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WO1999061615A1 - Polypeptide du domaine de kunitz, materiaux et procedes pour le realiser - Google Patents

Polypeptide du domaine de kunitz, materiaux et procedes pour le realiser Download PDF

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Publication number
WO1999061615A1
WO1999061615A1 PCT/US1999/011628 US9911628W WO9961615A1 WO 1999061615 A1 WO1999061615 A1 WO 1999061615A1 US 9911628 W US9911628 W US 9911628W WO 9961615 A1 WO9961615 A1 WO 9961615A1
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Prior art keywords
seq
protein
zkunδ
sequence
residues
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PCT/US1999/011628
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English (en)
Inventor
Darrell C. Conklin
Donald C. Foster
Zeren Gao
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Zymogenetics, Inc.
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Publication date
Application filed by Zymogenetics, Inc. filed Critical Zymogenetics, Inc.
Priority to AU42074/99A priority Critical patent/AU4207499A/en
Priority to JP2000550999A priority patent/JP2002516102A/ja
Priority to CA002329694A priority patent/CA2329694A1/fr
Priority to EP99925873A priority patent/EP1082430A1/fr
Publication of WO1999061615A1 publication Critical patent/WO1999061615A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/81—Protease inhibitors
    • C07K14/8107—Endopeptidase (E.C. 3.4.21-99) inhibitors
    • C07K14/811—Serine protease (E.C. 3.4.21) inhibitors
    • C07K14/8114—Kunitz type inhibitors

Definitions

  • proteinases are important in wound healing, extracellular matrix destruction, tissue reorganization, and in cascades leading to blood coagulation, fibrinolysis, and complement activation. Proteinases are released by inflammatory cells for destruction of pathogens or foreign materials, and by normal and cancerous cells as they move through their surroundings. The activity of proteinases is regulated by inhibitors; 10% of the proteins in blood serum are proteinase inhibitors (Roberts et al., Critical Reviews in Eukaryotic Gene Expression 5:385-436, 1995).
  • Kunitz inhibitors includes inhibitors of trypsin, chymotrypsin, elastase, kallikrein, plasmin, coagulation factors Xla and IXa, and cathepsin G. These inhibitors thus regulate a variety of physiological processes, including blood coagulation, fibrinolysis, and inflammation.
  • Proteinase inhibitors regulate the proteolytic activity of target proteinases by occupying the active site and thereby preventing occupation by normal substrates.
  • proteinase inhibitors fall into several unrelated structural classes, they all possess an exposed loop (variously termed an “inhibitor loop", a “reactive core”, a “reactive site”, or a “binding loop") which is stabilized by intermolecular interactions between residues flanking the binding loop and the protein core (Bode and Huber, Eur. J. Biochem. 204:433-451. 1992). Interaction between inhibitor and enzyme produces a stable complex which disassociates very slowly, releasing either virgin (uncleaved) inhibitor, or a modified inhibitor that is cleaved at the scissile bond of the binding loop.
  • Kunitz inhibitors are generally basic, low molecular weight proteins comprising one or more inhibitory domains ("Kunitz domains").
  • the Kunitz domain is a folding domain of approximately 50-60 residues which forms a central anti-parallel beta sheet and a short C-terminal helix. This characteristic domain comprises six cysteine residues that form three disulfide bonds, resulting in a double-loop structure. Between the N-terminal region and the first beta strand resides the active inhibitory binding loop. This binding loop is disulfide bonded through the P2 Cys residue to the hairpin loop formed between the last two beta strands.
  • Isolated Kunitz domains from a variety of proteinase inhibitors have been shown to have inhibitory activity (e.g., Petersen et al., Eur. J. Biochem. 125:310-316, 1996; Wagner et al., Biochem. Biophys. Res. Comm. 186:1138- 1145, 1992; Dennis et al., J. Biol. Chem. 270:25411-25417, 1995).
  • Proteinase inhibitors comprising one or more Kunitz domains include tissue factor pathway inhibitor (TFPI), tissue factor pathway inhibitor 2 (TFPI-2), amyloid ⁇ -protein precursor (A ⁇ PP), aprotinin, and placental bikunin.
  • TFPI tissue factor pathway inhibitor
  • TFPI-2 tissue factor pathway inhibitor 2
  • a ⁇ PP amyloid ⁇ -protein precursor
  • aprotinin aprotinin
  • placental bikunin TFPI, an extrinsic pathway inhibitor and a natural anticoagulant, contains three tandemly linked Kunitz inhibitor domains.
  • the amino-terminal Kunitz domain inhibits factor Vila, plasmin, and cathepsin G; the second domain inhibits factor Xa, trypsin, and chymotrypsin; and the third domain has no known activity (Petersen et al., ibid.).
  • TFPI-2 has been shown to be an inhibitor of the amidolytic and proteolytic activities of human factor Vila-tissue factor complex, factor Xla, plasma kallikrein, and plasmin (Sprecher et al., Proc. Natl. Acad. Sci. USA 91:3353-3357, 1994; Petersen et al., Biochem. 35:266-272, 1996).
  • the ability of TFPI-2 to inhibit the factor Vila-tissue factor complex and its relatively high levels of transcription in umbilical vein endothelial cells, placenta and liver suggests a specialized role for this protein in hemostasis (Sprecher et al., ibid.).
  • Aprotinin (bovine pancreatic trypsin inhibitor) is a broad spectrum Kunitz-type serine proteinase inhibitor that has been shown to prevent activation of the clotting cascade.
  • Aprotinin is a moderate inhibitor of plasma kallikrein and plamin, and blockage of fibrinolysis and extracorporeal coagulation have been detected in patients given aprotinin during open heart surgery (Davis and Whittington, Drugs 49:954-983, 1995; Dietrich et al., Thorac. Cardiovasc. Surg. 37:92-98, 1989).
  • Aprotinin has also been used in the treatment of septic shock, adult respiratory distress syndrome, acute pancreatitis, hemorrhagic shock, and other conditions (Westaby, Ann. Thorac.
  • aprotinin is believed to arise from its inhibitory activity towards plasma kallikrein or plasmin (Dennis et al., ibid.).
  • Placental bikunin is a serine proteinase inhibitor containing two Kunitz domains (Delaria et al., J. Biol. Chem. 272:12209-12214, 1997).
  • Kunitz-type inhibitors lack specificity and may have low potency. Lack of specificity can result in undesirable side effects, such as nephrotoxicity that occurs after repeated injections of high doses of aprotinin. These limitations may be overcome by preparing isolated Kunitz domains, which may have fewer side effects than traditional anticoagulants. Hence, there is a need in the art for additional Kunitz-type proteinase inhibitors.
  • the invention provides an isolated protein comprising a sequence of amino acid residues as shown in SEQ ID NO:5, wherein the sequence is at least 90% identical to residues 9 through 59 of SEQ ID NO:2 and wherein the protein has proteinase inhibiting activity, within one embodiment, the protein is from 51 to 81 amino acid residues in length.
  • the protein is from 51 to 67 residues in length, preferably from 55 to 62 residues in length.
  • the sequence is selected from the group consisting of residues 9 through 59 of SEQ ID NO:2 and residues 9 through 59 of SEQ ID NO:4.
  • the protein consists of from 51-557 contiguous amino acid residues of SEQ ID NO:10.
  • the protein further comprises an affinity tag. Suitable affinity tags include maltose binding protein, polyhistidine, and Glu-Tyr-Met-Pro-Met-Glu (SEQ ID NO: 18).
  • the invention provides an expression vector comprising the following operably linked elements: (a) a transcription promoter; (b) a DNA segment encoding a protein as disclosed above; and (c) a transcription terminator.
  • the expression vector further comprises a secretory signal sequence operably linked to the DNA segment.
  • the invention provides a cultured cell containing an expression vector as disclosed above, wherein the cell expresses the DNA segment.
  • a method of making a protein having proteinase inhibiting activity comprising culturing a cell as disclosed above under conditions whereby the DNA segment is expressed, and recovering the protein encoded by the DNA segment.
  • the Figure shows an amino acid sequence alignment of a representative polypeptide of the present invention (SEQ ID NO:2), designated "ZKUN5", with the sequence of the Kunitz domain of human alpha 3 type VI collagen (SEQ ID NO:8), designated "1KNT”.
  • affinity tag is used herein to denote a polypeptide segment that can be attached to a second polypeptide to provide for purification of the second polypeptide or provide sites for attachment of the second polypeptide to a substrate.
  • Affinity tags include a poly-histidine tract, protein A (Nilsson et al., EMBO J. 4:1075, 1985; Nilsson et al., Methods Enzymol. 198:3, 1991), glutathione S transferase (Smith and Johnson, Gene 67:31 , 1988), Glu-Glu affinity tag (Grussenmeyer et al., Proc. Natl.
  • allelic variant is used herein to denote any of two or more alternative forms of a gene occupying the same chromosomal locus. Allelic variation arises naturally through mutation, and may result in phenotypic polymorphism within populations. Gene mutations can be silent (no change in the encoded polypeptide) or may encode polypeptides having altered amino acid sequence.
  • allelic variant is also used herein to denote a protein encoded by an allelic variant of a gene.
  • amino-terminal and “carboxyl-terminal” are used herein to denote positions within polypeptides. Where the context allows, these terms are used with reference to a particular sequence or portion of a polypeptide to denote proximity or relative position. For example, a certain sequence positioned carboxyl-terminal to a reference sequence within a polypeptide is located proximal to the carboxyl terminus of the reference sequence, but is not necessarily at the carboxyl terminus of the complete polypeptide.
  • a "complement" of a polynucleotide molecule is a polynucleotide molecule having a complementary base sequence and reverse orientation as compared to a reference sequence.
  • the sequence 5' ATGCACGGG 3' is complementary to 5' CCCGTGCAT 3'.
  • degenerate nucleotide sequence denotes a sequence of nucleotides that includes one or more degenerate codons (as compared to a reference polynucleotide molecule that encodes a polypeptide).
  • Degenerate codons contain different triplets of nucleotides, but encode the same amino acid residue (i.e., GAU and GAC triplets each encode Asp).
  • a "DNA segment” is a portion of a larger DNA molecule having specified attributes.
  • a DNA segment encoding a specified polypeptide is a portion of a longer DNA molecule, such as a plasmid or plasmid fragment, that, when read from the 5' to the 3' direction, encodes the sequence of amino acids of the specified polypeptide.
  • expression vector is used to denote a DNA molecule, linear or circular, that comprises a segment encoding a polypeptide of interest operably linked to additional segments that provide for its transcription. Such additional segments include promoter and terminator sequences, and may also include one or more origins of replication, one or more selectable markers, an enhancer, a polyadenylation signal, etc. Expression vectors are generally derived from plasmid or viral DNA, or may contain elements of both.
  • isolated when applied to a polynucleotide, denotes that the polynucleotide has been removed from its natural genetic milieu and is thus free of other extraneous or unwanted coding sequences, and is in a form suitable for use within genetically engineered protein production systems.
  • isolated molecules are those that are separated from their natural environment and include cDNA and genomic clones.
  • isolated DNA molecules of the present invention are free of other genes with which they are ordinarily associated, but may include naturally occurring 5' and 3' untranslated regions such as promoters and terminators. The identification of associated regions will be evident to one of ordinary skill in the art (see for example, Dynan and Tijan, Nature 316:774-78. 1985).
  • an "isolated" polypeptide or protein is a polypeptide or protein that is found in a condition other than its native environment, such as apart from blood and animal tissue.
  • the isolated polypeptide is substantially free of other polypeptides, particularly other polypeptides of animal origin. It is preferred to provide the polypeptides in a highly purified form, i.e. greater than 95% pure, more preferably greater than 99% pure.
  • the term “isolated” does not exclude the presence of the same polypeptide in alternative physical forms, such as dimers or alternatively glycosylated or derivatized forms.
  • operably linked when referring to DNA segments, indicates that the segments are arranged so that they function in concert for their intended purposes, e.g., transcription initiates in the promoter and proceeds through the coding segment to the terminator.
  • ortholog denotes a polypeptide or protein obtained from one species that is the functional counterpart of a polypeptide or protein from a different species. Sequence differences among orthologs are the result of speciation.
  • polynucleotide is a single- or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5' to the 3' end.
  • Polynucleotides include RNA and DNA, and may be isolated from natural sources, synthesized in vitro, or prepared from a combination of natural and synthetic molecules. Sizes of polynucleotides are expressed as base pairs
  • bp nucleotides
  • kb kilobases
  • polypeptide is a polymer of amino acid residues joined by peptide bonds, whether produced naturally or synthetically. Polypeptides of less than about 10 amino acid residues are commonly referred to as “peptides”.
  • promoter is used herein for its art-recognized meaning to denote a portion of a gene containing DNA sequences that provide for the binding of RNA polymerase and initiation of transcription. Promoter sequences are commonly, but not always, found in the 5' non-coding regions of genes.
  • a “protein” is a macromolecule comprising one or more polypeptide chains.
  • a protein may also comprise non-peptidic components, such as carbohydrate groups. Carbohydrates and other non-peptidic substituents may be added to a protein by the cell in which the protein is produced, and will vary with the type of cell. Proteins are defined herein in terms of their amino acid backbone structures; substituents such as carbohydrate groups are generally not specified, but may be present nonetheless.
  • secretory signal sequence denotes a DNA sequence that encodes a polypeptide (a "secretory peptide") that, as a component of a larger polypeptide, directs the larger polypeptide through a secretory pathway of a cell in which it is synthesized.
  • the larger polypeptide is commonly cleaved to remove the secretory peptide during transit through the secretory pathway.
  • the term "splice variant" is used herein to denote alternative forms of RNA transcribed from a gene. Splice variation arises naturally through use of alternative splicing sites within a transcribed RNA molecule, or less commonly between separately transcribed RNA molecules, and may result in several mRNAs transcribed from the same gene. Splice variants may encode polypeptides having altered amino acid sequence.
  • the term splice variant is also used herein to denote a protein encoded by a splice variant of an mRNA transcribed from a gene.
  • the present invention provides, in part, novel serine proteinases comprising a Kunitz domain.
  • This Kunitz domain including sequence variants thereof and proteins containing it, is referred to herein as "zkun ⁇ ".
  • the zkun ⁇ polypeptide sequence shown in SEQ ID NO:2 comprises this Kunitz domain, which is bounded at the amino and carboxyl termini by cysteine residues at positions 9 and 59, respectively.
  • Zkun ⁇ has 50% residue identity with the kunitz domain in human alpha 3 type VI collagen (shown in SEQ ID NO:8).
  • the structure of the latter domain has been solved by X-ray crystallography and by NMR (Arnoux et al., J. Mol. Biol. 246:609-617, 1995; Sorensen et al., Biochemistry 36:10439- 10450, 1997).
  • An alignment of zkun ⁇ and the collagen Kunitz domain can be combined with a homology model of zkun ⁇ based on the X-ray structure to predict the function of certain residues in zkun ⁇ .
  • protease binding loop (P3-P4 1 ) is expected to comprise residues 17-23 of SEQ ID NO:2 (Asn-Cys-Gly-Glu-Tyr-Val-Val), with the P1 residue being Gly19, and the P1" residue being Glu20.
  • Zkun ⁇ further comprises a potential glycosylation site at position Asn43 of SEQ ID NO:2.
  • the kunitz domain of human alpha 3 type VI collagen is not known to have antiproteinase activity.
  • SEQ ID NO: ⁇ is a generalized Kunitz domain sequence that shows allowable amino acid substitutions based on such an alignment.
  • the ⁇ 1- residue sequence shown in SEQ ID NO:5 conforms to the pattern: C-X(8)-C-X( 15)-C-X(7)-C-X( 12)-C-X(3)-C wherein C denotes cysteine; X is any naturally occuring amino acid residue, subject to the limitations set forth in the attached Sequence Listing for SEQ ID NO: ⁇ ; and the numerals indicate the number of such variable residues.
  • the second cysteine residue is in the P2 position.
  • the present invention thus provides a family of proteins comprising a sequence of amino acid residues as shown in SEQ ID NO: ⁇ , wherein the sequence is at least 90% identical to residues 9 through ⁇ 9 of SEQ ID NO:2. It is preferred that the proteins of the present invention comprise such a sequence that is at least 9 ⁇ % identical to residues 9 through ⁇ 9 of SEQ ID NO:2.
  • Percent sequence identity is determined by conventional methods. See, for example, Altschul et al., Bull. Math. Bio. 48:603-616, 1986, and Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:1091 ⁇ -10919, 1992. Briefly, two amino acid sequences are aligned to optimize the alignment scores using a gap opening penalty of 10, a gap extension penalty of 1 , and the "BLOSUM62" scoring matrix of Henikoff and Henikoff (ibid.) as shown in Table 2 (amino acids are indicated by the standard one-letter codes). The percent identity is then calculated as:
  • the ten regions with the highest density of identities are then rescored by comparing the similarity of all paired amino acids using an amino acid substitution matrix, and the ends of the regions are "trimmed" to include only those residues that contribute to the highest score. If there are several regions with scores greater than the "cutoff' value (calculated by a predetermined formula based upon the length of the sequence and the ktup value), then the trimmed initial regions are examined to determine whether the regions can be joined to form an approximate alignment with gaps. Finally, the highest scoring regions of the two amino acid sequences are aligned using a modification of the Needleman-Wunsch-Sellers algorithm (Needleman and Wunsch, J. Mol. Biol. 48:444, 1970; Sellers, SIAM J. Appl. Math.
  • ktup 1
  • gap opening penalty 10
  • gap extension penalty 1
  • substitution matrix BLOSUM62.
  • SMATRIX scoring matrix file
  • FASTA can also be used to determine the sequence identity of nucleic acid molecules using a ratio as disclosed above.
  • the ktup value can range between one to six, preferably from four to six.
  • the proteins of the present invention can also comprise non- naturally occurring amino acid residues.
  • Non-naturally occurring amino acids include, without limitation, frat?s-3-methylproline, 2,4-methanoproline, c/s-4- hydroxyproline, frans-4-hydroxyproline, ⁇ /-methylglycine, a//o-threonine, methylthreonine, hydroxyethylcysteine, hydroxyethylhomocysteine, nitroglutamine, homoglutamine, pipecolic acid, thiazolidine carboxylic acid, dehydroproline, 3- and 4-methylproline, 3,3-dimethylproline, tetf-leucine, norvaline, 2-azaphenylalanine, 3-azaphenylalanine, 4-azaphenylalanine, and 4-fluorophenylalanine.
  • E. coli cells are cultured in the absence of a natural amino acid that is to be replaced (e.g., phenylalanine) and in the presence of the desired non-naturally occurring amino acid(s) (e.g., 2-azaphenylalanine, 3-azaphenylalanine, 4- azaphenylalanine, or 4-fluorophenylalanine). See, Koide et al., Biochem.
  • Naturally occurring amino acid residues can be converted to non-naturally occurring species by in vitro chemical modification. Chemical modification can be combined with site-directed mutagenesis to further expand the range of substitutions (Wynn and Richards, Protein Sci. 2:39 ⁇ -403, 1993). Additional polypeptides may be joined to the amino and/or carboxyl termini of the zkun ⁇ Kunitz domain (residues 9- ⁇ 9 of SEQ ID NO:2) or a derivative of the zkun ⁇ Kunitz domain as disclosed above. Within one embodiment, the extensions are those shown in SEQ ID NO: 10, wherein the zkun ⁇ Kunitz domain is located at residues ⁇ 04- ⁇ 4.
  • Particularly preferred proteins in this regard include residues 1-62 of SEQ ID NO:2 or SEQ ID NO:4.
  • Amino and carboxyl extensions of the zkun ⁇ Kunitz domain will be selected so as not to destroy or mask the proteinase-inhibiting activity of the protein by, for example, burying the Kunitz domain within the interior of the protein.
  • shorter extensions typically 10-15 residues in length, preferably not exceeding 8 residues in length.
  • cysteine residues in close proximity to the the Kunitz domain itself.
  • a zkun ⁇ protein can comprise residues 9- ⁇ 9 of SEQ ID NO:2 or SEQ ID NO:4 with amino- and carboxyl-terminal dipeptides, wherein the individual amino acid residues of the dipeptides are any amino acid residue except cysteine.
  • Other amino- and carboxyl-terminal extensions that can be included in the proteins of the present invention include, for example, an amino-terminal methionine residue, a small linker peptide of up to about 20-2 ⁇ residues, or an affinity tag as disclosed above.
  • a protein comprising such an extension may further comprise a polypeptide linker and/or a proteolytic cleavage site between the zkun ⁇ portion and the affinity tag.
  • Preferred cleavage sites include thrombin cleavage sites and factor Xa cleavage sites.
  • the zkun ⁇ protein shown in SEQ ID NO:2 may be expressed as a fusion comprising, from amino terminus to carboxyl terminus: maltose binding protein-polyhistidine-thrombin cleavage site (Leu-Val-Pro-Arg; SEQ ID NO:11)- SEQ ID NO:2.
  • Linker peptides and affinity tags provide for additional functions, such as binding to substrates, antibodies, binding proteins, and the like, and facilitate purification, detection, and delivery of zkun ⁇ proteins.
  • a zkun ⁇ Kunitz domain can be expressed as a secreted protein comprising a carboxyl-terminal receptor transmembrane domain, permitting the Kunitz domain to be displayed on the surface of a cell.
  • the Kunitz domain can be separated from the transmembrane domain by a spacer polypeptide, and can be contained within an extended polypeptide comprising a carboxyl-terminal transmembrane domain-spacer polypeptide-Kunitz domain-amino-terminal polypeptide.
  • the spacer polypeptide will generally be at least about ⁇ O amino acid residues in length, up to 200-300 or more residues.
  • the amino terminal polypeptide may be up to 300 or more residues in length.
  • the present invention further provides polynucleotide molecules, including DNA and RNA molecules, encoding zkun ⁇ proteins.
  • the polynucleotides of the present invention include the sense strand; the anti- sense strand; and the DNA as double-stranded, having both the sense and anti-sense strand annealed together by their respective hydrogen bonds.
  • Representative DNA sequences encoding zkun ⁇ proteins are set forth in SEQ ID NO:1 , SEQ ID NO:3, and SEQ ID NO:9.
  • DNA sequences encoding other zkun ⁇ proteins can be readily generated by those of ordinary skill in the art based on the genetic code.
  • Counterpart RNA sequences can be generated by substitution of U for T.
  • SEQ ID NO:6 is a degenerate DNA sequence that encompasses all DNAs that encode the zkun ⁇ polypeptide of SEQ ID NO:2.
  • SEQ ID NO:7 is a degenerate DNA sequence that encompasses all DNAs that encode the zkun ⁇ polypeptide of SEQ ID NO:4.
  • the degenerate sequences of SEQ ID NO:6 and SEQ ID NO:7 also provide all RNA sequences encoding SEQ ID NO:2 and SEQ ID NO:4, respectively, by substituting U for T.
  • zkun ⁇ polypeptide-encoding polynucleotides comprising nucleotide 1 to nucleotide 186 of SEQ ID NO:6, nucleotide 1 to nucleotide 186 of SEQ ID NO:7, and their respective RNA equivalents are contemplated by the present invention.
  • Table 2 sets forth the one-letter codes used within SEQ ID NOS:6 and 7 to denote degenerate nucleotide positions.
  • “Resolutions” are the nucleotides denoted by a code letter.
  • “Complement” indicates the code for the complementary nucleotide(s). For example, the code Y denotes either C or T, and its complement R denotes A or G, A being complementary to T, and G being complementary to C.
  • degenerate codons used in SEQ ID NOS:6 and 7, encompassing all possible codons for a given amino acid, are set forth in Table 3.
  • any X NNN One of ordinary skill in the art will appreciate that some ambiguity is introduced in determining a degenerate codon, representative of all possible codons encoding each amino acid.
  • the degenerate codon for serine WSN
  • the degenerate codon for arginine AGR
  • the degenerate codon for arginine MGN
  • some polynucleotides encompassed by the degenerate sequence may encode variant amino acid sequences, but one of ordinary skill in the art can easily identify such variant sequences by reference to the amino acid sequences shown in SEQ ID NOS:2 and 4. Variant sequences can be readily tested for functionality as described herein.
  • Preferred codons for a particular species can be introduced into the polynucleotides of the present invention by a variety of methods known in the art, thereby increasing translation efficiency within a particular cell type or species.
  • the degenerate codon sequences disclosed in SEQ ID NOS:6 and 7 serve as templates for optimizing expression of polynucleotides in various cell types and species commonly used in the art and disclosed herein. Sequences containing preferred codons can be tested and optimized for expression in various host cell species, and tested for functionality as disclosed herein.
  • zkun ⁇ polynucleotides hybridize to similar sized regions of SEQ ID NO:1 , or a sequence complementary thereto, under stringent conditions.
  • stringent conditions are selected to be about ⁇ °C lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH.
  • T m is the temperature (under defined ionic strength and pH) at which ⁇ 0% of the target sequence hybridizes to a perfectly matched probe.
  • Typical stringent conditions are those in which the salt concentration is up to about 0.03 M at pH 7 and the temperature is at least about 60°C.
  • zkun ⁇ polynucleotides provided by the present invention include DNA and RNA.
  • RNA is isolated from a tissue or cell that produces large amounts of zkun ⁇ RNA. Such tissues and cells are identified by Northern blotting (Thomas, Proc. Natl. Acad. Sci. USA 77:6201 , 1980), and include spinal cord, trachea, heart, colon, small intestine, and stomach. Total RNA can be prepared using guanidine-HCI extraction followed by isolation by centrifugation in a CsCI gradient (Chirgwin et al., Biochemistry 18:62-94, 1979). Poly (A) + RNA is prepared from total RNA using the method of Aviv and Leder (Proc. Natl. Acad. Sci.
  • Complementary DNA is prepared from poly(A) + RNA using known methods. In the alternative, genomic DNA can be isolated. Polynucleotides encoding zkun ⁇ polypeptides are then identified and isolated by, for example, hybridization or PCR. A full-length clone encoding zkun ⁇ can be obtained by conventional cloning procedures.
  • Complementary DNA (cDNA) clones are preferred, although for some applications (e.g., expression in transgenic animals) it may be preferable to use a genomic clone, or to modify a cDNA clone to include at least one genomic intron.
  • Methods for preparing cDNA and genomic clones are well known and within the level of ordinary skill in the art, and include the use of the sequence disclosed herein, or parts thereof, for probing or priming a library.
  • Expression libraries can be probed with antibodies to zkun ⁇ , receptor fragments, or other specific binding partners.
  • the polynucleotides of the present invention can also be synthesized using automated equipment ("gene machines"). Gene synthesis methods are well known in the art. See, for example, Glick and Pasternak, Molecular Biotechnology, Principles & Applications of Recombinant DNA, ASM Press, Washington, D.C., 1994; Itakura et al., Annu. Rev. Biochem. 63: 323-366, 1984; and Climie et al., Proc. Natl. Acad. Sci. USA 87:633-637, 1990.
  • the zkun ⁇ polynucleotide sequences disclosed herein can be used to isolate counterpart polynucleotides from other species (orthologs). These orthologous polynucleotides can be used, inter alia, to prepare the respective orthologous proteins. These other species include, but are not limited to mammalian, avian, amphibian, reptile, fish, insect and other vertebrate and invertebrate species. Of particular interest are zkun ⁇ polynucleotides abd polypeptides from other mammalian species, including murine, porcine, ovine, bovine, canine, feline, equine, and other primate polypeptides.
  • Orthologs of human zkun ⁇ can be cloned using information and compositions provided by the present invention in combination with conventional cloning techniques.
  • a cDNA can be cloned using mRNA obtained from a tissue or cell type that expresses zkun ⁇ as disclosed herein. Suitable sources of mRNA can be identified by probing Northern blots with probes designed from the sequences disclosed herein.
  • a library is then prepared from mRNA of a positive tissue or cell line.
  • a zkun ⁇ -encoding cDNA can then be isolated by a variety of methods, such as by probing with a complete or partial human cDNA or with one or more sets of degenerate probes based on the disclosed sequences.
  • a cDNA can also be cloned using the polymerase chain reaction, or PCR (Mullis, U.S. Patent No. 4,683,202), using primers designed from the representative human zkun ⁇ sequence disclosed herein.
  • the cDNA library can be used to transform or transfect host cells, and expression of the cDNA of interest can be detected with an antibody to zkun ⁇ polypeptide. Similar techniques can also be applied to the isolation of genomic clones.
  • SEQ ID NO:1 represents a single allele of human zkun ⁇ and that natural variation, including allelic variation and alternative splicing, is expected to occur. Allelic variants of this sequence can be cloned by probing cDNA or genomic libraries from different individuals according to standard procedures. Allelic variants of the DNA sequence shown in SEQ ID NO:1 , including those containing silent mutations and those in which mutations result in amino acid sequence changes, are within the scope of the present invention, as are proteins which are allelic variants of SEQ ID NO:2.
  • cDNAs generated from alternatively spliced mRNAs, which retain the proteinase inhibiting activity of zkun ⁇ are included within the scope of the present invention, as are polypeptides encoded by such cDNAs and mRNAs. Allelic variants and splice variants of these sequences can be cloned by probing cDNA or genomic libraries from different individuals or tissues according to standard procedures known in the art.
  • Zkun ⁇ proteins including variants of wild-type zkun ⁇ , are tested for activity in protease inhibition assays, a variety of which are known in the art.
  • Preferred assays include those measuring inhibition of trypsin, chymotrypsin, plasmin, cathepsin G, and human leukocyte elastase. See, for example, Petersen et al., Eur. J. Biochem. 236:310-316, 1996.
  • the inhibitory activity of a test compound is measured by incubating the test compound with the proteinase, then adding an appropriate substrate, typically a chromogenic peptide substrate. See, for example, Norris et al. (Biol. Chem.
  • the inhibition of coagulation factors (e.g., factor Vila, factor Xa) can be measured using chromogenic substrates or in conventional coagulation assays (e.g., clotting time of normal human plasma; Dennis et al., ibid.).
  • Zkun ⁇ proteins can be tested in animal models of disease, particularly tumor models, models of fibrinolysis, and models of imbalance of hemostasis. Suitable models are known in the art. For example, inhibition of tumor metastasis can be assessed in mice into which cancerous cells or tumor tissue have been introduced by implantation or injection (e.g., Brown, Advan. Enzyme Regul. 36:293-301 , 1996; Conway et al., Clin. Exp. Metastasis 14:116-124, 1996). Effects on fibrinolysis can be measured in a rat model wherein the enzyme batroxobin and radiolabeled fibrinogen are administered to test animals.
  • Zkun ⁇ proteins can be delivered to test animals by injection or infusion, or can be produced in vivo by way of, for example, viral or naked DNA delivery systems or transgenic expression.
  • Exemplary viral delivery systems include adenovirus, herpesvirus, vaccinia virus and adeno-associated virus (AAV).
  • Adenovirus a double-stranded DNA virus, is currently the best studied gene transfer vector for delivery of heterologous nucleic acid (for a review, see Becker et al., Meth. Cell Biol. 43:161-189, 1994; and Douglas and Curiel, Science & Medicine 4:44-63, 1997).
  • Adenovirus a double-stranded DNA virus
  • AAV adeno-associated virus
  • the essential E1 gene is deleted from the viral vector, and the virus will not replicate unless the E1 gene is provided by the host cell (e.g., the human 293 cell line).
  • the host cell e.g., the human 293 cell line.
  • adenovirus primarily targets the liver. If the adenoviral delivery system has an E1 gene deletion, the virus cannot replicate in the host cells. However, the host's tissue (e.g., liver) will express and process (and, if a signal sequence is present, secrete) the heterologous protein. Secreted proteins will enter the circulation in the highly vascularized liver, and effects on the infected animal can be determined.
  • An alternative method of gene delivery comprises removing cells from the body and introducing a vector into the cells as a naked DNA plasmid. The transformed cells are then re-implanted in the body. Naked DNA vectors are introduced into host cells by methods known in the art, including transfection, electroporation, microinjection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, use of a gene gun, or use of a DNA vector transporter. See, Wu et al., J. Biol. Chem. 263:14621-14624, 1988; Wu et al., J. Biol. Chem. 267:963-967, 1992; and Johnston and Tang, Meth. Cell Biol. 43:353-365, 1994.
  • Transgenic mice engineered to express a zkun ⁇ gene, and mice that exhibit a complete absence of zkun ⁇ gene function, referred to as "knockout mice” (Snouwaert et al., Science 267:1083, 1992), can also be generated (Lowell et al., Nature 366:740-742, 1993). These mice are employed to study the zkun ⁇ gene and the encoded protein in an in vivo system. Transgenic mice are particularly useful for investigating the role of zkun ⁇ proteins in early development because they allow the identification of developmental abnormalities or blocks resulting from the over- or underexpression of a specific factor.
  • the zkun ⁇ polypeptides of the present invention can be produced in genetically engineered host cells according to conventional techniques.
  • Suitable host cells are those cell types that can be transformed or transfected with exogenous DNA and grown in culture, and include bacteria, fungal cells, and cultured higher eukaryotic cells.
  • a DNA sequence encoding a zkun ⁇ polypeptide is operably linked to other genetic elements required for its expression, generally including a transcription promoter and terminator, within an expression vector.
  • the vector will also commonly contain one or more selectable markers and one or more origins of replication, although those skilled in the art will recognize that within certain systems selectable markers may be provided on separate vectors, and replication of the exogenous DNA may be provided by integration into the host cell genome. Selection of promoters, terminators, selectable markers, vectors and other elements is a matter of routine design within the level of ordinary skill in the art. Many such elements are described in the literature and are available through commercial suppliers.
  • a secretory signal sequence (also known as a leader sequence, prepro sequence or pre sequence) is provided in the expression vector.
  • the secretory signal sequence may be that of zkun ⁇ , or may be derived from another secreted protein (e.g., t-PA; see, U.S. Patent No. 5, 641 ,666) or synthesized de novo.
  • the secretory signal sequence is operably linked to the zkun ⁇ DNA sequence, i.e., the two sequences are joined in the correct reading frame and positioned to direct the newly sythesized polypeptide into the secretory pathway of the host cell.
  • Secretory signal sequences are commonly positioned ⁇ ' to the DNA sequence encoding the polypeptide of interest, although certain signal sequences may be positioned elsewhere in the DNA sequence of interest (see, e.g., Welch et al., U.S. Patent No. 6,037,743; Holland et al., U.S. Patent No. 5,143,830).
  • Cultured mammalian cells are suitable hosts for use within the present invention.
  • Methods for introducing exogenous DNA into mammalian host cells include calcium phosphate-mediated transfection (Wigler et al., Cell
  • Suitable cultured mammalian cells include the COS-1 (ATCC No. CRL 1650), COS-7 (ATCC No. CRL 1651), BHK (ATCC No. CRL 1632), BHK 570 (ATCC No. CRL 10314), 293 (ATCC No. CRL 1573; Graham et al., J. Gen. Virol. 36:59-72, 1977) and Chinese hamster ovary (e.g. CHO-K1 ; ATCC No.
  • CCL 61 CCL 61 cell lines. Additional suitable cell lines are known in the art and available from public depositories such as the American Type Culture Collection, Rockville, Maryland. In general, strong transcription promoters are preferred, such as promoters from SV-40 or cytomegalovirus. See, e.g., U.S. Patent No. 4,956,288. Other suitable promoters include those from metallothionein genes (U.S. Patent Nos. 4,579,821 and 4,601 ,978) and the adenovirus major late promoter. Expression vectors for use in mammalian cells include pZP-1 and pZP-9, which have been deposited with the American Type Culture Collection, Rockville, MD USA under accession numbers 98669 and 98668, respectively.
  • Drug selection is generally used to select for cultured mammalian cells into which foreign DNA has been inserted. Such cells are commonly referred to as “transfectants”. Cells that have been cultured in the presence of the selective agent and are able to pass the gene of interest to their progeny are referred to as “stable transfectants.”
  • a preferred selectable marker is a gene encoding resistance to the antibiotic neomycin. Selection is carried out in the presence of a neomycin-type drug, such as G-418 or the like.
  • Selection systems can also be used to increase the expression level of the gene of interest, a process referred to as "amplification.” Amplification is carried out by culturing transfectants in the presence of a low level of the selective agent and then increasing the amount of selective agent to select for cells that produce high levels of the products of the introduced genes.
  • a preferred amplifiable selectable marker is dihydrofolate reductase, which confers resistance to methotrexate.
  • Other drug resistance genes e.g. hygromycin resistance, multi-drug resistance, puromycin acetyltransferase
  • hygromycin resistance multi-drug resistance
  • puromycin acetyltransferase can also be used.
  • eukaryotic cells can also be used as hosts, including insect cells, plant cells and avian cells.
  • Agrobacterium rhizogenes as a vector for expressing genes in plant cells has been reviewed by Sinkar et al., J. Biosci. (Bangalore) 11:47-58, 1987. Transformation of insect cells and production of foreign polypeptides therein is disclosed by Guarino et al., U.S. Patent No. 6,162,222 and WIPO publication WO 94/06463.
  • Insect cells can be infected with recombinant baculovirus, commonly derived from Autographa californica nuclear polyhedrosis virus (AcNPV) using methods commonly known in the art.
  • AcNPV Autographa californica nuclear polyhedrosis virus
  • Recombinant baculovirus can also be produced through the use of a transposon-based system described by Luckow et al. (J. Virol. 67:4566- 4579, 1993). This system, which utilizes transfer vectors, is commercially available in kit form (Bac-to-BacTM kit; Life Technologies, Rockville, MD).
  • the transfer vector (e.g., pFastBadTM; Life Technologies) contains a Tn7 transposon to move the DNA encoding the protein of interest into a baculovirus genome maintained in E. coli as a large plasmid called a "bacmid.” See, Hill-Perkins and Possee, J. Gen. Virol. 71:971-976, 1990; Bonning et al., J. Gen. Virol. 75:1551-1556, 1994; and Chazenbalk and Rapoport, J. Biol. Chem. 270:1543-1549, 1995.
  • Fungal cells including yeast cells, can also be used within the present invention.
  • Yeast species of particular interest in this regard include Saccharomyces cerevisiae, Pichia pastoris, and Pichia methanolica.
  • Methods for transforming S. cerevisiae cells with exogenous DNA and producing recombinant polypeptides therefrom are disclosed by, for example, Kawasaki, U.S. Patent No. 4,599,311 ; Kawasaki et al., U.S. Patent No. 4,931 ,373; Brake, U.S. Patent No. 4,870,008; Welch et al., U.S. Patent No. 6,037,743; and Murray et al., U.S. Patent No.
  • Transformed cells are selected by phenotype determined by the selectable marker, commonly drug resistance or the ability to grow in the absence of a particular nutrient (e.g., leucine).
  • a preferred vector system for use in Saccharomyces cerevisiae is the POT1 vector system disclosed by Kawasaki et al. (U.S. Patent No. 4,931 ,373), which allows transformed cells to be selected by growth in glucose-containing media.
  • Suitable promoters and terminators for use in yeast include those from glycolytic enzyme genes (see, e.g., Kawasaki, U.S. Patent No. 4,599,311 ; Kingsman et al., U.S. Patent No. 4,615,974; and Bitter, U.S.
  • Patent No. 4,977,092) and alcohol dehydrogenase genes See also U.S. Patents Nos. 4,990,446; 5,063,154; 5,139,936 and 4,661 ,454. Transformation systems for other yeasts, including Hansenula polymorpha, Schizosaccharomyces pombe, Kluyveromyces lactis, Kluyveromyces fragilis, Ustilago maydis, Pichia pastoris, Pichia methanolica, Pichia guillermondii and Candida maltosa are known in the art. See, for example, Gleeson et al., J. Gen. Microbiol. 132:3459-3465, 1986 and Cregg, U.S. Patent No.
  • Aspergillus cells may be utilized according to the methods of McKnight et al., U.S. Patent No. 4,935,349. Methods for transforming Acremonium chrysogenum are disclosed by Sumino et al., U.S. Patent No. 5,162,228. Methods for transforming Neurospora are disclosed by Lambowitz, U.S. Patent No. 4,486,533. The use of Pichia methanolica as host for the production of recombinant proteins is disclosed in U.S. Patents Nos. 5,716,808, 5,736,383, 5,854,039, and 5,888,768; and WIPO Publications WO 97/17450 and W097/17451.
  • Prokaryotic host cells including strains of the bacteria Escherichia coli, Bacillus and other genera are also useful host cells within the present invention. Techniques for transforming these hosts and expressing foreign DNA sequences cloned therein are well known in the art (see, e.g., Sambrook et al., ibid.).
  • the polypeptide When expressing a zkun ⁇ polypeptide in bacteria such as E. coli, the polypeptide may be retained in the cytoplasm, typically as insoluble granules, or may be directed to the periplasmic space by a bacterial secretion sequence.
  • the cells are lysed, and the granules are recovered and denatured using, for example, guanidine isothiocyanate or urea.
  • the denatured polypeptide can then be refolded and dimerized by diluting the denaturant, such as by dialysis against a solution of urea and a combination of reduced and oxidized glutathione, followed by dialysis against a buffered saline solution.
  • the polypeptide can be recovered from the periplasmic space in a soluble and functional form by disrupting the cells (by, for example, sonication or osmotic shock) to release the contents of the periplasmic space and recovering the protein, thereby obviating the need for denaturation and refolding.
  • Transformed or transfected host cells are cultured according to conventional procedures in a culture medium containing nutrients and other components required for the growth of the chosen host cells.
  • suitable media including defined media and complex media, are known in the art and generally include a carbon source, a nitrogen source, essential amino acids, vitamins and minerals. Media may also contain such components as growth factors or serum, as required.
  • the growth medium will generally select for cells containing the exogenously added DNA by, for example, drug selection or deficiency in an essential nutrient which is complemented by the selectable marker carried on the expression vector or co-transfected into the host cell.
  • Zkun ⁇ polypeptides can also be prepared through chemical synthesis according to methods known in the art, including exclusive solid phase synthesis, partial solid phase methods, fragment condensation or classical solution synthesis. See, for example, Merrifield, J. Am. Chem. Soc. 86:2149, 1963; Stewart et al., Solid Phase Peptide Synthesis (2nd edition), Pierce Chemical Co., Rockford, IL, 1984; Bayer and Rapp, Chem. Pept. Prot. 3:3, 1986; and Atherton et al., Solid
  • proteins of the present invention it is preferred to purify the proteins of the present invention to >80% purity, more preferably to >90% purity, even more preferably >95% purity, and particularly preferred is a pharmaceutically pure state, that is greater than 99.9% pure with respect to contaminating macromolecules, particularly other proteins and nucleic acids, and free of infectious and pyrogenic agents.
  • a purified protein is substantially free of other proteins, particularly other proteins of animal origin.
  • Zkun ⁇ proteins are purified by conventional protein purification methods, typically by a combination of chromatographic techniques.
  • polypeptides comprising a polyhistidine affinity tag typically about 6 histidine residues
  • affinity chromatography on a nickel chelate resin. See, for example, Houchuli et al., Bio/Technol. 6: 1321-1325, 1988.
  • zkun ⁇ proteins can be produced glycosylated or non-glycosylated; pegylated or non-pegylated; and may or may not include an initial methionine amino acid residue.
  • the zkun ⁇ proteins are contemplated for the preparation of medicaments for use in the treatment or prevention of conditions associated with excessive proteinase activity, in particular an excess of trypsin, plasmin, kallikrein, elastase, cathepsin G, proteinase-3, thrombin, factor Vila, factor IXa, factor Xa, factor Xla, factor Xlla, or matrix metalloproteinases.
  • Such conditions include, but are not limited to, acute pancreatitis, cardiopulmonary bypass (CPB)-induced pulmonary injury, allergy-induced protease release, deep vein thrombosis, myocardial infarction, shock (including septic shock), hyperfibrinolytic hemorrhage, emphysema, rheumatoid arthritis, adult respiratory distress syndrome, chronic inflammatory bowel disease, psoriasis, and other inflammatory conditions.
  • CPB cardiopulmonary bypass
  • shock including septic shock
  • hyperfibrinolytic hemorrhage including septic shock
  • emphysema rheumatoid arthritis
  • adult respiratory distress syndrome chronic inflammatory bowel disease
  • psoriasis psoriasis
  • Zkun ⁇ -containing medicaments are also contemplated for use in preservation of platelet function, organ preservation, and wound healing.
  • Zkun ⁇ proteins may be useful in the treatment of conditions arising from an imbalance in hemostasis, including acquired coagulopathies, primary fibrinolysis and fibrinolysis due to cirrhosis, and complications from high-dose thrombolytic therapy.
  • Acquired coagulopathies can result from liver disease, uremia, acute disseminated intravascular coagulation, post- cardiopulmonary bypass, massive transfusion, or Warfarin overdose (Humphries, Transfusion Medicine 1:1181-1201 , 1994).
  • a deficiency or dysfunction in any of the procoagulant mechanisms predisposes the patient to either spontaneous hemorrhage or excess blood loss associated with trauma or surgery.
  • Acquired coagulopathies usually involve a combination of deficiencies, such as deficiencies of a plurality of coagulation factors, and/or platelet dysfunction.
  • patients with liver disease commonly experience increased fibrinolysis due to an inability to maintain normal levels of ⁇ 2 -antiplasmin and/or decreased hepatic clearance of plasminogen activators (Shuman, Hemorrhagic Disorders, in Bennet and Plum, eds. Cecil Textbook of Medicine. 20th ed., W.B. Saunders Co., 1996).
  • Primary fibrinolysis results from a massive release of plasminogen activator.
  • Conditions associated with primary fibrinolysis include carcinoma of the prostate, acute promyelocytic leukemia, hemangiomas, and sustained release of plasminogen activator by endothelial cells due to injection of venoms. The condition becomes critical when enough plasmin is activated to deplete the circulating level of ⁇ 2 -antiplasmin (Shuman, ibid.). Data suggest that plasmin on endothelial cells may be related to the pathophysiology of bleeding or rethrombosis observed in patients undergoing high-dose thrombolytic therapy for thrombosis. Plasmin may cause further damage to the thrombogenic surface of blood vessels after thrombolysis, which may result in rethrombosis
  • zkun ⁇ proteins include treatment or prevention of deep vein thrombosis, pulmonary embolism, and post-surgical thrombosis.
  • Zkun ⁇ proteins may also be used within methods for inhibiting blood coagulation in mammals, such as in the treatment of disseminated intravascular coagulation. Zkun ⁇ proteins may thus be used in place of known anticoagulants such as heparin, coumarin, and anti-thrombin III. Such methods will generally include administration of the protein in an amount sufficient to produce a clinically significant inhibition of blood coagulation.
  • Zkun ⁇ proteins may also find therapeutic use in the blockage of proteolytic tissue degradation. Proteolysis of extracellular matrix, connective tissue, and other tissues and organs is an element of many diseases. This tissue destruction is beleived to be initiated when plasmin activates one or more matrix metalloproteinases (e.g., collagenase and metallo-elastases).
  • matrix metalloproteinases e.g., collagenase and metallo-elastases.
  • Inhibition of plasmin by zkun ⁇ proteins may thus be beneficial in the treatment of these conditions.
  • Matrix metalloproteinases are believed to play a role in metastases of cancers, abdominal aortic aneurysm, multiple sclerosis, rheumatoid arthritis, osteoarthritis, trauma and hemorrhagic shock, and cornial ulcers. MMPs produced by tumor cells break down and remodel tissue matrices during the process of metastatic spread. There is evidence to suggest that MMP inhibitors may block this activity (Brown, Advan. Enzyme Regul. 36:293-301 , 1995). Abdominal aortic aneurysm is characterized by the degradation of extracellular matrix and loss of structural integrity of the aortic wall.
  • plasmin may be important in the sequence of events leading to this destruction of aortic matrix (Jean-Claude et al., Surgery 116:472-478, 1994).
  • Proteolytic enzymes are also believed to contribute to the inflammatory tissue damage of multiple sclerosis (Gijbels, J. Clin. Invest. 94:2177-2182, 1994).
  • Rheumatoid arthritis is a chronic, systemic inflammatory disease predominantly affecting joints and other connective tissues, wherein proliferating inflammatory tissue (panus) may cause joint deformities and dysfunction (see, Arnett, in Cecil Textbook of Medicine, ibid.).
  • Osteoarthritis is a chronic disease causing deterioration of the joint cartilage and other joint tissues and the formation of new bone (bone spurs) at the margins of the joints.
  • MMPs participate in the degradation of collagen in the matrix of osteoarthritic articular cartilage. Inhition of MMPs results in the inhibition of the removal of collagen from cartilage matrix (Spirito, Inflam. Res. 44 (supp. 2):S131-S132, 1995; O'Byrne, Inflam. Res. 44 (supp. 2):S117-S118, 1995; Karran, Ann. Rheumatic Disease 54:662-669, 1995). Zkun ⁇ proteins may also be useful in the treatment of trauma and hemorrhagic shock.
  • the zkun ⁇ proteins of the present invention may be combined with other therapeutic agents to augment the activity (e.g., antithrombotic or anticoagulant activity) of such agents.
  • a zkun ⁇ protein may be used in combination with tissue plasminogen activator in thrombolytic therapy.
  • Doses of zkun ⁇ proteins will vary according to the severity of the condition being treated and may range from approximately 10 ⁇ g/kg to 10 mg/kg body weight, preferably 100 ⁇ g/kg to ⁇ mg/kg, more preferably 100 ⁇ g/kg to 1 mg/kg.
  • the proteins formulated in a pharmaceutically acceptable carrier or vehicle may be formulated in a pharmaceutically acceptable carrier or vehicle.
  • compositions may further include one or more excipients, preservatives, solubilizers, buffering agents, albumin to prevent protein loss on vial surfaces, etc. Formulation methods are within the level of ordinary skill in the art. See, Remington: The Science and Practice of Pharmacy, Gennaro, ed., Mack Publishing Co., Easton, PA, 19th ed., 1996.
  • Gene therapy provides an alternative therapeutic approach for delivery of zkun ⁇ proteins.
  • a mammal has a mutated or absent zkun ⁇ gene
  • a polynucleotide encoding a zkun ⁇ protein can be introduced into the cells of the mammal.
  • a gene encoding a zkun ⁇ protein is introduced in vivo in a viral vector.
  • viral vectors include an attenuated or defective DNA virus, such as herpes simplex virus (HSV), papillomavirus, Epstein Barr virus (EBV), adenovirus, adeno-associated virus (AAV), and the like. Defective viruses, which entirely or almost entirely lack viral genes, are preferred.
  • a defective virus is not infective after introduction into a cell.
  • Use of defective viral vectors allows for administration to cells in a specific, localized area, without concern that the vector can infect other cells.
  • Examples of particular vectors include, without limitation, a defective herpes simplex virus 1 (HSV1) vector (Kaplitt et al., Molec. Cell. Neurosci. 2:320-30, 1991); an attenuated adenovirus vector, such as the vector described by Stratford-Perricaudet et al., J. Clin. Invest. 90:626-30, 1992; and a defective adeno-associated virus vector (Samulski et al., J. Virol.
  • HSV1 herpes simplex virus 1
  • a zkun ⁇ polynucleotide can be introduced in a retroviral vector, as described, for example, by Anderson et al., U.S. Patent No. 6,399,346; Mann et al. Cell 33:163, 1983; Temin et al., U.S. Patent No. 4,650,764; Temin et al., U.S. Patent No. 4,980,289; Markowitz et al., J. Virol. 62:1120, 1988; Temin et al., U.S. Patent No.
  • the vector can be introduced by lipofection in vivo using liposomes.
  • Synthetic cationic lipids can be used to prepare liposomes for in vivo transfection of a gene encoding a marker (Feigner et al., Proc. Natl. Acad. Sci. USA 84:7413-7, 1987; Mackey et al., Proc. Natl. Acad. Sci. USA 85:8027-31 , 1988).
  • target cells are removed from the body, and a vector is introduced into the cells as a naked DNA plasmid.
  • the transformed cells are then re-implanted into the body.
  • naked DNA vectors for gene therapy can be introduced into the desired host cells by methods known in the art, e.g., transfection, electroporation, microinjection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, use of a gene gun or use of a DNA vector transporter. See, for example, Wu et al., J. Biol. Chem. 267:963-7, 1992; Wu et al., J. Biol. Chem. 263:14621-4, 1988.
  • Zkun ⁇ proteins can also be used to prepare antibodies that specifically bind to zkun ⁇ proteins.
  • antibodies includes polyclonal antibodies, monoclonal antibodies, antigen-binding fragments thereof such as F(ab')2 and Fab fragments, single chain antibodies, and the like, including genetically engineered antibodies.
  • Non-human antibodies can be humanized by grafting only non-human CDRs onto human framework and constant regions, or by incorporating the entire non-human variable domains (optionally "cloaking" them with a human-like surface by replacement of exposed residues, wherein the result is a "veneered” antibody).
  • humanized antibodies may retain non-human residues within the human variable region framework domains to enhance proper binding characteristics.
  • humanizing antibodies biological half-life may be increased, and the potential for adverse immune reactions upon administration to humans is reduced.
  • One skilled in the art can generate humanized antibodies with specific and different constant domains (i.e., different Ig subclasses) to facilitate or inhibit various immune functions associated with particular antibody constant domains.
  • Alternative techniques for generating or selecting antibodies useful herein include in vitro exposure of lymphocytes to a zkun ⁇ protein, and selection of antibody display libraries in phage or similar vectors (for instance, through use of immobilized or labeled zkun ⁇ polypeptide).
  • Antibodies are defined to be specifically binding if they bind to a zkun ⁇ protein with an affinity at least 10-fold greater than the binding affinity to control (non-zkun ⁇ ) polypeptide.
  • the antibodies exhibit a binding affinity (K a ) of 10 6 M “1 or greater, preferably 10 7 M “1 or greater, more preferably 10 8 M “1 or greater, and most preferably 10 9 M '1 or greater.
  • K a binding affinity
  • the affinity of a monoclonal antibody can be readily determined by one of ordinary skill in the art (see, for example, Scatchard, Ann. NY Acad. Sci. 51: 660-672, 1949).
  • polyclonal antibodies can be generated from a variety of warm-blooded animals such as horses, cows, goats, sheep, dogs, chickens, rabbits, mice, and rats.
  • the immunogenicity of a zkun ⁇ protein may be increased through the use of an adjuvant such as alum (aluminum hydroxide) or Freund's complete or incomplete adjuvant.
  • Polypeptides useful for immunization also include fusion polypeptides, such as fusions of a zkun ⁇ protein or a portion thereof with an immunoglobulin polypeptide or with maltose binding protein.
  • the polypeptide immunogen may be a full-length molecule or a portion thereof. If the polypeptide portion is "hapten-like", such portion may be advantageously joined or linked to a macromolecular carrier (such as keyhole limpet hemocyanin (KLH), bovine serum albumin (BSA) or tetanus toxoid) for immunization.
  • KLH keyhole limpet hemocyanin
  • BSA bovine serum albumin
  • tetanus toxoid tetanus toxoid
  • Immunogenic zkun ⁇ polypeptides may be as small as ⁇ residues. It is preferred to use polypeptides that are hydrophilic or comprise a hydrophilic region. A preferred such region of SEQ ID NO:2 includes residues 43-59.
  • assays known to those skilled in the art can be utilized to detect antibodies that specifically bind to a zkun ⁇ protein. Exemplary assays are described in detail in Antibodies: A Laboratory Manual, Harlow and Lane (Eds.), Cold Spring Harbor Laboratory Press, 1988.
  • assays include concurrent immunoelectrophoresis, radio-immunoassays, radio-immunoprecipitations, enzyme-linked immunosorbent assays (ELISA), dot blot assays, Western blot assays, inhibition or competition assays, and sandwich assays.
  • ELISA enzyme-linked immunosorbent assays
  • dot blot assays Western blot assays
  • inhibition or competition assays and sandwich assays.
  • Antibodies to zkun ⁇ may be used for affinity purification of zkun ⁇ proteins; within diagnostic assays for determining circulating levels of zkun ⁇ proteins; for detecting or quantitating soluble zkun ⁇ protein as a marker of underlying pathology or disease; for immunolocalization within whole animals or tissue sections, including immunodiagnostic applications; for immunohistochemistry; for screening expression libraries; and for other uses that will be evident to those skilled in the art. For certain applications, including in vitro and in vivo diagnostic uses, it is advantageous to employ labeled antibodies.
  • Suitable direct tags or labels include radionuclides, enzymes, substrates, cofactors, inhibitors, fluorescent markers, chemiluminescent markers, magnetic particles and the like; indirect tags or labels may feature use of biotin-avidin or other complement/anti-complement pairs as intermediates.
  • Zkun ⁇ proteins may be used in the laboratory or commercial preparation of proteins from cultured cells. The proteins can be used alone to inhibit specific proteolysis or can be combined with other proteinase inhibitors to provide a "cocktail" with a broad spectrum of activity. Of particular interest is the inhibition of cellular proteases, which can be release during cell lysis. The proteins can also be used in the laboratory as a tissue culture additive to prevent cell detachment.
  • the present invention also provides reagents for use in diagnostic applications.
  • the zkun ⁇ gene a probe comprising zkun ⁇ DNA or RNA or a subsequence thereof can be used to determine if the zkun ⁇ gene is present on chromosome 7 or if a mutation has occurred.
  • Detectable chromosomal aberrations at the zkun ⁇ gene locus include, but are not limited to, aneuploidy, gene copy number changes, insertions, deletions, restriction site changes and rearrangements.
  • Such aberrations can be detected using polynucleotides of the present invention by employing molecular genetic techniques, such as restriction fragment length polymorphism (RFLP) analysis, short tandem repeat (STR) analysis employing PCR techniques, and other genetic linkage analysis techniques known in the art (Sambrook et al., ibid.; Ausubel et. al., ibid.; Marian, Chest 108:256-65, 1995).
  • molecular genetic techniques such as restriction fragment length polymorphism (RFLP) analysis, short tandem repeat (STR) analysis employing PCR techniques, and other genetic linkage analysis techniques known in the art (Sambrook et al., ibid.; Ausubel et. al., ibid.; Marian, Chest 108:256-65, 1995).
  • Zkun5 polynucleotides can also be used for chromosomal mapping.
  • the human zkun ⁇ gene has be localized to 7p22.2-p22.1. Localization of the zkun ⁇ gene facilitates the establishment of directly proportional physical distances between newly discovered genes of interest and previously mapped markers, including zkun ⁇ .
  • the precise knowledge of a gene's position can be useful for a number of purposes, including: 1) determining if a newly identified sequence is part of an previously identified gene or gene segment and obtaining additional surrounding genetic sequences in various forms, such as YACs, BACs or cDNA clones; 2) providing a possible candidate gene for an inheritable disease which shows linkage to the same chromosomal region; and 3) cross-referencing model organisms, such as mouse, which may aid in determining what function a particular gene might have.
  • a useful technique in this regard is radiation hybrid mapping, a somatic cell genetic technique developed for constructing high-resolution, contiguous maps of mammalian chromosomes (Cox et al., Science 250:246-50, 1990).
  • Radiomación or full knowledge of a gene's sequence allows one to design PCR primers suitable for use with chromosomal radiation hybrid mapping panels.
  • Radiation hybrid mapping panels which are commercially available (e.g., the Stanford G3 RH Panel and the GeneBridge 4 RH Panel, available from Research Genetics, Inc., Huntsville, AL), cover the entire human genome. These panels enable rapid, PCR-based chromosomal localizations and ordering of genes, sequence-tagged sites (STSs), and other nonpolymorphic and polymorphic markers within a region of interest.
  • STSs sequence-tagged sites
  • Sequence tagged sites can also be used independently for chromosomal localization.
  • An STS is a DNA sequence that is unique in the human genome and can be used as a reference point for a particular chromosome or region of a chromosome.
  • An STS is defined by a pair of oligonucleotide primers that are used in a polymerase chain reaction to specifically detect this site in the presence of all other genomic sequences.
  • STSs are based solely on DNA sequence they can be completely described within an electronic database (for example, Database of Sequence Tagged Sites (dbSTS), GenBank; National Center for Biological Information, National Institutes of Health, Bethesda, MD; http://www.ncbi.nlm.nih.gov) and can be searched with a gene sequence of interest for the mapping data contained within these short genomic landmark STS sequences.
  • dbSTS Database of Sequence Tagged Sites
  • the 139-nucleotide sequence of an expressed sequence tag was analyzed and found to encode a C-terminal portion of a Kunitz domain. A clone corresponding to this EST was obtained and sequenced. The clone contained the sequence shown in SEQ ID NO:1. This Kunitz domain sequence was designatied "zkun ⁇ ".
  • tissue distribution of zkun ⁇ was performed by Northern blotting (using Human Multiple Tissue Blots I, II, and III, and Human RNA Master blot from Clontech Laboratories, Inc., Palo Alto, CA).
  • a probe was made from a gel-purified EcoRI-Xhol fragment of the origninal zkun ⁇ clone, and was radioactively labeled using a commercially available labeling kit (RediprimeTM DNA labeling system, Amersham Corp., Arlington Heights, IL) 36
  • the probe was purified using a commercially available push column (NucTrap® column; Stratagene, La Jolla, CA; see U.S. Patent No. 6,336,412).
  • a commercially available hybridization solution (ExpressHybTM Hybridization Solution; Clontech Laboratories, Inc., Palo Alto, CA) was used for prehybridization and as a hybridization solution for the blots. Hybridization took place overnight at 65°C, and the blots were then washed in 2X SSC and 0.06% SDS at room temperature, followed by a wash in 0.1X SSC and 0.1% SDS at 5 ⁇ °C.
  • RNA appeared to be subject to a tissue specific splicing event since trachea, testis and placenta give different size bands from the others.
  • cDNAs made from several tissues including pancreas, heart, stomach and testis.
  • the cDNAs were prepared using a a commercially available kit (MarathonTM cDNA Amplification Kit from Clontech Laboratories, Inc., Palo Alto, CA) and an oligo(dT) primer.
  • reaction mixtures were incubated at 94°C for 2 minutes; 26 cycles of 94°C for 1 ⁇ seconds, 66°C for 20 seconds, and 72°C for 30 seconds; and a 1 -minute incubation at 72°C.
  • 1 ⁇ l each of 1/100 diluted first PCR product was used as template for a nested PCR.
  • 20 pmoles each of oligonucleotide primers ZC9719 (SEQ ID NO:14) and ZC15,998 (SEQ ID NO:1 ⁇ ), and 1 U of ExTaq/Pfu were used in 25- ⁇ l reaction mixtures.
  • the mixtures were incubated at 94°C for 2 minutes; 2 cycles of 94°C for 15 seconds, 66°C for 20 seconds, 72°C for 30 seconds; 25 cycles of 94°C for 15 seconds, 64°C for 20 seconds, 72°C for 30 seconds; and a 1 -minute incubation at 72°C.
  • the PCR products were gel purified and sequenced. Sequencing results indicated that the PCR products extended the original EST clone to include an intact Kunitz domain. The sequence of the PCR-generated clone is shown in SEQ ID NO:9.
  • PCR was performed on cDNA prepared from pancreas as disclosed above. Based on the domain comparison with other known Kunitz domains, primers were designed such that the PCR product would encode an intact Kunitz domain with restriction sites Bam HI in sense primer ZC17,238 (SEQ ID NO:16) and Xho I in antisense primer ZC17,240 (SEQ ID NO:17) to facilitate subcloning into an expression vector.
  • a silent mutation (nucleotide T to C) was introduced in the sense primer ZC17,238 (SEQ ID NO: 16) to remove an internal Bam HI site within the Kunitz domain sequence.
  • a mammalian expression vector was constructed with the dihyrofolate reductase gene selectable marker under control of the SV40 early promoter, SV40 polyadenylation site, a cloning site to insert the gene of interest under control of the mouse metallothionein 1 (MT-1) promoter and the hGH polyadenylation site.
  • the expression vector was designated pZP-9 and has been deposited at the American Type Culture Collection, 12301 Parklawn Drive, Rockville, MD under accession no 98668.
  • the pZP9 vector was modified by addition of a tissue plasminogen activator (t-PA) secretory signal sequence (see U.S. Patent No.
  • t-PA secretory signal sequence replaces the native secretory signal sequence for DNAs encoding polypeptides of interest that are inserted into this vector, and expression results in an N-terminally tagged protein.
  • the N-terminally tagged vector was designated pZP9NEE. The vector was digested with Bam HI and Xho I, and the zkun ⁇ fragment was inserted. The resulting construct was confirmed by sequencing.
  • the human zkun ⁇ gene was mapped to chromosome 7 using the commercially available GeneBridge 4 Radiation Hybrid Panel (Research Genetics, Inc., Huntsville, AL).
  • the GeneBridge 4 Radiation Hybrid Panel contains PCRable DNAs from each of 93 radiation hybrid clones, plus two control DNAs (the HFL donor and the A23 recipient).
  • a publicly available world-wide web server http://www-genome.wi.mit.edu/cgi- bin/contig/rhmapper.pl) allows mapping relative to the Whitehead Institute/MIT Center for Genome Research's radiation hybrid map of the human genome (the "WICGR" radiation hybrid map), which was constructed with the GeneBridge 4 Radiation Hybrid Panel.
  • mapping of the zkun ⁇ gene 20- ⁇ l reaction mixtures were set up in a PCRable 96-well microtiter plate (Stratagene, La Jolla, CA) and used in a thermal cycler (RoboCycler® Gradient 96; Stratagene).
  • Each of the 9 ⁇ PCR reaction mixtures contained 2 ⁇ l buffer (10X KlenTaq PCR reaction buffer; Clontech Laboratories, Inc., Palo Alto, CA), 1.6 ⁇ l dNTPs mix (2.5 mM each, PERKIN-ELMER, Foster City, CA), 1 ⁇ l sense primer (ZC16,523; SEQ ID NO:19), 1 ⁇ l antisense primer (ZC16,522; SEQ ID NO:20), 2 ⁇ l of a density increasing agent and tracking dye (RediLoad, Research Genetics, Inc., Huntsville, AL), 0.4 ⁇ l of a commercially available
  • DNA polymerase/antibody mix 50X AdvantageTM KlenTaq Polymerase Mix; Clontech Laboratories, Inc.
  • the mixtures were overlaid with an equal amount of mineral oil and sealed.
  • the PCR cycler conditions were as follows: an initial 5 minute denaturation at 95°C; 35 cycles of a 1 minute denaturation at 95°C, 1 minute annealing at 64°C, and 1.5 minute extension at 72°C; followed by a final extension of 7 minutes at 72°C.
  • the reaction products were separated by electrophoresis on a 2% agarose gel (Life Technologies, Gaithersburg, MD).

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Abstract

La présente invention concerne des inhibiteurs de protéinases comprenant un domaine de Künitz. Le domaine de Künitz comprend une séquence de résidus d'acides aminés représentés par le SEQ ID NO:5, la séquence étant pour 90 % identique au SEQ ID NO:2. L'invention concerne également, d'une part des procédés permettant de réaliser ces inhibiteurs de protéinases, mais aussi des vecteurs d'expression ainsi que des cellules de culture convenant dans le cadre de ces procédés. Ces inhibiteurs de protéinases, qui conviennent comme composantes du milieu de culture cellulaire, conviennent également pour la purification de protéines, et pour certaines applications thérapeutiques et diagnostiques.
PCT/US1999/011628 1998-05-28 1999-05-26 Polypeptide du domaine de kunitz, materiaux et procedes pour le realiser WO1999061615A1 (fr)

Priority Applications (4)

Application Number Priority Date Filing Date Title
AU42074/99A AU4207499A (en) 1998-05-28 1999-05-26 Kunitz domain polypeptide and materials and methods for making it
JP2000550999A JP2002516102A (ja) 1998-05-28 1999-05-26 Ｋｕｎｉｔｚドメインポリペプチド並びにその製造のための材料及び方法
CA002329694A CA2329694A1 (fr) 1998-05-28 1999-05-26 Polypeptide du domaine de kunitz, materiaux et procedes pour le realiser
EP99925873A EP1082430A1 (fr) 1998-05-28 1999-05-26 Polypeptide du domaine de kunitz, materiaux et procedes pour le realiser

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US8625398A 1998-05-28 1998-05-28
US09/086,253 1998-05-28

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Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001046230A3 (fr) * 1999-12-22 2002-01-03 Zymogenetics Inc Polypeptide zkun11 a domaine de kunitz
WO2001064888A3 (fr) * 2000-02-29 2002-02-28 Zymogenetics Inc Polypeptide zkun8 a domaine kunitz
US6544760B2 (en) 1999-12-22 2003-04-08 Zymogenetics, Inc. Kunitz domain polypeptide Zkun11
JP2004504838A (ja) * 2000-07-27 2004-02-19 カイロン　コーポレイション Ｇｓｋ３ポリペプチド
WO2007049065A3 (fr) * 2005-10-27 2007-08-09 Ares Trading Sa Proteine contenant des domaines vwfa, collagene et kunitz

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1995021601A2 (fr) * 1994-01-11 1995-08-17 Protein Engineering Corporation Proteines de 'domaine de kunitz' a activite antikallikreine, et leurs analogues
WO1996035788A2 (fr) * 1995-05-08 1996-11-14 Scios, Inc. Peptides inhibiteurs de proteases de type kunitz

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1995021601A2 (fr) * 1994-01-11 1995-08-17 Protein Engineering Corporation Proteines de 'domaine de kunitz' a activite antikallikreine, et leurs analogues
WO1996035788A2 (fr) * 1995-05-08 1996-11-14 Scios, Inc. Peptides inhibiteurs de proteases de type kunitz

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
DATABASE EMBL NUCLEOTIDE SEQU 1 January 1900 (1900-01-01), XP002114490, Database accession no. AI554767 *
DATABASE EMBL NUCLEOTIDE SEQU 1 January 1900 (1900-01-01), XP002114491, Database accession no. AI217375 *

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001046230A3 (fr) * 1999-12-22 2002-01-03 Zymogenetics Inc Polypeptide zkun11 a domaine de kunitz
US6544760B2 (en) 1999-12-22 2003-04-08 Zymogenetics, Inc. Kunitz domain polypeptide Zkun11
WO2001064888A3 (fr) * 2000-02-29 2002-02-28 Zymogenetics Inc Polypeptide zkun8 a domaine kunitz
JP2004504838A (ja) * 2000-07-27 2004-02-19 カイロン　コーポレイション Ｇｓｋ３ポリペプチド
WO2007049065A3 (fr) * 2005-10-27 2007-08-09 Ares Trading Sa Proteine contenant des domaines vwfa, collagene et kunitz

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AU4207499A (en) 1999-12-13
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EP1082430A1 (fr) 2001-03-14

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