FVIIa antagonists

Abstract

This invention provides novel compounds which prevent or block a FVIIa mediated or associated process or event such as the catalytic conversion of FX to FXa , FVII to FVIIa or FIX to FIXa. In particular aspects, the compounds of the invention bind Factor VIIa (FVIIa ), its zymogen Factor VII (FVII). The invention also provides pharmaceutical compositions comprising the novel compounds as well as their use in diagnostic, therapeutic, and prophylactic methods.

Description

FIELD OF THE INVENTION

[0001] This invention relates to novel compounds which prevent or block a Factor VIIa (FVIIa ) mediated or associated process or event such as the catalytic conversion of Factor X (FX) to Factor Xa (FXa ), Factor VII (FVII) to FVIIa or Factor IX (FIX) to Factor IXa (FIXa ). In particular aspects, the compounds of the invention bind FVIIa or its zymogen FVII. The invention also relates to pharmaceutical compositions comprising the novel compounds as well as their use in research, diagnostic, therapeutic, and prophylactic methods.

DESCRIPTION OF RELATED DISCLOSURES

[0002] The tissue factor-Factor VIIa (TF-FVIIa ) complex constitutes the primary initiator of the extrinsic pathway of blood coagulation (Carson, S. D., and Brozna, J. P., Blood Coag. Fibrinol. 4:281-292 (1993); Davie, E. W., et al., Biochemistry 30:10363-10370 (1991); Rapaport, S. I., and Rao, L. V. M., Arterioscler. Thromb. 12:1111-1121 (1992); Davie, E. W., Thromb. Haemost. 74: 1-6 (1995); Rapaport, S. I. and Rao, L. V. M., Thromb. Haemost. 74: 7-17 (1995); Mann, K. G., Thromb. Haemost. 82: 165-174 (1999); Edgington, T. S. et al., Thromb. Haemost. 78: 401-408 (1997)). The complex initiates the extrinsic pathway by activation of FX to FXa , FIX to FIXa , and additional FVII to FVIIa. The action of TF-FVIIa leads ultimately to the conversion of prothrombin to thrombin, which carries out many biological functions (Badimon, L., et al., Trends Cardiovasc. Med. 1:261-267 (1991)). Among the functions of thrombin is the conversion of fibrinogen to fibrin, which polymerizes to form a clot. The TF-FVIIa complex also participates as a secondary factor in extending the physiological effects of the contact activation system.

[0003] The involvement of these plasma protease systems has been suggested to play a significant role in a variety of clinical manifestations including arterial and venous thrombosis, septic shock, adult respiratory distress syndrome (ARDS), disseminated intravascular coagulation (DIC) and various other disease states (Haskel, E. J., et al., Circulation 84:821-827 (1991)); Holst, J., et al., Haemostasis 23(suppl. 1): 112-117 (1993); Creasey, A. A., et al., J. Clin. Invest. 91:2850-2860 (1993); see also, Colman, R. W., N. Engl. J. Med. 320:1207-1209 (1989); Bone, R. C., Arch. Intern. Med. 152:1381-1389 (1992) Presta, L. G. et al., Thromb. Haemost. 85: 379-389 (2001)).

[0004] Antibodies reactive with the protease domain of FVII have been shown to inhibit TF-FVIIa proteolytic function (Dickinson et al., J. Mol. Biol. 277:959-971 (1998)). Peptides corresponding to the EGF2 domain of FVII are potent inhibitors of TF-FVIIa mediated activation of FX (Husbyn et al., J. Peptide Res. 50:475-482 (1997); Presta supra). Several peptides corresponding to various regions of FVII (for example, amino acid sequence residues 372-337 and 103-112 of hFVII) have been proposed as therapeutic anticoagulants based upon their ability to inhibit TF-FVIIa mediated coagulation (International Publication No. WO 90/03390; International Publication No. W095/00541). Active site modified FVII variants capable of binding tissue factor (TF) have been proposed as pharmaceutical compositions for the prevention of TF/FVIIa mediated coagulation (International Publication No. WO 91/11514). U.S. Pat. Nos. 5,759,954, 5,863,893, 5,880,256 and 5,834,244 describe variant Kunitz-type serine protease inhibitors that inhibit TF-FVIIa activity and have been shown to prolong tissue factor initiated prothrombin time (PT). This is consistant with the ability of these TF-FVIIa active site inhibitors to prevent FX activation through inhibition of the TF-FVIIa complex.

[0005] The architecture of the active site of the serine proteases involved in the coagulation cascade is very similar. Although nonselective with respect to small chromogenic substrates, the proteases exhibit a strong specificity for their natural macromolecular substrates. Exosites on these enzymes play an important role in substrate recognition and specific cleavage. Blocking such interactions could result in the specific inhibition of a single protease in the coagulation pathway.

[0006] Two classes of peptide exosite inhibitors of human FVIIa have been identified (International Publication Number WO 01/10892; International Publication Number WO 01/01749; Dennis, M. S., et al. (2000) Nature,404: 465-470; Dennis, M. S., et al. (2001) Biochemistry, 40: 9513-9521; Roberge, M., et al. (2001) Biochemistry, 40: 9522-9531). The two peptides classes are typified by peptides designated E-76 (TF76; SEQ ID NO: 8, International Publication Number WO 01/01749) and A-183 (TF183; SEQ ID NO: 23, International Publication Number WO 01/10892), which bind to two distinct exosites on the protease domain of FVIIa and inhibit the activation of FX to FXa by TF-FVIIa with IC50 values in the nanomolar range. Similar potency was observed for the inhibition of the amidolytic activity of TF-FVIIa using the peptides. Although these peptides are potent inhibitors of TF-FVIIa activity, they do not completely inhibit the enzymatic activity of FVIIa. At saturating concentrations of peptide, E-76 and A-183 show a maximal inhibition of FX activation of 90% and 78%, respectively, whereas maximal extent of inhibition of the amidolytic activity was 50% and 32%, respectively.

SUMMARY OF THE INVENTION

[0007] The present invention provides compounds and compositions which inhibit a FVII/FVIIa mediated or associated process such as the catalytic conversion of FVII to FVIIa , FIX to FIXa , or FX to FXa and thereby block initial events of the extrinsic pathway of blood coagulation. In addition, the compositions of the present invention /are capable of neutralizing the thrombotic effects of endogenous TF by binding to FVII or FVIIa and preventing the TF-FVIIa mediated activation of FX. In preferred embodiments the compositions provide for the complete inhibition of FVIIa and the TF-FVIIa complex providing, in preferred embodiments, for low dose pharmaceutical formulations. The compositions of the present invention are therefore useful in therapeutic and prophylactic methods for inhibiting TF-FVIIa mediated or associated processes.

[0008] The invention provides, in certain embodiments, for substrates for FVIIa. The substrates for FVIIa in combination with peptide exosite inhibitors of FVIIa described in International Publication Number WO 01/10892 comprise selective and complete inhibitors of FVIIa. The invention provides compounds which, by virtue of binding FVII or FVIIa , inhibit a FVII or FVIIa mediated coagulation event. Such compounds preferably bind FVII or FVIIa with a Kd less than about 100 μM, preferably less than about 100 nM, and preferably do not substantially inhibit the activity of other proteases of the coagulation cascade. In preferred embodiments, the compositions are peptides. Specific examples of such compounds include linear or cyclic peptides and combinations thereof, preferably between about 10 and 100 amino acid residues in length, optionally modified at the N-terminus or C-terminus or both, as well as their salts and derivatives, functional analogues thereof and extended peptide chains carrying amino acids or polypeptides at the termini of the sequences for use in the inhibition of FVIIa mediated activation of FX.

[0009] The invention further provides a method of inhibiting the activation of FX to FXa comprising contacting FVII with TF under conditions which allow formation of a TF-FVIIa complex in the presence of a peptide compound of the invention and further contacting the TF-FVIIa complex with FX. According to this aspect of the invention, the contacting steps may occur in vivo or in vitro.

[0010] The invention includes compositions, including pharmaceutical compositions, comprising compounds such as peptides for the treatment of a FVII/FVIIa mediated disorder as well as kits and articles of manufacture. Kits and articles of manufacture preferably include:

[0011] (a) a container;

[0012] (b) a label on or associated with said container; and

[0013] (c) a composition comprising a compound of the present invention contained within said container; wherein the composition is effective for treating a FVII/FVIIa mediated disorder. Preferably, the label on said container indicates that the composition can be used for treating a FVII/FVIIa mediated disorder and the compound in said composition comprises a compound which binds FVII/FVIIa and prevents FVII/FVIIa mediated activation of FX. The kits optionally include accessory components such as a second container comprising a pharmaceutically-acceptable buffer and instructions for using the composition to treat a disorder.

[0014] Also disclosed are methods useful in the treatment of coagulopathic disorders, especially those characterized by the involvement of FVII/FVIIa or the TF-FVIIa complex. Therefore, the invention provides a method of treating a FVII/FVIIa or TF-FVIIa mediated disease or disorder in a host in need thereof comprising administering to the host a therapeutically effective amount of a compound of the invention. The methods are useful in preventing, blocking or inhibiting a FVII/FVIIa or TF-FVIIa associated event. In preferred embodiments, the methods of the present invention are employed to reduce or prevent the severity of or the degree of tissue injury associated with blood coagulation.

[0015] The present invention further provides various dosage forms of the compounds of the present invention, including but not limited to, those suitable for parenteral, oral, rectal and pulmonary administration of a compound. In preferred aspects of the present invention a therapeutic dosage form is provided suitable for inhalation and the invention provides for the therapeutic treatment of diseases or disorders involving a FVII/FVIIa mediated or associated process or event, such as the activation of FX, via pulmonary administration of a compound of the invention. More particularly, the invention is directed to pulmonary administration of the compounds of the invention, especially the peptide compounds, by inhalation. Thus, the present invention provides an aerosol formulation comprising an amount of a compound of the invention, more particularly a peptide compound of the invention, effective to block or prevent a FVII/FVIIa mediated or associated process or event and a dispersant. In one embodiment, the compound of the invention, particularly the peptide compound of the invention, can be provided in a liquid aerosol formulation. Alternatively, the compound can be provided as a dry powder aerosol formulation. Therefore, according to the present invention, formulations are provided which provide an effective noninvasive alternative to other parenteral routes of administration of the compounds of the present invention for the treatment of FVII/FVIIa or TF-FVIIa mediated or associated events.

BRIEF DESCRIPTION OF THE DRAWINGS

[0016] FIG. 1. Model of the protease domain of FVIIa. The protease domain of FVIIa is depicted as a model complexed with peptide A-183 at the A-exosite and D-Phe-L-Phe-L-Arg-chloromethylketone covalently bound to the active site (Roberge, M., et al., (2001) Biochemistry, 40: 9522-9531). The amino and carboxy terminal residues of A-183 are indicated.

[0017] FIG. 2. Model of FVIIa protease domain with A-183 extension peptide. The protease domain of FVIIa is depicted as a model complexed with peptide A-183 having a C-terminal extension. The model shows peptide A-183 linked to the sequence SGGGSGASGFR (SEQ ID NO: 1), where the C-terminal arginine is in the P1 pocket at the active site. The phenylalanine was chosen in analogy to the irreversible active site inhibitor (D-Phe-L-Phe-Arg-CMK) used in the crystal structure of the TF-FVIIa complex (Banner, D. W., et al., (1996) Nature, 380: 41-46).

[0018] FIG. 3. Amidolytic activity of immoblilized FVIIa. Wells were coated with four different concentrations (1, 5, 10, or 20 μg/ml) of FVIIa. Amidolytic activity was tested with Chromozym t-PA at pH 6.0 and pH 8.5 in the presence and absence of soluble TF (sTF).

[0019] FIG. 4. Phage selection strategy. The substrate phage libraries in binding buffer (pH 6.0) were incubated with immobilized FVIIa for 1 h. Unbound phage were removed by repetitive washing with binding buffer. Bound phage were immediately incubated for 5 min with cleavage buffer (pH 8.5 and sTF). The supernatants were incubated with immobilized tetra-His-monoclonal Antibody to pull out any uncleaved phage. These supernatants were then subjected to propagation and further rounds of selection.

[0020] FIG. 5. Library design. Four original libraries designated A, B, C, and D were designed to determine the preferred length and the sequence of the extension which goes into the active site. X refers to any amino acid. . . . P1, P1′, P2′ . . . refer to the putative . . . P1, P1′, P2′ . . . residues for serine protease substrates. Cleavage occurs between the P1 and P1′ residues. The fixed sequences for libraries A, B, and C are derived from FX, one of the natural protein substrates.

[0021] FIG. 6. Consensus Library. A consensus library resulted out of libraries A and D. Residues were either fixed, fully randomized (X) or partially randomized as indicated. The consensus library was sorted to determine the preferred extension of A-183X.

[0022] FIG. 7. Inhibition of TF-FVIIa catalyzed activation of FX. The inhibition of FX activation by Z-A-183X and Z-A-183 is shown. Z-A-183X exhibited complete inhibition (ca. 99%) of FX activation and an improvement in potency (IC50=12 pM) relative to Z-A-183, which inhibited the activity to 80% extent with an IC50 of 660 pM.

[0023] FIG. 8. Inhibition of FX activation with different extensions. The inhibition of FX activation by Z-A-183-[GGS]4, Z-A-183-[GGS]3GGR, Z-A-183X-EW, Z-A-183X-EWA is shown. A random extension showed a greater extent of inhibition of FX activation (88%) compared to Z-A-183 (FIG. 7) or A-183 as observed previously (Dennis, M. S., et al., (2001) Biochemistry, 40: 9513-9521), however the inhibition was still not complete. The C-terminal arginine is not required to obtain complete inhibition.

[0024] FIG. 9. Prolongation of TF-dependent clotting times. The fold prolongation of the clotting time upon initiation by TF and Ca2+ in the PT assay is shown for Z-A-183, Z-A-183X, Z-A-183-[GGS]4, and A-183. Compared to A-183 (1.6-fold) and the two control peptides, Z-A-183X showed a significant improvement (7.7-fold) in the fold prolongation of clotting.

[0025] FIG. 10. Amino acid sequences of selected peptides suitable for use in conjuction with the C terminal extension of the present invention (SEQ ID NOS: 2-39).

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

Definitions

[0026] Terms used in the claims and specification are defined as set forth below unless otherwise specified.

[0027] Abbreviations used throughout the description include: FIXa for Factor IXa and FIX for zymogen Factor IX; FXa for Factor Xa and FX for zymogen Factor X; FVII for zymogen factor VII; FVIIa for Factor VIIa ; TF for tissue factor; TF-FVIIa for the tissue factor-Factor VIIa complex; FVII/FVIIa for FVII and/or FVIIa ; sTF or TF1-129 for soluble tissue factor composed of the extracellular domain amino acid residues 1-219; TF1-243 for membrane tissue factor composed of the extracellular domain and transmembrane amino acid residues 1-243 (Paborsky et al., J. Biol. Chem. 266:21911-21916 (1991)); PT for prothrombin time; APTT for activated partial thromboplastin time.

[0028] The term “peptidell is used herein to refer to constrained (that is, having some element of structure as, for example, the presence of amino acids which initiate a β turn or β pleated sheet, or for example, cyclized by the presence of disulfide bonded Cys residues) or unconstrained (e.g., linear) amino acid sequences of less than about 50 amino acid residues, and preferably less than about 40 amino acids residues, including multimers, such as dimers thereof or there between.

[0029] The term “amino acid” within the scope of the present invention is used in its broadest sense and is meant to include the naturally occurring L α-amino acids or residues. The commonly used one- and three-letter abbreviations for naturally occurring amino acids are used herein (Lehninger, A. L., Biochemistry, 2d ed., pp. 71-92, (Worth Publishers, New York, N.Y., 1975). The term includes D-amino acids as well as chemically modified amino acids such as amino acid analogs, naturally occurring amino acids that are not usually incorporated into proteins such as norleucine, and chemically synthesized compounds having properties known in the art to be characteristic of an amino acid. For example, analogs or mimetics of phenylalanine or proline, which allow the same conformational restriction of the peptide compounds as natural Phe or Pro are included within the definition of amino acid. Such analogs and mimetics are referred to herein as “functional equivalents” of an amino acid. Other examples of amino acids are listed by Roberts and Vellaccio, The Peptides: Analysis, Synthesis, Biology, Gross and Meiehofer, Eds., Vol. 5, p. 341 (Academic Press, Inc., New York, N.Y., 1983), which is incorporated herein by reference.

[0030] The term “conservative” amino acid substitution as used within this invention is meant to refer to amino acid substitutions which substitute functionally equivalent amino acids. Conservative amino acid changes result in silent changes in the amino acid sequence of the resulting peptide. For example, one or more amino acids of a similar polarity act as functional equivalents and result in a silent alteration within the amino acid sequence of the peptide. The largest sets of conservative amino acid substitutions include:

[0031] (1) hydrophobic: His, Trp, Tyr, Phe, Met, Leu, Ile, Val, Ala;

[0032] (2) neutral hydrophilic: Cys, Ser, Thr;

[0033] (3) polar: Ser, Thr, Asn, Gln;

[0034] (4) acidic/negatively charged: Asp, Glu;

[0035] (5) charged: Asp, Glu, Arg, Lys, His;

[0036] (6) positively charged: Arg, Lys, His;

[0037] (7) basic: His, Lys, Arg;

[0038] (8) residues that influence chain orientation: Gly, Pro; and

[0039] (9) aromatic: Trp, Tyr, Phe, His.

[0040] In addition, structurally similar amino acids can substitute conservatively for some of the specific amino acids. Groups of structurally similar amino acids include: (Ile, Leu, and Val); (Phe and Tyr); (Lys and Arg); (Gln and Asn); (Asp and Glu); and (Gly and Ala). In this regard, it is understood that amino acids are substituted on the basis of side chain bulk, charge and/or hydrophobicity.

[0041] Amino acid residues can be further classified as cyclic or noncyclic, aromatic or non aromatic with respect to their side chain groups these designations being commonplace to the skilled artisan.

	Original	Exemplary Conservative	Preferred Conservative
	Residue	Substitution	Substitution
	Ala	Val, Leu, Ile	Val
	Arg	Lys, Gln, Asn	Lys
	Asn	Gln, His, Lys, Arg	Gln
	Asp	Glu	Glu
	Cys	Ser	Ser
	Gln	Asn	Asn
	Glu	Asp	Asp
	Gly	Pro	Pro
	His	Asn, Gln, Lys, Arg	Arg
	Ile	Leu, Val, Met, Ala	Leu
		Phe
	Leu	Ile, Val	Ile
		Met, Ala, Phe
	Lys	Arg, Gln, Asn	Arg
	Met	Leu, Phe, Ile	Leu
	Phe	Leu, Val, Ile, Ala	Leu
	Pro	Gly	Gly
	Ser	Thr	Thr
	Thr	Ser	Ser
	Trp	Tyr	Tyr
	Tyr	Trp, Phe, Thr, Ser	Phe
	Val	Ile, Leu, Met, Phe	Leu
	Ala

[0042] Peptides synthesized by the standard solid-phase synthesis techniques described here, for example, are not limited to amino acids encoded by genes for substitutions involving the amino acids. Commonly encountered amino acids which are not encoded by the genetic code include, for example, those described in International Publication No. WO 90/01940 and described in Table 1 below, as well as, for example, 2-amino adipic acid (Aad) for Glu and Asp; 2-aminopimelic acid (Apm) for Glu and Asp; 2-aminobutyric (Abu) acid for Met, Leu, and other aliphatic amino acids; 2-aminoheptanoic acid (Ahe) for Met, Leu and other aliphatic amino acids; 2-aminoisobutyric acid (Aib) for Gly; cyclohexylalanine (Cha) for Val, and Leu and Ile; homoarginine (Har) for Arg and Lys; 2,3-diaminopropionic acid (Dpr) for Lys, Arg and His; N-ethylglycine (EtGly) for Gly, Pro, and Ala; N-ethylglycine (EtGly) for Gly, Pro, and Ala; N-ethylasparigine (EtAsn) for Asn, and Gln; Hydroxyllysine (Hyl) for Lys; allohydroxyllysine (AHyl) for Lys; 3-(and 4)hydoxyproline (3Hyp, 4Hyp) for Pro, Ser, and Thr; allo-isoleucine (AIle) for Ile, Leu, and Val; p-amidinophenylalanine for Ala; N-methylglycine (MeGly, sarcosine) for Gly, Pro, and Ala; N-methylisoleucine (MeIle) for Ile; Norvaline (Nva) for Met and other aliphatic amino acids; Norleucine (Nle) for Met and other aliphatic amino acids; Ornithine (Orn or Or) for Lys, Arg and His; Citrulline (Cit) and methionine sulfoxide (MSO) for Thr, Asn and Gln; -methylphenylalanine (MePhe), trimethylphenylalanine, halo (F, Cl, Br, and I)phenylalanine, trifluoroylphenylalanine, for Phe.

TABLE 1
Abbreviations used in the specification
Compound	Abbreviation
Acetyl	Ac
Alanine	Ala	A
3-(2-Thiazolyl)-L-alanine	Tza
Arginine	Arg	R
Asparagine	Asn	N
Aspartic acid	Asp	D
t-Butyloxycarbonyl	Boc
Benzotriazol-1-yloxy-tris-(dimethylamino)-	Bop
phosphonium-hexafluorophosphate
β-Alanine	βAla
β-Valine	βVal
β-(2-Pyridyl)-alanine	Pal (2)
β-(3-Pyridyl)-alanine	Pal (3)
β-(4-Pyridyl)-alanine	Pal (4)
β-(3-N-Methylpyridinium)-alanine	PalMe (3)
t-Butyl	tBu, But
t-Butyloxycarbonyl	Boc
Caffeic acid	Caff
Cysteine	Cys	C
Cyclohexylalanine	Cha
Cyclohexylglycine	Chg
3,5-Dinitrotyrosine	Tyr (3,5-No2)
3,5-Diiodotyrosine	Tyr (3,5-I)
3,5-Dibromotyrosine	Tyr (3,5-Br)
9-Fluorenylmethyloxy-carbonyl	Fmoc
Glutamine	Gln	Q
Glutamic acid	Glu	E
γ-Carboxyglutamic acid	Gla
Glycine	Gly	G
Histidine	His	H
Homoarginine	hArg
3-Hydroxyproline	Hyp
Isoleucine	Ile	I
Leucine	Leu	L
tert-Leucine	Tle
Lysine	Lys	K
Mercapto-β,β-cyclopentamethylene-propionic	Mpp
acid
Mercaptoacetic acid	Mpa
Mercaptopropionic acid	Mpr
Methionine	Met	M
β-Naphthylalanine	Na
Nicotinic acid	Nic
Nipecotic acid	Npa
N-methyl nicotinic acid	NicMe
Norarginine	nArg
Norleucine	Nle nL
Norvaline	Nva
Ornithine	Orn or Or
Ornithine-derived dimethylamidinium	Orn (Nδ—C3H7N)
Phenylalanine	Phe	F
p-Guanidinophenylalanine	Phe (Gua)
p-Aminophenylalanine	Phe (NH2)
p- Chlorophenylalanine	Phe (Cl)
p-Flurophenylalanine	Phe (F)
p-Nitrophenylalanine	Phe (NO2)
p-Hydroxyphenylglycine	Pgl (OH)
p-Toluenesulfonyl	Tos
m-Amidinophenylalanine	mAph
p-Amidinophenylalanine	pAph
Phenylglycine	Pgl
Phenylmalonic acid	Pma
Proline	Pro	P
4-Quinolinecarboxy	4-Qca
Sarcosine	Sar
Serine	Ser	S
Succinyl	Suc
Threonine	Thr	T
Tryptophan	Trp	W
Tyrosine	Tyr	Y
3-iodotyrosine	Tyr (3-I)
O-Methyl tyrosine	Tyr (Me)
Valine	Val	V
* Amino acids of D configuration are denoted by D-prefix using three-letter code (eg., D-Ala, D-Cys, D-Asp, D-Trp).

[0043] A useful method for identification of certain residues or regions of the compound for amino acid substitution other than those described herein is called alanine scanning mutagenesis as described by Cunningham and Wells, Science 244:1081-1085 (1989). Here a residue or group of target residues are identified (e.g., charged residues such as Arg, Asp, His, Lys, and Glu) and replaced by a neutral or negatively charged amino acid to affect the interaction of the amino acids with the surrounding aqueous environment in or outside the cell. Those regions demonstrating functional sensitivity to the substitution are then refined by introducing further or other variations at or for the sites of substitution. Thus while the site for introducing an amino acid sequence variation is predetermined the nature of the mutation per se need not be predetermined. For example, to optimize the performance of a mutation at a given site, Ala scanning or random mutagenesis may be conducted at the target codon or region and the expressed compound screened for the optimal combination of desired activity.

[0044] Phage display of protein or peptide libraries offers another methodology for the selection of compounds with improved affinity, altered specificity, or improved stability (Smith, G. P., Curr. Opin. Biotechnol. 2:668-673 (1991); Lowman, Ann. Rev. Biophys. Biomol. Struct. 26:401-404 (1997)). High affinity proteins, displayed in a monovalent fashion as fusions with the M13 gene III coat protein (Clackson, T., et al., Trends Biotechnol. 12:173-183 (1994)), can be identified by cloning and sequencing the corresponding DNA packaged in the phagemid particles after a number of rounds of binding selection.

[0045] Preferred amino acid sequences within the context of the present invention are non-naturally occurring amino acid sequences. By non-naturally occurring is meant that the amino acid sequence is not found in nature. These include peptides, peptide analogs and mimetics containing naturally as well as non-naturally occurring amino acids. Especially preferred are sequences as described above consisting of naturally occurring amino acids.

[0046] A TF-FVIIa mediated or associated process or event, or equivalently, an activity associated with plasma FVII/FVIIa , according to the present invention is any event which requires the presence of FVIIa. The general mechanism of blood clot formation is reviewed by Ganong, in Review of Medical Physiology, 13th ed., pp.411-414 (Lange, Los Altos, Calif., 1987). Coagulation requires the confluence of two processes, the production of thrombin which induces platelet aggregation and the formation of fibrin which renders the platelet plug stable. The process comprises several stages each requiring the presence of discrete proenzymes and procofactors. The process ends in fibrin crosslinking and thrombus formation. Fibrinogen is converted to fibrin by the action of thrombin. Thrombin, in turn, is formed by the proteolytic cleavage of prothrombin. This proteolysis is effected by FXa which binds to the surface of activated platelets and in the presence of FVa and calcium, cleaves prothrombin. TF-FVIIa is required for the proteolytic activation of FX by the extrinsic pathway of coagulation. Therefore, a process mediated by or associated with TF-FVIIa , or an activity associated with FVII/FVIIa includes any step in the coagulation cascade from the formation of the TF-FVIIa complex to the formation of a fibrin platelet clot and which initially requires the presence FVII/FVIIa. For example, the TF-FVIIa complex initiates the extrinsic pathway by activation of FX to FXa , FIX to FIXa , and additional FVII to FVIIa.

[0047] TF-FVIIa mediated or associated process, or FVII/FVIIa mediated or associated activity, can be conveniently measured employing standard assays, such as those described in Roy, S., J. Biol. Chem. 266:4665-4668 (1991), O'Brien, D., et al., J. Clin. Invest. 82:206-212 (1988), Lee et al., Biochemistry 36:5607-5611 (1997), Kelly et al., J. Biol. Chem. 272:17467-17472 (1997), for the conversion of chromogenic substrates or Factor X to Factor Xa in the presence of Factor VII and other necessary reagents.

[0048] A TF-FVIIa related disease or disorder is meant to include chronic thromboembolic diseases or disorders associated with fibrin formation including vascular disorders such as deep venous thrombosis, arterial thrombosis, stroke, tumor metastasis, thrombolysis, arteriosclerosis and restenosis following angioplasty, acute and chronic indications such as inflammation, septic shock, septicemia, hypotension, adult respiratory distress syndrome (ARDS), disseminated intravascular coagulapathy (DIC) and other diseases. The TF-FVIIa related disorder is not limited to in vivo coagulopathic disorders such as those named above but includes inappropriate or undesirable coagulation related to circulation of blood through stents or artificial valves or related to extracorporeal circulation including blood removed in-line from a patient in such processes as dialysis procedures, blood filtration, or blood bypass during surgery.

[0049] As used herein, the term “pulmonary administration” refers to administration of a formulation of the invention through the lungs by inhalation. As used herein, the term “inhalation” refers to intake of air to the alveoli. In specific examples, intake can occur by self-administration of a formulation of the invention while inhaling, or by administration via a respirator, e.g., to a patient on a respirator. The term “inhalation” used with respect to a formulation of the invention is synonymous with “pulmonary administration.”

[0050] As used herein, the term “parenteral” refers to introduction of a compound of the invention into the body by other than the intestines, and in particular, intravenous (i.v.), intraarterial (i.a.), intraperitoneal (i.p.), intramuscular (i.m.), intraventricular, and subcutaneous (s.c.) routes.

[0051] As used herein, the term “aerosol” refers to suspension in the air. In particular, aerosol refers to the particlization of a formulation of the invention and its suspension in the air. According to the present invention, an aerosol formulation is a formulation comprising a compound of the present invention that is suitable for aerosolization, i.e., particlization and suspension in the air, for inhalation or pulmonary administration.

[0052] The term “treatment” as used within the context of the present invention is meant to include therapeutic treatment as well as prophylactic, or suppressive measures for the disease or disorder. Thus, for example, the term treatment includes the administration of an agent prior to or following the onset of a disease or disorder thereby preventing or removing all signs of the disease or disorder. As another example, administration of the agent after clinical manifestation of the disease to combat the symptoms of the disease comprises “treatment, of the disease. Further, administration of the agent after onset and after clinical symptoms have developed where administration affects clinical parameters of the disease or disorder, such as the degree of tissue injury or the amount or extent of leukocyte trafficking and perhaps amelioration of the disease, comprises “treatment” of the disease.

[0053] Those “in need of treatment” include mammals, such as humans, already having the disease or disorder, including those in which the disease or disorder is to be prevented.

MODES FOR CARRYING OUT THE INVENTION

Selection of Compounds

[0054] The present invention provides for, among other things, the specific and complete inhibition of FVIIa. In particular embodiments, the invention provides a molecule which specifically binds the FVIIa active site based upon the interaction of FVIIa with a peptide ligand of FVIIa described in International Publication Number WO 01/10892. In preferred embodiment the invention provides peptide inhibitors of FVIIa which comprise a peptide ligand of International Publication No. WO 01/10892 and a C-terminal peptide extension described herein. The peptide inhibitors of the present invention preferably provide complete inhibition of FVIIa enzymatic and amidolytic activity.

[0055] In order to determine both the length and the sequence of the peptide extension of the present invention, a novel substrate phage display strategy may be employed. Substrate phage display has been successfully employed to determine preferred cleavage sequences for proteases (Matthews, D. A. and Wells, J. A. (1993) Science 260: 1113-1117; Smith, M. M. et al. (1995) J. Biol. Chem. 270:6440-6449; Harris J. L. et al. (1998) J. Biol. Chem. 273: 27364-27373; Ke S. H. et al. (1997) J. Biol. Chem. 272: 20456-20462; Kridel, S. J. et al. (2001) Anal. Biochem. 294: 176-184). According to certain aspects of the present invention, a substrate phage library is displayed between an anchor that binds to a specific target protease such as FVIIa and one of the phage coat proteins. The activation of the immobilized protease results in the release of phage displaying preferred protease substrate sequences. Phage in the supernatant are subjected to propagation and preferred substrate sequences are determined by sequencing of selected phage. The immobilization of the phage library by the protease and the selective propagation of released phage due to proteolytic cleavage, creates the basis for selection in this assay. According to the present invention preferred the preferred protease is FVIIa and preferred anchors for the selection of peptide extensions are the peptide ligands described in International Publication Number WO 01/10892.

[0056] In the context of the present invention, a peptide ligand, such as the inhibitor A-183 of International Publication Number WO 01/10892 serves as an anchor to bind FVIIa which serves as both binding target and the cleavage enzyme. A peptide ligand such as A-183 is used as the anchor to bring the substrate library in close proximity to the active site of FVIIa under conditions where the enzyme is not active. Upon activation of FVIIa by addition of its obligate cofactor TF and modification of the pH, only phage with suitable sequences for enzymatic cleavage by TF-FVIIa are released and propagated (FIG. 4).

[0057] Employing this strategy, peptide extensions may be obtained which show complete (>˜99%) inhibition of FX activation an improvement in potency (IC50=12 pM) over the peptide ligand itself and a more dramatic effect as an anticoagulant in PT clotting assays.

Peptides Ligards

[0058] According to the invention a peptide extension described herein forms a C-terminal extension of a peptide ligand of International Publication No. WO 01/10892. Preferred peptides of International Publication No. WO 01/10892 are fifteen (15) amino acid peptides having the following formula:

Xi-Cys1-Xj-Cys2-Xk

[0059] wherein Xi is absent or is a peptide of 6 amino acids; Xj is 5 amino acids and Xk is a peptide of 2 amino acids.

[0060] Preferred peptides include peptides such as those described above comprising the following sequence:

[0061] Glu3-Glu2-Trp1-Glu3-Val1-Leu1-Cys1-Trp2-Thr1-Trp3-Glu4-Thr2-Cys2-Glu5-Arg (SEQ ID NO: 16)

[0062] wherein Glu1 and Glu2 are optionally absent or any amino acid, Trp1 is Trp or an amino acid selected from the group consisting of, Phe, Tyr, Leu, Ile, Met, Val and Ala; Glu3 is Glu or any other amino acid; Val1 is Val or an amino acid selected from the group consisting of Trp, Phe, Tyr, Leu, Ile, Met and Ala; Leu, is Leu or an amino acid selected from the group consisting of Leu, Trp, Phe, Tyr, Ile Met, Val and Ala; Trp2 is amino acid selected from the group consisting of Trp, Phe, Tyr, Leu, Ile, Met, Val and Ala; Thr1 is any amino acid; Trp3 is an amino acid selected from the group consisting of Trp, Phe, Tyr, Leu, Ile, Met, Val and Ala; Glu4 is any amino acid; Thr2 is any amino acid; Glu5 is any amino acid and Arg is an amino acid selected from the group consisting of Arg, Lys, Leu, Trp, His, Met and Ile. Peptides of this variety may contain N-terminal amino acid extensions.

[0063] Preferred amino acids according to this aspect of the invention comprise the sequence Trp1-Glu1-Val-Leu-Cys1-Trp2-Thr1-Trp3-Glu2-Thr2-Cys2-Glu3-Arg (SEQ ID NO: 40) or having between 1 and 8 amino acids of SEQ ID NO: 40 substituted; or between 1 and 6 amino acids of SEQ ID NO: 40 substituted, or between 1 and 4 amino acids substituted, or between 1 or 2 amino acids of SEQ ID NO: 40 substituted. According to this aspect of the invention; Trp1 is an amino acid selected from the group consisting of Trp, Phe and Leu; Glu1 is any amino acid; Val is an amino acid selected from the group consisting of Val and Ile; Leu is an amino acid selected from the group consisting of Leu, Ile, Met, Val and Ala;Trp2 is amino acid selected from the group consisting of Trp, Phe, Tyr, Leu and Met; Thr1 is any amino acid; Trp3 is an amino acid selected from the group consisting of Trp, Phe and Tyr; Glu2 is any amino acid; Thr2 is any amino acid; Glu3 is any amino acid and Arg is an amino acid selected from the group consisting of Arg, Lys, Leu and Trp.

[0064] The foregoing peptides preferably have an IC50 for FVII/FVIIa of less than 1 μM, more preferably less than 100 nM and more preferably less than 10 nM. In addition the peptides preferably binds FVII/FVIIa and inhibits activity associated with FVIIa selected from the group consisting of activation of FVII, activation of FIX and activation of FX. Preferably the peptide competes with a peptide of the present invention for binding FVII/FVIIa and blocks activation of FX. Preferably the peptide has an IC50 for inhibiting FX activation of less than 10 μM, more preferably of less than 100 nM and more preferably less than 5 nM.

[0065] In this context reference can be made to the exemplary peptides listed in FIG. 10 (SEQ ID NOS: 2-39).

Methods of Use

[0066] The invention further provides a method of inhibiting FVIIa activity comprising the step of contacting FVII/FVIIa with a peptide of the invention, such as those described above, in the presence of tissue factor and under conditions which allow binding of the compound to FVIIa to occur.

[0067] The invention also provides a method for selecting a compound which blocks FVII/FVIIa activation of FX comprising the step of:

[0068] (1) contacting FVII/FVIIa with a peptide compound of the invention in the presence and absence of a candidate compound under conditions which allow specific binding of the peptide compound of the invention to FVII/FVIIa to occur;

[0069] (2) detecting the amount of specific binding of the peptide compound of the invention to FVII/FVIIa that occurs in the presence and absence of the candidate compound; and

[0070] (3) selecting a candidate compound based upon a decrease in the amount of binding of the peptide compound of the invention in the presence of the candidate compound.

[0071] The invention further provides a method of inhibiting the activation of FX comprising contacting FVII/FVIIa with a compound that prevents the interaction of FVII/FVIIa with a peptide of the invention. The contacting step may occur in vivo or in vitro.

Chemical Synthesis

[0072] One method of producing the compounds of the invention involves chemical synthesis. This can be accomplished by using methodologies well known in the art (see Kelley, R. F., and Winkler, M. E., in Genetic Engineering Principles and Methods, Setlow, J. K, ed., vol. 12, pp. 1-19 (Plenum Press, New York, N.Y., 1990); Stewart, J. M., and Young, J. D., Solid Phase Peptide Synthesis (Pierce Chemical Co., Rockford, Ill., 1984); see also U.S. Pat. Nos. 4,105,603; 3,972,859; 3,842,067; and 3,862,925).

[0073] Peptides of the invention can be conveniently prepared using solid phase peptide synthesis (Merrifield, J. Am. Chem. Soc. 85:2149 (1964); Houghten, Proc. Natl. Acad. Sci. USA 82:5132 (1985)). Solid phase synthesis begins at the carboxyl terminus of the putative peptide by coupling a protected amino acid to an inert solid support. The inert solid support can be any macromolecule capable of serving as an anchor for the C-terminus of the initial amino acid. Typically, the macromolecular support is a cross-linked polymeric resin (e.g., a polyamide or polystyrene resin), as shown in FIGS. 1-1 and 1-2, on pages 2 and 4 of Stewart and Young, supra. In one embodiment, the C-terminal amino acid is coupled to a polystyrene resin to form a benzyl ester. A macromolecular support is selected such that the peptide anchor link is stable under the conditions used to deprotect the α-amino group of the blocked amino acids in peptide synthesis. If a base-labile α-protecting group is used, then it is desirable to use an acid-labile link between the peptide and the solid support. For example, an acid-labile ether resin is effective for base-labile Fmoc-amino acid peptide synthesis, as described on page 16 of Stewart and Young, supra. Alternatively, a peptide anchor link and α-protecting group that are differentially labile to acidolysis can be used. For example, an aminomethyl resin such as the phenylacetamidomethyl (Pam) resin works well in conjunction with Boc-amino acid peptide synthesis, as described on pages 11-12 of Stewart and Young, supra.

[0074] After the initial amino acid is coupled to an inert solid support, the α-amino protecting group of the initial amino acid is removed with, for example, trifluoroacetic acid (TFA) in methylene chloride and neutralizing in, for example, triethylamine (TEA). Following deprotection of the initial amino acid's α-amino group, the next α-amino and sidechain protected amino acid in the synthesis is added. The remaining α-amino and, if necessary, side chain protected amino acids are then coupled sequentially in the desired order by condensation to obtain an intermediate compound connected to the solid support. Alternatively, some amino acids may be coupled to one another to form a fragment of the desired peptide followed by addition of the peptide fragment to the growing solid phase peptide chain.

[0075] The condensation reaction between two amino acids, or an amino acid and a peptide, or a peptide and a peptide can be carried out according to the usual condensation methods such as the axide method, mixed acid anhydride method, DCC (N,N′-dicyclohexylcarbodiimide) or DIC (N,N′-diisopropylcarbodiimide) methods, active ester method, p-nitrophenyl ester method, BOP (benzotriazole-1-yl-oxy-tris [dimethylamino] phosphonium hexafluorophosphate) method, N-hydroxysuccinic acid imido ester method, etc, and Woodward reagent K method.

[0076] It is common in the chemical syntheses of peptides to protect any reactive side-chain groups of the amino acids with suitable protecting groups. Ultimately, these protecting groups are removed after the desired polypeptide chain has been sequentially assembled. Also common is the protection of the α-amino group on an amino acid or peptide fragment while the C-terminal carboxyl group of the amino acid or peptide fragment reacts with the free N-terminal amino group of the growing solid phase polypeptide chain, followed by the selective removal of the α-amino group to permit the addition of the next amino acid or peptide fragment to the solid phase polypeptide chain. Accordingly, it is common in polypeptide synthesis that an intermediate compound is produced which contains each of the amino acid residues located in the desired sequence in the peptide chain wherein individual residues still carry side-chain protecting groups. These protecting groups can be removed substantially at the same time to produce the desired polypeptide product following removal from the solid phase.

[0077] aα- and ε-amino side chains can be protected with benzyloxycarbonyl (abbreviated Z), isonicotinyloxycarbonyl (iNOC), o-chlorobenzyloxycarbonyl [Z(2Cl)], p-nitrobenzyloxycarbonyl [Z(NO2)], p-methoxybenzyloxycarbonyl [Z(OMe)], t-butoxycarbonyl (Boc), t-amyloxycarbonyl (Aoc), isobornyloxycarbonyl, adamantyloxycarbonyl, 2-(4-biphenyl)-2-propyloxycarbonyl (Bpoc), 9-fluorenylmethoxycarbonyl (Fmoc), methylsulfonyethoxycarbonyl (Msc), trifluoroacetyl, phthalyl, formyl, 2-nitrophenylsulphenyl (NPS), diphenylphosphinothioyl (Ppt), and dimethylphosphinothioyl (Mpt) groups, and the like.

[0078] Protective groups for the carboxyl functional group are exemplified by benzyl ester (OBzl), cyclohexyl ester (Chx), 4-nitrobenzyl ester (ONb), t-butyl ester (Obut), 4-pyridylmethyl ester (OPic), and the like. It is often desirable that specific amino acids such as arginine, cysteine, and serine possessing a functional group other than amino and carboxyl groups are protected by a suitable protective group. For example, the guanidino group of arginine may be protected with nitro, p-toluenesulfonyl, benzyloxycarbonyl, adamantyloxycarbonyl, p-methoxybenzesulfonyl, 4-methoxy-2,6-dimethylbenzenesulfonyl (Nds), 1,3,5-trimethylphenysulfonyl (Mts), and the like. The thiol group of cysteine can be protected with p-methoxybenzyl, trityl, and the like.

[0079] Many of the blocked amino acids described above can be obtained from commercial sources such as Novabiochem (San Diego, Calif.), Bachem CA (Torrence, Calif.) or Peninsula Labs (Belmont, Calif.).

[0080] Stewart and Young, supra, provides detailed information regarding procedures for preparing peptides. Protection of α-amino groups is described on pages 14-18, and side chain blockage is described on pages 18-28. A table of protecting groups for amine, hydroxyl and sulfhydryl functions is provided on pages 149-151.

[0081] After the desired amino acid sequence has been completed, the peptide can be cleaved away from the solid support, recovered and purified. The peptide is removed from the solid support by a reagent capable of disrupting the peptide-solid phase link, and optionally deprotects blocked side chain functional groups on the peptide. In one embodiment, the peptide is cleaved away from the solid phase by acidolysis with liquid hydrofluoric acid (HF), which also removes any remaining side chain protective groups. Preferably, in order to avoid alkylation of residues in the peptide (for example, alkylation of methionine, cysteine, and tyrosine residues), the acidolysis reaction mixture contains thio-cresol and cresol scavengers. Following HF cleavage, the resin is washed with ether, and the free peptide is extracted from the solid phase with sequential washes of acetic acid solutions. The combined washes are lyophilized, and the peptide is purified.

Disulfide Linked Peptides

[0082] Some embodiments of the invention include cyclic peptides formed by a disulfide bond between cysteine residues. Such peptides can be made by chemical synthesis as described above and then cyclized by any convenient method used in the formation of disulfide linkages. For example, peptides can be recovered from solid-phase synthesis with sulfhydryls in reduced form, dissolved in a dilute solution wherein the intramolecular cysteine concentration exceeds the intermolecular cysteine concentration in order to optimize intramolecular disulfide bond formation, such as a peptide concentration of 25 mM to 1 μM, and more preferably 500 μM to 1 μM, and more preferably 25 μM to 1 μM, and then oxidized by exposing the free sulfhydryl groups to a mild oxidizing agent that is sufficient to generate intramolecular disulfide bonds, e.g., molecular oxygen with or without catalysts such as metal cations, potassium ferricyanide, sodium tetrathionate, etc. The peptides can be cyclized as described in Pelton et al., J. Med. Chem. 29:2370-2375 (1986).

[0083] Cyclization can be achieved by the formation, for example, of a disulfide bond or a lactam bond between Cys residues. Residues capable of forming a disulfide bond include for example Cys, Pen, Mpr, and Mpp and its 2-amino group-containing equivalents. Residues capable of forming a lactam bridge include, for example, Asp, Glu, Lys, Orn, -diaminobutyric acid, diaminoacetic acid, aminobenzoic acid and mercaptobenzoic acid. The compounds herein can be cyclized, for example, via a lactam bond which can utilize the side chain group of a non-adjacent residue to form a covalent attachment to the N-terminus amino group of Cys or other amino acid. Alternative bridge structures also can be used to cyclize the compounds of the invention, including, for example, peptides and peptidomimetics, which can cyclize via S—S, CH2—S, CH2—O—CH2, lactam ester or other linkages.

Recombinant Synthesis

[0084] In a further embodiment, the present invention encompasses a composition of matter comprising isolated nucleic acid, preferably DNA, encoding a peptide described herein. DNAs encoding the peptides of the invention can be prepared by a variety of methods known in the art. These methods include, but are not limited to, chemical synthesis by any of the methods described in Engels et al.,Agnew. Chem. Int. Ed. Engl. 28:716-734 (1989), the entire disclosure of which is incorporated herein by reference, such as the triester, phosphite, phosphoramidite and H-phosphonate methods. In one embodiment, codons preferred by the expression host cell are used in the design of the encoding DNA. Alternatively, DNA encoding the peptide can be altered to encode one or more variants by using recombinant DNA techniques, such as site-specific mutagenesis (Kunkel et al., Methods Enzymol. 204:125-139 (1991); Carter, P., et al., Nucl. Acids. Res. 13:4331 (1986); Zoller, M. J., et al., Nucl. Acids Res. 10:6487 (1982)), cassette mutagenesis (Wells, J. A., et al., Gene 34:315 (1985)), restriction selection mutagenesis (Wells, J. A., et al., Philos. Trans, R. Soc. London, SerA 317, 415), and the like.

[0085] The invention further comprises an expression control sequence operably linked to the DNA molecule encoding a peptide of the invention, and an expression vector, such as a plasmid, comprising the DNA molecule, wherein the control sequence is recognized by a host cell transformed with the vector. In general, plasmid vectors contain replication and control sequences which are derived from species compatible with the host cell. The vector ordinarily carries a replication site, as well as sequences which encode proteins that are capable of providing phenotypic selection in transformed cells.

[0086] Suitable host cells for expressing the DNA include prokaryote, yeast, or higher eukaryote cells. Suitable prokaryotes include but are not limited to eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as E. coli. Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC No. 31,446); E. coli X1776 (ATCC No. 31,537); E. coli strain W3110 (ATCC No. 27,325) and K5 772 (ATCC No. 53,635).

[0087] In addition to prokaryotes, eukaryotic organisms, such as yeasts, or cells derived from multicellular organisms can be used as host cells. For expression in yeast host cells, such as common baker's yeast or Saccharomyces cerevisiae, suitable vectors include episomally replicating vectors based on the 2-micron plasmid, integration vectors, and yeast artificial chromosome (YAC) vectors. Suitable host cells for expression also are derived from multicellular organisms. Examples of invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells. For expression in insect host cells, such as Sf9 cells, suitable vectors include baculoviral vectors. For expression in plant host cells, particularly dicotyledonous plant hosts, such as tobacco, suitable expression vectors include vectors derived from the Ti plasmid of Agrobacterium tumefaciens.

[0088] Examples of useful mammalian host cells include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 cells subcloned for growth in suspension culture, Graham et al., J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK, ATCC CCL 10); Chinese hamster ovary cells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci. USA 77:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251 (1980)); monkey kidney cells (CV1 ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al., Annals N.Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma cell line (Hep G2).

[0089] For expression in prokaryotic hosts, suitable vectors include pBR322 (ATCC No. 37,017), phGH107 (ATCC No. 40,011), pBO475, pS0132, pRIT5, any vector in the pRIT20 or pRIT30 series (Nilsson and Abrahmsen, Meth. Enzymol. 185:144-161 (1990)), pRIT2T, pKK233-2, pDR540 and pPL-lambda. Prokaryotic host cells containing the expression vectors of the present invention include E. coli K12 strain 294 (ATCC NO. 31,446), E. coli strain JM101 (Messing et al., Nucl. Acid Res. 9:309 (1981)), E. coli strain B, E. coli strain X1776 (ATCC No. 31,537), E. coli c600 (Appleyard, Genetics 39:440 (1954)), E. coli W3110 (F-, gamma-, prototrophic, ATCC No. 27,325), E. coli strain 27C7 (W3110, tonA, phoA E15, (argF-lac)169, ptr3, degP41, ompT, kanr) (U.S. Pat. No. 5,288,931, ATCC No. 55,244), Bacillus subtilis, Salmonella typhimurium, Serratia marcesans, and Pseudomonas species.

[0090] For expression in mammalian host cells, useful vectors include vectors derived from SV40, vectors derived from cytomegalovirus such as the pRK vectors, including pRK5 and pRK7 (Suva et al., Science 237:893-896 (1987); EP 307,247 (3/15/89), EP 278,776 (8/17/88)) vectors derived from vaccinia viruses or other pox viruses, and retroviral vectors such as vectors derived from Moloney's murine leukemia virus (MoMLV).

[0091] Optionally, the DNA encoding the peptide of interest is operably linked to a secretory leader sequence resulting in secretion of the expression product by the host cell into the culture medium. Examples of secretory leader sequences include stII, ecotin, lamB, herpes GD, lpp, alkaline phosphatase, invertase, MIP.5 and alpha factor. Also suitable for use herein is the 36 amino acid leader sequence of protein A (Abrahmsen et al., EMBO J. 4:3901 (1985)).

[0092] Host cells are transfected and preferably transformed with the above-described expression or cloning vectors of this invention and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.

[0093] Transfection refers to the taking up of an expression vector by a host cell whether or not any coding sequences are in fact expressed. Numerous methods of transfection are known to the ordinarily skilled artisan, for example, CaPO4 precipitation and electroporation. Successful transfection is generally recognized when any indication of the operation of this vector occurs within the host cell.

[0094] Transformation means introducing DNA into an organism so that the DNA is replicable, either as an extrachromosomal element or by chromosomal integrant. Depending upon the host cell used, transformation is done using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride, as described in section 1.82 of Sambrook et al., Molecular Cloning, 2nd ed. (Cold Spring Harbor Laboratory, New York, 1989), is generally used for prokaryotes or other cells that contain substantial cell-wall barriers. Infection with Agrobacterium tumefaciens is used for transformation of certain plant cells, as described by Shaw et al., Gene 23:315 (1983) and WO 89/05859, published Jun. 29, 1989. For mammalian cells without such cell walls, the calcium phosphate precipitation method described in sections 16.30-16.37 of Sambrook et al., supra, is preferred. General aspects of mammalian cell host system transformations have been described by Axel in U.S. Pat. No. 4,399,216, issued Aug. 16, 1983. Transformations into yeast are typically carried out according to the method of Van Solingen et al., J. Bact. 130:946 (1977) and Hsiao et al., Proc. Natl. Acad. Sci. USA 76:3829 (1979). However, other methods for introducing DNA into cells such as by nuclear injection, electroporation, or by protoplast fusion may also be used.

[0095] Other preferred vectors can be constructed using standard techniques by combining the relevant traits of the vectors described above. Relevant traits include the promoter, the ribosome binding site, the gene of interest or gene fusion (the Z domain of protein A and gene of interest and a linker), the antibiotic resistance markers, and the appropriate origins of replication.

[0096] A variation on the above procedures contemplates the use of gene fusions, wherein the gene encoding the desired peptide is associated, in the vector, with a gene encoding another protein or a fragment of another protein. This results in the desired peptide being produced by the host cell as a fusion with another protein or peptide. The “other” protein or peptide is often a protein or peptide which can be secreted by the cell, making it possible to isolate and purify the desired peptide from the culture medium and eliminating the necessity of destroying the host cells which arises when the desired peptide remains inside the cell. Alternatively, the fusion protein can be expressed intracellularly. It is useful to use fusion proteins that are highly expressed.

[0097] The use of gene fusions, though not essential, can facilitate the expression of heterologous peptides in insect cells as well as the subsequent purification of those gene products. Protein A fusions are often used because the binding of protein A, or more specifically the Z domain of protein A, to IgG provides an “affinity handle” for the purification of the fused protein. For example, a DNA sequence encoding the desired peptide ligand can be fused by site-directed mutagenesis to the genen for a consensus domain of protein A known as the Z domain (Nilsson et al., Protein Engineering 1:107-113 (1987)). After expression and secretion the fusion protein can be enzymatically cleaved to yield free peptide which can be purified from the enzymatic mix (see, e.g., Varadarajan et al., Proc. Natl. Acad. Sci USA 82:5681-5684 (1985); Castellanos-Serra et al., FEBS Letters 378:171-176 (1996); Nilsson et al., J. Biotechnol. 48:241-250 (1996)).

[0098] Fusion proteins can be cleaved using chemicals, such as cyanogen bromide, which cleaves at a methionine, or hydroxylamine, which cleaves between an Asn and Gly residue. Using standard recombinant DNA methodology, the nucleotide base pairs encoding these amino acids may be inserted just prior to the 5′ end of the gene encoding the desired peptide.

[0099] Alternatively, one can employ proteolytic cleavage of fusion protein. Carter, in Protein Purification: From Molecular Mechanisms to Large-Scale Processes, Ladisch et al., eds., Ch. 13, pp. 181-193 (American Chemical Society Symposium Series No. 427, 1990).

[0100] Proteases such as enterokinase, Factor Xa, thrombin, and subtilisin or its mutants, and a number of others have been successfully used to cleave fusion proteins. Preferred according to the present invention for the production of peptide ligands of less than about 30 amino acids is the protease trypsin which is highly specific for Arg and Lys residues. Trypsin cleavage is discussed generally in Nilsson et al., J. Biotech. 48:241 (1996) and Smith et al., Methods Mol. Biol. 32:289 (1994). Typically, a peptide linker that is amenable to cleavage by the protease used is inserted between the “other” protein (e.g., the Z domain of protein A) and the desired peptide. Using recombinant DNA methodology, the nucleotide base pairs encoding the linker are inserted between the genes or gene fragments coding for the other proteins. Proteolytic cleavage of the partially purified fusion protein containing the correct linker can then be carried out on either the native fusion protein, or the reduced or denatured fusion protein.

[0101] The peptide may or may not be properly folded when expressed as a fusion protein. Also, the specific peptide linker containing the cleavage site may or may not be accessible to the protease. These factors determine whether the fusion protein must be denatured and refolded, and if so, whether these procedures are employed before or after cleavage.

[0102] When denaturing and refolding are needed, typically the peptide is treated with a chaotrope, such a guanidine HCl, and is then treated with a redox buffer, containing, for example, reduced and oxidized dithiothreitol or glutathione at the appropriate ratios, pH, and temperature, such that the peptide is refolded to its native structure.

[0103] The host cells referred to in this disclosure encompass cells in in vitro culture as well as cells that are within a host animal.

[0104] In cyclized embodiments of the invention, the recombinantly produced peptide can be cyclized by formation of an intramolecular disulfide bond as described above.

[0105] The peptide compounds of the invention can be modified at the N-terminus or the C-terminus using an amino-protecting group or carboxyl-protecting group, respectively. Numerous such modifications will be apparent to those skilled in the art. For example, the N-terminus of a peptide or peptide analog can be chemically modified such that the N-terminal amino group is substituted for example by an acetyl, cyclopentylcarboxy, isoquinolylcarboxy, furoyl, tosyl, pyrazinecarboxy, or other such group, which can be sustituted by a substituent as described herein. The N-terminal amino group also can be substituted, for example, with a reverse amide bond. It should be recognized that the term amino group is used broadly herein to refer to any free amino group, including a primary, secondary, or tertiary amino group, present in a peptide. By contrast the term N-terminus refers to the α-amino group of the first amino acid present in a peptide written in the conventional manner.

[0106] The N-terminus of a peptide of the invention can be protected by linking thereto an amino protecting group. The term “amino protecting group” is used broadly herein to refer to a chemical group that can react with a free amino group, including, for example, the α-amino group present at the N-terminus of an peptide of the invention. By virtue of reacting therewith, an amino protecting group protects the otherwise reactive amino group against undesirable reactions, as can occur, for example, during a synthetic procedure or due to exopeptidase activity on a final compound.

[0107] Modification of an amino group also can provide additional advantages, including, for example, increasing the solubility or the activity of the compound. Compounds having these modifications are meant to be included within the compounds of the present invention since their construction is within the ability of the skilled artisan given the present disclosure. Various amino protecting groups are known in the art and include, for example, acyl groups such as an acetyl, picolyl, tert-butylacetyl, tert-butyloxycarbonyl, benzyloxycarbonyl, benzoyl groups, including for example a benzyloxime such as a 2-aryl-2-o-benzyloxime as well as an amino acyl residue which itself can be modified by an amino-protecting group. Other amino-protecting groups are described, for example, in The Peptides, Gross and Meienhofer, eds., Vol. 3 (Academic Press, Inc., New York, N.Y., 1981) and Greene and Wuts, in Protective groups in Organic Synthesis, 2d ed., pp. 309-405 (John Wiley & sons, New York, N.Y., 1991), each of which is incorporated herein by reference. The product of any such modification of the N-terminus amino group of a peptide or peptide analog of the invention is referred to herein as an “N-terminal derivative”.

[0108] Similarly, a carboxyl group such as the carboxyl group present at the C-terminus of a peptide can be chemically modified using a carboxyl-protecting group. The terms “carboxyl group” and ” ° C-terminus” are used in a manner consistent with the terms amino groups and N-terminus as defined above. A carboxyl group such as that present at the C-terminus of a peptide can be modified by reduction of the C-terminal carboxyl group to an alcohol or aldehyde or by formation of an oral ester or by substitution of the carboxyl group with a substituent such as a thiazolyl, cyclohexyl, or other group. Oral esters are well known in the art and include, for example, alkoxymethyl groups such as methoxymethyl, ethoxymethyl, propoxymethyl, isopropoxy methyl, and the like.

Research and Diagnostic Compositions

[0109] In a preferred embodiment, the peptides of the invention are non-covalently adsorbed or covalently bound to a macromolecule, such as a solid support. It will be appreciated that the invention encompasses both macromolecules complexed with the peptides. In general, the solid support is an inert matrix, such as a polymeric gel, comprising a three-dimensional structure, lattice or network of a material. Almost any macromolecule, synthetic or natural, can form a gel in a suitable liquid when suitably cross-linked with a bifunctional reagent. Preferably, the macromolecule selected is convenient for use in affinity chromatography. Most chromatographic matrices used for affinity chromatography are xerogels. Such gels shrink on drying to a compact solid comprising only the gel matrix. When the dried xerogel is resuspended in the liquid, the gel matrix imbibes liquid, swells and returns to the gel state. Xerogels suitable for use herein include polymeric gels, such as cellulose, cross-linked dextrans (e.g., Sepharose), agarose, cross-linked agarose, polyacrylamide gels, and polyacrylamide-agarose gels.

[0110] Alternatively, aerogels can be used for affinity chromatography. These gels do not shrink on drying but merely allow penetration of the surrounding air. When the dry gel is exposed to liquid, the latter displaces the air in the gel. Aerogels suitable for use herein include porous glass and ceramic gels.

[0111] Also encompassed herein are the peptides of the invention coupled to derivatized gels wherein the derivative moieties facilitate the coupling of the peptide ligands to the gel matrix and avoid steric hindrance of the peptide-FVII/FVIIa interaction in affinity chromatography. Alternatively, spacer arms can be interposed between the gel matrix and the peptide ligand for similar benefits.

Pharmaceutical Compositions

[0112] Pharmaceutical compositions which comprise the compounds, including the hybrid molecules of the invention, may be formulated and delivered or administered in a manner best suited to the particular FVII/FVIIa mediated disease or disorder being treated, including formulations suitable for parental, topical, oral, local, aerosol or transdermal administration or delivery of the compounds. In indications where the reduction of TF-FVIIa dependent coagulation is related to circulation of blood through stents or artificial valves or related to extracorporeal circulation, including blood removed in-line from a patient in such processes as dialysis procedures, blood filtration, or blood bypass during surgery, suitable formulations include those appropriate for coating devices such as stents, valves and filtration devices.

[0113] Somewhat more particularly, suitable compositions of the present invention comprise any of the compounds described herein along with a pharmaceutically acceptable carrier, the nature of the carrier differing with the mode of administration delivery or use, for example, in oral administration, usually using a solid carrier and in i.v. administration, a liquid salt solution carrier. For local administration, such as may be appropriate where TF-FVIIa dependent coagulation is related to circulation of blood through artificial devices such as stents or valves, the peptides may be linked, for example, covalently, to the artificial device preventing local thrombus formation. Alternatively, the peptide may be provided in a formulation that would allow for the peptide to slowly elute from the device providing both local and systemic protection against events associated with TF-FVIIa dependent coagulation. As but one example, stents adsorbed with peptides can be employed following angioplasty or other surgical procedure.

[0114] The compositions of the present invention include pharmaceutically acceptable components that are compatible with the subject and the compound of the invention. These generally include suspensions, solutions and elixirs, and most especially biological buffers, such as phosphate buffered saline, saline, Dulbecco's Media, and the like. Aerosols may also be used, or carriers such as starches, sugars, microcrystalline cellulose, diluents, granulating agents, lubricants, binders, disintegrating agents, and the like (in the case of oral solid preparations, such as powders, capsules, and tablets).

[0115] As used herein, the term “pharmaceutically acceptable” generally means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.

[0116] The formulation of choice can be made using a variety of the aforementioned buffers, or even excipients including, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin cellulose, magnesium carbonate, and the like. “PEGylation” of the compositions may be achieved using techniques known to the art (see for example International Patent Publication No. W092/16555, U.S. Pat. No. 5,122,614 to Enzon, and International Patent Publication No. W092/00748).

[0117] A preferred route of administration of the present invention is in the aerosol or inhaled form. The compounds of the present invention, combined with a dispersing agent, or dispersant, can be administered in an aerosol formulation as a dry powder or in a solution or suspension with a diluent.

[0118] As used herein, the term “dispersant” refers to a agent that assists aerosolization of the compound or absorption of the protein in lung tissue, or both. Preferably the dispersant is pharmaceutically acceptable. As used herein, the term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. Suitable dispersing agents are well known in the art, and include, but are not limited to, surfactants and the like. For example, surfactants that are generally used in the art to reduce surface-induced aggregation of the compound, especially the peptide compound, caused by atomization of the solution forming the liquid aerosol may be used. Nonlimiting examples of such surfactants include polyoxyethylene fatty acid esters and alcohols, and polyoxyethylene sorbitan fatty acid esters. Amounts of surfactants used will vary, being generally within the range of 0.001 and 4% by weight of the formulation. In a specific aspect, the surfactant is polyoxyethylene sorbitan monooleate or sorbitan trioleate. Suitable surfactants are well known in the art, and can be selected on the basis of desired properties, depending upon the specific formulation, concentration of the compound, diluent (in a liquid formulation) or form of powder (in a dry powder formulation), etc.

[0119] Moreover, depending upon the choice of the compound, the desired therapeutic effect, the quality of the lung tissue (e.g., diseased or healthy lungs), and numerous other factors, the liquid or dry formulations can comprise additional components, as discussed further below.

[0120] The liquid aerosol formulations generally contain the compound and a dispersing agent in a physiologically acceptable diluent. The dry powder aerosol formulations of the present invention consist of a finely divided solid form of the compound and a dispersing agent. With either the liquid or dry powder aerosol formulation, the formulation must be aerosolized. That is, it must be broken down into liquid or solid particles in order to ensure that the aerosolized dose actually reaches the alveoli. In general, the mass median dynamic diameter will be 5 micrometers or less in order to ensure that the drug particles reach the lung alveoli (Wearley, L. L., Crit. Rev. in Ther. Drug Carrier Systems 8:333 (1991)). The term “aerosol particle” is used herein to describe the liquid or solid particle suitable for pulmonary administration, i.e., that will reach the alveoli. Other considerations such as construction of the delivery device, additional components in the formulation, and particle characteristics are important. These aspects of pulmonary administration of a drug are well known in the art, and manipulation of formulations, aerosolization means and construction of a delivery device require, at most, routine experimentation by one of ordinary skill in the art.

[0121] With regard to construction of the delivery device, any form of aerosolization known in the art, including, but not limited to, nebulization, atomization or pump aerosolization of a liquid formulation, and aerosolization of a dry powder formulation, can be used in the practice of the invention. A delivery device that is uniquely designed for administration of solid formulations is envisioned. Often, the aerosolization of a liquid or a dry powder formulation will require a propellent. The propellent may be any propellant generally used in the art. Specific nonlimiting examples of such useful propellants are a chlorofluorocarbon, a hydrofluorocarbon, a hydrochlorofluorocarbon, or a hydrocarbon, including trifluoromethane, dichlorodifluoromethane, dichlorotetrafluoroethanol, and 1,1,1,2-tetrafluoroethane, or combinations thereof.

[0122] In a preferred aspect of the invention, the device for aerosolization is a metered dose inhaler. A metered dose inhaler provides a specific dosage when administered, rather than a variable dose depending upon administration. Such a metered dose inhaler can be used with either a liquid or a dry powder aerosol formulation. Metered dose inhalers are well known in the art.

[0123] Once the compound reaches the lung, a number of formulation-dependent factors effect the drug absorption. It will be appreciated that in treating a disease or disorder that requires circulatory levels of the compound, such factors as aerosol particle size, aerosol particle shape, the presence or absence of infection, lung disease or emboli may affect the absorption of the compounds. For each of the formulations described herein, certain lubricators, absorption enhancers, protein stabilizers or suspending agents may be appropriate. The choice of these additional agents will vary depending upon the goal. It will be appreciated that in instances where local delivery of the compounds is desired or sought, such variables as absorption enhancement will be less critical.

Liquid Aerosol Formulations

[0124] The liquid aerosol formulations of the present invention will typically be used with a nebulizer. The nebulizer can be either compressed-air driven or ultrasonic. Any nebulizer known in the art can be used in conjunction with the present invention, such as, but not limited to: Ultravent, (Mallinckrodt, Inc., St. Louis, Mo.); the Acorn II nebulizer (Marquest Medical Products, Englewood Colo.). Other nebulizers useful in conjunction with the present invention are described in U.S. Pat. Nos. 4,624,251, issued Nov. 25, 1986; 3,703,173, issued Nov. 21, 1972; 3,561,444, issued Feb. 9, 1971; and 4,635,627, issued Jan. 13, 1971.

[0125] The formulation may include a carrier. The carrier is a macromolecule which is soluble in the circulatory system and which is physiologically acceptable where physiological acceptance means that those of skill in the art would accept injection of said carrier into a patient as part of a therapeutic regime. The carrier preferably is relatively stable in the circulatory system with an acceptable plasma half life for clearance. Such macromolecules include, but are not limited to, Soya lecithin, oleic acid and sorbitan trioleate, with sorbitan trioleate preferred.

[0126] The formulations of the present embodiment may also include other agents useful for protein stabilization or for the regulation of osmotic pressure. Examples of the agents include, but are not limited to, salts, such as sodium chloride, or potassium chloride, and carbohydrates, such as glucose, galactose or mannose, and the like.

Aerosol Dry Powder Formulations

[0127] It is also contemplated that the present pharmaceutical formulation will be used as a dry powder inhaler formulation comprising a finely divided powder form of the compound and a dispersant. The form of the compound will generally be a lyophilized powder. Lyophilized forms of peptide compounds can be obtained through standard techniques.

[0128] In another embodiment, the dry powder formulation will comprise a finely divided dry powder containing one or more compounds of the present invention, a dispersing agent and also a bulking agent. Bulking agents useful in conjunction with the present formulation include such agents as lactose, sorbitol, sucrose, or mannitol, in amounts that facilitate the dispersal of the powder from the device.

Therapeutic Methods

[0129] The compounds of the present invention can be used therapeutically to prevent the biological activity of the TF-FVIIa complex. The inhibition of TF-FVIIa is desirable in indications where the reduction of TF-FVIIa dependent coagulation is implicated. These situations include but are not limited to the prevention of arterial thrombosis in combination with thrombolytic therapy. It has been suggested that the TF-FVIIa plays a significant role in a variety of clinical states including deep venous thrombosis, arterial thrombosis, stroke, DIC, septic shock, cardiopulmonary bypass surgery, adult respiratory distress syndrome, hereditary angioedema. Inhibitors of TF-FVIIa may therefore play important roles in the regulation of inflammatory and/or thrombotic disorders.

[0130] Thus the present invention encompasses a method for preventing TF-FVIIa mediated event in a human comprising administering to a patient in need thereof a therapeutically effective amount of the compound of the present invention. A therapeutically effective amount of the compound of the present invention is predetermined to achieve the desired effect. The amount to be employed therapeutically will vary depending upon therapeutic objectives, the routes of administration and the condition being treated. Accordingly, the dosages to be administered are sufficient to bind to available FVII/FVIIa and form an inactive complex leading to decreased coagulation in the subject being treated.

[0131] The therapeutic effectiveness is measured by an improvement in one or more symptoms associated with the TF-FVIIa dependant coagulation. Such therapeutically effective dosages can be determined by the skilled artisan and will vary depending upon the age, sex and condition of the subject being treated. Suitable dosage ranges for systemic administration are typically between about 1 μg/kg to up to 100 mg/kg or more and depend upon the route of administration. According to the present invention, a preferred therapeutic dosage is between about 1 μg/kg body weight and about 5 mg/kg body weight. For example, suitable regimens include intravenous injection or infusion sufficient to maintain concentration in the blood in the ranges specified for the therapy contemplated.

[0132] The conditions characterized by abnormal thrombosis include those involving the arterial and venous vasculature. With respect to the coronary arterial vasculature, abnormal thrombus formation characterizes, for example, the rupture of an established atherosclerotic plaque which is the major cause of acute myocardial infarction and unstable angina, as well as also characterizing the occlusive coronary thrombus formation resulting from either thrombolytic therapy or percutaneous transluminal coronary angioplasty (PTCA). With respect to the venous vasculature, abnormal thrombus formation characterizes the condition observed in patients undergoing surgery in the lower extremities or the abdominal area who often suffer from thrombus formation in the venous vasculature resulting in reduced blood flow to the affected extremity and a predisposition to pulmonary embolism. Abnormal thrombus formation further characterizes disseminated intravascular coagulopathy commonly associated with both vascular systems during septic shock, certain viral infections and cancer, a condition wherein there is a rapid consumption of coagulation factors and systemic coagulation which results in the formation of life-threatening thrombi occurring throughout the microvasculature leading to wide-spread organ failure.

[0133] The following examples are offered by way of illustration and not by way of limitation. The disclosures of all citations in the specification are expressly incorporated herein by reference.

EXAMPLES

Example 1

[0134] In order to identify peptides of the invention that extend from the FVIIa exosite identified by A-183 into the active site of FVIIa , a substrate phage display approach was utilized. This approach required optimal conditions for specific phage binding under conditions where FVIIa is inactive followed by activation of FVIIa in the presence of bound phage in order to select only those phage that are released due to enzymatic cleavage by FVIIa.

[0135] Since A-183 inhibits TF-FVIIa activity, albeit incompletely, special conditions were selected. The amidolytic activity of FVIIa has been studied under a variety of different conditions such as changes in pH, different salts at various concentrations and the effect of TF (Neuenschwander, P. F., et al. (1993). Thromb. Haemostasis, 70: 970-977). In the absence of TF, FVIIa exhibits very low enzymatic activity. Addition of TF enhances the activity for the cleavage of FX by about 1000-fold, whereas the increase in amidolytic activity is ca. 70-fold, depending on the pH (Neuenschwander, P. F., et al. (1993). Thromb. Haemostasis, 70: 970-977). In the absence of TF, FVIIa showed no detectable amidolytic activity at or below pH 6.0 or above pH 10.5. The binding of A-183 to FVIIa also varies as a function of pH, having a determined binding constant of Kd=2.8 nM to FVIIa at pH 7.2 (Roberge, M., et al. (2001) Biochemistry, 40: 9522-9531).

[0136] The activity of immobilized FVIIa coated on plates was determined and controlled simultaneously. Maxisorp plates were coated with 4 different concentrations of FVIIa (1, 5, 10 and 20 μg). Each concentration was tested in the absence and presence of sTF (soluble TF; TF1-219) (Kelley, R. F., et al. (1997) Blood, 89: 3219-3227) at pH 6.0 and pH 8.5. Comparing the activities at the 20 μg FVIIa concentration, the presence of sTF showed an 11-fold increase in activity at pH 8.5, whereas amidolytic actvity was basically undetectable at pH 6.0 and the absence of sTF (FIG. 3). The activity increased with the amount of FVIIa coated on the plate.

[0137] As previously described, A-183 shows potent but incomplete inhibition of amidolytic activity (Dennis, M. S., et al. (2001) Biochemistry, 40: 9513-9521). To test whether amidolytic activity was still sufficient in the presence of A-183, we designed a substrate comprising A-183 fused to Z-domain of protein A. This fusion contained a linker with the cleavage sequence of FX (..NLTRIVGG..) where the putative P1 arginine was 11 residues from the C-terminal arginine of A-183. This fusion peptide was incubated with FVIIa in the presence and absence of sTF at pH 6.0 and pH 8.5. The reaction mix was incubated at room temperature for 2 hours and separated by HPLC. Collected peaks were analyzed by SDS-PAGE, N-terminal sequencing and mass spectrometry. This data confirmed that the fusion peptide was cleaved after the putative P1 arginine only under enzymatically favorable conditions (sTF, pH 8.5); no cleavage was observed at pH 6.0 and the absence of sTF the fusion peptide. Based on these studies, suitable conditions for controlling both binding (pH 6.0) and catalysis (sTF, pH 8.5) were determined.

[0138] Clotting Assay

[0139] The prothrombin time (PT) assay was performed in citrated pooled normal human plasma as described previously (Dennis, M. S., et al., (2000) Nature, 404: 465-470). Clotting times were determined using an ACL 300 Coagulation Analyzer (Coulter Corp., Miami, Fla.) using Innovin (human relipidated TF and Ca2+) from Dade International Inc. to initiate the assay.

Examples 2

[0140] The crystal structure of the protease domain of FVII in complex with A-183 revealed the orientation of the bound peptide at its binding site (Eigenbrot, C., et al. (2001) Structure, 9: 627-636). FIG. 1 depicts a model based on the crystal structure of peptide A-183 (green) at the A exosite and D-Phe-L-Arg-chloromethylketone (salmon) covalently bound to the active site (Roberge, M. et al., (2001) Biochemistry, 40:9522-9531. The amino and carboxy terminal residues of A-183 are indicated. The C-terminal arginine of A-183 is in close proximity to the protease active site. We modeled a hypothetical extension onto the C-terminus of A-183, attempting to find the shortest path to the active site of FVIIa (FIG. 2). Taking the shape of the surface and the constraints in flexibility due to peptide bonds, an extension of 11 residues was estimated to be sufficient to reach the active site. Substrate phage library design

[0141] A hexa-His-A183-(protease resistant linker)-g3p fusion was constructed for monovalent display of a A-183-extension peptide library on filamentous phage. The previously described clone AD (Dennis, M. S., et al., (2001) Biochemistry, 40: 9513-9521) was used as a template for Kunkel mutagenesis (Kunkel, T. A, et al., (1987) Methods Enzymol., 154: 367-382) to create a template phagemid containing DNA encoding hexa-His, peptide A-183, 3 stop codons, and the sequence TPTDPPTTPPT (SEQ ID NO: 41) (a protease resistant linker), which was fused to the N-terminus of g3. The following primers were used:

[0142] (5′ TGC TGG ACG TGG GAG ACC TGC GAA CGT GGT GAA GGT CAG TAA TAA TAA ACC CCG ACC GAT CCG CCG ACC ACC CCG CCG ACC GAT TTT GAT TAT3′) (SEQ ID NO: 42) and (5′-ACA AAT GCC TAT GCA CAT CAC CAT CAC CAT CAC TCC GAA GAG TGG GAG-3′) (SEQ ID NO: 43).

[0143] Four random sequence peptide libraries were constructed based on the template phagemid above, which was used as the template:

[0144] hexa-His-A183-XXXXXXXBNLTRIVGG-(protease resistant linker)-g3, library A

[0145] hexa-His-A183-XXXXXXXJLTRIVGG-(protease resistant linker)-g3, library B

[0146] hexa-His-A183-XXXXXXXUTRIVGG-(protease resistant linker)-g3, library C

[0147] hexa-His-A183-GGSGGSGXXXXXXXGG-(protease resistant linker)-g3, library D

[0148] At positions B, J and U codons were tailored to randomly coding only the residue sets (S,N,K), (N,K) and (L,Q), respectively, whereas at position X all 20 residues were allowed using NNS codons. The oligonucleotides 5′-GAG ACC TGC GAA CGT NNS NNS NNS NNS NNS NNS NNS ARM AAC CTG ACC CGT ATC GTG GGT GGT ACC CCG ACC GAT CCG-31 (SEQ ID NO: 44), 5′-GAG ACC TGC GAA CGT NNS NNS NNS NNS NNS NNS NNS AAM CTG ACC CGT ATC GTG GGT GGT ACC CCG ACC GAT CCG-3′ (SEQ ID NO: 45), 5′-GAG ACC TGC GAA CGT NNS NNS NNS NNS NNS NNS NNS CWG ACC CGT ATC GTG GGT GGT ACC CCG ACC GAT CCG-3′ (SEQ ID NO: 46) and 5′-GAG ACC TGC GAA CGT GGT GGT AGC GGT GGT AGC GGT NNS NNS NNS NNS NNS NNS NNS GGT GGT ACC CCG ACC GAT CCG-3′ (SEQ ID NO: 47) were used to generate libraries A, B, C, and D, respectively, which yielded 4.7×1010, 3.5×1010, 1.5×1010, and 1.7×1010 E. coli transformanants, respectively. N stands for A, C, G, and T; S stands for G and C; R stands for A and G; M stands for A and C; W stands for A and T.

[0149] Next, substrate phage libraries were captured on immobilized FVIIa at pH 6.0. In principle, the change to enzymatically favored conditions (sTF, pH 8.5), should result in the release of only those phage displaying preferred substrate sequences. However, the increase in pH results in a new equilibrium of phage bound, as evidenced by the release of uncleaved phage. In order to overcome this background of uncleaved phage, an N-terminal hexa-His tag was introduced on the A-183 phage libraries. Anti-tetra-His monoclonal antibodies were immobilized to a plate to pull out any uncleaved phage, i.e. those containing both the his tag and the phage, from solution. The cleaved phage, which remained in solution, were then propagated and sorted further for enrichment. Control phage displaying hexa-His-A-183 were captured 1000-fold more selectively by the anti-His antibody compared with phage displaying only A-183. About 2×106 phage forming units were captured by 500 ng of immobilized antibody, which was determined by propagating a serial dilution of both test phage.

[0150] Peptide Library Selection Conditions

[0151] Individual wells of Maxi-Sorp plates were separately coated with 100 μl FVIIa (10 μg/ml) and 100 μl Tetra-His monoclonal Antibody (Qiagen, Valencia, Calif.) in 50 mM carbonate buffer pH 9.6 at 4° C. overnight. Wells were blocked for 1 hour with Casein in TBS or Superblock in TBS (Pierce, Rockford, Ill.) at room temperature before each round of panning. FVIIa coated wells were incubated with peptide phage libraries in binding buffer (50 mM MES pH 6.0, 100 mM NaCl, 0.5% BSA and 0.05% Tween 20) for 1 hour. Unbound phage were removed by repetitive washing in binding buffer. Individual wells were immediately treated with 100 μl cleavage buffer (50 mM Tris pH 8.5, 100 mM NaCl, 5 mM CaCl2, 5 mM MgCl2, 0.05% Tween 20, 1% BSA, 100 μg/ml sTF) (Note: sTF stands for soluble TF; TF1-219) and incubated for 5 min. The supernatant was removed and incubated with Tetra-His monoclonal Antibody coated wells. After 1 hour, supernatant was removed and phage were propagated in XL-1 Blue cells with VCSM13 helper phage (Stratagene, La Jolla, Calif.). After several rounds of panning, individual clones from each library were picked and sequenced. Enrichment was monitored by titering the number of phage released by FVIIa in cleavage buffer compared to phage released by FVIIa in binding buffer.

[0152] FVIIa Control Substrate

[0153] Because A-183 inhibits the activity of FVIIa a synthetic substrate was constructed to test whether FVIIa had sufficient activity to cleave the synthetic substrate in the presence of A-183. An expression plasmid was constructed using Kunkel mutagenesis (Kunkel, T. A, et al., (1987) Methods Enzymol., 154: 367-382) by inserting a DNA sequence encoding (GGGSGGSNLTRIVGGSGG) (SEQ ID NO: 48) into pA-100-Z (Dennis, M. S., et al., (2001) Biochemistry, 40: 9513-9521) between A-183 and the Z-domain. The A-183-CS-Z-fusion peptide, which contains a FVIIa cleavage site, was expressed and purified as described above for the Z-fusion peptides. 20 μg of A-183-CS-Z-fusion peptide was incubated for 2 hours at room temperature with FVIIa and sTF in a molar ration of 10:1:10, respectively. The reaction mix was separated by reversed-phase HPLC using a water/acetonitrile gradient containing 0.1% TFA. Peaks were collected and analyzed by SDS-PAGE, N-terminal sequencing and MALDI-TOF mass spectrometry.

[0154] Library Design and Sorting Results

[0155] 7 positions in the linker were fully randomized at once, which created a theoretical diversity of 6.8×1010 variants. Four different libraries were designed to determine the optimal length and sequence of the extension (FIG. 5). Libraries A, B and C contained an arginine at position 10, 11 or 12, respectively, whereas the first 7 residues were fully randomized. The position number refers to the number of residues following the c-terminal arginine of A-183. The residual positions were filled with residues according to those found in the FX cleavage sites of human, bovine and pig. These three libraries were designed to select for preferred residues in the beginning of the linker, considering 3 different positions for the arginine. The linker for Library D contained a flexible (GGS)2G spacer followed by fully randomized residues from positions 8 to 14, addressing the question of which residues are preferred in the cleavage site. In natural and synthetic substrates proteolysis occurs after arginine, defining it as the preferred residue at the P1 position. Thus, the position in which arginine was observed most frequently was used to determine the length of the extension.

[0156] After six rounds of sorting, 100 clones were randomly picked from each library and sequenced. A statistical analysis was used to determine the frequency of each residue at any randomized position. The frequencies were normalized by the codon bias to compare the probabilities. In library D, this analysis resulted in the consensus sequence XVEWRGX (SEQ ID NO: 49) for positions 8 through 14, respectively, with arginine preferred at position 12, where X represents no clear residue preference. Limiting the statistical analysis for only those sequences containing arginine at position 12 showed consistency in the sequence motif around the arginine (XXEWRGW) (SEQ ID NO: 50). These results lead to library A, where arginine was fixed at position 12. Statistical analysis of library A resulted in the consensus sequence GEVGEEE (SEQ ID NO: 51) for the first 7 randomized positions, with strong preference for glutamate in position 2, 5 and 7. Glycine was exclusively chosen at position 1. Library B showed similar preferences for acidic residues, comparable to library A.

[0157] Randomly picked sequences from library A after 6 rounds of selection. Shaded positions were partially or fully randomized; others were fixed. Positions with a dash contained DNA sequence that was not clearly identifiable.

Library A                    1
position in linker library A 2
                             3
                             4
                             5
                             6
                             7

[0158] Randomly picked sequences from library D after 6 rounds of selection Shaded positions were fully randomized; others were fixed. Positions with a dash contained DNA sequence that was not clearly identifiable.

positions in linker library D 8
                              9
                              10
                              11
                              12
                              13
                              14

[0159] The results from library A and D were combined to create a complete consensus for residues 1 through 14 (GEGVEEEXXEWRGX) (SEQ ID NO: 208). A new library was designed based on these results and positions with limited preference, such as 2, 3, 4 and 6 were patially randomized, whereas positions with no significant preference, such as 8, 9, 14 and 15, were fully randomized again. This new substrate library was panned 6 rounds and 200 clones were picked randomly for sequence analysis. The statistical analysis lead to a consensus sequence (GEGVEEELWEWR) (SEQ ID NO: 209) in the context of previously chosen and fixed residues.

[0160] Randomly picked sequences from the consensus library after 6 rounds of selection. Shaded positions were partially or fully randomized; others were fixed. Positions with a dash contained DNA sequence that was not clearly identifiable.

15
16
17
18
19
20
21
22
23
24
25
26
27

[0161] Extracted sequences from above containing the LW sequence at 26 positions 8 and 9

28
Consensus Library—Statistical Analysis
29

[0162] Positions 3 through 6 contained tailored (partially randomized) codon usage, allowing only the depicted residues. Only one codon per residue was used. There was no clear preference at these positions for a specific residue. However, Asp at position 4 was less frequently observed than Gly or Val.

[0163] Frequency of finding a given residue

Residue/
Position	G	E	D	V
3	40.9%	22.7%		35%
4	44%		5.8%	49%
5		60%	35%
6	55.8%	42%

[0164]

Consensus Library—Statistical Analysis
30

[0165] Positions 8 and 9 were completely randomized. To determine the probability of each residue at positions 8 and 9, the frequency of each residue was normalized by the codon bias. The preference of a given residue at a position is related to the sigma value. The relative significance of any given residue is related to the number of standard deviation units (sigma) above a random chance occurrence of a given residue in the library assuming a binomial distribution of amino acids (see Lowman and Wells, J. Mol. Biol. (1993) 234: 564-578). At position 8, there was a high preference for Leu; Ile, Val, and Phe were also preferred. At position 9, Trp and Phe were highly preferred; Ile, Leu, Pro, and Val were also preferred. Thus positions 8 and 9 had preferences for hydrophobic amino acids.

Example III

[0166] Production of Z-A-183-Extension Variants

[0167] An expression plasmid for Z-A-183 was constructed using Kunkel mutagenesis (Kunkel, T. A, et al., (1987) Methods Enzymol., 154: 367-382) by inserting a DNA sequence encoding a linker with an enterokinase recognition site (GGSGGDDDDK) (SEQ ID NO. 346) and A-183 with a stop codon (EEWEVLCWTWETCERstop) (SEQ ID NO: 16) into the vector pZCT after the C-terminus of the Z consensus domain from protein A (Starovasnik, M. A., et al., (1999)Protein Sci., 8: 1423-1431). The resulting plasmid pZCT-A-183 was confirmed by DNA sequencing and used as expression vector as well as a template for Kunkel mutagenensis. The extension variants pZCT-A-183X, pZCT-A-183(GGS)3GGR, pZCT-A-183(GGS)4, pZCT-A-183EWA, pZCT-A-183EW were constructed by Kunkel mutagenesis (Kunkel, T. A, et al., (1987) Methods Enzymol., 154: 367-382) using pZCT-A183 as template by inserting DNA sequence encoding (GEGVEEELWEWR) (SEQ ID NO: 209), (GGSGGSGGSGGR) (SEQ ID NO: 347), (GGSGGSGGSGGS) (SEQ ID NO: 348), (GEGVEEELWEWA) (SEQ ID NO: 349), (GEGVEEELWEW) (SEQ ID NO: 350), respectively, between the C-terminus of A-183 and the stop codon. All constructs were transformed into E.coli strain 27C7 and grown in low phosphate minimal media as previously described (Dennis, M. S., et al., (2001) Biochemistry, 40: 9513-9521). All Z-fusion peptides were secreted into and harvested from the media and initially purified using IgG-Sepharose (Amersham Pharmacia Biotech, Piscataway, N.J.) as described previously (Dennis, M. S., et al. (1993). Proteins: Struct., Funct., Genet., 15: 312-321). In order to obtain greater purity Z-fusion peptides were further purified by size exclusion on Superdex 75 (Amersham Pharmacia Biotech, Piscataway, N.J.) at 0.5 ml/min flow rate using Tris buffer pH 7.5 and 200 mM NaCl. Fractions from gel filtration containing monomeric Z-fusion peptides were loaded on a Resource Q (1 ml) column (Amersham Pharmacia Biotech, Piscataway, N.J.) for concentration and final purification by ion exchange chromatography, using a salt gradient from 0.2 M to 0.8 M NaCl over 12 column volumes at 3 ml/min flow rate.

		SEQ ID
Peptide	Sequence	NO:
A-183	EEWEVLCWTWETCER	16
Z-A-183	Z-GGSGGDDDDK-EEWEVLCWTWETCER	346 and
		16
Z-A-183X	Z-GGSGGDDDDK-EEWEVLCWTWETCERGEGVEEELWEWR	346, 16,
		209
Z-A-	Z-GGSGGDDDDK-EEWEVLCWTWETCERGGSGGSGGSGGR	346, 16,
183 (GGS)3GGR		347
Z-A-183 (GGS)4	Z-GGSGGDDDDK-EEWEVLCWTWETCERGGSGGSGGSGGS	346, 16
		348
Z-A-183X-EWA	Z-GGSGGDDDDK-EEWEVLCWTWETCERGEGVEEELWEWA	346, 16
		349
Z-A-183X-EW	Z-GGSGGDDDDK-EEWEVLCWTWETCERGEGVEEELWEW	346, 16,
		350
Z—Z domain of protein A
GGSGGDDDDK—enterokinase cleavage linker 346

Example IV

[0168] Amidolytic Activity of Immobilized FVIIa

[0169] Maxi-Sorp plates were separately coated with different concentrations of FVIIa (1, 5, 10 and 20 μg/ml) in 50 mM carbonate buffer pH 9.6 at 4° C. overnight. Amidolytic acivity was monitored at 405 nm over 5 min with 1 mM Chromozym t-PA at pH 6.0 and pH 8.5 in the absence and presence of 5-fold excess of sTF over FVIIa.

[0170] Inhibition of FX Activation and Amidolytic Activity

[0171] Inhibition of FX activation by TF-VIIa was determined with 300 pM relipidated TF1-243, 20 pM FVIIa , and 165 nM FX at 25° C. as a function of peptide concentration essentially as described (Dennis, M. S., et al., (2000) Nature, 404: 465-470; Kelley, R. F., et al., (1997) Blood, 89: 3219-3227). TF was incorporated into phospholipid vesicles and quantified as previously described (Kelley, R. F., et al., (1997) Blood, 89: 3219-3227). The linear rates of FXa generation can be expressed as mOD405/min/min or as fractional activities (vi/v0). Control experiments showed that the peptides tested did not inhibit the FXa chromogenic activity.

[0172] Inhibition of amidolytic activity of TF-FVIIa was monitored as a function of peptide concentration, as described previously (Dennis, M. S., et al., (2000) Nature, 404: 465-470) using Chromozym t-PA as amidolytic substrate. The linear rates of the increase in absorbance at 405 nm can be expressed as mOD405/min or as fractional activities (vi/v0).

[0173] Z-A-183-GEGVEEELWEWR (SEQ ID NO: 209) (Z-A-183X) and Z-A-183 were tested for their ability to inhibit the TF-FVIIa catalyzed activation of FX (FIG. 7 and FIG. 8). Z-A-183X inhibited 99% of the activity upon saturation. This is in contrast to the 80% inhibition of activity observed for Z-A-183. Furthermore, the IC50 value in the FX activation assay for Z-A-183X improved to 12 pM, whereas Z-A-183 showed an IC50 of 660 pM. Thus, in addition to the complete inhibition of FX activation, the A-183 C-terminal extension of provided a 55-fold improvement in the affinity for TF-FVIIa.

[0174] To address the question whether the extension has to be specific to obtain complete inhibition of FX activation, a random extension consisting of a GGS-motif with and without arginine at the carboxy-terminus (Z-A-183 [GGS]3GGR and Z-A-183 [GGS]4, respectively) was tested. An Arg to Ala mutant Z-A-183-GEGVEEELWEWA (SEQ ID NO: 349) (Z-A-183 EW) and an Arg truncation Z-A-183-GEGVEEELWEW (SEQ ID NO: 350) (Z-A-183 EW) in the selected extension to determine its importance for blocking the active site and extent of inhibition were also tested. It has been previously shown, that Z-domain C-terminally fused to A-183 increases the extent of inhibition in FX activation. Consistent with these findings, the random extensions do improve the extent of inhibition of FX activation, but only up to 88%, which is independent of the arginine. Interestingly, the specific extension does not depend on the C-terminal arginine as well. Both truncation of the arginine (Z-A-183 EW) or mutation to alanine (Z-A-183 EW) resulted in complete inhibition of FX activation. (FIG. 8)

Example V

[0175] Clotting Assay

[0176] The prothrombin time (PT) assay was performed in citrated pooled normal human plasma as described previously (Dennis, M. S., et al., (2000) Nature, 404: 465-470). Clotting times were determined using an ACL 300 Coagulation Analyzer (Coulter Corp., Miami, Fla.) using Innovin (human relipidated TF and Ca2+) from Dade International Inc. to initiate the assay. The fold prolongation of the clotting time upon initiation by TF and Ca2+ in the PT assay is shown for Z-A-183, Z-A-183X, Z-A-183-[GGS]4, and A-183. Compared to A-183 (1.6-fold) and the two control peptides, Z-A-183X showed a significant improvement (7.7-fold) in the fold prolongation of clotting. (FIG. 9)

Claims

1. A peptide which: i) comprises the sequence: GEGVEEELWEWR (SEQ ID NO: 209) GEEVEEELWEWR (SEQ ID NO: 351) GEVVEEELWEWR (SEQ ID NO: 352) GEVGDGELWEWR or (SEQ ID NO: 353) GEEGEEELWEWR (SEQ ID NO: 354).

2. The peptide of claim 1 which: i) comprises the sequence Glu1-Glu2-Trp1-Glu3-Val-Leu-Cys1-Trp2-Thr1-Trp3-Glu4-Thr2-Cys2-Glu5-Arg (SEQ ID NO: 16), or ii) competes with SEQ ID NO: 16 for binding FVII/FVIIa in an in vitro assay and having between 1 and 8 amino acids of SEQ ID NO: 16 substituted according to the following: Glu1 and Glu2 are optionally absent or any amino acid; Trp1 is an amino acid selected from the group consisting of Trp, Phe and Leu; Glu3 is any amino acid; Val is an amino acid selected from the group consisting of Val and Ile; Leu is an amino acid selected from the group consisting of Leu, Ile, Met, Val and Ala; Trp2 is amino acid selected from the group consisting of Trp, Phe, Tyr, Leu and Met; Thr1 is any amino acid; Trp3 is an amino acid selected from the group consisting of Trp, Phe and Tyr; Glu4 is any amino acid; Thr2 is any amino acid; Glu5 is any amino acid; Arg is an amino acid selected from the group consisting of Arg, Lys, Leu and Trp; and iii) comprises the peptide of claim 1.

3. A method of inhibiting FVIIa activity comprising the step of contacting FVIIa with a peptide of claim 2 in the presence of tissue factor and under conditions which allow binding of the compound to FVIIa to occur.

4. A pharmaceutical composition comprising a compound of claim 2 and a pharmaceutically acceptable carrier.