Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/12—Antivirals
  • A61P31/20—Antivirals for DNA viruses
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
  • C12N2770/00011—Details
  • C12N2770/24011—Flaviviridae
  • C12N2770/24211—Hepacivirus, e.g. hepatitis C virus, hepatitis G virus
  • C12N2770/24222—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes

Definitions

• Hepatitis C virus is considered to be the major etiological agent of non-A non-B (NANB) hepatitis, chronic liver disease, and hepatocellular carcinoma (HCC) around the world.
• NANB non-A non-B
• HCC hepatocellular carcinoma
• the viral infection accounts for greater than 90% of transfusion -associated hepatitis in U.S. and it is the predominant form of hepatitis in adults over 40 years of age. Almost all of the infections result in chronic hepatitis and nearly 20% develop liver cirrhosis.
• the virus particle has not been identified due to the lack of an efficient in vitro replication system and the extremely low amount of HCV particles in infected liver tissues or blood.
• molecular cloning of the viral genome has been accomplished by isolating the messenger RNA (mRNA) from the serum of infected chimpanzees then cloned using recombinant methodologies.
• mRNA messenger RNA
• HCV contains a positive strand RNA genome comprising approximately 9400 nucleotides, whose organization is similar to that of f la vi viruses and pestiviruses.
• the genome of HCV like that of flavi- and pestiviruses, encodes a single large polyprotein of about 3000 amino acids which undergoes proteolysis to form mature viral proteins in infected cells.
• HCV polyprotein is processed by cellular and viral proteases to produce the putative structural and nonstructural (NS) proteins.
• At least nine mature viral proteins are produced from the polyprotein by specific proteolysis.
• the order and nomenclature of the cleavage products are as follows: NH 2 -C-El-E2-NS2-NS3-NS4A-NS4B-NS5A-NS5B-COOH.
• C capsid
• El two envelope glycoproteins
• the host enzyme is also responsible for generating the amino terminus of NS2 .
• the proteolytic processing of the nonstructural proteins are carried out by the viral proteases: NS2-3 and NS3, contained within the viral polyprotein.
• the NS2-3 protease catalyzes the cleavage between NS2 and NS3. It is a metalloprotease and requires both NS2 and the protease domain of NS3.
• the NS3 protease catalyzes the rest of the cleavages of the substrates in the nonstructural part of the polyprotein.
• the NS3 protein contains 631 amino acid residues and is comprised of two enzymatic domains: the protease domain contained within amino acid residues 1-181 and a helicase ATPase domain contained within the rest of the protein. It is not known if the 70 kD NS3 protein is cleaved further in infected cells to separate the protease domain from the helicase domain, however, no cleavage has been observed in cell culture expression studies.
• the NS3 protease is a member of the serine proteinase class of enzymes. It contains His, Asp, and Ser as the catalytic triad. Mutation of the catalytic triad residues abolishes the cleavages at substrates NS3/4A, NS4A/4B, NS4B/5A, and NS5A/5B.
• the cleavage between NS3 and NS4A is mediated through an intramolecular enzymatic reaction, whereas the cleavages at NS4A/4B, 4B/5A, 5A/5B sites occur in a trans enzymatic reaction.
• NS polyproteins in mammalian cells have established that the NS3 serine protease is necessary but not sufficient for efficient processing of all these cleavages.
• the HCV NS3 protease also requires a cofactor to catalyze some of these cleavage reactions.
• the NS4A protein is absolutely required for the cleavage of the substrate at the NS3/4A and 4B/5A sites and increases the efficiency of cleavage of the substrate between 5A/5B, and possibly 4A/4B.
• the HCV NS3 protease cleaves the non-structural HCV proteins which are necessary for the HCV replication, the NS3 protease can be a target for the development of therapeutic agents against the HCV virus. Thus there is a need for the development of inhibitors of the HCV protease.
• the present invention fills this need by providing for a bivalent inhibitor of an hepatitis C NS3 protease comprised of a first peptide linked to a second peptide, said first peptide being a subsequence, mutated subsequence or a mutated full-length sequence of a substrate of the hepatitis C NS3 protease and said second peptide being a subsequence, a mutated subsequence or a mutated full-length sequence of a hepatitis C NS4A polypeptide.
• the present application further provides for an inhibitor of an HCV protease comprised of a peptide, said peptide being a subsequence, a mutated subsequence, or a mutated full-length sequence of a substrate of the HCV NS3 protease.
• the present application further provides for an inhibitor of an HCV NS3 protease comprised of a peptide, said peptide being a subsequence, a mutated subsequence or a mutated full-length sequence of an HCV NS4A polypeptide.
• the present invention further comprises a method for treating an individual infected with the HCV virus comprising administering an inhibitor of an HCV NS3 protease to said individual, said inhibitor being comprised of a first peptide linked to a second peptide, said first peptide being a subsequence, a mutated subsequence or a mutated full- length sequence of a substrate of the hepatitis C NS3 protease and said second peptide being a subsequence, a mutated subsequence or a mutated full-length sequence of a hepatitis C NS4A polypeptide.
• the present invention further comprises a method for treating an individual infected with the HCV virus comprising administering an inhibitor of an HCV NS3 protease to said individual, said inhibitor being comprised of a peptide, said peptide being a subsequence, a mutated subsequence or a mutated full-length sequence of a substrate of the HCV NS3 protease.
• the present invention further comprises a method for treating an individual infected with the HCV virus comprising administering an inhibitor of an HCV NS3 protease to said individual, said inhibitor being comprised of a peptide, said peptide being a subsequence, a mutated subsequence or a mutated full-length sequence of an HCV NS4A polypeptide.
• the present invention further comprises a pharmaceutical composition for treating an individual infected with hepatitis C virus, said pharmaceutical composition being an inhibitor of an HCV NS3 protease, said inhibitor being comprised of a first peptide linked to a second peptide, said first peptide being a subsequence, a mutated subsequence or a mutated full-length sequence of a substrate of the hepatitis C NS3 protease and said second peptide being a subsequence, a mutated subsequence or a mutated full-length sequence of a hepatitis C NS4A polypeptide, and a pharmaceutical carrier.
• a pharmaceutical composition for treating an individual infected with hepatitis C virus said pharmaceutical composition being an inhibitor of an HCV NS3 protease, said inhibitor being comprised of a first peptide linked to a second peptide, said first peptide being a subsequence, a mutated
• the present invention further provides for a pharmaceutical composition for treating an individual infected with hepatitis C virus, said pharmaceutical composition being comprised of an inhibitor of an HCV NS3 protease and a pharmaceutical carrier, said inhibitor being a subsequence, a mutated subsequence or a mutated full-length sequence of a substrate of the HCV NS3 protease.
• the present invention further provides for a pharmaceutical composition for treating an individual infected with hepatitis C virus, said pharmaceutical composition being comprised of an inhibitor of an HCV NS3 protease and a pharmaceutical carrier, wherein said inhibitor is comprised of a peptide, said peptide being a subsequence, a mutated subsequence or a mutated full-length subsequence of an HCV NS4A polypeptide.
• Figure 1 schematically depicts an embodiment of a bivalent inhibitor of the present invention.
• Figure 2 depicts the recombinant synthesis of plasmid pBJ1015.
• Figure 3 depicts the recombinant synthesis of plasmid pTS56-9.
• Figure 4 depicts the recombinant synthesis of plasmid pJB1006.
• Figure 5 depicts the recombinant synthesis of plasmid pBJ1022.
• Figure 6 depicts the recombinant synthesis of plasmid pNB(-V)182 ⁇ 4AHT.
• Figure 7 depicts the recombinant synthesis of plasmid pT5His/HIV/183.
• the present invention are inhibitors of the HCV NS3 protease.
• the present invention relates to inhibitors of the HCV NS3 protease which inhibit either the interaction of a substrate or cofactor NS4A with the NS3 protease or a bivalent inhibitor which inhibits the interaction of the NS3 protease with both cofactor NS4A and a substrate of the NS3 protease.
• bivalent enzyme inhibitors may provide additional advantages in terms of higher binding affinity (potency), as well as enhanced specificity against similar cellular host enzymes for reduced toxicity effects.
• the basic strategy for the design of bivalent inhibitors of HCV NS3 protease involved the devise of a molecular framework consisting of three individual components: 1. a region appropriate for binding to a substrate binding site;
• Figure 1 Schematically, this is represented by Figure 1 in which the substrate subsequence is depicted as block, 10, being attached to linker 12, and said linker 12 being attached to the polypeptide NS4A designated 14.
• a substrate inhibitor which is a subsequence of the inhibitor should be a subsequence which is prior to or after the cleavage site but preferably should not contain the cleavage site.
• a mutated subsequence or mutated full-length sequence of the substrate can be used if the cleavage site is mutated so that the cleavage of the substrate does not occur cleavage leads to mechanism-based inactivation of the protease.
• the NS3/4A cleavage site contains the following sequence:
• the cleavage site is between the threonine at position 10 and the serine at position 11.
• Any subsequence inhibitor should preferably be before the serine or after the threonine residue.
• a mutated subsequence or sequence can be produced by changing the threonine /serine cleavage site at position 10-11 to eliminate the cleavage site.
• NS4A/4B contains the following sequence.
• the cleavage site is between the cysteine residue at position 10 and the serine at position 11. Any subsequence should preferably be before the serine or after the cysteine, but should preferably not contain both the cysteine and the serine. Alternatively, a mutated subsequence or sequence can be produced by changing the cysteine /serine cleavage site at position 10 - 11 to eliminate the cleavage site.
• NS4B/5A contains the following sequence.
• Trp He Ser Ser Glu Cys Thr Thr Pro Cys Ser Gly Ser Trp Leu 5 10 15
• the cleavage site is between the cysteine at position 10 and serine at position 11. Any subsequence should preferably end before the serine or start after the cysteine but should preferably not contain both the serine and the cysteine. Alternatively, a mutated subsequence or sequence can be produced by changing the cysteine /serine cleavage sit at position 10 - 11 to eliminate the cleavage site.
• NS5A/5B contains the following sequence. Asp Thr Glu Asp Val Val Cys Cys Ser Met Ser Tyr Thr Trp Thr
• the cleavage site is between the cysteine at position 8 and the serine at position 9. Any subsequence should preferably end at the cysteine or start at the serine, but should preferably not contain both the cysteine and the serine. Alternatively, a mutated sequence or subsequence can be produced by changing the cysteine /serine cleavage site at position 8 - 9 to eliminate the cleavage site.
• Linker 12 can be any chemical entity that can form a bond with polypeptides 10 and 14. Preferably the linker should be equivalent in length to a carbon chain having about 7-14 carbon residues. Examples of suitable linkers are two 6-aminocaproic acid (Acp) residues or an Acp and Lys wherein one of the polypeptides 10 or 14 form a peptide bond with the ⁇ amine of lysine.
• bivalent inhibitors of the present invention are the following:
• Xaa is a lysine residue having a peptide bond between its ⁇ -amino and the carboxyl group of the following lysine which forms a peptide bond with the glycine at position 10.
• the glutamic acid residue at position 1 may or may not be acety lated.
• Xaa is Lysine having a peptide bond between its ⁇ -amino and the carboxyl group of the following lysine which forms a peptide bond with the Gly; furthermore, the carboxyl group of the Xaa forms a peptide bond with the ⁇ -amino group of another lysine (not shown);
• Glu-Asp-Val-Val-Cys-Cys-Acp-Acp-Lys-Gly-Ser-Leu-Val- Ile-Arg-Gly-Val-Ile-Val-Val-Cys (SEQ ID NO: 5) wherein the amino acids at positions 9-21 are preferably D-amino acids;
• the lysine residue at position 8 has a peptide bond between the carboxyl of Acp and the ⁇ amino group of the lysine, and the ⁇ amino group of the lysine at position 8 forms a peptide bond with the carboxyl group of the cysteine residue at position 9 and the amino acid residues at positions 9-21 are preferably D-amino acid residues;
• amino acid residues at positions 8-20 are preferably D- amino acid residues
• Xaa is a Lys which forms a peptide bond between its ⁇ - amino acid and the carboxyl group of the Cys residue at position 8 and the carboxyl group of the Lys residue forms a peptide bond with an alpha amino group of another Lys residue (not shown), preferably the amino acid residues at positions 8 - 20 are D- amino acids.
• Suitable monovalent inhibitors of the present invention are the following:
• Lys-Gly-Ser-Leu-Val-Ile-Arg-Gly-Val-Ile-Val-Val-Cys-Lys (SEQ ID NO.: 9) wherein the amino acid residues at positions 1- 13 are preferably D-amino acid residues;
• Lys-Gly-Ser-Leu-Val-Ile-Arg-Gly-Val-Ile-Val-Lys (SEQ ID NO.: 10) wherein amino acid residues at positions 1 - 11 are preferably D-amino acid residues; Cys-Val-Val-Ile-Val-Gly-Arg-Ile-Val-Leu-Ser-Gly-Lys (SEQ ID NO.: 11) wherein the amino acid residues are preferably D-amino acid residues;
• amino acid residues are preferably D-amino acid residues and the serine residue at position 1 has been preferably acety lated;
• Lys-Gly-Ser-Leu-Val-Ile-Arg-Gly-Val-Ile-Val-Val-Cys (SEQ ID NO.: 13) wherein the amino acid residues are preferably D-amino acid residues the lysine residue at position 1 is preferably acetylated;
• Xaa-Lys-Gly-Ser-Leu-Val-Ile-Arg-Gly-Val-Ile Val-Val-Cys-Lys-Lys (SEQ ID NO.: 14); wherein Xaa is biotin and the amino acid residues at positions 2 - 14 are preferably D-amino acid residues;
• Xaa is a lysine residue in which the ⁇ amino group of the lysine forms a peptide bond with a biotin, and amino acid residues at positions 1 - 13 are preferably D-amino acid residues.
• the inhibitors of the present invention can be synthesized by a suitable method such as by exclusive solid phase synthesis, partial solid phase methods, fragment condensation or classical solution synthesis.
• the polypeptides are preferably prepared by solid phase peptide synthesis as described by Merrifield, J. Am. Chem. Soc. 85:2149 (1963). The synthesis is carried out with amino acids that are protected at the alpha-amino terminus. Trifunctional amino acids with labile side- chains are also protected with suitable groups to prevent undesired chemical reactions from occurring during the assembly of the polypeptides.
• the alpha-amino protecting group is selectively removed to allow subsequent reaction to take place at the amino-terminus. The conditions for the removal of the alpha-amino protecting group do not remove the side-chain protecting groups.
• alpha-amino protecting groups are those known to be useful in the art of stepwise polypeptide synthesis. Included are acyl type protecting groups (e.g., formyl, trifluoroacetyl, acetyl), aryl type protecting groups (e.g.
• biotinyl aromatic urethane type protecting groups [e.g., benzyloxycarbonyl (Cbz), substituted benzyloxycarbonyl and 9-fluorenylmethyloxy-carbonyl (Fmoc)], aliphatic urethane protecting groups [e.g., t-butyloxycarbonyl (tBoc), isopropyloxycarbonyl, cyclohexyloxycarbonyl] and alkyl type protecting groups (e.g., benzyl, triphenylmethyl).
• the preferred protecting groups are tBoc and Fmoc, thus the peptides are said to be synthesized by tBoc and Fmoc chemistry, respectively.
• the side-chain protecting groups selected must remain intact during coupling and not be removed during the deprotection of the amino-terminus protecting group or during coupling conditions.
• the side-chain protecting groups must also be removable upon the completion of synthesis, using reaction conditions that will not alter the finished polypeptide.
• the side-chain protecting groups for trifunctional amino acids are mostly benzyl based.
• Fmoc chemistry they are mostly tert.-butyl or trityl based.
• the preferred side-chain protecting groups are tosyl for Arg, cyclohexyl for Asp, 4-methylbenzyl (and acetamidomethyl) for Cys, benzyl for Glu, Ser and Thr, benzyloxymethyl (and dinitrophenyl) for His, 2-Cl-benzyloxycarbonyl for Lys, formyl for Trp and 2-bromobenzyl for Tyr.
• the preferred side-chain protecting groups are 2,2,5,7,8- pentamethylchroman-6-sulfonyl (Pmc) or 2,2,4,6,7- pentamethyldihydrobenzofuran-5-sulfonyl (Pbf) for Arg, trityl for Asn, Cys, Gin and His, tert-butyl for Asp, Glu, Ser, Thr and Tyr, tBoc for Lys and Trp.
• Solid phase synthesis is usually carried out from the carboxyl- terminus by coupling the alpha-amino protected (side-chain protected) amino acid to a suitable solid support.
• An ester linkage is formed when the attachment is made to a chloromethyl, chlortrityl or hydroxymethyl resin, and the resulting polypeptide will have a free carboxyl group at the C-terminus.
• an amide resin such as benzhydrylamine or p-methylbenzhydrylamine resin (for tBoc chemistry) and Rink amide or PAL resin (for Fmoc chemistry) is used, an amide bond is formed and the resulting polypeptide will have a carboxamide group at the C-terminus.
• the C-terminal amino acid is attached to a hydroxylmethyl resin using various activating agents including dicyclohexylcarbodiimide (DCC), N,N'-diisopropylcarbodiimide DIPCDI) and carbonyldiimidazole (CDI). It can be attached to chloromethyl or chlorotrityl resin directly in its cesium tetramethylammonium salt form or in the presence of triethylamine (TEA) or diisopropylethylamine (DIE A).
• DCC dicyclohexylcarbodiimide
• DIPCDI N,N'-diisopropylcarbodiimide
• CDI carbonyldiimidazole
• the alpha- amino protecting group is removed using various reagents depending on the protecting chemistry (e.g. , tBoc, Fmoc). The extent of Fmoc removal can be monitored at 300-320 nm or by a conductivity cell. After removal of the alpha-amino protecting group, the remaining protected amino acids are coupled stepwise in the required order to obtain the desired sequence.
• activating agents can be used for the coupling reactions including DCC, DIPCDI, 2-chloro-l,3-dimethylimidium hexafluorophosphate (CIP), benzotriazol-1-yl-oxy-tris- (dimethylamino)-phosphonium hexafluorophosphate (BOP) and its pyrrolidine analog (PyBOP), bromo-tris-pyrrolidino-phosphonium hexafluorophosphate (PyBroP), N- [(lH-benzotriazol-1-yl) - (dimethylamino) methylene] -N-methylmethanaminium hexaflourophosphate N-oxide (HBTU) and its tetrafluoroborate analog (TBTU) or its pyrrolidine analog (HBPyU), (HATU) and its tetrafluoroborate analog (TATU) or pyrrolidine analog (HAPyU).
• DCC di
• the most common catalytic additives used in coupling reactions include 4-dimethylaminopyridine (DMAP), 3-hydroxy-3,4-dihydro-4-oxo- 1,2,3-benzotriazine (HODhbt), N-hydroxybenzotriazole (HOBt) and 1- hydroxy-7-azabenzotriazole (HOAt).
• DMAP 4-dimethylaminopyridine
• HODhbt 3-hydroxy-3,4-dihydro-4-oxo- 1,2,3-benzotriazine
• HOBt N-hydroxybenzotriazole
• 1- hydroxy-7-azabenzotriazole HOAt
• Amino acid flourides or chlorides may be used for difficult couplings. Each protected amino acid is used in excess (>2.0 equivalents), and the couplings are usually carried out in N-methylpyrrolidone (NMP) or in DMF, CH2O2 or mixtures thereof.
• NMP N-methylpyrrolidone
• the extent of completion of the coupling reaction can be monitored at each stage, e.g., by the ninhydrin reaction as described by Kaiser et al, Anal. Biochem. 34:595 (1970). In cases where incomplete coupling is found, the coupling reaction is extended and repeated and may have chaotropic salts added.
• the coupling reactions can be performed automatically with commercially available instruments such as ABI model 430A, 431A and 433A peptide synthesizers.
• the peptide- resin is cleaved with a reagent with proper scavengers.
• the Fmoc peptides are usually cleaved and deprotected by TFA with scavengers (e.g., H2O, ethanedithiol, phenol and thioanisole).
• the tBoc peptides are usually cleaved and deprotected with liquid HF for 1-2 hours at -5 to 0°C, which cleaves the polypeptide from the resin and removes most of the side-chain protecting groups.
• Scavengers such as anisole, dimethylsulfide and p-thiocresol are usually used with the liquid HF to prevent cations formed during the cleavage from alkylating and acylating the amino acid residues present in the polypeptide.
• the formyl group of Trp and dinitrophenyl group of His need to be removed, respectively, by piperidine and thiophenol in DMF prior to the HF cleavage.
• the acetamidomethyl group of Cys can be removed by mercury(II) acetate and alternatively by iodine, thallium (III) trifluoroacetate or silver tetrafluoroborate which simultaneously oxidize cysteine to cystine.
• Other strong acids used for tBoc peptide cleavage and deprotection include trifluoromethanesulfonic acid (TFMSA) and trimethylsilyltrifluoroacetate (TMSOTf).
• peptides of the present invention were assembled from a Fmoc-Amide resin or a Fmoc-L-Lys- (tBoc) - Wang resin on an ABI model 433A synthesizer (Applied Biosystems, Foster City, CA) by solid phase peptide synthesis method as originally described by Merrifield, J. Am.Chem.Soc. 85:2149 (1963) but with Fmoc chemistry.
• the side chains of trifunctional amino acids were protected by tert.-butyl for Glu, Asp and Ser, trityl for Cys, tert.-butyloxycarbonyl (tBoc) for Lys and 2,2,5,7,8-pentamethylchroman-6-sulfonyl (Pmc) or 2,2,4,6,7- pentamethyldihydrobenzofuran-5-sulfonyl (Pbf) for Arg.
• N-a-Fmoc protected amino acids were pre-activated by HATU and 1 -hydroxy- 7- azabenzotriazole (HOAt) prior to coupling to the resin.
• Dimethylsulfoxide (20%) was added during conditional extended coupling and Fmoc deprotection reactions.
• the synthesis of the inhibitors SEQ ID NOs: 1, 2, 5, 7, and 9-15 was accomplished by sequential and linear assembly of appropriate D- and L-amino acids and achiral amino acids (Gly and Ahx).
• the synthesis of the inhibitors SEQ ID NOs: 3, 4, 6, and 8 required orthogonal chain assembly anchored at a Lys residue whose side chain amino group was protected by l-(4,4- dimethyl-2,6-dioxocyclohex-l-ylidene)-ethyl (Dde).
• SPA scintillation proximity assay
• SPA technology involves the use of beads coated with scintillant.
• acceptor molecules such as antibodies, receptors or enzyme substrates which interact with ligands or enzymes in a reversible manner.
• the substrate peptide is biotinylated at one end and the other end is radiolabelled with low energy emitters such as 125 I or 3 H.
• the labeled substrate is then incubated with the enzyme.
• Avidin coated SPA beads are then added which bind to the biotin.
• the radioactive emitter is no longer in proximity to the scintillant bead and no light emission takes place.
• Inhibitors of the protease will leave the substrate intact and can be identified by the resulting light emission which takes place in their presence.
• a suitable assay technique is an HPLC assay in which the resultant reaction mixture containing the NS3 protease, the substrate products and the potential inhibitor is resolved on an HPLC column to determine the extent of the cleavage of the substrate. If the substrate has not been cleaved or the cleavage has been inhibited, then only the intact substrate would be present or a reduced amount of the cleaved product will be shown to be present. If this is the case, then the compound is an effective inhibitor of the NS3 protease.
• the dosage level of inhibitors necessary for effective therapy to inhibit the HCV NS3 protease will depend upon many different factors, including means of administration, target site, physiological state of the patient, and other medicants administered. Thus, treatment dosages should be titrated to optimize safety and efficacy. Typically, dosages used in vitro may provide useful guidance in the amounts useful for in situ administration of these reagents. Animal testing of effective doses for treatment of particular disorders will provide further predictive indication of human dosage. Various considerations are described, e.g., in Gilman, et al. (eds.) (1990) Goodman and Gilman's: The Pharmacological Bases of Therapeutics, 8th Ed., Pergamon Press; and Remington's Pharmaceutical Sciences. 17th ed.
• Pharmaceutically acceptable carriers will include water, saline, buffers, and other compounds described, e.g., in the Merck Index. Merck & Co., Rahway, New Jersey, l ⁇ g per kilogram weight of the patient to 500 mg per kilogram weight of the patient with an appropriate carrier is a range from which the dosage can be chosen. Slow release formulations, or a slow release apparatus will often be utilized for continuous administration.
• the inhibitors of the HCV NS3 protease of the present invention may be administered directly to the host to be treated or, depending on the size of the compounds, it may be desirable to conjugate them to carrier proteins such as ovalbumin or serum albumin prior to their administration.
• Therapeutic formulations may be administered in any conventional dosage formulation. While it is possible for the active ingredient to be administered alone, it is preferable to present it as a pharmaceutical formulation.
• Formulations typically comprise at least one active ingredient, as defined above, together with one or more acceptable carriers thereof. Each carrier should be both pharmaceutically and physiologically acceptable in the sense of being compatible with the other ingredients and not injurious to the patient.
• Formulations include those suitable for oral, rectal, nasal, or parenteral (including subcutaneous, intramuscular, intravenous and intradermal) administration.
• the formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. See, e.g., Gilman, et al. (eds.) (1990) Goodman and Gilman's: The Pharmacological Bases of Therapeutics. 8th Ed., Pergamon Press, Parrytown, NY; Remington's Pharmaceutical Sciences. 17th ed. (1990), Mack Publishing Co., Easton, Perm.; Avis, et al. (eds.)(1993) Pharmaceutical Dosage Forms: Parenteral Medications 2d ed., Dekker, NY; Lieberman, et al.
• compositions Tablets 2d ed., Dekker, NY; and Lieberman, et al. (eds.)(1990) Pharmaceutical Dosage Forms: Disperse Systems Dekker, NY.
• the therapy of this invention may be combined with or used in association with other chemotherapeutic or chemopreventive agents.
• bivalent inhibitors of defined by SEQ ID NOs.: 1-10 were synthetically produced as described above and tested for their ability to inhibit the HCV NS3 protease as follows.
• aqueous solution containing 25 mM TRIS, 50 mM NaCl, .5 mM EDTA, 10% glycerol and .1% NP40 was placed the potential inhibitor, the HCV NS3 protease at a concentration of 0.05 ⁇ M - 0.1 mM, the HCV NS4A cofactor at a concentration of 0.05 ⁇ M - 0.1 ⁇ M and the 5A/5B substrate at a concentration of 50 ⁇ M.
• This solution was then incubated for approximately 2 hours at 30°C after which the solution was applied to an HPLC to determine if the 5A/5B remained intact and thus the compound was determined to be an inhibitor.
• Examples of monovalent inhibitors of the HCV NS3 protease are as follows.
• plasmids were designed and constructed using standard recombinant DNA techniques (Sambrook,Fritsch & Maniatis) to express the HCV protease in E. coli (Fig 2-7). All HCV specific sequences originated from the parental plasmid pBRTM/HCV 1-3011 (Grakoui et ⁇ Z.1993). To express the N-terminal 183 amino acid versions of the protease, a stop codon was inserted into the HCV genome using synthetic oligonucleotides (Fig. 3). The plasmids designed to express the N-terminal 246 amino acid residues were generated by the natural Ncol restriction site at the C-terminus.
• the plasmid pBRTM/HCV 1-3011 containing the entire HCV genome was digested with the restriction enzymes Sea I and Hpa I and the 7138 bp (base pair) DNA fragment was isolated and cloned to the Sma I site of pSP72 (Promega) to produce the plasmid, pRJ201.
• the plasmid pRJ 201 was digested with Mse I and the 2106 bp Mse I fragment was isolated and cloned into the Sma I site of the plasmid pBD7.
• the resulting plasmid pMBM48 was digested with Kas I and Nco I, and the 734 bp DNA fragment after blunt ending with Klenow polymerase was isolated and cloned into Nco I digested, klenow polymerase treated pTrc HIS B seq expression plasmid (Invitrogen). The ligation regenerated a Nco I site at the 5' end and Nsi I site at the 3' end of HCV sequence.
• the plasmid pTHB HCV NS3 was then digested with Nco I and Nsi I, and treated with klenow polymerase and T4 DNA polymerase, to produce a blunt ended 738 bp DNA fragment which was isolated and cloned into Asp I cut, klenow polymerase treated expression plasmid pQE30 (HIV).
• the resulting plasmid pBJ 1015 expresses HCV NS3 (246 amino acids) protease.
• the plasmid pTHB HCV NS3 was digested with Nco I, treated with klenow polymerase, then digested with Bst Y I; and the DNA fragment containing HCV sequence was isolated and cloned into Sma I and Bgl II digested pSP72.
• the resulting plasmid pTS 49-27 was then digested with Bgl II and Hpa I and ligated with a double stranded oligonucleotide:
• the plasmid pTS 56-9 was digested with Sph I and Bgl II and the DNA fragment containing HCV sequence was isolated and cloned into a Sph I, Bgl II cut pSP72.
• the resulting plasmid pJB 1002 digested with Age I and Hpal and ligated to a double stranded oligonucleotide,
• the plasmid pJB 1006 was digested with NgoM I and Nhe I and the 216 bp DNA fragment was isolated and cloned into Ngo M I, Nhe I cut pBJ 1015 to construct plasmid pBJ 1019.
• the plasmid pBJ 1019 was digested with Nar I and Pvu II, and treated with Klenow polymerase to fill in 5' ends of Nar I fragments.
• the expression plasmid pQE31 (Invitrogen) was digested with BamH I, blunt ended with Klenow polymerase.
• the 717 bp Nar I- Pvu II DNA fragment was isolated and ligated to the 2787 bp BamH I/Klenowed -Mse I (Bal I) fragment of the expression plasmid pQE31 (Invitrogen).
• the recombinant plasmid, pBJ 1022 obtained after transformation into E.coli expresses His NS3(2-183)-HT which does not contain any HIV protease cleavage site sequence.
• the plasmid also contains a large deletion in the CAT (Chloramphenicol Acetyl Transferase) gene.
• the 220 bp DNA fragment was isolated and cloned into the expression plasmid pQE30 which was digested with BamH I and blunt ended with Klenow polymerase prior to ligation.
• the resulting plasmid pJB 1011 was digested with NgoM I and Hind III and ligated to a double stranded oligonucleotide ,
• the plasmid pNB 4AHT was digested with Msl I and Xba I.
• the 1218 bp DNA fragment was isolated and cloned into Age I cut, klenow polymerase treated, Xba I cut vector DNA of pBJ 1019.
• the ligation results in a substitution of the 183rd amino acid residue valine by a gly cine residue in NS3, and a deletion of amino terminal three amino acid residues of NS4A at the junction.
• the recombinant plasmid pNB182 ⁇ 4A HT comprising NS3(182aa)-G- NS4A(4-54 amino acid) does not contain NS3/NS4A cleavage site sequence at the junction and is not cleaved by the autocatalytic activity of NS3.
• the plasmid pNB182 ⁇ 4A HT (SEQ ID NO 8) was digested with Stu I and Nhe I, the 803 bp DNA fragment was isolated and cloned into Stu I and Nhe I cut plasmid pBJ 1022.
• the resulting plasmid pNB(- V)182- ⁇ 4A HT contains a deletion of the HIV sequence from the amino terminus end of the NS3 sequence and in the CAT gene (SEQ ID NO 23).
• the recombinant plasmids ⁇ BJ1022 and pNB(-V)182 ⁇ 4A were used to transform separate cultures of E. coli strain M15 [pREP4] (Qiagen), which over-expresses the lac repressor, according to methods recommended by the manufacturer.
• M15 [pREP4] bacteria harboring recombinant plasmids were grown overnight in broth containing 20g/L bactotrypton, lOg/L bacto-yeast extract, 5g/L NaCl (20-10-5 broth) and supplemented with lOO ⁇ g/ml ampicillin and 25 ⁇ g/ml kanamycin.
• Cultures were diluted down to O.D.600 of 0.1, then grown at 30°C to O.D.600 of 0.6 to 0.8, after which IPTG was added to a final concentration of lmM. At post-induction 2 to 3 hours, the cells were harvested by pelleting, and the cell pellets were washed with lOOmM Tris, pH 7.5. Cell lysates were prepared as follows: to each ml equivalent of pelleted fermentation broth was added 50 ⁇ l sonication buffer (50mM sodium phosphate, pH 7.8, 0.3M NaCl) with lmg/ml lysozyme; cell suspension was placed on ice for 30 min.
• 50 ⁇ l sonication buffer 50mM sodium phosphate, pH 7.8, 0.3M NaCl
• NTA Ni 2+ -Nitrosyl acetic acid
• the proteins were then purified by placing the extracted lysate on an NTA agarose column.
• NTA agarose column chromatography was used because the histidine tag which was fused to the N-terminus of the proteases readily binds to the nickel column. This produces a powerful affinity chromatographic technique for rapidly purifying the soluble protease.
• the column chromatography was performed in a batch mode.
• the Ni 2+ NTA resin (3ml) was washed twice with 50 ml of Buffer A ( 50mM sodium phosphate pH 7.8 containing 10% glycerol, 0.2% Tween- 20, lOmM BME).
• the lysate obtained from a 250 ml fermentation (12.5 ml) was incubated with the resin for one hour at 4°C. The flow through was collected by centrifugation. The resin was packed into a 1.0 x 4 cm column and washed with buffer A until the baseline was reached. The bound protein was then eluted with a 20 ml gradient of imidazole (0- 0.5M) in buffer A. Eluted fractions were evaluated by SDS-PAGE and western blot analysis using a rabbit polyclonal antibody to His-HrV 183.
• the lysate containing the proteins were applied to a POROS metal-chelate affinity column.
• Perfusion chromatography was performed on a POROS MC metal chelate column (4.6 x 50mm, 1.7 ml) precharged with Ni 2+ .
• the sample was applied at 10 ml/min and the column was washed with buffer A.
• the column was step eluted with ten column volumes of buffer A containing 25 mM imidazole.
• the column was further eluted with a 25 column volume gradient of 25-250 mM imidazole in buffer A. All eluted fractions were evaluated by SDS-PAGE and western blot analysis using rabbit polyclonal antibody.
• the peptides 5A/5B and 4B/5A substrates (SEQ ID NOs 16, 18, 19, 20 and 21) were synthesized using Fmoc chemistry on an ABI model 431 A peptide synthesizer.
• the manufacture recommended FastMocTM activation strategy (HBTU/HOBt) was used for the synthesis of 4A activator peptide.
• a more powerful activator, HATU with or without the additive HO At were employed to assemble 5A/5B substrate peptides on a preloaded Wang resin.
• the peptides were cleaved off the resin and deprotected by standard TFA cleavage protocol.
• the peptides were purified on reverse phase HPLC and confirmed by mass spectrometric analysis.
• the DTEDWCC SMSYTWTGK (SEQ ID NO 16) and soluble HCV NS3 (SEQ ID NO 27) were placed together in an assay buffer.
• the assay buffer was 50mM sodium phosphate pH 7.8, containing 15% glycerol, lOmM DTT, 0.2% Tween20 and 200 mM NaCl).
• the protease activity of SEQ ID NO 27 cleaved the substrate into two byproduct peptides, namely 5A and 5B. The substrate and two byproduct peptides were separated on a reversed- phase HPLC column.
• Xaa is lysine having a peptide bond between its ⁇ -amino group and the carboxyl group of lysine at position 8.
• the carboxyl group of the Xaa forms a peptide bond with the ⁇ -amino group of another lysine (not shown);
• the lysine residue at position 8 has a peptide bond between the carboxyl group of Acp and the a amino group of the lysine, and the ⁇ amino group of the lysine at position 8 forms a peptide bond with the carboxyl group of the cysteine residue at position 9 and the amino acid residues at positions 9-21 are preferably D-amino acid residues;
• Xaa is a lysine wherein the ⁇ amino group of which forms a peptide bond with the carboxyl group of the cysteine residue at position 8 and the carboxyl group of the lysine residue forms a peptide bond with an ⁇ amino group of another lysine residue (not shown), preferably the amino acid residues at positions 8 - 20 are D- amino acid residues.
• amino acid residues at positions 1- 13 are preferably D-amino acid residues and lysine at position 14 is preferably an L-amino acid residue;
• amino acid residues are preferably D-amino acid residues.
• amino acid residues are preferably D-amino acids and the serine residue at position 1 is preferably acetylated;
• Xaa is biotin and the amino acid residues at positions 2 - 14 are preferably D-amino acids;
• Xaa is a lysine residue in which the ⁇ amino group of the lysine forms a peptide bond with a biotin and amino acid residues at positions 1 - 13 are preferably D-amino acid residues.
• NAME/KEY NS4A AGC ACC TGG GTG CTC GTT GGC GGC GTC CTG GCT GCT CTG GCC GCG 45 Ser Thr Trp Val Leu Val Gly Gly Val Leu Ala Ala Leu Ala Ala 1 5 10 15
• NAME/KEY NS4A/4B Cleavage Site Tyr Gin Glu Phe Asp Glu Met Glu Glu Cys Ser Gin His Leu Pro
• Trp He Ser Ser Glu Cys Thr Thr Pro Cys Ser Gly Ser Trp Leu

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