOs: 4 and 5),

FIG. 9 shows plasmid PEPIab2 containing a DNA sequence encoding (Asp1-Thr161)-EPI, and

FIGS. 10A and 10B together show the DNA and amino acid sequence for (Asp1-Thr161)-EPI preceded by the EPI signal (SEQ ID NOs: 6 and 7).

The invention is further described in the following examples which are not in any ways intended to limit the scope or spirit of the invention as claimed.

Assay for EPI activity: EPI was measured in a chromogenic microplate assay, modified after the method of Sandset et al., (Thromb. Res. 47 (1989), 389-400). Heat treated plasma pool was used as a standard. This standard is set to contain 1 U/ml of EPI activity. Standards and samples were diluted in buffer A (0.05M tris/0.1M NaCl/0.1M Na-citrate/0.02% NaN.sub.3 /pH 8.0) containing 2 .mu.g/ml polybrene and 0.2% bovine serum albumin. FVIIa/TF/FX/CaCl.sub.2 combination reagent was prepared in buffer A and contained 1.6 ng/ml FVIIa (Novo-Nordisk a/s), human tissue factor diluted 60 fold (Hjort, Scand. J. Clin. Lab. Invest. 9 (1957), 50 ng/ml FX (Sigma) and 18 mM CaCl.sub.2. The assay was performed in microplate strips at 37.degree. C. 50 .mu.l of samples and standards were pipetted into the strips and 100 .mu.l combination reagent was added to each well. After 10 minutes incubation, 25 .mu.l of FX (3.2 .mu.g/ml) was added to each well and after another 10 minutes 25 l of chromogenic substrate for FXa (S2222) was added 10 minutes after the addition of substrate. The reaction was stopped by addition of 50 .mu.l 1.0M citric acid pH 3.0. The microplate was read at 405 nm.

Assay for anti Xa activity: HeLa EPI purified on heparin sepharose (PCTDK90/00016) was used as a standard. This standard was assigned an amount of Xa inhibition units corresponding to the amount of EPI units measured in the EPI assay. Samples and standards were diluted in 50 mM tris/0.2% bovine serum albumin pH 7.3. 100 .mu.l of diluted samples and standard were incubated 30 minutes at 37.degree. C. with 100 .mu.l FXa (Stago, 14 ng/ml). 25 .mu.l of S2222 (2 mg/ml) was added after another 2 hours at 37.degree. C. The assay was stopped and read like the EPI assay.

Synthetic oligonucleotides were synthesized by the phosphoramidite method using an Applied Biosystem DNA synthesizer.

M13 sequencing primers and gamma-[.sup.32p ]-ATP (5000 Ci/mmol, 10 mCi/ml) for labelling of primers were obtained from Amersham.

Restriction endonucleases and T4 DNA-ligase were obtained from New England Biolabs. Modified T7 DNA-polymerase (Sequenase) was obtained from United States Biochemicals. pBS+ (Stratagene) was used as cloning vector for synthetic DNA fragments.

A mammalian expression vector denoted pJR77 (FIG. 3) containing the human cytomegalovirus IE1 gene promoter and the human growth hormone gene polyadenylation signal was used for expression of various EPI related proteins in COS-7 cells.

XL-1 Blue (Stratagene) a derivative of E. coli K12 as used as bacterial recipient for plasmid transformations and as host for propagation and preparation of plasmid DNA.

Green monkey kidney cell-line COS-7 (ATCC #CRL 1651) was grown in Dulbecco's modified eagle medium (DMEM) (Gibco 041-1965)+50 .mu.g/ml gentamycin+110 .mu.g/ml pyruvate+10% fetal calf serum (FCS) or DMEM+50 .mu.g/ml gentamycin+110 .mu.g/ml pyruvate +1% ITS.sup.+ (insulin, transferrin, serum albumin).

Restriction endonucleases and other enzymes were used in accordance with the manufacturers recommendations. Standard recombinant DNA-techniques were carried out as described (Maniatis et al., Molecular cloning. Cold Spring Harbor Laboratory, 1982).

DNA sequences were determined by the dideoxy chain termination method (Sanger et al., Proc. Natl. Acad. Sci. 74 (1977), 5463-67) using double stranded plasmid DNA as template and .sup.32 P-labelled primers and Sequenase.

Plasmid DNA was introduced into COS-7 cells by calcium phosphate coprecipitation (Graham & van der Eb, Virology 52 (1973), 456-457).

7.times.10.sup..ident. cells were seeded in 20 cm.sup.2 dishes in 5 ml DMEM+FCS. The following day each dish was added 20 .mu.g plasmid DNA in 0.5 precipitate and 50 .mu.l 10 mM chloroquine diphosphate. Cells were incubated overnight with precipitate. The following day fresh medium DMEM+ITS.sup.+ was added. After two days of incubation media were harvested and assayed for EPI-activity and anti Xa-activity.

The EPI cDNA sequence is described by Wun et al. (J. Biol. Chem. 263 (1988), 6001-6004). Based on the known sequence synthetic DNA-sequences encoding EPI and EPI analogues were constructed by silent mutations introducing restriction endonuclease recognition sites at suitable locations.

Expression cassettes encoding EPI fragments using the tPA signal sequence (FIGS. 7 and 8) and an expression cassette encoding the entire EPI protein were assembled by sequentially insertion into the cloning vector pBS+ of annealed complementary synthetic oligonucleotides. Following assembly of DNA fragment sequences were verified by DNA sequencing as described.

Finally expression casettes were transferred to expression vector pJR77 giving rise to the following expression plasmids:

pEPIb1 encoding the tPA signal followed by EPI analogue Ser-(Thr88-Thr161)-EPI (SEQ ID NO: 2). pEPIab encoding the tPA signal followed by EPI analogue Ser-(Glu15-Thr161)-EPI (SEQ ID NO: 4). pCMVEPIhGH encoding the entire EPI protein.

COS-7 cells were transfected as indicated in Table 1. After 2 days of incubation with DMEM+ITS. media were harvested. Table 1 shows assay results for EPI-activity and anti-Xa activity.

The results in table 1 show that the EPI-fragment Ser-(Thr88Thr161)-EPI (SEQ ID No. 3) containing only the second Kunitz domain has no activity whereas the EPI-fragment Ser-(Glu15-Thr161)-EPI (SEQ ID NO: 5) containing the first and second Kunitz domain has retained the EPI activity.

COS transfections with EPI plasmids were performed as described in example 1 and media were harvested after 48 hours. 5 columns were packed, each with 300 ul of heparin sepharose. The columns were equilibrated with 20 mM tris/10% glycerol, pH 7.5. (buffer B). 1.3 ml culture medium was applied to each column. Then the columns were washed with 1.5 ml buffer B and each column was eluted with steps of 1.5 ml buffer B with increasing amounts of NaCl. For comparison is given data from another experiment where EPI from HeLa and HepG2 cells were fractionated on heparin-sepharose. In this experiment other NaCl concentrations were used for elution. Table 2 shows that Ser-(Glu15-Thr161)-EPI (SEQ ID NO: 5) not bind to heparin at physiological pH and ionic strength.

Construction of expression plasmids, transformation and expression in COS-7 cell was performed using materials and methods as described in Example 1.

Sequences between SalI and BamHI of expression plasmid pEPIab (FIG. 6) encoding the t-PA signal and Ser-(Glu15-Thr161)-EPI (SEQ ID NO: 5) was replaced by a synthetic DNA-sequence encoding the authentic EPI signal and (Asp1-Thr161)-EPI (SEQ ID NO: 6).

The resulting plasmid pEPIab2 is shown in FIG. 9 and the expression cassette of pEPIab2 is shown in FIG. 10.

Culture medium from pEPIab2 transfected COS cells were applied to Heparin-Sepharose as described in Example 2. 3.8 ml culture medium containing 31.2 U/ml of EPI was applied to a 0.5 ml heparin column. Flow through contained 77% and B wash contained 16% of the applied EPI activity. No EPI was detected in eluates with 0.25, 0.75 and 1.5M NaCl respectively.

(Asp1-Thr161)-EPI (SEQ ID NO: 7) has one potential N-linked glycosylation site (Asn117) and the importance of this glycosylation for activity was investigated.

(Asp1-Thr161)-EPI (SEQ ID NO: 7) was purified from COS culture medium by affinity chromatography of FXa-Sepharose. In SDS-PAGE the purified protein appeared as a glycosylated band near 27 kDa and an unglycosylated band near 22 kDa (shown by treatment with endogylcosidase F). The glycosylated and unglycosylated forms were separated in unreduced SDS-PAGE and were extracted from the gel. Both forms were active in the EPI assay and showed the same specific activity as judged from the staining intensities in the SDS-gel. Glycosylation at Asn117 is therefore apparently not essential for EPI activity and active (Asp1-Thr161)-EPI (SEQ ID NO: 7) can thus be obtained in efficient expression systems where mammalian N-linked glycosylation is not obtained, e.g. in procaryots, or as unsecreted protein in yeast.