WO2009021121A2 - Identification and characterization of hcv replicon variants with reduced susceptibility to a combination of polymerase and protease inhibitors, and methods related thereto - Google Patents

Identification and characterization of hcv replicon variants with reduced susceptibility to a combination of polymerase and protease inhibitors, and methods related thereto Download PDF

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Publication number
WO2009021121A2
WO2009021121A2 PCT/US2008/072492 US2008072492W WO2009021121A2 WO 2009021121 A2 WO2009021121 A2 WO 2009021121A2 US 2008072492 W US2008072492 W US 2008072492W WO 2009021121 A2 WO2009021121 A2 WO 2009021121A2
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Prior art keywords
hepatitis
subject
amino acid
hcv
acid sequence
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PCT/US2008/072492
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French (fr)
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WO2009021121A3 (en
WO2009021121A4 (en
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Michael James Flint
Anita Y.M. Howe
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Wyeth
Viropharma Incorporated
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Publication of WO2009021121A4 publication Critical patent/WO2009021121A4/en

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/335—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin
    • A61K31/34—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin having five-membered rings with one oxygen as the only ring hetero atom, e.g. isosorbide
    • A61K31/343—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin having five-membered rings with one oxygen as the only ring hetero atom, e.g. isosorbide condensed with a carbocyclic ring, e.g. coumaran, bufuralol, befunolol, clobenfurol, amiodarone
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/04—Peptides having up to 20 amino acids in a fully defined sequence; Derivatives thereof
    • A61K38/06—Tripeptides
    • 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
    • A61P31/14—Antivirals for RNA viruses
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/576—Immunoassay; Biospecific binding assay; Materials therefor for hepatitis
    • G01N33/5767—Immunoassay; Biospecific binding assay; Materials therefor for hepatitis non-A, non-B hepatitis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/005—Assays involving biological materials from specific organisms or of a specific nature from viruses
    • G01N2333/08—RNA viruses
    • G01N2333/18—Togaviridae; Flaviviridae
    • G01N2333/183—Flaviviridae, e.g. pestivirus, mucosal disease virus, bovine viral diarrhoea virus, classical swine fever virus (hog cholera virus) or border disease virus
    • G01N2333/186—Hepatitis C; Hepatitis NANB
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2469/00—Immunoassays for the detection of microorganisms
    • G01N2469/10—Detection of antigens from microorganism in sample from host
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/56—Staging of a disease; Further complications associated with the disease

Definitions

  • the present invention relates to treatment-resistant hepatitis C viral infections and inhibitors of hepatitis C virus RNA-dependent RNA polymerase NS5B (RdRp) and serine protease NS3.
  • the present invention relates to the NS3 serine protease inhibitor boceprevir, as well as benzofuran inhibitors of NS5B, more particularly 5-cyclopropyl-2-(4-fluorophenyl)- 6-[(2-hydroxyethyl)(methylsulfonyl)amino]-N-methyl-l -benzofuran- 3-carboxamide (HCV-796).
  • Hepatitis C is a common viral infection that can lead to chronic hepatitis, cirrhosis, liver failure, and hepatocellular carcinoma.
  • Infection with the hepatitis C virus (HCV) leads to chronic hepatitis in at least 85% of cases, is the leading reason for liver transplantation, and is responsible for at least 10,000 deaths annually in the United States ((1997) Hepatology 26:2S- 10S).
  • HCV hepatitis C virus
  • HCV hepatitis C virus
  • the hepatitis C virus is a member of the Flaviviridae family and displays genetic heterogeneity; at least 6 genotypes and more than 50 subtypes have been identified (Wong and Lee, supra).
  • the genome of HCV is a single-stranded linear RNA of positive sense that encodes a 3,010 amino acid polyprotein (Purcell (1997) Hepatology 26: 1 I S- 14S).
  • the polyprotein is cleaved by a combination of host- and virus-encoded proteases to yield individual viral proteins, including both structural and nonstructural proteins.
  • the nonstructural proteins are: NS2, NS3, NS4A, NS4B, NS5A, and NS5B (Bartenschlager and Lohmann (2000) J. Gen. Virol. 81 : 1631 -48).
  • NS5B RdRp is the principal catalytic enzyme for HCV replication, and represents a viable target for anti-HCV therapeutics (Walker and Hong (2002) Curr. Opin. Pharm. 2:534-40). Recent research efforts have led to the discovery of inhibitors that specifically target NS5B, as well as therapeutics that target other HCV viral proteins (Carroll et al.
  • NIs nucleoside inhibitors
  • NNIs nonnucleoside inhibitors
  • NNIs on NS5B Three distinct binding sites for NNIs on NS5B have been described: one near a GTP-binding site within the thumb domain (for benzimidazoles and indoles); one at the base of the thumb (for thiophene, phenylalanine, dihydropyranone and pyranoindole derivatives); and one in the palm domain adjacent to the active site (for benzothiadiazine, proline sulphonamide, benzylidene and acrylic acid analogs).
  • the NNIs appear to act through allosteric mechanisms that inhibit the initiation or elongation of RNA synthesis by NS5B.
  • HIV human immunodeficiency virus
  • HBV hepatitis B virus
  • numerous mutations have been identified in patients treated with protease inhibitors as well as NIs and NNIs.
  • NIs and NNIs hepatitis B virus
  • emergence of resistant viruses is anticipated to be one of the largest challenges in developing effective antiviral therapies against HCV infection.
  • an optimal antiviral regimen is likely to include several drugs targeting different steps in replication. Such combinations provide the best chance of achieving maximal efficacy and inhibiting the development of resistance.
  • HCV-796 and boceprevir demonstrate antiviral activities in patients infected with HCV.
  • mutations occurring in NS5B or NS3 sometimes lead to decreased sensitivity to their respective inhibitors. Such mutations can result in the emergence of treatment-resistant hepatitis C viral infections.
  • the combination of HCV-796 and boceprevir has an additive inhibitory effect on the HCV replicon, signaling a need to identify methods by which combination therapy with HCV-796 and boceprevir may reduce the emergence of treatment-resistant hepatitis C viral infections. Additionally, there is a need to identify the mutation sites in the NS5B polymerase and NS3 serine protease that result in treatment-resistant hepatitis C viral infections. Once identified, these sites will serve as: (1) markers to monitor the course of an anti-hepatitis C therapy for developing an.
  • NS5B polymerase inhibitors e.g., benzofurans, such as HCV-796
  • NS3 protease inhibitors e.g., boceprevir
  • markers to identify individuals with a decreased likelihood of responding to an anti-hepatitis C virus therapy e.g., boceprevir
  • markers to monitor and prognose a hepatitis C viral infection This information is additionally useful to optimize second-generation hepatitis C viral inhibitors or other HCV inhibitor combinations that exhibit significantly reduced, minimal, or no susceptibility to resistance caused by mutations at these sites.
  • the present invention provides methods of decreasing the frequency of emergence, decreasing the level of resistance, and delaying the emergence of a treatment-resistant hepatitis C viral infection, by administering to a subject, either in combination or in series, an inhibitor of the hepatitis C RNA-dependent RNA polymerase NS5B (e.g., a benzofuran, such as 5-cyclopropyl-2-(4-fluorophenyl)- 6-[(2-hydroxyethyl)(methylsulfonyl)arnino]-N-methyl-l -benzofuran-3- carboxamide (HCV-796)) and an inhibitor of the HCV NS3 serine protease (e.g., boceprevir).
  • the present invention also describes further administering at least one additional anti-hepatitis C agent, e.g., a ribavirin product or an immunomodulator, such as an interferon product.
  • the present invention relates to methods of monitoring the course of treatment of a hepatitis C viral infection, methods of monitoring and prognosing a hepatitis C viral infection, and methods of identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy.
  • the present invention also provides useful information and methods related to optimizing second-generation anti-hepatitis C agents, e.g., optimizing identification and chemical synthesis of second-generation anti-hepatitis C agents, for treating, e.g., a benzofuran- or boceprevir-resistant hepatitis C viral infection in a subject.
  • the invention provides a method of decreasing the frequency of emergence of a treatment-resistant hepatitis C viral infection, comprising administering a benzofuran inhibitor of a hepatitis C virus in combination with an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof.
  • the invention provides a method of delaying the emergence of a treatment-resistant hepatitis C viral infection, comprising administering a benzofuran inhibitor of a hepatitis C virus in combination with an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof.
  • the invention provides a method of decreasing the level of resistance of a treatment-resistant hepatitis C viral infection, comprising administering a benzofuran inhibitor of a hepatitis C virus in combination with an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof.
  • the benzofuran inhibitor of a hepatitis C virus is HCV-796.
  • the NS3 protease inhibitor is boceprevir.
  • at least one additional anti-hepatitis C virus agent is also administered.
  • the at least one additional anti-hepatitis C virus agent may be an immunomodulator, a ribavirin product, and/or a small molecule inhibitor such as a nucleoside analogue, a nonnucleoside, or an inhibitor of heat shock proteins.
  • the invention provides a method of decreasing the emergence of an HCV-796-resistant hepatitis C viral infection, comprising administering HCV-796 in combination with an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof.
  • the invention provides a method of decreasing the emergence of an HCV-796-resistant hepatitis C viral infection, comprising administering HCV-796 either before or after administration of an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof.
  • at least one additional anti-hepatitis C virus agent is also administered.
  • the at least one additional anti-hepatitis C virus agent may be an immunomodulator, a ribavirin product, and/or a small molecule inhibitor such as a nucleoside analogue, a nonnucleoside, or an inhibitor of heat shock proteins.
  • the invention provides a method of identifying an individual with a decreased likelihood of responding to an anti- hepatitis C viral therapy, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the individual at a first time point; and determining the amino acid sequence of the nonstructural gene in a sample from the individual at a second time point, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the individual at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the individual at the first time point, indicates a decreased likelihood that the individual will respond to an anti-hepatitis C viral therapy.
  • the invention provides a method of identifying an individual with a decreased likelihood of responding to an anti- hepatitis C viral therapy, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the individual; and comparing the amino acid sequence of the nonstructural gene in the sample from the individual to the amino acid sequence of the nonstructural gene in a reference sample, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the individual, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, indicates a decreased likelihood that the individual will respond to an anti-hepatitis C viral therapy.
  • the invention provides a method for monitoring the course of treatment of a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; administering a benzofuran compound and an NS3 protease inhibitor to the subject; and determining the amino acid sequence of the nonstructural gene in a sample from the subject following administration of the benzofuran compound and NS3 protease inhibitor to the subject, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject following administration of the benzofuran compound and NS3 protease inhibitor, in comparison to the amino acid sequence of the nonstructural gene in the sample from the subject prior to administration of the benzofuran compound and NS3 protease inhibitor, provides a negative indication of the effect of the treatment of the hepatitis C viral infection in the subject.
  • the invention provides a method for monitoring the course of treatment of a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; administering HCV-796 and boceprevir to the subject; and determining the amino acid sequence of the nonstructural gene in a sample from the subject following administration of HCV-796 and boceprevir to the subject, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject following administration of HCV-796 and boceprevir, in comparison to the amino acid sequence of the nonstructural gene in the sample from the subject prior to administration of HCV-796 and boceprevir, provides a negative indication of the effect of the treatment of the hepatitis C viral infection in the subject.
  • the invention provides a method for monitoring the course of treatment of a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; administering HCV-796, boceprevir, and at least one additional anti-hepatitis C agent to the subject; and determining the amino acid sequence of the nonstructural gene in a sample from the subject following administration of HCV-796, boceprevir and at least one additional anti- hepatitis C agent to the subject, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject following administration of HCV-796, boceprevir, and at least one additional anti-hepatitis C agent, in comparison to the amino acid sequence of the nonstructural gene in the sample from the subject prior to administration of HCV-796, boceprevir, and at least one additional anti-hepatitis C agent, provides a negative indication of the effect of the treatment of the hepatit
  • the at least one additional anti-hepatitis C virus agent is an immunomodulator, a ribavirin product, and/or a small molecule inhibitor such as a nucleoside analogue, a nonnucleoside, or an inhibitor of heat shock proteins.
  • the invention provides a method for prognosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject at a first time point; and determining the amino acid sequence of the nonstructural gene in a sample from the subject at a second time point, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject at the second time point, in comparison to the amino acid sequence from the subject at the first time point, indicates an increased likelihood that the subject will develop a treatment- resistant hepatitis C viral infection.
  • the invention provides a method for prognosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; and comparing the amino acid sequence of the nonstructural gene in the sample from the subject to the amino acid sequence of the nonstructural gene in a reference sample, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, indicates an increased likelihood that the subject will •> develop a treatment-resistant hepatitis C viral infection.
  • the invention provides a method for monitoring a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject at a first time point; and determining the amino acid sequence of the nonstructural gene in a sample from the subject at a second time point, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the subject at the first time point, provides an indication that the hepatitis C viral infection has changed in severity.
  • the invention provides a method for monitoring a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; and comparing the amino acid sequence of the nonstructural gene in the sample from the subject to the amino acid sequence of the nonstructural gene in a reference sample, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, provides an indication that the hepatitis C viral infection has changed in severity.
  • the invention provides a method for diagnosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HGV nonstructural gene in a sample from the subject at a first time point; and determining the amino acid sequence of the nonstructural gene in a sample from the subject at a second time point, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the subject at the first time point, indicates an increased likelihood that the subject has developed or will develop a treatment-resistant hepatitis C viral infection.
  • the invention provides a method for diagnosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; and comparing the amino acid sequence of the nonstructural gene in the sample from the subject to the amino acid sequence of the nonstructural gene in a reference sample, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, indicates an increased likelihood that the subject has developed or will develop a treatment-resistant hepatitis C viral infection.
  • the nonstructural gene is selected from the group of NS3, NS5A, and NS5B.
  • the change in the amino acid sequence of the nonstructural gene is an amino acid change selected from the group consisting of those set forth in Table 3A.
  • the hepatitis C RNA-dependent RNA polymerase NS5B is derived from a hepatitis C virus genotype selected from the group consisting of genotypes Ia, Ib, 2, 3, 4, 5, and 6.
  • Figure 1 shows the frequency of selection of replicons resistant to combinations of HCV-796 and boceprevir.
  • Huh7-BB7 cells bearing a subgenomic genotype Ib HCV replicon were seeded at 20,000 per 100 mm dish and treated with 1 mg/ml G418 and the indicated combinations of HCV-796 and boceprevir.
  • Fresh medium, G418, and compounds at the appropriate concentration were added every 3 or 4 days. After 7 days the cultures were split 1 : 10 into a new 100 mm dish and, after 20 days, the surviving cell colonies were fixed and stained with crystal violet. Shown is a representative of three independent experiments.
  • Figure 2 shows a time course of treatment of HCV replicon cells with combinations of HCV-796 and boceprevir (SCH-503034).
  • HCV replicon cells were propagated in the presence of combinations of HCV-796 and/or boceprevir, but in the absence of G418. Cells were passaged every 2-3 days, and each time the cultures were split, a sample of the cells was taken. RNA was extracted from cell lysates, and HCV and rRNA levels were determined by qRT-PCR. Each point is a mean HCV RNA/rRNA value from eight independent experiments, each comprising triplicate replicon cell cultures. Error bars above each point represent the standard error of the mean.
  • Figure 3 shows HCV replicon variants resistant to the combination of HCV-796 and boceprevir can be cleared by Peg-IFN.
  • the previously selected 40/800 and 0/0 cells were incubated for 30 days in the presence of 40 nM HCV-796 and 800 nM boceprevir, and treated with Peg-IFN as described infra. After 30 days, the Peg-IFN was withdrawn and 0.25 mg/ml G418 was added to select for cells that had retained the replicon. Three replicate cultures were treated, HCV and ribosomal RNA was quantitated, and the mean and standard error at each time point was plotted. No cells that were treated with ⁇ 100x EC 50 Peg-IFN survived the selection process.
  • Figures 4A-F show competition with the parental replicon sequence as a measure of mutant relative replicative capacity.
  • Huh7 cells were electroporated either with parental replicon RNA, mutant replicon RNA or with equal amounts of parental and mutant replicon RNAs.
  • RNA was extracted from the replicon cell populations and the NS3 and NS5B genes were amplified. Sequences of the PCR product populations were determined. 4A. NS3-V 158M; 4B. NS3-V170A; 4C. NS3-E176G; 4D. NS5B-C316Y; 4E. NS5B- C445F; 4F.
  • NS3-V 17OA / NS5B-C316Y Representative sequencing chromatograms (from at least two sequencing reactions), nucleotide sequence and the inferred amino acid sequence at the mutant codon are shown. Sequences from cells electroporated with only the parent replicon and only the mutant replicon RNA are shown above the co-electroporated cells.
  • a replicon is a subgenomic RNA that contains all essential elements and genes required for replication in the absence of structural genes.
  • the HCV replicon also contains a foreign gene encoding a drug-selectable marker (neomycin phosphotransferase) to allow for G418 (neomycin) selection of cells that contain a functional replicon. Transfection of the HCV replicon into human hepatoma cells (Huh-7) leads to an autonomous HCV replication.
  • the present invention provides, e.g., methods of monitoring the course of treatment of a hepatitis C viral infection, methods of diagnosing the development of a treatment-resistant hepatitis C viral infection, methods of monitoring and prognosing a hepatitis C viral infection, and methods of identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy.
  • hepatitis C virus means all genotypes of hepatitis C (e.g., hepatitis C Ia, Ib, 2, 3, and 4), and all subtypes and isolates thereof ⁇ see, e.g., Wong and Lee (2006) Canadian Med. Assoc. J. 174:649-59).
  • anti-hepatitis C viral therapy means any treatment (e.g., administration of an agent) or course of treatment for HCV infection.
  • Such therapies include administration of an agent alone, e.g., administration of an anti-hepatitis C virus agent, such as an immunomodulator (e.g., an interferon product), or administration of agents in combination, e.g., administration of an immunomodulator either concurrently or in series with a ribavirin product.
  • an agent alone e.g., administration of an anti-hepatitis C virus agent
  • an immunomodulator e.g., an interferon product
  • administration of agents in combination e.g., administration of an immunomodulator either concurrently or in series with a ribavirin product.
  • a single or sustained treatment which may be an agent alone or in combination with at least one additional agent, is included within the meaning of "anti-hepatitis C viral therapy” and the like.
  • anti-hepatitis C virus agent and the like means any agent that may be used to treat HCV infection, e.g., interferon products and other immunomodulators, ribavirin products, inhibitors of HCV enzymes, antifibrotics, etc.
  • agents include those disclosed in, e.g., Carroll et al., supra; Dhanak et al., supra; Howe et al.
  • VIRAMIDINE® VALeant Pharmaceuticals
  • MERIMEPODIB® Vertex Pharmaceuticals
  • mycophenolic acid Roche
  • amantadine ACTILON® (Coley)
  • BILN-2061 Boehringer Ingelheim
  • Sch-6 Sch-6
  • VX-950 Vertex Pharmaceuticals
  • VALOPICITABINE® Idenix Pharmaceuticals
  • JDK-003 Akros Pharmaceuticals
  • HCV-796 (Wyeth/ViroPharma), ISIS-14803 (Isis Pharmaceuticals), ENBREL® (Wyeth); IP-501 (Indevus Pharmaceuticals), ID- 6556 (Idun Pharmaceuticals), RITUXIMAB® (Genentech), XLT-6865 (XTL), ANA-971 (Anadys), ANA-245 (Anadys) and TARVACIN® (Peregrine).
  • Additional anti-hepatitis C virus agents include immunomodulators, e.g., interferons (e.g., LFN- ⁇ , ⁇ , and ⁇ ) and interferon products (e.g., pegylated interferons and albumin interferons), which includes both natural and recombinant or modified interferons.
  • immunomodulators e.g., interferons (e.g., LFN- ⁇ , ⁇ , and ⁇ ) and interferon products (e.g., pegylated interferons and albumin interferons), which includes both natural and recombinant or modified interferons.
  • interferon products include, but are not limited to, ALBUFERON® (Human Genome Sciences), MULTIFERON® (Viragen), PEG-ALFACON® (Inter-Mune), OMEGA INTERFERON® (Biomedicines), INTRON® A (Schering), ROFERON® A (Roche), INFERGEN® (Amgen), PEG-INTRON® (Schering), PEGASYS® (Roche), MEDUSA INTERFERON® (Flamel Technologies), REBIF® (Ares Serono), ORAL INTERFERON ALFA® (Amarillo Biosciences), consensus interferon (CIFN) (Aladag et al. (2006) Turk. J. Gastroenterol.
  • immunomodulator and the like means any agent capable of regulating an immune response or a portion of an immune response in a subject. Examples include, but are not limited to, agents that may regulate T- cell function (e.g., thymosin alfa-1, ZADAXFN® (Sci-Clone)), agents that enhance IFN activation of immune cells (e.g., histamine dihydrochloride, CEPLEME® (Maxim Pharmaceutical)), and interferon products.
  • T- cell function e.g., thymosin alfa-1, ZADAXFN® (Sci-Clone)
  • agents that enhance IFN activation of immune cells e.g., histamine dihydrochloride, CEPLEME® (Maxim Pharmaceutical)
  • interferon products e.g., interferon products.
  • Additional anti-hepatitis C virus agents include antiviral agents (e.g., nucleoside analogs), such as ribavirin products.
  • antiviral agents e.g., nucleoside analogs
  • ribavirin product and the like means any agent that contains ribavirin (1 - ⁇ -D- ribofuranosyl-lH-l ,2,4-triazole-3-carboxamide).
  • examples of such ribavirin products include COPEGUS® (Roche); R1BASPHERE® (Three Rivers Pharmaceuticals); VIRAZOLE® (Valeant Pharmaceuticals); and REBETOL® (Schering).
  • HCV-796 and the like means 5-cyclopropyl-2-(4- fluorophenyl)-6-[(2-hydroxyethyl)(methylsulfonyl)amino]-N-methyl-l - benzofuran-3-carboxamide, which is disclosed in, e.g., U.S. Patent Application No. 10/699,336 (i.e., U.S. Published Patent Application No. 2004/0162318) and U.S. Provisional Patent Application Nos. 60/735, 190 and 60/735, 191 , the contents of which are hereby incorporated by reference herein in their entireties.
  • hepatitis C RNA-dependent RNA polymerase NS5B means the RNA-dependent RNA polymerase from any hepatitis C virus (i.e., any HCV genotype or any subtype or isolate thereof).
  • hepatitis C RNA-dependent RNA polymerase NS5B gene and the like means a nucleic acid that encodes a hepatitis C RNA-dependent RNA polymerase NS5B.
  • polypeptide sequences from various hepatitis C genotypes and isolates may be found in the literature, e.g., HCV genotype Ib isolates include GenBank Accession Nos.
  • HCV genotype Ia isolates include, e.g., GenBank Accession Nos. NC_004102.1; AY100171.1; AF516387.1; AY100128.1; AY100114.1; AF516389.1; AY1OO185.1; AF516391.1; AY100136.1; AY100132.1; AY100133.1; AY100179.1; AY100120.1; AY100135.1; AY100173.1; AYlOOl 18.1 ; AY 100147.1; AY100176.1; AY100181.1; AY100193.1; AY 100124.1; AF516388.1; AY 100139.1; AY100161.1; AYlOOl 15.1; AY100122.1; AY100129.1; AY100131.1; AY100146.1; AY100166.1; AY100169.1; AY100130.1; AF516386.1; AY100183.1; AY100151.1; AY
  • HCV genotype 2 isolates include, e.g., GenBank Accession Nos. AX057088.1; AX057090.1; AX057092.1; AX057094.1; D31973.1; D50409.1; AF238486.1; AB030907.1; U14293.1; U14294.1; AF238481.1;
  • HCV genotype 3 isolates include, e.g., GenBank Accession Nos. D49374.1; D17763.1; D10585.1; AF046866.1; AY100061.1; AY100033.1; AY100080.1; AY100088.1; AY100036.1; AF516379.1; AY100064.1; AY 100059.1; AY 100062.1; AY 100065.1; AY 100078.1; AF516374.1; AY 100090.1; AY 100042.1; AY 100075.1 ; AF516369.1; AY 100067.1; AY100045.1; AF516377.1; AY100058.1; AF516378.1; AY100026.1; AY 100044.1; AY 100055.1; AY 100056.1; AY 100092.1; AY 100097.1; AY100047.1; AY100029.1; AY100028.1; AY100091.1; AF516368.1; AY10008
  • HCV genotype 4 isolates include, e.g., GenBank Accession Nos. Y l 1604.1 ; AF271807.1 ; AF271800; AJ291255.1 ; AJ291293.1 ; AJ291258.1 ; AJ291291.1 ; AJ291282.1 ; AJ291284.1 ; AJ291263.1 ; AJ291286.1 ; AJ291272.1 ; AJ291275.1 ; AJ291271.1 ; AF271814.1
  • HCV genotype 5 isolates include, e.g., GenBank Accession Nos. Y 13184.1 ; AJ291281.1 ; L23472.1 ; and L23471.1.
  • HCV genotype 6 isolates include, e.g., GenBank Accession Nos. Y 12083.1 ; L38379.1 ; L23475.1 ; and L38339.1.
  • nonstructural gene product and the like means NS2, NS3, NS4A, NS4B, NS5A and NS5B polynucleotides and polypeptides and fragments thereof (e.g., mRNA, RNA, rRNA, cDNA, protein, peptides and fragments thereof).
  • amino acid change and the like means a deviation from the amino acid residue at a given position in a hepatitis C nonstructural gene.
  • amino acid change and the like means both single and multiple changes or differences in, between or among sequences.
  • HCV-796 binding pocket and the like means the portion of a hepatitis C RNA-dependent RNA polymerase NS5B responsible for interacting with HCV-796.
  • the HCV-796-binding pocket of NS5B from HCV genotype I b is contained within about amino acid residues 120 to 450.
  • determining "the amino acid sequence of a nonstructural gene” and the like includes, but is not limited to, (1 ) determining the amino acid sequence of any nonstructural gene; (2) determining the amino acid structure of a nonstructural gene or a portion thereof, e.g., determining the amino acid structure of the HCV-796 binding pocket of the hepatitis C RNA-dependent RNA polymerase NS5B or a portion thereof; and/or (3) determining the nucleic acid sequence encoding any nonstructural gene.
  • Such methods may employ routine nucleotide sequencing or routine protein sequencing (see also U. S. S.N. 60/840,353, filed August 25, 2006 (the entire contents of which are hereby incorporated by reference herein)).
  • the instant invention contemplates methods of decreasing the frequency of emergence, decreasing the level of resistance, and delaying the emergence of a treatment-resistant hepatitis C viral infection, by administering to a subject, either in combination or in series, an inhibitor of the hepatitis C RNA- dependent RNA polymerase NS5B (e.g., a benzofuran, such as HCV-796) and an inhibitor of the NS3 serine protease (e.g., boceprevir).
  • the present invention also provides for the administration of at least one additional anti-hepatitis C agent (including but not limited to, a ribavirin product or an immunomodulator, such as an interferon product).
  • inhibitors and agents e.g., HCV-796 and boceprevir, with or without an additional agent, e.g., an interferon product and/or a ribavirin product
  • additional agent e.g., an interferon product and/or a ribavirin product
  • exemplary agents useful to decrease the frequency of emergence, decrease the level of resistance, and delay the emergence of a treatment-resistant hepatitis C viral infection include agents that target the hepatitis C protease inhibitor NS3, e.g. boceprevir.
  • Other agents include agents that target the hepatitis C RNA-dependent RNA polymerase NS5B, e.g., benzofuran compounds.
  • Such compounds are disclosed in, e.g., U.S. Provisional Patent Appln. Nos. 60/735,190 and 60/735,191 , and U.S. Patent Publication No. 2004/0162318, the disclosures of which are hereby incorporated by reference herein.
  • the benzofuran compound is 5-cyclopropyl-2-(4-fluorophenyl)-6-[(2-hydroxyethyl) (methylsulfonyl)amino]-N-methyl- l-benzofuran-3-carboxarnide (HCV-796).
  • HCV-796 5-cyclopropyl-2-(4-fluorophenyl)-6-[(2-hydroxyethyl) (methylsulfonyl)amino]-N-methyl- l-benzofuran-3-carboxarnide
  • a hepatitis C virus with resistance to an anti-hepatitis C viral therapy of choice, e.g., a benzofuran anti-hepatitis C viral therapy (such as a benzofuran-based anti-hepatitis C viral therapy employing HCV-796) or an NS3 serine protease inhibitor (such as boceprevir).
  • an anti-hepatitis C viral therapy of choice e.g., a benzofuran anti-hepatitis C viral therapy (such as a benzofuran-based anti-hepatitis C viral therapy employing HCV-796) or an NS3 serine protease inhibitor (such as boceprevir).
  • "delaying the emergence” and the like may refer to postponing the development of a treatment-resistant hepatitis C viral infection relative to a reference sample (e.g., a reference mean or median rate of development of a treatment-resistant hepatitis C virus in a reference population). Such postponement may be by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or any other method of assessing a delay of emergence of resistance known in the art.
  • decreasing the frequency of emergence means reducing the rate of occurrence, e.g., of the development of a hepatitis C virus with resistance to an anti-hepatitis C viral therapy of choice.
  • “decreasing the frequency of emergence” and the like may refer to a reduction in the rate of occurrence of a treatment-resistant hepatitis C viral infection relative to a reference sample (e.g., a reference mean or median rate of occurrence of a treatment-resistant hepatitis C virus in a reference population). Such reduction may be by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or any other method of assessing a decrease of frequency of emergence of resistance known in the art.
  • decreasing the level of resistance means reducing the strength or the ability of a hepatitis C virus to withstand an anti- hepatitis C viral therapy.
  • “decreasing the level of resistance” and the like may refer to a reduction in the strength or the ability of a hepatitis C virus to withstand an anti-hepatitis C viral therapy relative to a reference sample (e.g., a reference mean or median ability to withstand an anti-hepatitis C viral therapy in a reference population). Such reduction may be by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or any other method of assessing a decrease in the level of resistance known in the art.
  • treatment-resistant hepatitis C viral infection and the like means a hepatitis C viral infection that displays an abrogated response to an anti-hepatitis C viral therapy (e.g., a delayed (or absent) response to treatment, or a lessened (i.e., abrogated) reduction in hepatitis C viral load in response to treatment).
  • the treatment-resistant hepatitis C viral infection is a benzofuran-resistant hepatitis C viral infection, particularly an HCV-796 resistant hepatitis C viral infection.
  • the treatment-resistant hepatitis C viral infection is a boceprevir- resistant hepatitis C viral infection.
  • nucleotide sequence or polynucleotide as set forth herein encompasses a DNA molecule (e.g., a cDNA molecule) with the specified sequence (or a complement thereof), and encompasses an RNA molecule (e.g., an mRNA or an rRNA molecule) with the specified sequence in which U is substituted for T, unless context requires otherwise.
  • RNA molecule e.g., an mRNA or an rRNA molecule
  • Such polynucleotides and nucleic acids additionally include allelic variants of the disclosed polynucleotides, e.g., polynucleotides and nucleic acids of various subtypes of the hepatitis C virus genotypes.
  • allelic variants are naturally occurring alternative forms of the disclosed polynucleotides that encode polypeptides that are identical to or have significant similarity to the polypeptides encoded by the disclosed polynucleotides.
  • allelic variants have at least 90% sequence identity (more preferably, at least 95% identity; most preferably, at least 99% identity) with the disclosed polynucleotides.
  • significant similarity exists when the nucleic acid segments will hybridize under selective hybridization conditions (e.g., highly stringent hybridization conditions) to the disclosed polynucleotides.
  • Such polynucleotides and nucleic acids additionally include DNAs having sequences encoding polypeptides homologous to the disclosed polynucleotides. These homologs are polynucleotides and polypeptides isolated from a different species than that of the disclosed polypeptides and polynucleotides, or within the same species, but with significant sequence similarity to the disclosed polynucleotides and polypeptides.
  • polynucleotide homologs have at least 50% sequence identity (more preferably, at least 75% identity; most preferably, at least 90% identity) with the disclosed polynucleotides, whereas polypeptide homologs have at least 30% sequence identity (more preferably, at least 45% identity; most preferably, at least 60% identity) with the disclosed polypeptides.
  • homologs of the disclosed polynucleotides and polypeptides are those isolated from mammalian species.
  • sequence identity is calculated by means well known to those of skill in the art. For example, one general means for calculating sequence identity is described as follows.
  • the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment, and nonhomologous sequences can be disregarded for comparison purposes).
  • the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, still more preferably at least 60%, and even more preferably at least 70%, 80%, 90%, or 100% of the length of the reference sequence.
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position.
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the comparison of sequences and determination of percent sequence identity between two sequences may be accomplished using a mathematical algorithm. In one exemplary embodiment, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (( 197O) J MoI. Biol.
  • the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available at www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1 , 2, 3, 4, 5, or 6.
  • One exemplary set of parameters is a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
  • the percent identity between two amino acid or nucleotide sequences can also be determined using the algorithm of Meyers and Miller ((1989) CABIOS 4: 1 1 -17), which has been incorporated into the ALIGN program (version 2.0), using a PAM 120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • Anti-hepatitis C virus agents include, e.g., polynucleotides, protein biologies, antibodies and small molecules.
  • small molecule refers to compounds that are not macromolecules ⁇ see, e.g., Karp (2000) Bioinformatics Ontology 16:269-85; Verkman (2004) AJP-CeIl Physiol. 286:465-74). Thus, small molecules are often considered those compounds that are, e.g., less than one thousand daltons (e.g., Voet and Voet, Biochemistry, 2 nd ed, ed. N. Rose, Wiley and Sons, New York, 14 (1995)). For example, Davis et al.
  • FCD Full Chemicals Database
  • SMID Small Molecule Interaction Database
  • ChEBI Certical Entities of Biological Interest
  • CSD Cambridge Structural Database
  • SMIPTM small modular immunopharmaceutical
  • SMIPs are single-chain polypeptides composed of a binding domain for a cognate structure such as an antigen, a counterreceptor or the like, a hinge-region polypeptide having either one or no cysteine residues, and immunoglobulin CH2 and CH3 domains (see also www.trubion.com).
  • SMIPs and their uses and applications are disclosed in, e.g., U.S. Published Patent Application. ⁇ os.
  • the term "antibody” includes a protein comprising at least one, and typically two, VH domains or portions thereof, and/or at least one, and typically two, VL domains or portions thereof.
  • the antibody is a tetramer of two heavy immunoglobulin chains and two light immunoglobulin chains, wherein the heavy and light immunoglobulin chains are interconnected by, e.g., disulfide bonds.
  • the antibodies, or a portion thereof can be obtained from any origin, including but not limited to, rodent, primate (e.g., human and nonhuman primate), camelid, shark, etc., or they can be recombinantly produced, e.g., chimeric, humanized, and/or in v;7ro-generated, e.g., by methods well known to those of skill in the art.
  • binding fragments encompassed within the term "antigen- binding fragment" of an antibody include, but are not limited to, (i) an Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CH l domains; (ii) an F(ab') 2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) an Fd fragment consisting of the VH and CH l domains; (iv) an Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment, which consists of a VH domain; (vi) a single chain Fv (scFv; see below); (vii) a camelid or camelized heavy chain variable domain (VHH; see below); (viii) a bispecific antibody (see below); and (ix) one or more fragments of an immunoglobulin molecule fused to an Fc region.
  • an Fab fragment a
  • the two domains of the Fv fragment, VL and VH are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv)); see, e.g., Bird et al. (1988) Science 242:423-26; Huston et al. (1988) Proc. Natl. Acad. Sci. U.S.A. 85:5879-83).
  • single chain Fv single chain Fv
  • Such single chain antibodies are also intended to be encompassed within the term "antigen-binding fragment" of an antibody.
  • the term "antigen-binding fragment” encompasses single domain antibodies.
  • Single domain antibodies can include antibodies whose CDRs are part of a single domain polypeptide. Examples include, but are not limited to, heavy chain antibodies, antibodies naturally devoid of light chains, single domain antibodies derived from conventional four-chain antibodies, engineered antibodies and single domain scaffolds other than those derived from antibodies.
  • Single domain antibodies may be any of those known in the art, or any future single domain antibodies.
  • Single domain antibodies may be derived from any species including, but not limited to, mouse, human, camel, llama, goat, rabbit, bovine, and shark.
  • a single domain antibody as used herein is a naturally occurring single domain antibody known as heavy chain antibody devoid of light chains.
  • Such single domain antibodies are disclosed in, e.g., WO 94/04678.
  • This variable domain derived from a heavy chain antibody naturally devoid of light chain is known herein as a VHH or nanobody, to distinguish it from the conventional VH of four-chain immunoglobulins.
  • VHH molecule can be derived from antibodies raised in Camelidae species, for example in camel, llama, dromedary, alpaca and guanaco. Other species besides Camelidae may produce heavy chain antibodies naturally devoid of light chain; such VHH molecules are within the scope of the invention.
  • composition means any composition that contains at least one therapeutically or biologically active agent (e.g., an anti- hepatitis C virus agent(s), such as HCV-796, boceprevir, a ribavirin product, an interferon product, etc.) and is suitable for administration to a subject.
  • therapeutically or biologically active agent e.g., an anti- hepatitis C virus agent(s), such as HCV-796, boceprevir, a ribavirin product, an interferon product, etc.
  • Pharmaceutical compositions and appropriate formulations thereof can be prepared by well-known and accepted methods of the art. See, for example, Remington: The Science and Practice of Pharmacy, 21 s1 Ed., (ed. A. R. Gennaro), Lippincott Williams & Wilkins, Baltimore, MD (2005).
  • the hepatitis C RNA-dependent RNA polymerase NS5B that is analyzed as part of the disclosed methods may be a variant polypeptide that differs from an NS5B sequence set forth herein. Such a variation may occur in a relatively irrelevant site of NS5B, e.g., outside of the HCV-796-binding domain.
  • NS5B polypeptides are contemplated as useful in the instant methods because such methods rely on the identification of a change in sequence or structure of an NS5B polypeptide from an individual (over time, i.e., between a first and second time point, or relative to a reference sample) infected with HCV.
  • NS3 polypeptides and changes in sequence or structure related to an HCV infection and administration of, e.g., boceprevir.
  • viral mutation may replace residues that form NS5B and/or NS3 protein tertiary structure, provided that residues that perform a similar function are used.
  • the type of residue may be completely irrelevant if an alteration occurs in a noncritical area.
  • the invention further utilizes NS5B and/or NS3 variants that show substantial NS5B-type and/or NS3-type biological activities.
  • Such variants include deletions, insertions, inversions, repeats, and type substitutions (for example, substituting one hydrophilic residue for another, but not a strongly hydrophilic residue for a strongly hydrophobic residue).
  • Small changes or "neutral" amino acid substitutions will often have little impact on protein function (Taylor (1986) J. Theor. Biol. 1 19:205-18).
  • Conservative substitutions may include, but are not limited to, replacements among the aliphatic amino acids, substitutions between amide residues, exchanges of basic residues, and replacements among the aromatic residues. Further guidance concerning which amino acid changes are likely to be phenotypically silent (i.e., are unlikely to significantly affect function) can be found in Bowie et al. (1990) Science 247: 1306-10 and Zvelebil et al. (1987) J. MoI. Biol. 195:957-61.
  • the present invention provides methods for monitoring the course of treatment of a hepatitis C viral infection, methods for monitoring and prognosing the development of a treatment-resistant hepatitis C viral infection, and methods for diagnosing the development of a treatment-resistant hepatitis C viral infection, by, e.g., determining the sequence or structure of a nonstructural HCV gene in a sample from the subject, and comparing the sequence or structure of the gene product(s) or a portion(s) thereof in the sample from the subject to the sequence or structure of a nonstructural gene product(s) or a portion(s) thereof in a reference sample.
  • these methods may include determining a test sequence or structure of a nonstructural gene product(s) or portion(s) thereof in biological sample taken from a subject at a first time point, and comparing the sequence or structure of the nonstructural gene product(s) or portion(s) thereof to the sequence or structure of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from the subject at a second time point.
  • the invention provides methods of diagnosing, prognosing and monitoring, e.g., by determining changes in the sequence of a nonstructural gene product(s) or a portion(s) thereof (e.g., NS5B or NS3) in a sample from a subject infected with HCV.
  • sequence or structure of a nonstructural gene product(s) or a portion(s) thereof may also be measured in a reference cell or sample of interest to produce or obtain a reference sequence of a nonstructural gene, or such reference sequence or structure may be obtained through other methods, or may be generally known, by one of skill in the art.
  • sequence of the nonstructural gene product(s) or a portion(s) thereof may be obtained from a subject at a first time point and compared to the sequence of the nonstructural gene product(s) or portion(s) thereof from the subject at a second time point to identify the development of amino acid changes in the nonstructural gene product(s) or a portion(s) thereof.
  • These methods may be performed by, e.g., utilizing prepackaged diagnostic kits comprising at least one of a polynucleotide (or portion(s) thereof, e.g., an NS5B sequencing probe(s) or an NS5B hybridization probe(s)), or an antibody against, e.g., an NS5B polypeptide (or a portion thereof), which may be conveniently used, for example, in a clinical setting.
  • a polynucleotide or portion(s) thereof, e.g., an NS5B sequencing probe(s) or an NS5B hybridization probe(s)
  • an antibody against e.g., an NS5B polypeptide (or a portion thereof)
  • Diagnostic means identifying the presence or absence of a pathologic condition, e.g., diagnosing the development of a treatment- resistant hepatitis C viral infection in a subject. Diagnostic methods include, but are not limited to, detecting changes in the sequence of a nonstructural gene by determining the sequence of a nonstructural gene product(s) or a portion(s) thereof in a biological sample from a subject (e.g., human or nonhuman mammal), and comparing the test sequence or structure with, e.g., a normal (or relatively normal) sequence of the same nonstructural gene product.
  • the present invention also provides methods for prognosing the development of a treatment-resistant hepatitis C viral infection in a subject by determining, for example, the sequence or structure of a nonstructural gene product(s) or a portion(s) thereof in a biological sample from a subject (e.g., human or nonhuman mammal). "Prognostic” or “prognosing” means predicting the probable development and/or severity of a pathologic condition.
  • Prognostic methods include determining the sequence of a nonstructural gene product(s) or a portion(s) thereof in a biological sample from a subject, and comparing the sequence of the nonstructural gene product(s) or portion(s) thereof to a prognostic sequence of the nonstructural gene product(s) or portion(s) thereof (e.g., an NS5B sequence or structure from a reference sample).
  • a prognostic sequence of the nonstructural gene product(s) or portion(s) thereof e.g., an NS5B sequence or structure from a reference sample.
  • prognostic methods may include determining a test sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from a subject at a first time point, and comparing the sequence of the nonstructural gene product(s) or portion(s) thereof to the sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from the subject at a second time point. Changes in a particular portion(s) or amino acid residue(s) of the nonstructural gene product(s) are consistent with certain prognoses for the development of a treatment-resistant hepatitis C viral infection.
  • the present invention also provides methods for monito ⁇ ng a hepatitis C viral infection in a subject by determining, for example, the sequence of a nonstructural gene product(s) or a portion(s) thereof in a biological sample from a human or nonhuman mammalian subject
  • Monitonng methods include determining a test sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from a subject at a first time point, and comparing the sequence of the nonstructural gene product(s) or portion(s) thereof to the sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from the subject at a second time point
  • monito ⁇ ng methods may include comparing the test sequence or structure with, e g , a normal sequence of a nonstructural gene product(s) or portion(s) thereof (e g , an NS5B sequence or structure from a reference sample) A change in the sequence of a nonstructural
  • the present invention also provides methods for identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy, comprising determining the sequence of a nonstructural gene product(s) or a portion(s) thereof, and comparing the test sequence or structure with, e g , a normal nonstructural gene product sequence or structure (e g , an NS5B sequence or structure from a reference sample)
  • identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy may include determining a test sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from a subject at a first time point, and comparing the sequence of the nonstructural gene product(s) or port ⁇ on(s) thereof to the sequence of a nonstructural gene product(s) or port ⁇ on(s) thereof in a biological sample taken from the subject at a second time point.
  • a change(s) in a particular portion(s) is consistent with a decreased likelihood that the individual will respond to an anti-hepatitis C viral therapy. Closely associated methods of determining whether an individual will likely respond to an anti-hepatitis C viral therapy with little or no resistance are also contemplated.
  • this information is useful in methods of selecting combinations of, e.g., anti-hepatitis C agents and/or second-generation anti-hepatitis C agents with additive or synergistic effects to reduce the susceptibility to resistance caused by such mutations in, e.g., the hepatitis C RNA-dependent RNA polymerase NS5B and serine protease NS3.
  • HCV variants generated in response to combination treatment of HCV with a benzofuran and boceprevir which also may include the administration of at least one additional anti-HCV agent as described herein, such as a ribavirin product and/or an interferon product
  • HTS high throughput screening
  • Determining the sequence (or structure) of a nonstructural gene product(s) or a portion(s) thereof as used in the disclosed methods may be measured in a variety of biological samples, including bodily fluids (e.g., whole blood, plasma, and urine), cells (e.g., whole cells, cell fractions, and cell extracts), and other tissues.
  • biological samples also include sections of tissue, such as biopsies and frozen sections taken for histological purposes.
  • Preferred biological samples include blood, plasma, lymph, and liver tissue biopsies. It will be appreciated that analysis of a biological sample need not necessarily require removal of cells or tissue from the subject.
  • appropriately labeled agents e.g., antibodies, nucleic acids
  • a subject may be administered to a subject and visualized (when bound to the target) using standard imaging technology (e.g., CAT, NMR (MRI), and PET).
  • standard imaging technology e.g., CAT, NMR (MRI), and PET.
  • the sequence or structure of a nonstructural gene product(s) or a portion(s) thereof is determined to yield a test sequence or structure.
  • the test sequence or structure is then compared with, e.g., a baseline/normal nonstructural gene sequence.
  • baseline sequence(s) or structure(s) of a nonstructural gene product(s) or a portion(s) thereof are determined by determining the sequence(s) or structure(s) of a reference nonstructural gene product(s) or a portion(s) thereof from a corresponding HCV genotype and/or subtype (or isolate) that is not resistant to the anti-hepatitis C viral therapy or anti-hepatitis C virus agent (e.g., HCV-796 and/or boceprevir) of interest.
  • anti-hepatitis C viral therapy or anti-hepatitis C virus agent e.g., HCV-796 and/or boceprevir
  • baseline (normal) sequence(s) or structure(s) of the nonstructural gene product(s) or a portion(s) thereof may be ascertained by determining the sequence(s) or structure(s) of a reference nonstructural gene product(s) or a portion(s) thereof from a sample taken from the subject prior to initiation of an anti-hepatitis C viral therapy or administration of the anti-hepatitis C virus agent (e.g., HCV-796 and/or boceprevir) of interest.
  • an anti-hepatitis C viral therapy e.g., HCV-796 and/or boceprevir
  • the methods of the present invention involve determining the sequence (or structure) of a hepatitis C nonstructural gene product(s) or portion(s) thereof, e.g., the sequence of an NS5B or NS3 polynucleotide or polypeptide.
  • the sequence or structure of a hepatitis C nonstructural gene product(s) or portion(s) thereof can be measured using methods well known to those skilled in the art, those described in the Examples section (e.g., RT-PCR), and additional techniques described herein.
  • further methods related to determining the sequence and/or structure of HCV nonstructural gene product(s) or portion(s) thereof are disclosed in, e.g., U. S. S.N.
  • Determination of a sequence and/or structural change(s) in a nonstructural gene may employ various methods well known in the art, e.g., routine nucleotide sequencing, PCR amplification, Northern Blotting, or routine protein sequencing (i.e., sequencing of the NS5B polypeptide or a portion thereof (e.g., the portion(s) of the NS5B polypeptide responsible for interacting with HCV-796)), isoelectric focusing, spectroscopy or antibody-based detection of structural changes.
  • Nonstructural gene mRNA can be isolated and reverse transcribed to cDNA, and then directly sequenced by various well-known methods, or alternatively probed for the presence or absence of certain amino acid encoding sequences.
  • the nonstructural gene mRNA itself may be probed for certain amino acid encoding sequences using hybridization-based assays, such as Northern hybridization, in situ hybridization, dot and slot blots, and oligonucleotide arrays.
  • Hybridization-based assays refer to assays in which a probe nucleic acid is hybridized to a target nucleic acid. In some formats, the target, the probe, or both are immobilized.
  • the immobilized nucleic acid may be DNA, RNA, or another oligonucleotide or polynucleotide, and may comprise naturally or nonnarurally occurring nucleotides, nucleotide analogs, or backbones.
  • Methods of selecting nucleic acid probe sequences for use in the present invention e.g., based on the nucleic acid sequences of, e.g., NS5B, NS5A, or NS3 are well known in the art and can be easily determined, e.g., based on the sequences set forth in SEQ ID NO: 1 and SEQ ID NO:2, which are the nucleic acid and amino acid sequences (respectively) of HCV, genotype Ib complete genome, isolate Con 1.
  • mRNA may be amplified before sequencing and/or probing.
  • amplification-based techniques are well known in the art and include polymerase chain reaction (PCR), reverse-transcription-PCR (RT-PCR), PCR-enzyme-linked immunosorbent assay (PCR-ELISA), and ligase chain reaction (LCR).
  • Primers and probes for producing and detecting amplified nonstructural gene products may be readily designed and produced without undue experimentation by those of skill in the art based on the nucleic acid sequences of the nonstructural gene.
  • Amplified nonstructural gene products may be directly analyzed, for example, by restriction digest followed by gel electrophoresis; by hybridization to a probe nucleic acid; by sequencing; by detection of a fluorescent, phosphorescent, or radioactive signal; or by any of a variety of well-known methods.
  • methods are known to those of skill in the art for increasing the signal produced by amplification of target nucleic acid sequences.
  • the present invention provides methods for decreasing the frequency of emergence, decreasing the level of resistance, and delaying the emergence of a treatment-resistant hepatitis C viral infection, by, e.g., administering a benzofuran inhibitor (e.g., HCV-796) of hepatitis C virus in combination with an NS3 serine protease inhibitor (e.g., boceprevir) to a subject in need thereof.
  • a benzofuran inhibitor e.g., HCV-796
  • an NS3 serine protease inhibitor e.g., boceprevir
  • At least one additional anti-hepatitis C virus agent may also be administered.
  • Benzofuran compounds and additional anti-hepatitis C virus agents are disclosed herein.
  • the anti-hepatitis C virus agent is an immunomodulator, particularly an interferon product, or an antiviral agent, particularly a ribavirin product.
  • the invention features methods for decreasing the frequency of emergence, decreasing the level of resistance, or delaying the emergence of a treatment-resistant hepatitis C viral infection.
  • These methods may comprise contacting a population of cells (e.g., by administering to a subject suffering from or at risk for fibrosis or a fibrosis-associated disorder) with an anti-hepatitis C virus agent (e.g., an immunomodulator, particularly an interferon product; an antiviral agent, particularly a ribavirin product; a benzofuran, particularly HCV-796; an NS3 protease inhibitor, particularly boceprevir) in an amount sufficient to decrease the frequency of emergence, decrease the level of resistance, or delay the emergence of a treatment-resistant hepatitis C viral infection.
  • an anti-hepatitis C virus agent e.g., an immunomodulator, particularly an interferon product; an antiviral agent, particularly a ribavirin product; a benzofuran, particularly HCV
  • Anti-hepatitis C virus agents for decreasing the frequency of emergence, decreasing the level of resistance, or delaying the emergence of a treatment- resistant hepatitis C viral infection may be used as a pharmaceutical composition when combined with a pharmaceutically acceptable carrier.
  • a pharmaceutically acceptable carrier may contain, in addition to the anti-hepatitis C virus agent(s) and carrier, various diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials well known in the art.
  • pharmaceutically acceptable means a nontoxic or relatively nontoxic material that does not interfere with the effectiveness of the biological activity of the active ingredient(s). The characteristics of the carrier will depend on the route of administration, and are generally well known in the art.
  • the pharmaceutical composition of the invention may be in the form of a liposome in which an anti-hepatitis C virus agent(s) is combined with, in addition to other pharmaceutically acceptable carriers, amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers which exist in aqueous solution.
  • Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithin, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, e.g., in U.S. Patent Nos.
  • the term "therapeutically effective amount” means the amount of each active component of the pharmaceutical composition or method that is sufficient to show a meaningful subject benefit, e.g., amelioration or reduction of symptoms of, prevention of, healing of, or increase in rate of healing of such conditions.
  • a meaningful subject benefit e.g., amelioration or reduction of symptoms of, prevention of, healing of, or increase in rate of healing of such conditions.
  • the term refers to that ingredient alone.
  • the term refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
  • an anti-hepatitis C virus agent(s) is administered to a subject, e.g., a mammal (e.g., a human).
  • An anti-hepatitis C virus agent(s) may be administered in accordance with the method of the invention either alone or in combination with other therapies as described in more detail herein.
  • an anti-hepatitis C virus agent(s) may be administered either simultaneously with the second agent, or sequentially.
  • an anti-hepatitis C virus agent(s) used in a pharmaceutical composition of the present invention or to practice a method of the present invention may be carried out in a variety of conventional ways, such as oral ingestion, inhalation, or cutaneous, subcutaneous, or intravenous injection. Intravenous administration to the subject is sometimes preferred.
  • the binding agent will be in the form of a tablet, capsule, powder, solution or elixir.
  • the pharmaceutical composition of the invention may additionally contain a solid carrier such as a gelatin or an adjuvant.
  • a solid carrier such as a gelatin or an adjuvant.
  • the tablet, capsule, and powder contain from about 5 to 95% binding agent, and preferably from about 25 to 90% binding agent.
  • a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil (albeit keeping in mind the frequency of peanut allergies in the population), mineral oil, soybean oil, or sesame oil, or synthetic oils may be added.
  • the liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol.
  • the pharmaceutical composition contains from about 0.5 to 90% by weight of the binding agent, and preferably from about 1 to 50% of the binding agent.
  • an anti-hepatitis C virus agent(s) When a therapeutically effective amount of an anti-hepatitis C virus agent(s) is administered by intravenous, intramuscular, cutaneous or subcutaneous injection, the binding agent will be in the form of a pyrogen-free, parenterally acceptable aqueous solution.
  • a preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection should contain, in addition to a binding agent, an isotonic vehicle such as sodium chloride injection, Ringer's injection, dextrose injection, dextrose and sodium chloride injection, lactated Ringer's injection, or other vehicle as known in the art.
  • the pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additive known to those of skill in the art.
  • 0096) The amount of an anti-hepatitis C virus agent(s) in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments that the subject has undergone. Ultimately, the attending physician will decide the amount of anti-hepatitis C virus agent(s) with which to treat each individual subject. Initially, the attending physician will administer low doses of anti-hepatitis C virus agent(s) and observe the subject's response.
  • anti- hepatitis C virus agent(s) may be administered until the optimal therapeutic effect is obtained for the subject, and at that point the dosage is not generally increased further.
  • the various pharmaceutical compositions used to practice the method of the present invention should contain about 0.01 ⁇ g to about 2000 mg anti-hepatitis C virus agent(s) per kg body weight.
  • Dosing schedules for ribavirin products and interferon products are well known to those of skill in the art and may be found throughout the literature, e.g., in Jen et al. (2002) Clin. Pharmacol. Ther. 72:349-61 , Krawitt et al. (2006) Am. J. Gastroenterol.
  • pegylated-interferon may be administered at a range of 0.01 ⁇ g/kg/dose to 50 ⁇ g/kg/dose, e.g., 0.1 ⁇ g/kg/dose to 3 ⁇ g/kg/dose, one or more times a week.
  • HCV-796 may be administered in doses at a range of 1 mg to 2000 mg, e.g., 50 mg to 1500 mg, one or more times a day.
  • boceprevir may be administered in doses at a range of 1 mg to 4000 mg, e.g. 200 mg to 800 mg, three or more times a day.
  • an interferon product (including pegylated interferon), is administered intramuscularly.
  • ribavirin is administered orally.
  • HCV-796 and/or boceprevir are administered orally.
  • the duration of intravenous therapy using the pharmaceutical composition of the present invention will vary, depending on the severity of the disease being treated and the condition and potential idiosyncratic response of each individual subject. If administered intravenously, it is contemplated that the duration of each application of an anti-hepatitis C virus agent(s) may be in the range of approximately 12 to 24 hours of continuous i.v. administration. Also contemplated is subcutaneous (s.c.) therapy using a pharmaceutical composition of the present invention. These therapies can be administered, e.g., daily, several times a day, weekly, biweekly, or monthly. Typically, anti-hepatitis C viral therapy lasts from 12 to 48 weeks.
  • the anti- hepatitis C virus agent is a small molecule (e.g., for oral delivery)
  • the therapies may be administered daily, twice a day, three times a day, etc.
  • the attending physician will decide on the appropriate duration of i.v. or s.c. therapy, or therapy with a small molecule, and the timing of administration of the therapy using the pharmaceutical composition of the present invention.
  • the polynucleotide and proteins of the present invention are expected to exhibit one or more of the uses or biological activities (including those associated with assays cited herein) identified below.
  • a pharmaceutical composition comprising a benzofuran inhibitor of an NS5B (e.g., HCV-796) and an inhibitor of NS3 serine protease (e.g., boceprevir) is administered in further combination therapy.
  • NS5B e.g., HCV-796
  • NS3 serine protease e.g., boceprevir
  • the term "in combination" in this context means that the benzofuran inhibitor and the inhibitor of NS3 protease are given substantially contemporaneously, either simultaneously or sequentially, including in further combination with other agents. If given sequentially, at the onset of administration of a later compound(s), the earlier compound(s) may still be detectable at effective concentrations at the site of treatment.
  • the combination therapy can include at least one benzofuran inhibitor of an NS5B (e.g., HCV-796) coformulated with, and/or coadministered with, or otherwise administered in combination with, an inhibitor of NS3 (e.g., boceprevir), and additionally at least one other anti-HCV agent.
  • Additional anti- hepatitis C virus agents may include at least one immunomodulator, antiviral, antifibrotics, small interfering RNA compounds, antisense compounds, polymerase inhibitors (such as nucleotide or nucleoside analogs), protease inhibitors or other small molecule anti-HCV agents, immunoglobulins, hepatoprotectants, anti-inflammatory agents, antiviral vaccine, antibiotics, anti- infectives, etc.
  • Such combination therapies may advantageously utilize lower dosages of the administered therapeutic agents, thus avoiding possible toxicities or complications associated with the various monotherapies.
  • Therapeutic agents used in combination with an anti-hepatitis C virus agent may be those agents that interfere at different stages in the autoimmune and subsequent inflammatory response.
  • At least one anti- hepatitis C virus agent described herein may be coadministered with at least one benzofuran compound and an inhibitor of NS3 (e.g., boceprevir).
  • the benzofuran compound may include any of those set forth in, e.g., U.S. Provisional Patent App. Nos. 60/735,190 and 60/735,191 , and U.S. Published Patent Application No. 2004/0162318.
  • anti-hepatitis C virus agents examples include VIRAMIDINE® (Valeant Pharmaceuticals); MERIMEPODIB® (Vertex Pharmaceuticals); mycophenolic acid (Roche); amantadine; additional benzofurans; ACTILON® (Coley); BILN-2061 (Boehringer Ingelheim); Sch-6 (Schering); VX-950 (Vertex .
  • VALOPICITABINE® (Idenix Pharmaceuticals); JDK-003 (Akros Pharmaceuticals); HCV-796 (Wyeth/ViroPharma); ISlS- 14803 (Isis Pharmaceuticals); ENBREL® (Wyeth); IP-501 (Indevus Pharmaceuticals); ID-6556 (Idun Pharmaceuticals); RITUXIMAB® (Genentech); XLT-6865 (XTL); ANA-971 (Anadys); ANA-245 (Anadys) and TARVACIN® (Peregrine).
  • Additional anti-hepatitis C virus agents include immunomodulators, e.g., interferons (e.g., IFN ⁇ , ⁇ , and ⁇ ) and interferon products (e.g., pegylated interferons), which includes both natural and recombinant or modified interferons.
  • immunomodulators e.g., interferons (e.g., IFN ⁇ , ⁇ , and ⁇ ) and interferon products (e.g., pegylated interferons), which includes both natural and recombinant or modified interferons.
  • interferon products include, but are not limited to, ALBUFERON® (Human Genome Sciences), MULTIFERON® (Viragen), PEG- ALFACON® (Inter-Mune), OMEGA INTERFERON® (Biomedicines), INTRON® A (Schering), ROFERON® A (Roche), INFERGEN® (Amgen), PEG-INTRON® (Schering), PEGASYS® (Roche), MEDUSA INTERFERON® (Flamel Technologies), REBIF® (Ares Serono), and ORAL INTERFERON ALFA® (Amarillo Biosciences).
  • anti-hepatitis C virus agents include, but are not limited to, agents that may regulate T-cell function (e.g., thymosin alfa- 1 , ZADAXIN® (Sci-Clone)), agents that enhance IFN activation of immune cells (e.g., histamine dihydrochloride, CEPLEME® (Maxim Pharmaceutical)), and interferon products.
  • agents that may regulate T-cell function e.g., thymosin alfa- 1 , ZADAXIN® (Sci-Clone)
  • agents that enhance IFN activation of immune cells e.g., histamine dihydrochloride, CEPLEME® (Maxim Pharmaceutical)
  • interferon products e.g., interferon products.
  • Additional anti-hepatitis C virus agents also include antiviral agents (e.g., nucleoside analogs), such as ribavirin products, e.g., COPEGUS® (Roche); RIBASPHERE® (Three Rivers Pharmaceuticals); VIRAZOLE® (Valeant Pharmaceuticals); and REBETOL® (Schering).
  • antiviral agents e.g., nucleoside analogs
  • ribavirin products e.g., COPEGUS® (Roche); RIBASPHERE® (Three Rivers Pharmaceuticals); VIRAZOLE® (Valeant Pharmaceuticals); and REBETOL® (Schering).
  • HCV human immunodeficiency virus
  • Current guidelines suggest an initial antiretroviral therapy consisting of two NIs of the HIV RT, in combination with an NNI or HIV protease inhibitor(s) (Hammer et al. (2006) JAMA 296:827-43. Such combinations provide the best chance of achieving maximal efficiency and curtailing the development of resistance.
  • an optimal antiviral regimen is also likely to include several drugs that target different steps in replication.
  • HCV-796 an NNI of HCV NS5B
  • boceprevir an inhibitor of the NS3 serine protease
  • HCV-796 and boceprevir both demonstrated antiviral activity in HCV-infected patients
  • combinations of HCV-796 and boceprevir had an additive inhibitory effect.
  • replicon variants resistant to one agent were fully susceptible to the other (Howe et al. (2007) 42 nd Annual Meeting of the European Association for the Study of the Liver, Barcelona, Spain.
  • HCV-796 and 800 nM boceprevir were also resistant to two anthranilate derivatives (Table 2). This cross-resistance is explained by anthranilates and HCV-796 having overlapping binding sites on NS5B.
  • the replicon cells resistant to the combination of HCV-796 and boceprevir were fully sensitive to inhibition by another NNI (HCV-371, a pyranoindole), the NI 2'-C-methylcytidine, Peg-IFN, and inhibitors of Hsp90 that have recently been reported to modulate HCV replication.
  • the replicon cells could be cleared by extended treatment with Peg-IFN ( Figure 3).
  • these inhibitors may diminish the emergence of mutants resistant to both HCV-796 and boceprevir, and increase efficacy in a three-part combination.
  • Several mutations were identified in the replicon variants selected with HCV-796 and/or boceprevir.
  • NS5B-C316Y conferred a 242-fold increase in resistance to HCV-796 (Table 4).
  • the NS5B-C316Y mutation was associated with a reduced replicative capacity as the mutant was out-competed by the parental replicon when both were introduced into cells ( Figure 4D) and the NS5B-C316Y change decreased the efficiency of colony formation by approximately two-fold (Table 4).
  • NS5B-C445F mutation was detected during selection with anthranilate inhibitors of NS5B (data not shown) and in previous selection experiments with HCV-796 alone (Howe et al. (2006), supra), but was not previously characterized for its effect on susceptibility to HCV-796.
  • NS5B-C445F conferred an eight-fold reduced susceptibility to HCV-796 (Table 4).
  • NS5B-C445F did not have a detectable effect on HCV replication, as it was not out-competed when electroporated together with the parental replicon, nor did it have a significant effect on the efficiency of colony formation.
  • boceprevir Long exposure or high concentrations of boceprevir were necessary to induce the appearance of mutations at A 156 (Tong et al., supra). The boceprevir concentrations used in our experiments may have been too low, and the duration of selection too short, to select for A 156T.
  • the individual resistance mutations NS5B-C316Y and NS3-V 170A were detected by population sequencing of the NS5B and NS3 genes. To determine if replicons bearing both mutations in the same genome had arisen during the selection process, the entire nonstructural region from the 40/800 combination- resistant replicons was amplified, cloned, and sequenced. The NS3-V 170A mutation was not abundant in these sequences, probably due to the low concentrations of boceprevir used for selection, but a clone was isolated that bore both NS3-V 17OA and NS5B-C316Y. This suggests that these two resistance mutations can be selected together and co-exist in the same genome.
  • a luciferase replicon engineered with both these changes exhibited resistance to both compounds in a transient expression assay.
  • the extent of this resistance was similar to that conferred by the individual mutations to their respective compounds.
  • the data suggest that dually-resistant viral variants bearing both these resistance mutations may arise in response to treatment with the combination of HCV-796 and boceprevir.
  • the fitness of the NS3-V170A and NS5B-C316Y double mutant was debilitated, as it was out-competed by the parental replicon sequence in the competition experiment (Figure 4F) and had a reduced efficiency of colony formation (Table 4).
  • NS3-V158M has not previously been shown to confer resistance to boceprevir, though it is in the proximity of A 156, changes at which confer high levels of resistance to NS3 protease inhibitors.
  • NS3-V158M has not previously been shown to confer resistance to boceprevir, though it is in the proximity of A 156, changes at which confer high levels of resistance to NS3 protease inhibitors.
  • NS3-V158M nor NS5B-I424V affected susceptibility to HCV-796 or boceprevir, but both had a debilitating effect on replicative capacity. These may be secondary changes that arose after other mutations and may not have such deleterious effects in that context. The interactions of these mutations and other changes remains to be investigated.
  • Example 1 Frequency of Selection of Replicons Resistant to Combinations of
  • Example 1.1 Cells and Materials
  • Huh7.5 cells, and Huh7-BB7 cells bearing the Con l strain, genotype Ib subgenomic HCV replicon, and the parental plasmid pHCVreplb.BB7 were licensed from Apath, LLC (St Louis, MO).
  • Cell monolayers were propagated at 37°C in 5% CCb in Dulbecco's minimal essential medium (DMEM; Invitrogen, Carlsbad, CA), supplemented with 10% (v/v) fetal bovine serum (FBS; Hyclone, Logan, UT), penicillin-streptomycin, and nonessential amino acids.
  • DMEM Dulbecco's minimal essential medium
  • FBS fetal bovine serum
  • This medium was also supplemented with 1 mg/ml Geneticin (G418; Invitrogen) for the Huh7- BB7 cells.
  • Pegylated-interferon (Peg-IFN) was obtained from Schering Corporation (Kenilworth, NJ); 2'-C-methylcytidine from CHEMOS GmbH (Regenstauf, Germany); and 17-dimethylaminoethylamino- 17-demethoxygeldanamycin ( 17-DMAG) from Sigma (St. Louis, MO). All other reagents were obtained from suppliers as indicated.
  • Huh7-BB7 cells were seeded at a density of 20,000 cells per 100 mm dish and treated with various concentrations of HCV-796 and/or boceprevir in 0.5% (v/v) DMSO in DMEM supplemented with 2% FBS and 1 mg/ml G418. The cells were incubated at 37 0 C, 5% CO 2 . The medium was removed and replaced with fresh medium supplemented with the appropriate compound concentrations every three or four days. After seven days, the cells were split 1 : 10 into fresh 100 mm dishes and incubated with medium with the appropriate compound concentrations. After twenty days, the medium was removed, the surviving cell colonies were fixed with 7% (w/v) formaldehyde and stained with 1% (w/v) crystal violet in 50% (v/v) ethanol.
  • HCV-796 and boceprevir affected the frequency with which resistant replicons emerged, a genotype I b subgenomic HCV replicon with the neo selectable marker was used, and HCV replicon cells were treated with combinations of the two compounds.
  • the medium was supplemented with 1 mg/ml G418.
  • the concentrations of HCV-796 used were 40 nM and 80 nM (approximately ten- and twenty-times the EC50 in a three-day replicon inhibition assay ⁇ see Example 3.1), respectively).
  • the concentrations of boceprevir used were 400 nM and 800 nM (approximately two- and four-times the EC 50 ). Combinations hereafter are referred to as x/y for the nM concentrations of HCV-796 / boceprevir (i.e., 40/800 refers to cell populations treated with 40 nM HCV-796 and 800 nM boceprevir).
  • Cell death became apparent after 14 days in culture. After 27 days, the surviving cells were fixed and stained with crystal violet ( Figure 1). A confluent cell monolayer was apparent in the DMSO-only, vehicle control (0/0), but selection with increasing HCV-796 or boceprevir concentrations caused fewer cell colonies to survive. The number of colonies was further reduced when the compounds added were in combination.
  • Huh7-BB7 cells were seeded at a density of 7.5 x 10 5 cells per 25 cm 2 tissue-culture flask and cultured in the absence of G418 in DMEM supplemented with 2% FBS, penicillin-streptomycin, 0.5% (v/v) DMSO, and various combinations of HCV-796 and boceprevir, at 37°C and 5% CO 2 . Each concentration of compound was tested in triplicate. When the cells reached about 80% confluence (about 2-3 days); cells were passaged 1 :3 into fresh medium containing the appropriate concentration of each compound.
  • Example 2.2 Quantitative Reverse Transcription-Polymerase Chain Reaction
  • Quantitative reverse transcription-polymerase chain reaction was performed using the ABI Prism 7900HT Sequence Detection System (Applied Biosystems, Foster City, CA), as described previously (Howe et al. (2004), supra). Briefly, the levels of HCV replicon RNA and 18S rRNA were determined in a single-step duplexed reaction using HCV primers and probe against the neomycin phosphotransferase gene and rRNA Pre-Development reagent (Applied Biosystems). The RT reaction was carried out at 48°C for 30 minutes, followed by a denaturation step at 95°C for 10 minutes.
  • RNA extracted from replicon- bearing cells was used to construct standard curves: HCV RNA copies were quantified by the National Genetics Institute, and total RNA concentration was determined by UV-spectrophotometry.
  • the amount of HCV, 18S rRNA or GAPDH in each sample was determined by comparison to standard curves and was expressed as the number of HCV RNA copies per ⁇ g of total RNA (using rRNA as a marker for total RNA measurement) or GAPDH relative to total RNA.
  • replicon cells were cultured in the absence of G418, but in the presence of HCV-796 or boceprevir, alone or in combination. The same compound concentrations were used as for the colony formation assay (see Example 1.2, supra) and three separate cultures were propagated for each of the eight tested conditions. Cell cultures were passaged every two or three days, and fresh medium and compounds were added each time. At every passage, a sample of cells was taken and the HCV RNA and rRNA levels were determined ( Figure 2). (01261 Over the treatment period, the control cells (0/0) showed little change in their HCV replicon content. Levels of GAPDH and rRNA also remained approximately constant for each culture over the course of the experiment (data not shown).
  • the cells were approximately 25% confluent at the time of seeding, and 80 to 90% confluent after three days.
  • the medium was removed and total RNA extracted using the RNeasy 96 Kit.
  • the extracted RNA was eluted in 150 ⁇ L of nuclease-free water and the amounts of HCV, ribosomal and GAPDH RNAs determined by qRT- PCR (see Example 2.2, supra).
  • HCV-796 and boceprevir have been discovered. To evaluate their potential utility against HCV variants resistant to the combination of HCV-796 and boceprevir, several inhibitors with diverse mechanisms were tested in three-day replicon inhibition assays ⁇ see Example 3.1 , supra) against the 0/0 and 40/800 cells.
  • HCV-371 is a pyranoindole NNI of HCV NS5B that binds to the thumb domain of NS5B and inhibits RdRp activity (Gopalsamy et al. (2004) J. Med. Chem. 47:6603-08; Howe et al. (2006) Antimicrob. Agents Chemother. 50:4103- 13; Howe et al. (2004) Antimicrob. Agents Chemother. 48:4813-21 ).
  • the sensitivities of the 0/0 and 40/800 cells to HCV-371 in a three-day replicon assay were not significantly different (EC 50 values of 4832 and 7840 nM, respectively, Table 2), indicating that the 40/800 cell replicons were not cross-resistant to HCV-371.
  • the 40/800 cells were much less sensitive (> 15-fold) to inhibition by anthranilate derivatives than were the 0/0 cells.
  • Anthranilate derivatives are also NNIs of HCV NS5B, binding approximately 7.5A from the NS5B active site (Nittoli et al. (2007) J Med. Chem. 50:2108-16).
  • the clearance assay was done essentially as described (Lin et al. (2004) Antimicrob. Agents Chemother. 48:4784-92; Lin et al. (2006) Antimicrob. Agents Chemother. 50: 1813-22).
  • the 40/800 combination-selected replicon cells were passaged twice in the absence of G418, then following a third passage, were treated with 0, 1 10, or 1 100 ng/ml Peg-IFN for 30 days in the absence of G418. Confluent monolayers were passaged every 3-4 days. Each time the cells were split, a sample of 10 5 cells was lysed for qRT-PCR.
  • the cultures were seeded into medium without Peg-IFN and incubated for 24 hours, and then Peg-IFN was added (see Blight et al. (2002) / Virol. 76: 13001 -14). After 30 days, the Peg- IFN was withdrawn and 0.25 mg/ml G418 was added to expand cells that had not cleared the replicon. After ⁇ 7 days with G418, cell death was observed in several of the cultures. Any surviving cells were permitted to grow back to confluency in the presence of 0.25 mg/ml G418, and the amounts of HCV, ribosomal, and GAPDH were determined by qRT-PCR.
  • the cells grew normally and were split every 2 or 3 days, and at each passage, a sample of cells was collected and HCV and 18S rRNAs were quantitated.
  • the Peg-IFN treatment was performed with three separate 40/800 cell cultures, in the presence ( Figure 3) or absence (data not shown) of 40 nM HCV-796 and 800 nM boceprevir. Three 0/0 cell cultures were similarly treated. After 30 days, the Peg-IFN was withdrawn and 0.25 mg/ml G418 was added to the culture medium to expand any cells that retained the replicon RJSIA.
  • Each untreated cell culture grew normally and, when assayed after 55 and 58 days, contained similar HCV RNA levels as they did at the start of the experiment ( Figure 3).
  • the replicon variants resistant to the combination of HCV-796 and boceprevir were also resistant to the anthranilate derivatives but were susceptible to each of the other tested agents, including the NI (NM 107) and Peg-IFN.
  • the replicon could be cleared from the resistant cells by extended treatment with Peg-IFN.
  • the reaction was incubated at 55°C for 30 min, 94°C for 2 min, followed by 40 cycles of 94°C for 15 sec, 55 0 C for 30 sec, 68°C for 2 min with a final extension at 68°C for 7 min.
  • the amplicons were evaluated by agarose gel electrophoresis, and purified with QIAquick PCR Purification Kit (Qiagen) before sequencing. Sequencing of the PCR amplicons was performed using the ABI Prism BigDye Terminator Cycle Sequencing Ready Reaction kit v3.0 (Applied Biosystems) according to the manufacturer's instructions.
  • sequenced products were gel purified using the Performa® Dye Terminator Removal System (Edge BioSystems; Gaithersburg, MD), dried down, denatured with formaldehyde and separated by electrophoresis using an ABI Prism 3700 DNA Sequencer. Sequence data were analyzed using Sequencher v4.0. (0140) To generate single RT-PCR products encompassing NS3 to NS5B, RT was performed with total cellular RNA, oligonucleotide A9412 (SEQ ID NO: 3; 5 '-CAGG ATGGCCTATTGGCCTGG AG-3') and Superscript III reverse transcriptase (Invitrogen) at 55 0 C for 1 hr.
  • oligonucleotide A9412 SEQ ID NO: 3; 5 '-CAGG ATGGCCTATTGGCCTGG AG-3'
  • Superscript III reverse transcriptase Invitrogen
  • RNA strands were removed by the addition of RNase H (2U per reaction) and incubation at 37 0 C for 20 min.
  • RNase H (2U per reaction)
  • a 6.4 kb product was then amplified according to the manufacturer's instructions with the Expand Long Template PCR System (Roche; Indianapolis, IN) with oligonucleotides 1419F (SEQ ID NO:4; 5'-
  • the primary mutation known to confer resistance to HCV-796 is NS5B- C316Y (Howe et al. (2006), supra). Consistent with this, C316Y was found in cultures that had been selected with HCV-796, either alone or in combination with boceprevir. The changes C316S, C316N, C316F were not observed (previously shown to confer 10-, 26- and 130-fold reduced susceptibilities to HCV-796, respectively).
  • the NS5B amino acids at positions 314, 363, 365 and 414 have been shown to directly interact with HCV-796, and changes at these positions confer varying degrees of resistance to HCV-796. However, no changes at any of these positions was detected in any of the selected cell cultures.
  • the serine protease domain resides in the N-terminal third of NS3, while the helicase domain constitutes the remainder. Mutations in both protease and helicase domains were identified in the combination-resistant cell populations.
  • the NS3 mutation V 170A is known to confer resistance to boceprevir (Tong et al., supra). This change was detected in 3 of 3 cultures selected with 0/800, and in 1 of 3 selected with 40/800, though not in the 0/400 or 40/400 cells. Thus, boceprevir at 800 nM, but not 400 nM, exerted sufficient pressure for the V 17OA mutation to emerge.
  • the NS3-Q86K and -K.583T changes not previously reported to be an adaptive mutation were detected in several cultures, though K583E conferred a weakly adapted phenotype (Lohmann et al. (2003), supra; Lohmann et al. (2001 ), supra).
  • the NS3-E176G mutation was not found in the 0/0 cells, but was detected in the majority of the compound- treated replicons, suggesting that it may have been co-selected with resistance mutations that cause a debilitation in replicative capacity.
  • the mutation NS5B- C445F was detected in replicons treated with HCV-796 alone.
  • the clonal sequencing of the 40/800 replicon cells was generally consistent with the population sequencing, with NS3-V 158M, -E 176G, -G282S and NS5B- C316Y, -P353L and -I424V being notably prevalent among the sequenced clones.
  • the HCV-796 resistance mutation NS5B-C316Y was found in thirteen of the fourteen clones sequenced. Only one clone did not carry this mutation, and this particular clone (40/800-C #2) also carried changes that were not present in any of the other clones, NS5B-C445F, -E440G and -F572L.
  • the boceprevir- resistance mutation NS3-V170A was found in only a single clone from the 40/800 cultures (40/800-C # 1 , Table 3B), which also carried NS5B-C316Y, indicating that these two resistance mutations can coexist in the same replicon genome.
  • Example 7 Identification and characterization of mutations responsible for reduced susceptibility to HCV-796 and boceprevir
  • Example 7.1 Materials and Methods
  • Example 7.1.1 Cloning and Mutagenesis
  • An HCV replicon expressing a secreted luciferase protein was constructed by replacing the neo gene from the parental pHCVrepl b.BB7 plasmid with the luciferase gene from Gaussia princeps, amplified from pCMV-G-luc (New England Biolabs; Ipswich, MA), to generate the plasmid pHCVrep lb.BB7.G-luc. Following transcription and electroporation of the replicon RNA encoded by this plasmid, the Gaussia luciferase protein was secreted from expressing cells and activity was measured in the culture medium.
  • Mutagenesis was performed using the QuikChange II site-directed mutagenesis kit (Stratagene; La Jolla, CA) following the manufacturer's standard protocols. Mutations were generated in the appropriate shuttle vector pMUT-middle (containing the BsrGI-XhoI fragment from pHCVreplb.BB7, encompassing part of NS3, NS4A, NS4B and most of NS5A) or pMUT-back (containing the Xhol- HindIII site from pHCVrepl b.BB7, with part of NS5A, NS5B and the 3'UTR).
  • pMUT-middle containing the BsrGI-XhoI fragment from pHCVreplb.BB7, encompassing part of NS3, NS4A, NS4B and most of NS5A
  • pMUT-back containing the Xhol- HindIII site from pHCVrepl b.BB7, with part of NS5A, NS5
  • Fragments of interest were subcloned back into the appropriate replicon vector, either into pHCVreplb.BB7 for generation of stable cell lines, or into pHCVrepl b.BB7.G-luc for transient expression. The presence of each mutation was confirmed by sequencing of the final replicon plasmids. Amino acid mutations are designated by the single letter amino acid code of the parental sequence, the residue number of the individual protein, and the altered amino acid present in the mutant construct.
  • Example 7.1.2 RNA Transcription and Electroporation of Cultured Cells
  • the cells were washed twice by centrifugation at 250 x g for 5 min and resuspension in room temperature Dulbecco's PBS (D-PBS; 50 ml per flask), then pelleted again and resuspended at a concentration of 1 x 10 7 cells/ml in Cytomix (120 mM potassium chloride, 0.15 mM calcium chloride, 2 mM EGTA, 5 mM magnesium chloride, 25 mM HEPES, 10 mM potassium phosphate buffer pH 7.6).
  • D-PBS Dulbecco's PBS
  • Example 7.1.3 Evaluation of the Efficiency of Replicon Colony Formation [0150) Following electroporation of Huh7.5 cells with RNA generated from pHCVreplb.BB7 templates, a ten-fold serial dilution of the electroporated cells was generated and 15 ml of the 1 : 10, 1 : 100 and 1 :000 dilutions were seeded in 100 mm dishes ( ⁇ 10 5 , 10 4 and 10 3 electroporated cells, respectively). To select for replicon-bearing cells, the culture medium was supplemented with G418 at 0.375 mg/ml.
  • Example 7.1.4 Transient Replication Assay
  • Luciferase activity was measured from 25 ⁇ l of culture medium, using the Gaussia luciferase assay kit (New England Biolabs). To calculate the relative fitness of different replicon mutants, the luciferase signal from the sample taken 48 hours post-electroporation was normalized to the luciferase signal 4 hours post-electroporation (to account for electroporation efficiency) and then expressed relative to the parental replicon RNA (relative fitness for the parental RNA is 1.0). To determine the susceptibility of mutant replicons to inhibition by compounds, the medium was removed 48 hours post- electroporation and replaced with DMEM supplemented with 2% FBS and the compound under test.
  • luciferase activity was measured.
  • the EC 5 O was determined as the compound concentration necessary to inhibit 50% of the luciferase activity determined from untreated cells, following the deduction of background signal.
  • Example 7.2 Results
  • Example 7.2.1 Susceptibility
  • each individual mutation was reintroduced into the parental replicon that had the neo gene replaced with luciferase from Gaussia princeps.
  • the susceptibility of each mutant to HCV-796 and boceprevir was tested in a transient expression assay following electroporation of the replicon RNA.
  • the Gaussia luciferase protein was secreted from expressing cells and was assayed in the culture medium 72 hours after the addition of compound.
  • the ECso's for HCV-796 and boceprevir for the parental replicon in the transient assay were comparable to those obtained in the three-day inhibition assay with the stable replicon cells; the EC50 for HCV- 796 in the transient assay was 14 nM, compared to 5 nM for the stable replicon, and the EC 50 for boceprevir in the transient assay was 608 nM, compared with 201 nM in the stable (compare Tables 4 & 1).
  • NS5B-C316Y conferred a 142-fold reduced susceptibility to HCV-796, but had no effect on susceptibility to boceprevir.
  • the NS3-V 170A mutation conferred a five-fold reduced susceptibility to boceprevir, but had no effect on susceptibility to HCV-796.
  • both primary resistance- mutations NS3-V 170A and NS5B-C316Y, were introduced together, the double- mutant exhibited reduced susceptibility to both compounds: seven-fold to boceprevir and ⁇ 140-fold to HCV-796.
  • the NS5B-C445F mutation conferred a 17-fold reduced susceptibility to HCV-796 but had no effect upon inhibition by boceprevir.
  • the resistance to HCV-796 contributed by NS5B-C316Y and - C445F was additive, as a replicon bearing both mutations had ⁇ 1800-fold reduced susceptibility.
  • NS3-E176G The cell-culture-adaptive mutation, NS3-E176G, showed a slightly reduced susceptibility to inhibition by both HCV-796 (three-fold) and boceprevir (four-fold). This is likely due to an increased replication level and not a specific mechanism of resistance. A similar mechanism may explain the slightly reduced susceptibility to both compounds conferred by NS3-G282S. Three mutations found in the selected replicons did not effect susceptibility to either HCV-796 or boceprevir in the transient assay; NS3-V158M, -K583T and NS5B-I424V.
  • Gaussia luciferase protein compared to the Firefly luciferase used by others, may cause this assay to poorly resolve fitness phenotypes. Instead, other methods to evaluate mutant fitness was used.
  • Huh-7 cells were electroporated with either the parental replicon, the mutant replicon or with equal amounts of parental and mutant replicon. After G418 selection and expansion (sixteen to twenty days post-electroporation), the NS3 and NS5B genes were amplified and sequenced to determine if the mutant or the parental sequence predominated in the selected cell population ( Figures 4A-F).
  • the competition experiment was performed three times and each time similar results were obtained, except for one occasion when the NS5B-C445F mutant electroporated alone reverted and possessed a mixed mutant and parental sequence at NS5B-445 (data not shown). (0157J T° obtain a further measure of mutant fitness, the efficiency of colony formation following electroporation was determined (Table 4).
  • the parental replicon had an efficiency of 15 x 10 3 cfu/ ⁇ g of RNA.
  • the mutations could be divided into three groups. The first group was those that increased the efficiency of colony formation above that of the parental replicon, including the cell-culture adaptive change NS3-E176G, but also -G282S (36 and 27 x 10 3 cfu/ ⁇ g, respectively).
  • the second group of mutations did not significantly alter the efficiency of colony formation and included NS3-V 170A, -K.583T and NS5B- C445F (14, 19 and 12 x 10 3 cfu/ ⁇ g).
  • the final group of mutants caused a decrease in the efficiency of colony formation and included NS3-V 158M, NS5B- C316Y and -I424V (5, 7 and 6 x 10 3 cfu/ ⁇ g), consistent with these changes debilitating HCV replication.
  • Replicon-bearing cell populations selected under the indicated treatments, were tested for their susceptibility to HCV-796 or boceprevir in a three-day inhibition assay.
  • the mean EC 5 0 ⁇ standard deviation is indicated from n independent determinations. Fold resistance relative to the DMSO-only, vehicle-control treated culture (0/0) is shown.
  • Replicon cell populations selected DMSO-only (0/0) or 40 nM HCV-796 and 800 nM boceprevir (40/800), were tested for their susceptibility to miscellaneous anti-HCV inhibitors in a three-day inhibition assay.
  • the mean EC 5O ⁇ S. D. is indicated from n independent determinations.
  • Table 3 A Population sequence analysis of nonstructural genes from cells selected with combinations of HCV-796 and/or boceprevir
  • Table 3B Clonal sequence analysis of nonstructural genes from cells selected with combinations of HCV-796 and/or boceprevir
  • RNA from independently selected replicon cultures (0/0-A or 40/800-A, -B or -C) was extracted and cDNA encoding the nonstructural coding region was amplified and cloned.
  • Five different clones derived from each selected culture were sequenced (#1 -5). Only amino acid positions noted as being of interest from the population sequencing are shown. Amino acid numbering within NS3 and NS5B, the predicted amino acids present in the parental pBB7 plasmid and polyprotein numbering according to the Conl sequence (accession # AJ238799) is shown.
  • the susceptibility of replicon mutants to HCV-796 or boceprevir was determined using a transient luciferase replicon. The EC 50 and the fold resistance compared to the parental replicon sequence are indicated.
  • the efficiency of colony formation was determined following electroporation of Huh7.5 cells with replicon RNA and selection with G418. The efficiency of colony formation was determined for each mutant replicon in three separate electroporations on different days, with independently derived RNA preparations. Mean efficiency of colony formation ⁇ S. D. is shown.
  • a replication defective RNA (Pol -) is shown as a negative control.

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Abstract

The present invention provides methods of decreasing the frequency of emergence, decreasing the level of resistance, and delaying the emergence of a treatment-resistant hepatitis C viral infection, by administering to a subject, either in combination or in series, an inhibitor of the hepatitis C RNA-dependent RNA polymerase NS5B, e.g., a benzofuran, such as 5-cyclopropyl-2-(4-fluorophenyl)- 6-[(2-hydroxyethyl)(methylsulfonyl)amino]-N-methyl-l-benzofuran- 3-carboxamide (HCV-796), and an inhibitor of the serine protease NS3, e.g., boceprevir. Additionally, the invention relates to methods of monitoring the course of treatment of a hepatitis C viral infection, methods of monitoring and prognosing a hepatitis C viral infection, and methods of identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy. These methods use the sequence(s) of HCV nonstructural gene(s) to identify the emergence of a treatment-resistant hepatitis C viral infection, particularly a benzofuran (e.g., HCV-796) and NS3 inhibitor (e.g., boceprevir) treatment- resistant hepatitis C viral infection.

Description

IDENTIFICATION AND CHARACTERIZATION OF HCV REPLICON
VARIANTS WITH REDUCED SUSCEPTIBILITY TO A COMBINATION
OF POLYMERASE AND PROTEASE INHUiITORS, AND METHODS
RELATED THERETO
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional Application No. 60/954,665, filed August 8, 2007, which is incorporated herein by reference in its entirety.
BACKGROUND OF THE INVENTION
Field of the Invention
|0002) The present invention relates to treatment-resistant hepatitis C viral infections and inhibitors of hepatitis C virus RNA-dependent RNA polymerase NS5B (RdRp) and serine protease NS3. In particular, the present invention relates to the NS3 serine protease inhibitor boceprevir, as well as benzofuran inhibitors of NS5B, more particularly 5-cyclopropyl-2-(4-fluorophenyl)- 6-[(2-hydroxyethyl)(methylsulfonyl)amino]-N-methyl-l -benzofuran- 3-carboxamide (HCV-796).
Related Background Art
|00031 Hepatitis C is a common viral infection that can lead to chronic hepatitis, cirrhosis, liver failure, and hepatocellular carcinoma. Infection with the hepatitis C virus (HCV) leads to chronic hepatitis in at least 85% of cases, is the leading reason for liver transplantation, and is responsible for at least 10,000 deaths annually in the United States ((1997) Hepatology 26:2S- 10S). [0004) There is no vaccine currently available to prevent HCV infection. Current therapy for HCV infection includes monotherapy treatment with pegylated-interferon (Peg- INF), or a combination therapy consisting of Peg- INF with the nucleoside analog ribavirin (Bartenschlager (1997) Antiviral Chem. Chemo. 8:281-301). However, even with combination treatment, many patients fail to develop a sustained viral response (Wong and Lee (2006) Canadian Med. Assoc. J. 174:649-59). A therapeutic response will depend on, inter alia, viral genotype, e.g., HCV genotype Ib is more resistant to IFN therapy than genotypes 2 and 3 (id.).
[0005] The hepatitis C virus is a member of the Flaviviridae family and displays genetic heterogeneity; at least 6 genotypes and more than 50 subtypes have been identified (Wong and Lee, supra). The genome of HCV is a single-stranded linear RNA of positive sense that encodes a 3,010 amino acid polyprotein (Purcell (1997) Hepatology 26: 1 I S- 14S). The polyprotein is cleaved by a combination of host- and virus-encoded proteases to yield individual viral proteins, including both structural and nonstructural proteins. The nonstructural proteins are: NS2, NS3, NS4A, NS4B, NS5A, and NS5B (Bartenschlager and Lohmann (2000) J. Gen. Virol. 81 : 1631 -48).
|0006] The heterogeneity of HCV is due to the high rate of replication (~l x lθ12 virions per day) and the error-prone nature of the RdRp. These characteristics result in high mutation rates of 10"4 to 10"5 mutations/nucleotide in HCV (Patel and Preston (1994) Proc. Natl. Acad. ScL U.S.A. 91 :549-53; Preston et al. (1988) Science 242: 1 168-71 ). As a consequence, quasi-species of viral variants have been found in HCV-infected patients (Cabot et al. (2000) J Virol. 74:805- 1 1 ; Davis (1999) Am. J. Med. 107:21 S-26S; Farci and Purcell (2000) Sem. Liver Disease 20: 103-26). Taken together, these factors are likely to result in the rapid selection of drug-resistant HCV variants. Therefore, the development of successful anti-HCV therapies requires an understanding of the nature and fitness of variants that are likely to emerge upon treatment. In this endeavor, the structural basis for resistance will help in the design of therapies that may not be readily circumvented by the virus. [0007| The most intensively studied viral proteins with regard to therapeutic intervention have been two of the nonstructural proteins, the NS3 serine protease and the NS5B RNA-dependent RNA polymerase (RdRp) (De Francesco and Migliaccio (2005) Nature 436:953-60). NS5B RdRp is the principal catalytic enzyme for HCV replication, and represents a viable target for anti-HCV therapeutics (Walker and Hong (2002) Curr. Opin. Pharm. 2:534-40). Recent research efforts have led to the discovery of inhibitors that specifically target NS5B, as well as therapeutics that target other HCV viral proteins (Carroll et al.
(2003) J. Biol. Chem. 278: 1 1979-84; Dhanak et al. (2002) J. Biol. them. 277 :38322-27; Howe et al. (2004) Antimicrobial Agents Chemo. 48:4813-21 ; Love et al. (2003) J. Virol. 77:7575-81 ; Shim et al. (2003) Antiviral Res. 58:243-51 ; Summa et al. (2004) J. Med. Chem. 47: 14-17; Olsen et al. (2004) Antimicrobial Agents Chemo. 48:3944-53; Nguyen et al. (2003) Antimicrobial Agents Chemo. 47:3525-30; Ludmerer et al. (2005) Antimicrobial Agents Chemo. 49:2059-69; Mo et al. (2005) Antimicrobial Agents Chemo. 49: 4305- 14; Lu et al.
(2004) Antimicrobial Agents Chemo. 48:2260-66; U.S. Provisional Patent App. Nos. 60/735,190 and 60/735,191 (both disclosing benzofuran derivatives); U.S. Patent No. 6,964,979 (disclosing pyranoindole derivatives); U.S. Patent Publication Nos. 2006/0063821 (disclosing arbazole and cyclopentaindole derivatives), 2004/0162318 (disclosing benzofuran derivatives), and 2004/0082643 (disclosing pyranoindole derivatives).
|0008| Both nucleoside inhibitors (NIs) and nonnucleoside inhibitors (NNIs) of the NS5B RdRp have been reported. For example, the 5 '-triphosphates of 2'-C- methyl nucleosides were demonstrated to be potent inhibitors of the HCV RdRp (Carroll and Olsen (2006) Infect. Disord. Drug Targets 6: 17-29). Following conversion to the active 5 '-triphosphate, NIs function as competitive substrate analogs that terminate nascent RNA chains (Id.).
[0009] Numerous structurally diverse NNIs of NS5B have been shown (Carroll and Olsen, supra; Koch and Narjes (2006) Infect. Disord. Drug Targets 6:31-41 ; Wu et al. (2005) Mini Rev. Med. Chem. 5: 1 103- 12). Three distinct binding sites for NNIs on NS5B have been described: one near a GTP-binding site within the thumb domain (for benzimidazoles and indoles); one at the base of the thumb (for thiophene, phenylalanine, dihydropyranone and pyranoindole derivatives); and one in the palm domain adjacent to the active site (for benzothiadiazine, proline sulphonamide, benzylidene and acrylic acid analogs). The NNIs appear to act through allosteric mechanisms that inhibit the initiation or elongation of RNA synthesis by NS5B. For the NIs and NNIs characterized to date, single amino acid changes reduce susceptibility to the compounds (Migliaccio et al. (2003) J. Biol. Chem. 278:49164-70; Tomei et al. (2003) J. Virol. 77: 13225-31 ). 10010) The NS3 serine protease, in a complex with its cofactor NS4A, is responsible for cleavage of the polyprotein at sites downstream of NS3. Recent clinical trials demonstrated proof-of-concept in humans and validated the NS3 protease as a target (Lamarre et al. (2003) Nature 426: 186-9; Reeskin et al. (2006) Gastroenterology 131 :997-1002; Sarrazin et al. (2007) Gastroenterology 132: 1270-8). Replicon resistance studies, subsequently confirmed in biochemical assays, revealed that, like NIs and NNIs, single amino acid mutations were capable of reducing susceptibility to NS3 protease inhibitors (Lin et al. (2005) J. Biol. Chem. 280:36784-91 ; Lin et al. (2004) J Biol. Chem. 279: 17508-14; Sarrazin et al. (2007) Gastroenterology 132: 1767-77; Tong et al. (2006) Antivirol Res. 70:28-38.
[0011 ] In the case of human immunodeficiency virus (HIV) and hepatitis B virus (HBV), numerous mutations have been identified in patients treated with protease inhibitors as well as NIs and NNIs. Likewise, emergence of resistant viruses is anticipated to be one of the largest challenges in developing effective antiviral therapies against HCV infection. For HCV, as is the case for HIV, an optimal antiviral regimen is likely to include several drugs targeting different steps in replication. Such combinations provide the best chance of achieving maximal efficacy and inhibiting the development of resistance.
SUMMARY OF THE INVENTION
[0012] Individually, both HCV-796 and boceprevir demonstrate antiviral activities in patients infected with HCV. However, mutations occurring in NS5B or NS3 sometimes lead to decreased sensitivity to their respective inhibitors. Such mutations can result in the emergence of treatment-resistant hepatitis C viral infections.
|00131 Interestingly, the combination of HCV-796 and boceprevir has an additive inhibitory effect on the HCV replicon, signaling a need to identify methods by which combination therapy with HCV-796 and boceprevir may reduce the emergence of treatment-resistant hepatitis C viral infections. Additionally, there is a need to identify the mutation sites in the NS5B polymerase and NS3 serine protease that result in treatment-resistant hepatitis C viral infections. Once identified, these sites will serve as: (1) markers to monitor the course of an anti-hepatitis C therapy for developing an. increased resistance to NS5B polymerase inhibitors (e.g., benzofurans, such as HCV-796) and NS3 protease inhibitors (e.g., boceprevir); (2) markers to identify individuals with a decreased likelihood of responding to an anti-hepatitis C virus therapy; and (3) markers to monitor and prognose a hepatitis C viral infection. This information is additionally useful to optimize second-generation hepatitis C viral inhibitors or other HCV inhibitor combinations that exhibit significantly reduced, minimal, or no susceptibility to resistance caused by mutations at these sites. |0014| The present invention provides methods of decreasing the frequency of emergence, decreasing the level of resistance, and delaying the emergence of a treatment-resistant hepatitis C viral infection, by administering to a subject, either in combination or in series, an inhibitor of the hepatitis C RNA-dependent RNA polymerase NS5B (e.g., a benzofuran, such as 5-cyclopropyl-2-(4-fluorophenyl)- 6-[(2-hydroxyethyl)(methylsulfonyl)arnino]-N-methyl-l -benzofuran-3- carboxamide (HCV-796)) and an inhibitor of the HCV NS3 serine protease (e.g., boceprevir). The present invention also describes further administering at least one additional anti-hepatitis C agent, e.g., a ribavirin product or an immunomodulator, such as an interferon product.
[0015| Additionally, the present invention relates to methods of monitoring the course of treatment of a hepatitis C viral infection, methods of monitoring and prognosing a hepatitis C viral infection, and methods of identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy. The present invention also provides useful information and methods related to optimizing second-generation anti-hepatitis C agents, e.g., optimizing identification and chemical synthesis of second-generation anti-hepatitis C agents, for treating, e.g., a benzofuran- or boceprevir-resistant hepatitis C viral infection in a subject.
|0016) Thus, in at least one embodiment, the invention provides a method of decreasing the frequency of emergence of a treatment-resistant hepatitis C viral infection, comprising administering a benzofuran inhibitor of a hepatitis C virus in combination with an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof. In at least one other embodiment, the invention provides a method of delaying the emergence of a treatment-resistant hepatitis C viral infection, comprising administering a benzofuran inhibitor of a hepatitis C virus in combination with an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof. In at least one other embodiment, the invention provides a method of decreasing the level of resistance of a treatment-resistant hepatitis C viral infection, comprising administering a benzofuran inhibitor of a hepatitis C virus in combination with an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof. In some embodiments, the benzofuran inhibitor of a hepatitis C virus is HCV-796. In some embodiments, the NS3 protease inhibitor is boceprevir. In some embodiments, at least one additional anti-hepatitis C virus agent is also administered. The at least one additional anti-hepatitis C virus agent may be an immunomodulator, a ribavirin product, and/or a small molecule inhibitor such as a nucleoside analogue, a nonnucleoside, or an inhibitor of heat shock proteins.
|0017] In at least one embodiment, the invention provides a method of decreasing the emergence of an HCV-796-resistant hepatitis C viral infection, comprising administering HCV-796 in combination with an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof. In at least one other embodiment, the invention provides a method of decreasing the emergence of an HCV-796-resistant hepatitis C viral infection, comprising administering HCV-796 either before or after administration of an inhibitor of a hepatitis C virus NS3 serine protease to a subject in need thereof. In some embodiments, at least one additional anti-hepatitis C virus agent is also administered. The at least one additional anti-hepatitis C virus agent may be an immunomodulator, a ribavirin product, and/or a small molecule inhibitor such as a nucleoside analogue, a nonnucleoside, or an inhibitor of heat shock proteins. |0018] In at least one embodiment, the invention provides a method of identifying an individual with a decreased likelihood of responding to an anti- hepatitis C viral therapy, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the individual at a first time point; and determining the amino acid sequence of the nonstructural gene in a sample from the individual at a second time point, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the individual at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the individual at the first time point, indicates a decreased likelihood that the individual will respond to an anti-hepatitis C viral therapy. ' |0019) In at least one embodiment, the invention provides a method of identifying an individual with a decreased likelihood of responding to an anti- hepatitis C viral therapy, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the individual; and comparing the amino acid sequence of the nonstructural gene in the sample from the individual to the amino acid sequence of the nonstructural gene in a reference sample, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the individual, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, indicates a decreased likelihood that the individual will respond to an anti-hepatitis C viral therapy. [0020] In at least one embodiment, the invention provides a method for monitoring the course of treatment of a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; administering a benzofuran compound and an NS3 protease inhibitor to the subject; and determining the amino acid sequence of the nonstructural gene in a sample from the subject following administration of the benzofuran compound and NS3 protease inhibitor to the subject, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject following administration of the benzofuran compound and NS3 protease inhibitor, in comparison to the amino acid sequence of the nonstructural gene in the sample from the subject prior to administration of the benzofuran compound and NS3 protease inhibitor, provides a negative indication of the effect of the treatment of the hepatitis C viral infection in the subject. (0021) In at least one embodiment, the invention provides a method for monitoring the course of treatment of a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; administering HCV-796 and boceprevir to the subject; and determining the amino acid sequence of the nonstructural gene in a sample from the subject following administration of HCV-796 and boceprevir to the subject, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject following administration of HCV-796 and boceprevir, in comparison to the amino acid sequence of the nonstructural gene in the sample from the subject prior to administration of HCV-796 and boceprevir, provides a negative indication of the effect of the treatment of the hepatitis C viral infection in the subject.
[0022] In at least one embodiment, the invention provides a method for monitoring the course of treatment of a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; administering HCV-796, boceprevir, and at least one additional anti-hepatitis C agent to the subject; and determining the amino acid sequence of the nonstructural gene in a sample from the subject following administration of HCV-796, boceprevir and at least one additional anti- hepatitis C agent to the subject, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject following administration of HCV-796, boceprevir, and at least one additional anti-hepatitis C agent, in comparison to the amino acid sequence of the nonstructural gene in the sample from the subject prior to administration of HCV-796, boceprevir, and at least one additional anti-hepatitis C agent, provides a negative indication of the effect of the treatment of the hepatitis C viral infection in the subject. In some embodiments-, the at least one additional anti-hepatitis C virus agent is an immunomodulator, a ribavirin product, and/or a small molecule inhibitor such as a nucleoside analogue, a nonnucleoside, or an inhibitor of heat shock proteins. |0023) In at least one embodiment, the invention provides a method for prognosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject at a first time point; and determining the amino acid sequence of the nonstructural gene in a sample from the subject at a second time point, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject at the second time point, in comparison to the amino acid sequence from the subject at the first time point, indicates an increased likelihood that the subject will develop a treatment- resistant hepatitis C viral infection.
|0024) In at least one embodiment, the invention provides a method for prognosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; and comparing the amino acid sequence of the nonstructural gene in the sample from the subject to the amino acid sequence of the nonstructural gene in a reference sample, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, indicates an increased likelihood that the subject will •> develop a treatment-resistant hepatitis C viral infection. [0025| In at least one embodiment, the invention provides a method for monitoring a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject at a first time point; and determining the amino acid sequence of the nonstructural gene in a sample from the subject at a second time point, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the subject at the first time point, provides an indication that the hepatitis C viral infection has changed in severity. |0026] In at least one embodiment, the invention provides a method for monitoring a hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; and comparing the amino acid sequence of the nonstructural gene in the sample from the subject to the amino acid sequence of the nonstructural gene in a reference sample, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, provides an indication that the hepatitis C viral infection has changed in severity. |00271 In at least one embodiment, the invention provides a method for diagnosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HGV nonstructural gene in a sample from the subject at a first time point; and determining the amino acid sequence of the nonstructural gene in a sample from the subject at a second time point, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the subject at the first time point, indicates an increased likelihood that the subject has developed or will develop a treatment-resistant hepatitis C viral infection.
[0028) In at least one embodiment, the invention provides a method for diagnosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising: determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; and comparing the amino acid sequence of the nonstructural gene in the sample from the subject to the amino acid sequence of the nonstructural gene in a reference sample, wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, indicates an increased likelihood that the subject has developed or will develop a treatment-resistant hepatitis C viral infection.
[0029) In at least some of the above embodiments provided by the invention, the nonstructural gene is selected from the group of NS3, NS5A, and NS5B. In some embodiments, the change in the amino acid sequence of the nonstructural gene is an amino acid change selected from the group consisting of those set forth in Table 3A. In some further embodiments, the hepatitis C RNA-dependent RNA polymerase NS5B is derived from a hepatitis C virus genotype selected from the group consisting of genotypes Ia, Ib, 2, 3, 4, 5, and 6.
BRIEF DESCRIPTION OF THE DRAWINGS
[0030) Figure 1 shows the frequency of selection of replicons resistant to combinations of HCV-796 and boceprevir. Huh7-BB7 cells bearing a subgenomic genotype Ib HCV replicon were seeded at 20,000 per 100 mm dish and treated with 1 mg/ml G418 and the indicated combinations of HCV-796 and boceprevir. Fresh medium, G418, and compounds at the appropriate concentration were added every 3 or 4 days. After 7 days the cultures were split 1 : 10 into a new 100 mm dish and, after 20 days, the surviving cell colonies were fixed and stained with crystal violet. Shown is a representative of three independent experiments.
[0031) Figure 2 shows a time course of treatment of HCV replicon cells with combinations of HCV-796 and boceprevir (SCH-503034). HCV replicon cells were propagated in the presence of combinations of HCV-796 and/or boceprevir, but in the absence of G418. Cells were passaged every 2-3 days, and each time the cultures were split, a sample of the cells was taken. RNA was extracted from cell lysates, and HCV and rRNA levels were determined by qRT-PCR. Each point is a mean HCV RNA/rRNA value from eight independent experiments, each comprising triplicate replicon cell cultures. Error bars above each point represent the standard error of the mean.
[0032) Figure 3 shows HCV replicon variants resistant to the combination of HCV-796 and boceprevir can be cleared by Peg-IFN. The previously selected 40/800 and 0/0 cells were incubated for 30 days in the presence of 40 nM HCV-796 and 800 nM boceprevir, and treated with Peg-IFN as described infra. After 30 days, the Peg-IFN was withdrawn and 0.25 mg/ml G418 was added to select for cells that had retained the replicon. Three replicate cultures were treated, HCV and ribosomal RNA was quantitated, and the mean and standard error at each time point was plotted. No cells that were treated with ~100x EC50 Peg-IFN survived the selection process.
[0033) Figures 4A-F show competition with the parental replicon sequence as a measure of mutant relative replicative capacity. Huh7 cells were electroporated either with parental replicon RNA, mutant replicon RNA or with equal amounts of parental and mutant replicon RNAs. Following G418 selection, RNA was extracted from the replicon cell populations and the NS3 and NS5B genes were amplified. Sequences of the PCR product populations were determined. 4A. NS3-V 158M; 4B. NS3-V170A; 4C. NS3-E176G; 4D. NS5B-C316Y; 4E. NS5B- C445F; 4F. NS3-V 17OA / NS5B-C316Y. Representative sequencing chromatograms (from at least two sequencing reactions), nucleotide sequence and the inferred amino acid sequence at the mutant codon are shown. Sequences from cells electroporated with only the parent replicon and only the mutant replicon RNA are shown above the co-electroporated cells.
DETAILED DESCRIPTION OF THE INVENTION
[0034) In the absence of an efficient infectious tissue culture for HCV, viral resistance can be studied in the HCV replicon system (Blight et al. (2000) Science 290: 1972-74; Lohmann et al. (2003) J. Virol. 77:3007- 19). A replicon is a subgenomic RNA that contains all essential elements and genes required for replication in the absence of structural genes. The HCV replicon also contains a foreign gene encoding a drug-selectable marker (neomycin phosphotransferase) to allow for G418 (neomycin) selection of cells that contain a functional replicon. Transfection of the HCV replicon into human hepatoma cells (Huh-7) leads to an autonomous HCV replication.
|0035| Replicon resistance studies help validate enzyme targets, delineate antiviral mechanisms of action, and identify mutations that may be useful diagnostic and prognostic markers for drug susceptibility in patients. These systems also allow evaluations of the genetic barrier a virus like HCV must overcome to acquire resistance and, therefore, the likelihood that resistant variants will emerge during clinical use. The fitness of resistant mutants is likely to be a critical determinant of the efficacy of an anti-HCV therapy. [0036) The invention provides methods for the selection and characterization of replicon variants that have reduced susceptibility to HCV-796 and boceprevir (see also U. S. S. N. 1 1/704,505, filed February 9, 2007 (International Application No. PCT/US07/003807, filed February 9, 2007); see also, e.g., U.S. Published Application No. 2004/0162318; all of which are hereby incorporated by reference herein in their entireties). Mapping of the amino acid changes encoded by HCV nonstructural genes derived from the replicon variants demonstrated several mutations. These mutations were shown to be responsible for the reduced susceptibility to HCV-796 in recombinant replicons and enzymes molecularly engineered with the single mutations. Additionally, the drug susceptibility of the replicon variants was evaluated in a panel of antiviral agents including pegylated interferon (PegIFN) and ribavirin (RBV). Similar susceptibility to PegIFN, RBV, and other HCV specific inhibitors was detected.
|0037] Using the sequence and/or structure of the hepatitis C RNA-dependent RNA polymerase NS5B (hereinafter "NS5B") or a portion of NS5B (e.g., the HCV-796 binding pocket of the hepatitis C RNA-dependent RNA polymerase NS5B), and/or using the sequence and/or structure of the NS3 serine protease ("hereinafter "NS3") or a portion of NS3, the present invention provides, e.g., methods of monitoring the course of treatment of a hepatitis C viral infection, methods of diagnosing the development of a treatment-resistant hepatitis C viral infection, methods of monitoring and prognosing a hepatitis C viral infection, and methods of identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy. [0038] As used herein, "hepatitis C virus," "hepatitis C," "HCV," and the like means all genotypes of hepatitis C (e.g., hepatitis C Ia, Ib, 2, 3, and 4), and all subtypes and isolates thereof {see, e.g., Wong and Lee (2006) Canadian Med. Assoc. J. 174:649-59).
|0039) As used herein, "anti-hepatitis C viral therapy" and the like means any treatment (e.g., administration of an agent) or course of treatment for HCV infection. Such therapies include administration of an agent alone, e.g., administration of an anti-hepatitis C virus agent, such as an immunomodulator (e.g., an interferon product), or administration of agents in combination, e.g., administration of an immunomodulator either concurrently or in series with a ribavirin product. Thus either a single or sustained treatment, which may be an agent alone or in combination with at least one additional agent, is included within the meaning of "anti-hepatitis C viral therapy" and the like. [0040] As used herein, "anti-hepatitis C virus agent" and the like means any agent that may be used to treat HCV infection, e.g., interferon products and other immunomodulators, ribavirin products, inhibitors of HCV enzymes, antifibrotics, etc. Such agents include those disclosed in, e.g., Carroll et al., supra; Dhanak et al., supra; Howe et al. (2004), supra; Love et al., supra; Shim et al, supra; Summa et al., supra; Olsen et al., supra; Nguyen et al., supra; Ludmerer et al., supra; Mo et al., supra; Lu et al., supra; Leyssen et al. (2000) Clin. Microbiol. Rev. 13:67-82; Oguz et al. (2005) W. J. Gastroenterol. 1 1 :580-83; U.S. Provisional Patent App. Nos.: 60/735,190 and 60/735, 191 ; U.S. Patent No. 6,964,979; U.S. Patent Publication Nos. 2006/0063821 , 2004/0162318, 2006/0040944, 2006/0035848, 2005/0159345, 2005/0075309, 2005/0059647, 2005/0049204,2005/0048062, 2005/0031588, 2004/0266723, 2004/0209823, 2004/0077587, 2004/0067877, 2004/0028754 and 2004/0082643; and PCT Publication No. WO 2001/032153. Examples of such agents include VIRAMIDINE® (Valeant Pharmaceuticals), MERIMEPODIB® (Vertex Pharmaceuticals), mycophenolic acid (Roche), amantadine, ACTILON® (Coley), BILN-2061 (Boehringer Ingelheim), Sch-6 (Schering), VX-950 (Vertex Pharmaceuticals), VALOPICITABINE® (Idenix Pharmaceuticals); JDK-003 (Akros Pharmaceuticals); HCV-796 (Wyeth/ViroPharma), ISIS-14803 (Isis Pharmaceuticals), ENBREL® (Wyeth); IP-501 (Indevus Pharmaceuticals), ID- 6556 (Idun Pharmaceuticals), RITUXIMAB® (Genentech), XLT-6865 (XTL), ANA-971 (Anadys), ANA-245 (Anadys) and TARVACIN® (Peregrine). Additional anti-hepatitis C virus agents include immunomodulators, e.g., interferons (e.g., LFN-α, β, and γ) and interferon products (e.g., pegylated interferons and albumin interferons), which includes both natural and recombinant or modified interferons. Examples of interferon products include, but are not limited to, ALBUFERON® (Human Genome Sciences), MULTIFERON® (Viragen), PEG-ALFACON® (Inter-Mune), OMEGA INTERFERON® (Biomedicines), INTRON® A (Schering), ROFERON® A (Roche), INFERGEN® (Amgen), PEG-INTRON® (Schering), PEGASYS® (Roche), MEDUSA INTERFERON® (Flamel Technologies), REBIF® (Ares Serono), ORAL INTERFERON ALFA® (Amarillo Biosciences), consensus interferon (CIFN) (Aladag et al. (2006) Turk. J. Gastroenterol. 17(l ):35-39, and albumin-interferon-alpha (Balan et al. (2006) Antivir. Ther. 1 1 :35-45). [00411 As used herein, "immunomodulator" and the like means any agent capable of regulating an immune response or a portion of an immune response in a subject. Examples include, but are not limited to, agents that may regulate T- cell function (e.g., thymosin alfa-1, ZADAXFN® (Sci-Clone)), agents that enhance IFN activation of immune cells (e.g., histamine dihydrochloride, CEPLEME® (Maxim Pharmaceutical)), and interferon products. [0042] Additional anti-hepatitis C virus agents include antiviral agents (e.g., nucleoside analogs), such as ribavirin products. As used herein, "ribavirin product" and the like means any agent that contains ribavirin (1 -β-D- ribofuranosyl-lH-l ,2,4-triazole-3-carboxamide). Examples of such ribavirin products include COPEGUS® (Roche); R1BASPHERE® (Three Rivers Pharmaceuticals); VIRAZOLE® (Valeant Pharmaceuticals); and REBETOL® (Schering).
|00431 As used herein, "HCV-796" and the like means 5-cyclopropyl-2-(4- fluorophenyl)-6-[(2-hydroxyethyl)(methylsulfonyl)amino]-N-methyl-l - benzofuran-3-carboxamide, which is disclosed in, e.g., U.S. Patent Application No. 10/699,336 (i.e., U.S. Published Patent Application No. 2004/0162318) and U.S. Provisional Patent Application Nos. 60/735, 190 and 60/735, 191 , the contents of which are hereby incorporated by reference herein in their entireties. [0044| As used herein, "hepatitis C RNA-dependent RNA polymerase NS5B," "NS5B," "RdRp," and the like means the RNA-dependent RNA polymerase from any hepatitis C virus (i.e., any HCV genotype or any subtype or isolate thereof). As used herein, "hepatitis C RNA-dependent RNA polymerase NS5B gene" and the like means a nucleic acid that encodes a hepatitis C RNA-dependent RNA polymerase NS5B. Polynucleotide and polypeptide sequences from various hepatitis C genotypes and isolates (including NS5B sequences) may be found in the literature, e.g., HCV genotype Ib isolates include GenBank Accession Nos. AB049091.1; AB049088.1; AB049101.1; AB049093.1; AF165059.1; AF165060.1; AB049099.1; AB049090.1; AB049097.1; AB049098.1; AF165062; AF165061.1; AF165049.1; AB049095.1; AJ238799.1; D50485.1; D50481.1; AB049087.1; AF165050.1; AF165057.1; AF165051.1; AF165058.1; U45476.1; AF165052.1; AF176573.1; AF139594.2; AB049089.1; D89872.1; AB049100.1; AJ132996.1; AF165055.1; AJ238800.1; AF356827.1; AF165056.1; AB049096.1; AF165063.1; AF165064.1; AF483269.1; AF165054.1; AB049094.1; AF165053.1; D50480.1; D50483.1; D50482.1; AB049092.1; D50484.1; AB031322.1; U14286.1; U14320.1; U14284.1; U14282.1; U14287.1; U14281.1; U14283.1; U14316.1; U14318.1; U14292.1; U14290.1; AY003962.1; AY003965.1; U14291.1; AY003963.1; AY003966.1; AY003969.1; AY003977.1; AY003978.1; U 14285.1; AY003967.1; AY003968.1; AY003979.1; U14289.1; AY003964.1; AY003953.1; AY003954.1; AY003959.1; U14295.1; AY003955.1; AY003956.1; AY003958.1; AY004032.1; AY003960.1; AY004034.1; AY004035.1; AY003957.1; AY003961.1; AY004033.1; U14304.1; L38356.1; L38360.1; L38372.1; AJ291248.1; AF071973.1; U14297.1; L29575.1; U14310.1; AB001040.1; AF071978.1; U14308.1; AJ291273.1; U14307.1; U14305.1; AF071962.1; AF107041.1; U14302.1; U14309.1; AF071987.1; AF071977.1; U14296.1; AF071976.1; X91416.1; AF071956.1; L23442.1; L23445.1; AJ231477.1; U14298.1; AJ231475.1; AF149894.1; AF149895.1; AJ231480.1; L23443.1; L23444.1; AJ231473.1; AJ231474.1; AJ231476.1; AY149711.1; AF149898.1; AF149901.1; AF149903.1; AF149904.1; AJ231472.1; AJ231478.1; AF149899.1; AF149900.1; AJ231469.1; AJ231471.1; AF149897.1; AF071957.1; AF149896.1; AF149902.1; AJ231470.1; AY149693.1; AY149708.1; AY149709.1; AF462285.1; AF462296.1; AF462283.1; AF462287.1; AF462295.1; AF462286.1 ; AF462294.1 ; S79604.1 ; AF462284.1 ; AF462291.1 ; AF462292.1 ; AF462288.1 ; and AF042790.1. |0045] HCV genotype Ia isolates include, e.g., GenBank Accession Nos. NC_004102.1; AY100171.1; AF516387.1; AY100128.1; AY100114.1; AF516389.1; AY1OO185.1; AF516391.1; AY100136.1; AY100132.1; AY100133.1; AY100179.1; AY100120.1; AY100135.1; AY100173.1; AYlOOl 18.1 ; AY 100147.1; AY100176.1; AY100181.1; AY100193.1; AY 100124.1; AF516388.1; AY 100139.1; AY100161.1; AYlOOl 15.1; AY100122.1; AY100129.1; AY100131.1; AY100146.1; AY100166.1; AY100169.1; AY100130.1; AF516386.1; AY100183.1; AY100151.1; AY100145.1; AY100160.1; AY100172.1; AF516395.1; AY100134.1; AY100143.1; AY100144.1; AY100137.1; AY100155.1; AF516383.1; AYlOOl 19.1; AY 100138.1; AY 100154.1 ; AY100180.1; AY 100162.1; AF516394.1; AY100123.1; AY100186.1; AY100152.1; AY100164.1; AY100167.1; AY100187.1; AY100141.1-; AY100159.1; AY100188.1; AYlOOl 16.1; AY 100121.1; AY 100125.1; AY 100163.1; AY 100178.1; AF516392.1; AY100140.1; AY100189.1; AY100142.1; AY100149.1; AY100191.1; AY100127.1; AY100156.1; AY100184.1; AF516390.1; AF516393.1; AF516384.1; AY100168.1; AY100148.1; AY100170.1; AY100157.1; AY100174.1; AY100153.1; AY100126.1; AF516385.1; AYlOOl 17.1; AY 100150.1; AY 100165.1; AYlOO 177.1; AY 100182.1; AY100158.1; AF516382.1; AY100190.1; AY100175.1; AY100192.1; AF009071.1; S82227.1 ; AY003951.1; AY003947.1 ; A Y003948.1 ; AY003949.1 ; AY003950.1 ; U 14303.1 ; AY003952.1 ; AY004021.1; AY004022.1 ; AY004020.1; AY004019.1; AY004023.1; L38359.1; U 14299.1; U 14300.1; AF071960.1; AF071961.1; AF071983.1|; AJ291260.1; AF071959.1; AF071963.1; AJ291247.1; Z99042.1; AF071982.1 ; Z99040.1; Z99043.1; AF071953.1; AF071975.1 ; Z99041.1; AF071984.1; AF071985.1 ; AF071986.1; AY149700.1; AF071965.1; AF071974.1; AF071958.1; AF071979.1; AF071981.1; AF071968.1; AF071980.1; AY149698.1; L23435.1; L23436.1; AF071966.1; AY149701.1; AY149704.1; AF071955.1; AF071964.1; AY149692.1; L23437.1; L23440.1; AJ231490.1; AJ231491.1; L23439.1; L23438.1; L23441.1; AJ231489.1; AF009073.1; AF462276.1; AF009072.1; AF462279.1 ; AF462278.1 ; AF462281.1; AF009069.1 ; AF462277.1 ; AF462280.1; AF009070.1; AF462275.1; AF462282.1; AJ231493.1; and AJ231494.1. [0046| HCV genotype 2 isolates include, e.g., GenBank Accession Nos. AX057088.1; AX057090.1; AX057092.1; AX057094.1; D31973.1; D50409.1; AF238486.1; AB030907.1; U14293.1; U14294.1; AF238481.1; |AF238485.1; AF238484.1; U14288.1; AF238482.1; AF169002.1; AF169005.1; AF238483.1; AX057086.1; AF169003.1; AF169004.1; AY004014.1; AY004015.1; AY004016.1; AY004017.1; AY004024.1; AY004025.1; AY004026.1; AY004027.1 ; AY004028.1 ; AY004029.1 ; AY004030.1 ; AY004031.1 ; and AF107040.1.
(0047) HCV genotype 3 isolates include, e.g., GenBank Accession Nos. D49374.1; D17763.1; D10585.1; AF046866.1; AY100061.1; AY100033.1; AY100080.1; AY100088.1; AY100036.1; AF516379.1; AY100064.1; AY 100059.1; AY 100062.1; AY 100065.1; AY 100078.1; AF516374.1; AY 100090.1; AY 100042.1; AY 100075.1 ; AF516369.1; AY 100067.1; AY100045.1; AF516377.1; AY100058.1; AF516378.1; AY100026.1; AY 100044.1; AY 100055.1; AY 100056.1; AY 100092.1; AY 100097.1; AY100047.1; AY100029.1; AY100028.1; AY100091.1; AF516368.1; AY100087.1; AY100052.1; AF516376.1; AY100027.1; AY100066.1; AYlOOlOl.1; AF516373.1; AF516375.1; AY100057.1; AY100032.1; AY100038.1; AY100069.1; AY100082.1; AY100083.1; AY100098.1; AF516370.1; AY100040.1; AY100093.1; AY100035.1; AY100046.1; AY 100049.1; AY 100050.1; AY100070.1; AY100073.1; AY100077.1; AY100085.1; AF516380.1; AY100084.1; AY100030.1; AY100109.1; AY100111.1; AY100041.1; AY1OOO53.1; AY100095.1; AF516367.1; AF516372.1; AY100039.1; AY100043.1; AY100060.1; AY100063.1; AY100068.1; AY100072.1; AY100100.1; AYlOOl 13.1; AY100071.1; AY100076.1; AY100102.1; AY100031.1; AY100048.1; AY100108.1; AF516371.1; AY100037.1; AY100074.1; AY100096.1; AYlOOl 10.1; AY100024.1; AY100051.1; AY100079.1; AY100086.1; AY100103.1; AY100105.1; AY100107.1; AY100099.1; AF516381.1; AY100089.1; AY100094.1; AY100104.1; AY100025.1; AY100054.1; AY100081.1; AY100106.1; AYlOOl 12.1; U14315.1; U14317.1; U14313.1; AY003970.1; U 14314.1 ; U 14319.1 ; X91303.1 ; AY003975.1 ; AY003976.1 ; AY003974.1 ; AY004018.1; AF216791.1; U14301.1; AY003971.1; AY003973.1; AF388454.1; U 14312.1; AY003972.1; and L23466.1. [0048] HCV genotype 4 isolates include, e.g., GenBank Accession Nos. Y l 1604.1 ; AF271807.1 ; AF271800; AJ291255.1 ; AJ291293.1 ; AJ291258.1 ; AJ291291.1 ; AJ291282.1 ; AJ291284.1 ; AJ291263.1 ; AJ291286.1 ; AJ291272.1 ; AJ291275.1 ; AJ291271.1 ; AF271814.1|AF271814; AJ291254.1 ; AJ291289.1 ; AJ291288.1 |; AJ291249.1 ; L38370.1 ; AF388477.1 ; and AF271815.1. |0049| HCV genotype 5 isolates include, e.g., GenBank Accession Nos. Y 13184.1 ; AJ291281.1 ; L23472.1 ; and L23471.1. [0050| HCV genotype 6 isolates include, e.g., GenBank Accession Nos. Y 12083.1 ; L38379.1 ; L23475.1 ; and L38339.1.
[00511 As used herein, "nonstructural gene product" and the like means NS2, NS3, NS4A, NS4B, NS5A and NS5B polynucleotides and polypeptides and fragments thereof (e.g., mRNA, RNA, rRNA, cDNA, protein, peptides and fragments thereof).
|0052] As used herein, "amino acid change" and the like means a deviation from the amino acid residue at a given position in a hepatitis C nonstructural gene. The phrase "amino acid change" and the like means both single and multiple changes or differences in, between or among sequences. |0053] As used herein, "HCV-796 binding pocket" and the like means the portion of a hepatitis C RNA-dependent RNA polymerase NS5B responsible for interacting with HCV-796. For example, the HCV-796-binding pocket of NS5B from HCV genotype I b is contained within about amino acid residues 120 to 450. In relation to the methods disclosed herein, determining "the amino acid sequence of a nonstructural gene" and the like includes, but is not limited to, (1 ) determining the amino acid sequence of any nonstructural gene; (2) determining the amino acid structure of a nonstructural gene or a portion thereof, e.g., determining the amino acid structure of the HCV-796 binding pocket of the hepatitis C RNA-dependent RNA polymerase NS5B or a portion thereof; and/or (3) determining the nucleic acid sequence encoding any nonstructural gene. Such methods may employ routine nucleotide sequencing or routine protein sequencing (see also U. S. S.N. 60/840,353, filed August 25, 2006 (the entire contents of which are hereby incorporated by reference herein)). |0054| In addition, the instant invention contemplates methods of decreasing the frequency of emergence, decreasing the level of resistance, and delaying the emergence of a treatment-resistant hepatitis C viral infection, by administering to a subject, either in combination or in series, an inhibitor of the hepatitis C RNA- dependent RNA polymerase NS5B (e.g., a benzofuran, such as HCV-796) and an inhibitor of the NS3 serine protease (e.g., boceprevir). The present invention also provides for the administration of at least one additional anti-hepatitis C agent (including but not limited to, a ribavirin product or an immunomodulator, such as an interferon product). As discussed herein, administration of these inhibitors and agents (e.g., HCV-796 and boceprevir, with or without an additional agent, e.g., an interferon product and/or a ribavirin product) may be concurrent or in series.
|0055| As described in further detail herein, exemplary agents useful to decrease the frequency of emergence, decrease the level of resistance, and delay the emergence of a treatment-resistant hepatitis C viral infection include agents that target the hepatitis C protease inhibitor NS3, e.g. boceprevir. Other agents include agents that target the hepatitis C RNA-dependent RNA polymerase NS5B, e.g., benzofuran compounds. Such compounds are disclosed in, e.g., U.S. Provisional Patent Appln. Nos. 60/735,190 and 60/735,191 , and U.S. Patent Publication No. 2004/0162318, the disclosures of which are hereby incorporated by reference herein. In one embodiment of the invention, the benzofuran compound is 5-cyclopropyl-2-(4-fluorophenyl)-6-[(2-hydroxyethyl) (methylsulfonyl)amino]-N-methyl- l-benzofuran-3-carboxarnide (HCV-796). Thus, as used herein "benzofuran inhibitor of a hepatitis C virus" and the like means a benzofuran anti-hepatitis C virus agent.
|0056] ,As used herein, "delaying the emergence" and the like means postponing the development, e.g., of a hepatitis C virus with resistance to an anti-hepatitis C viral therapy of choice, e.g., a benzofuran anti-hepatitis C viral therapy (such as a benzofuran-based anti-hepatitis C viral therapy employing HCV-796) or an NS3 serine protease inhibitor (such as boceprevir). Thus, "delaying the emergence" and the like may refer to postponing the development of a treatment-resistant hepatitis C viral infection relative to a reference sample (e.g., a reference mean or median rate of development of a treatment-resistant hepatitis C virus in a reference population). Such postponement may be by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or any other method of assessing a delay of emergence of resistance known in the art. |0057] As used herein, "decreasing the frequency of emergence" and the like means reducing the rate of occurrence, e.g., of the development of a hepatitis C virus with resistance to an anti-hepatitis C viral therapy of choice. Thus, "decreasing the frequency of emergence" and the like may refer to a reduction in the rate of occurrence of a treatment-resistant hepatitis C viral infection relative to a reference sample (e.g., a reference mean or median rate of occurrence of a treatment-resistant hepatitis C virus in a reference population). Such reduction may be by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or any other method of assessing a decrease of frequency of emergence of resistance known in the art.
|0058] As used herein, "decreasing the level of resistance" and the like means reducing the strength or the ability of a hepatitis C virus to withstand an anti- hepatitis C viral therapy. Thus, "decreasing the level of resistance" and the like may refer to a reduction in the strength or the ability of a hepatitis C virus to withstand an anti-hepatitis C viral therapy relative to a reference sample (e.g., a reference mean or median ability to withstand an anti-hepatitis C viral therapy in a reference population). Such reduction may be by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or any other method of assessing a decrease in the level of resistance known in the art.
|0059] As used herein, "treatment-resistant hepatitis C viral infection" and the like means a hepatitis C viral infection that displays an abrogated response to an anti-hepatitis C viral therapy (e.g., a delayed (or absent) response to treatment, or a lessened (i.e., abrogated) reduction in hepatitis C viral load in response to treatment). In one embodiment of the invention, the treatment-resistant hepatitis C viral infection is a benzofuran-resistant hepatitis C viral infection, particularly an HCV-796 resistant hepatitis C viral infection. In one embodiment of the invention, the treatment-resistant hepatitis C viral infection is a boceprevir- resistant hepatitis C viral infection.
[0060| Reference to a nucleotide sequence or polynucleotide as set forth herein encompasses a DNA molecule (e.g., a cDNA molecule) with the specified sequence (or a complement thereof), and encompasses an RNA molecule (e.g., an mRNA or an rRNA molecule) with the specified sequence in which U is substituted for T, unless context requires otherwise. Such polynucleotides and nucleic acids additionally include allelic variants of the disclosed polynucleotides, e.g., polynucleotides and nucleic acids of various subtypes of the hepatitis C virus genotypes. Allelic variants are naturally occurring alternative forms of the disclosed polynucleotides that encode polypeptides that are identical to or have significant similarity to the polypeptides encoded by the disclosed polynucleotides. Preferably, allelic variants have at least 90% sequence identity (more preferably, at least 95% identity; most preferably, at least 99% identity) with the disclosed polynucleotides. Alternatively, significant similarity exists when the nucleic acid segments will hybridize under selective hybridization conditions (e.g., highly stringent hybridization conditions) to the disclosed polynucleotides.
(0061 ) Such polynucleotides and nucleic acids additionally include DNAs having sequences encoding polypeptides homologous to the disclosed polynucleotides. These homologs are polynucleotides and polypeptides isolated from a different species than that of the disclosed polypeptides and polynucleotides, or within the same species, but with significant sequence similarity to the disclosed polynucleotides and polypeptides. Preferably, polynucleotide homologs have at least 50% sequence identity (more preferably, at least 75% identity; most preferably, at least 90% identity) with the disclosed polynucleotides, whereas polypeptide homologs have at least 30% sequence identity (more preferably, at least 45% identity; most preferably, at least 60% identity) with the disclosed polypeptides. Preferably, homologs of the disclosed polynucleotides and polypeptides are those isolated from mammalian species.
(0062) .Calculations of "homology" or "sequence identity" between two sequences are performed by means well known to those of skill in the art. For example, one general means for calculating sequence identity is described as follows. The sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment, and nonhomologous sequences can be disregarded for comparison purposes). In a preferred embodiment, the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, still more preferably at least 60%, and even more preferably at least 70%, 80%, 90%, or 100% of the length of the reference sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences. |0063] The comparison of sequences and determination of percent sequence identity between two sequences may be accomplished using a mathematical algorithm. In one exemplary embodiment, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (( 197O) J MoI. Biol. 48:444-53) algorithm, which has been incorporated into the GAP program in the GCG software package (available at www.gcg.com), using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1 , 2, 3, 4, 5, or 6. In yet another embodiment, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available at www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1 , 2, 3, 4, 5, or 6. One exemplary set of parameters is a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5. The percent identity between two amino acid or nucleotide sequences can also be determined using the algorithm of Meyers and Miller ((1989) CABIOS 4: 1 1 -17), which has been incorporated into the ALIGN program (version 2.0), using a PAM 120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
|0064) Anti-hepatitis C virus agents include, e.g., polynucleotides, protein biologies, antibodies and small molecules. The term "small molecule" refers to compounds that are not macromolecules {see, e.g., Karp (2000) Bioinformatics Ontology 16:269-85; Verkman (2004) AJP-CeIl Physiol. 286:465-74). Thus, small molecules are often considered those compounds that are, e.g., less than one thousand daltons (e.g., Voet and Voet, Biochemistry, 2nd ed, ed. N. Rose, Wiley and Sons, New York, 14 (1995)). For example, Davis et al. (2005) Proc. Natl. Acad. Sci. USA 102:5981 -86, use the phrase small molecule to indicate folates, methotrexate, and neuropeptides, while Halpin and Harbury (2004) PLos Biology 2: 1022-30, use the phrase to indicate small molecule gene products, e.g., DNAs, RNAs and peptides. Examples of natural and synthesized small molecules include, but are not limited to, cholesterols, neurotransmitters, siRNAs, and various chemicals listed in numerous commercially available small molecule databases, e.g., FCD (Fine Chemicals Database), SMID (Small Molecule Interaction Database), ChEBI (Chemical Entities of Biological Interest), and CSD (Cambridge Structural Database) (see, e.g., Alfarano et al. (2005) Nwc. Acids Res. Database Issue 33 :D416-24).
[0065| In addition, the present invention contemplates the use of small modular immunopharmaceutical (SMIP™) drugs (Trubion Pharmaceuticals, Seattle, WA). SMIPs are single-chain polypeptides composed of a binding domain for a cognate structure such as an antigen, a counterreceptor or the like, a hinge-region polypeptide having either one or no cysteine residues, and immunoglobulin CH2 and CH3 domains (see also www.trubion.com). SMIPs and their uses and applications are disclosed in, e.g., U.S. Published Patent Application. Νos. 2003/01 18592, 2003/0133939, 2004/0058445, 2005/0136049, 2005/0175614, 2005/0180970, 2005/0186216, 2005/0202012, 2005/0202023, 2005/0202028, 2005/0202534, and 2005/0238646, and related patent family members thereof, all of which are hereby incorporated by reference herein in their entireties. (0066] As used herein, the term "antibody" includes a protein comprising at least one, and typically two, VH domains or portions thereof, and/or at least one, and typically two, VL domains or portions thereof. In certain embodiments, the antibody is a tetramer of two heavy immunoglobulin chains and two light immunoglobulin chains, wherein the heavy and light immunoglobulin chains are interconnected by, e.g., disulfide bonds. The antibodies, or a portion thereof, can be obtained from any origin, including but not limited to, rodent, primate (e.g., human and nonhuman primate), camelid, shark, etc., or they can be recombinantly produced, e.g., chimeric, humanized, and/or in v;7ro-generated, e.g., by methods well known to those of skill in the art.
|0067) Examples of binding fragments encompassed within the term "antigen- binding fragment" of an antibody include, but are not limited to, (i) an Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CH l domains; (ii) an F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) an Fd fragment consisting of the VH and CH l domains; (iv) an Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment, which consists of a VH domain; (vi) a single chain Fv (scFv; see below); (vii) a camelid or camelized heavy chain variable domain (VHH; see below); (viii) a bispecific antibody (see below); and (ix) one or more fragments of an immunoglobulin molecule fused to an Fc region. Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv)); see, e.g., Bird et al. (1988) Science 242:423-26; Huston et al. (1988) Proc. Natl. Acad. Sci. U.S.A. 85:5879-83). Such single chain antibodies are also intended to be encompassed within the term "antigen-binding fragment" of an antibody. These fragments may be obtained using conventional techniques known to those skilled in the art, and the fragments are evaluated for function in the same manner as are intact antibodies. |0068| In some embodiments, the term "antigen-binding fragment" encompasses single domain antibodies. Single domain antibodies can include antibodies whose CDRs are part of a single domain polypeptide. Examples include, but are not limited to, heavy chain antibodies, antibodies naturally devoid of light chains, single domain antibodies derived from conventional four-chain antibodies, engineered antibodies and single domain scaffolds other than those derived from antibodies. Single domain antibodies may be any of those known in the art, or any future single domain antibodies. Single domain antibodies may be derived from any species including, but not limited to, mouse, human, camel, llama, goat, rabbit, bovine, and shark. According to at least one aspect of the invention, a single domain antibody as used herein is a naturally occurring single domain antibody known as heavy chain antibody devoid of light chains. Such single domain antibodies are disclosed in, e.g., WO 94/04678. This variable domain derived from a heavy chain antibody naturally devoid of light chain is known herein as a VHH or nanobody, to distinguish it from the conventional VH of four-chain immunoglobulins. Such a VHH molecule can be derived from antibodies raised in Camelidae species, for example in camel, llama, dromedary, alpaca and guanaco. Other species besides Camelidae may produce heavy chain antibodies naturally devoid of light chain; such VHH molecules are within the scope of the invention. [0069J The term "pharmaceutical composition" means any composition that contains at least one therapeutically or biologically active agent (e.g., an anti- hepatitis C virus agent(s), such as HCV-796, boceprevir, a ribavirin product, an interferon product, etc.) and is suitable for administration to a subject. Pharmaceutical compositions and appropriate formulations thereof can be prepared by well-known and accepted methods of the art. See, for example, Remington: The Science and Practice of Pharmacy, 21s1 Ed., (ed. A. R. Gennaro), Lippincott Williams & Wilkins, Baltimore, MD (2005). [0070) In all aspects of the invention, the hepatitis C RNA-dependent RNA polymerase NS5B that is analyzed as part of the disclosed methods may be a variant polypeptide that differs from an NS5B sequence set forth herein. Such a variation may occur in a relatively irrelevant site of NS5B, e.g., outside of the HCV-796-binding domain. These NS5B polypeptides are contemplated as useful in the instant methods because such methods rely on the identification of a change in sequence or structure of an NS5B polypeptide from an individual (over time, i.e., between a first and second time point, or relative to a reference sample) infected with HCV. A similar paradigm applies to, e.g., NS3 polypeptides and changes in sequence or structure related to an HCV infection and administration of, e.g., boceprevir. In general, viral mutation may replace residues that form NS5B and/or NS3 protein tertiary structure, provided that residues that perform a similar function are used. In other instances, the type of residue may be completely irrelevant if an alteration occurs in a noncritical area. Thus, the invention further utilizes NS5B and/or NS3 variants that show substantial NS5B-type and/or NS3-type biological activities. Such variants include deletions, insertions, inversions, repeats, and type substitutions (for example, substituting one hydrophilic residue for another, but not a strongly hydrophilic residue for a strongly hydrophobic residue). Small changes or "neutral" amino acid substitutions will often have little impact on protein function (Taylor (1986) J. Theor. Biol. 1 19:205-18). Conservative substitutions may include, but are not limited to, replacements among the aliphatic amino acids, substitutions between amide residues, exchanges of basic residues, and replacements among the aromatic residues. Further guidance concerning which amino acid changes are likely to be phenotypically silent (i.e., are unlikely to significantly affect function) can be found in Bowie et al. (1990) Science 247: 1306-10 and Zvelebil et al. (1987) J. MoI. Biol. 195:957-61.
Methods for Monitoring the Course of Treatment of a Hepatitis C Viral Infection, Methods for Monitoring and Prognosing a Hepatitis C Viral Infection, and Methods for Diagnosing the Development of a Treatment-Resistant Hepatitis C Viral Infection
|0071 J The present invention provides methods for monitoring the course of treatment of a hepatitis C viral infection, methods for monitoring and prognosing the development of a treatment-resistant hepatitis C viral infection, and methods for diagnosing the development of a treatment-resistant hepatitis C viral infection, by, e.g., determining the sequence or structure of a nonstructural HCV gene in a sample from the subject, and comparing the sequence or structure of the gene product(s) or a portion(s) thereof in the sample from the subject to the sequence or structure of a nonstructural gene product(s) or a portion(s) thereof in a reference sample. Alternatively, these methods may include determining a test sequence or structure of a nonstructural gene product(s) or portion(s) thereof in biological sample taken from a subject at a first time point, and comparing the sequence or structure of the nonstructural gene product(s) or portion(s) thereof to the sequence or structure of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from the subject at a second time point. |0072] For example, the invention provides methods of diagnosing, prognosing and monitoring, e.g., by determining changes in the sequence of a nonstructural gene product(s) or a portion(s) thereof (e.g., NS5B or NS3) in a sample from a subject infected with HCV. The sequence or structure of a nonstructural gene product(s) or a portion(s) thereof may also be measured in a reference cell or sample of interest to produce or obtain a reference sequence of a nonstructural gene, or such reference sequence or structure may be obtained through other methods, or may be generally known, by one of skill in the art. In addition, the sequence of the nonstructural gene product(s) or a portion(s) thereof may be obtained from a subject at a first time point and compared to the sequence of the nonstructural gene product(s) or portion(s) thereof from the subject at a second time point to identify the development of amino acid changes in the nonstructural gene product(s) or a portion(s) thereof. These methods may be performed by, e.g., utilizing prepackaged diagnostic kits comprising at least one of a polynucleotide (or portion(s) thereof, e.g., an NS5B sequencing probe(s) or an NS5B hybridization probe(s)), or an antibody against, e.g., an NS5B polypeptide (or a portion thereof), which may be conveniently used, for example, in a clinical setting.
(0073) "Diagnostic" or "diagnosing" means identifying the presence or absence of a pathologic condition, e.g., diagnosing the development of a treatment- resistant hepatitis C viral infection in a subject. Diagnostic methods include, but are not limited to, detecting changes in the sequence of a nonstructural gene by determining the sequence of a nonstructural gene product(s) or a portion(s) thereof in a biological sample from a subject (e.g., human or nonhuman mammal), and comparing the test sequence or structure with, e.g., a normal (or relatively normal) sequence of the same nonstructural gene product. Although a particular diagnostic method may not provide a definitive diagnosis of the development of a treatment-resistant hepatitis C viral infection, it suffices if the method provides a positive indication that aids in diagnosis. |0074) The present invention also provides methods for prognosing the development of a treatment-resistant hepatitis C viral infection in a subject by determining, for example, the sequence or structure of a nonstructural gene product(s) or a portion(s) thereof in a biological sample from a subject (e.g., human or nonhuman mammal). "Prognostic" or "prognosing" means predicting the probable development and/or severity of a pathologic condition. Prognostic methods include determining the sequence of a nonstructural gene product(s) or a portion(s) thereof in a biological sample from a subject, and comparing the sequence of the nonstructural gene product(s) or portion(s) thereof to a prognostic sequence of the nonstructural gene product(s) or portion(s) thereof (e.g., an NS5B sequence or structure from a reference sample). Alternatively, prognostic methods may include determining a test sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from a subject at a first time point, and comparing the sequence of the nonstructural gene product(s) or portion(s) thereof to the sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from the subject at a second time point. Changes in a particular portion(s) or amino acid residue(s) of the nonstructural gene product(s) are consistent with certain prognoses for the development of a treatment-resistant hepatitis C viral infection. |00751 The present invention also provides methods for monitoπng a hepatitis C viral infection in a subject by determining, for example, the sequence of a nonstructural gene product(s) or a portion(s) thereof in a biological sample from a human or nonhuman mammalian subject Monitonng methods include determining a test sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from a subject at a first time point, and comparing the sequence of the nonstructural gene product(s) or portion(s) thereof to the sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from the subject at a second time point Alternatively, monitoπng methods may include comparing the test sequence or structure with, e g , a normal sequence of a nonstructural gene product(s) or portion(s) thereof (e g , an NS5B sequence or structure from a reference sample) A change in the sequence of a nonstructural gene product(s) or portion(s) thereof between the first and second time points (or between the test sample and the reference sample) indicates that the hepatitis C viral infection has increased in severity Such monitoring assays are also useful for evaluating the efficacy of a particular anti- hepatitis C virus agent or an anti-hepatitis C viral therapy in patients being treated for hepatitis C infection, i e , monitoring the course of treatment of a HCV infection in a subject, e g , a HCV-796 and boceprevir combination treatment (with or without administration of at least one additional anti-hepatitis C virus agent)
Methods of Identifying an Individual with a Decreased Likelihood of Responding to an Anti-Hepatitis C Viral Therapy
I0076J The present invention also provides methods for identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy, comprising determining the sequence of a nonstructural gene product(s) or a portion(s) thereof, and comparing the test sequence or structure with, e g , a normal nonstructural gene product sequence or structure (e g , an NS5B sequence or structure from a reference sample) Alternatively, identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy may include determining a test sequence of a nonstructural gene product(s) or portion(s) thereof in a biological sample taken from a subject at a first time point, and comparing the sequence of the nonstructural gene product(s) or portιon(s) thereof to the sequence of a nonstructural gene product(s) or portιon(s) thereof in a biological sample taken from the subject at a second time point. A change(s) in a particular portion(s) is consistent with a decreased likelihood that the individual will respond to an anti-hepatitis C viral therapy. Closely associated methods of determining whether an individual will likely respond to an anti-hepatitis C viral therapy with little or no resistance are also contemplated.
Second-Generation Anti-Hepatitis C Virus Agents
|00771 The information regarding the sequence of hepatitis C RNA-dependent RNA polymerase NS5B and serine protease NS3 variants that emerge in response to treatment with boceprevir and a benzofuran (such as HCV-796) is additionally useful to optimize second-generation anti-hepatitis C agents (e.g., hepatitis C viral inhibitors or HCV inhibitor combinations that exhibit significantly reduced, minimal, or no susceptibility to resistance caused by mutations in these variants). In addition, this information is useful in methods of selecting combinations of, e.g., anti-hepatitis C agents and/or second-generation anti-hepatitis C agents with additive or synergistic effects to reduce the susceptibility to resistance caused by such mutations in, e.g., the hepatitis C RNA-dependent RNA polymerase NS5B and serine protease NS3.
|0078] For example, using the HCV variants generated in response to combination treatment of HCV with a benzofuran and boceprevir (which also may include the administration of at least one additional anti-HCV agent as described herein, such as a ribavirin product and/or an interferon product), one may screen, e.g., using high throughput screening (HTS), for novel anti- hepatitis C agents useful to treat a benzofuran and boceprevir treatment-resistant hepatitis C viral infection, and thus optimize identification and chemical synthesis of second-generation anti-hepatitis C agents. In addition, using the methods disclosed herein, one may identify a change in the amino acid sequence of a nonstructural HCV gene generated in response to a benzofuran and boceprevir combination treatment of HCV in a subject, and then administer an optimized second-generation anti-hepatitis C agent to treat the resistant hepatitis C viral infection in the subject.
Determining the Sequence (or Structure) of a Nonstructural Gene Product(s) or a Portion(s) Thereof
[0079| Determining the sequence (or structure) of a nonstructural gene product(s) or a portion(s) thereof as used in the disclosed methods may be measured in a variety of biological samples, including bodily fluids (e.g., whole blood, plasma, and urine), cells (e.g., whole cells, cell fractions, and cell extracts), and other tissues. Biological samples also include sections of tissue, such as biopsies and frozen sections taken for histological purposes. Preferred biological samples include blood, plasma, lymph, and liver tissue biopsies. It will be appreciated that analysis of a biological sample need not necessarily require removal of cells or tissue from the subject. For example, appropriately labeled agents (e.g., antibodies, nucleic acids) that interact with the nonstructural gene, or that interact with particular amino acids (or nucleotides encoding certain amino acids) within the nonstructural gene, may be administered to a subject and visualized (when bound to the target) using standard imaging technology (e.g., CAT, NMR (MRI), and PET).
[0080) In diagnostic, prognostic, and monitoring assays and methods of the present invention, the sequence or structure of a nonstructural gene product(s) or a portion(s) thereof is determined to yield a test sequence or structure. The test sequence or structure is then compared with, e.g., a baseline/normal nonstructural gene sequence.
(0081) Normal sequences or structures of nonstructural gene product(s) or a portion(s) thereof from different HCV genotypes, subtypes, and isolates may be
• determined for any particular sample type and population. Generally, baseline (e.g., normal) sequence(s) or structure(s) of a nonstructural gene product(s) or a portion(s) thereof are determined by determining the sequence(s) or structure(s) of a reference nonstructural gene product(s) or a portion(s) thereof from a corresponding HCV genotype and/or subtype (or isolate) that is not resistant to the anti-hepatitis C viral therapy or anti-hepatitis C virus agent (e.g., HCV-796 and/or boceprevir) of interest. Alternatively, baseline (normal) sequence(s) or structure(s) of the nonstructural gene product(s) or a portion(s) thereof may be ascertained by determining the sequence(s) or structure(s) of a reference nonstructural gene product(s) or a portion(s) thereof from a sample taken from the subject prior to initiation of an anti-hepatitis C viral therapy or administration of the anti-hepatitis C virus agent (e.g., HCV-796 and/or boceprevir) of interest. |0082| It will be appreciated that the methods of the present invention do not necessarily require determining the entire sequence or structure of a hepatitis C nonstructural gene product(s), as determining the sequence or structure of a portion of a hepatitis C nonstructural gene product(s) is sufficient for many applications of these methods.
Characterization of a Sequence (or Structural) Change in a Nonstructural Gene Product
|0083) The methods of the present invention involve determining the sequence (or structure) of a hepatitis C nonstructural gene product(s) or portion(s) thereof, e.g., the sequence of an NS5B or NS3 polynucleotide or polypeptide. The sequence or structure of a hepatitis C nonstructural gene product(s) or portion(s) thereof can be measured using methods well known to those skilled in the art, those described in the Examples section (e.g., RT-PCR), and additional techniques described herein. In addition, further methods related to determining the sequence and/or structure of HCV nonstructural gene product(s) or portion(s) thereof are disclosed in, e.g., U. S. S.N. 60/840,353, filed August 25, 2006 (the entire contents of which are hereby incorporated by reference herein). [0084| One may determine changes in the amino acid sequence or structure of the nonstructural gene product by: (1) determining the amino acid sequence of the nonstructural gene or a portion thereof; (2) determining the amino acid structure of a nonstructural gene or a portion thereof, e.g., determining the amino acid structure of the HCV-796 binding pocket of the hepatitis C RNA-dependent RNA polymerase NS5B or a portion thereof; and/or (3) determining the nucleic acid sequence encoding the nonstructural gene or a portion thereof. [0085J Determination of a sequence and/or structural change(s) in a nonstructural gene may employ various methods well known in the art, e.g., routine nucleotide sequencing, PCR amplification, Northern Blotting, or routine protein sequencing (i.e., sequencing of the NS5B polypeptide or a portion thereof (e.g., the portion(s) of the NS5B polypeptide responsible for interacting with HCV-796)), isoelectric focusing, spectroscopy or antibody-based detection of structural changes.
|0086| Nonstructural gene mRNA can be isolated and reverse transcribed to cDNA, and then directly sequenced by various well-known methods, or alternatively probed for the presence or absence of certain amino acid encoding sequences. Alternatively, the nonstructural gene mRNA itself may be probed for certain amino acid encoding sequences using hybridization-based assays, such as Northern hybridization, in situ hybridization, dot and slot blots, and oligonucleotide arrays. Hybridization-based assays refer to assays in which a probe nucleic acid is hybridized to a target nucleic acid. In some formats, the target, the probe, or both are immobilized. The immobilized nucleic acid may be DNA, RNA, or another oligonucleotide or polynucleotide, and may comprise naturally or nonnarurally occurring nucleotides, nucleotide analogs, or backbones. Methods of selecting nucleic acid probe sequences for use in the present invention (e.g., based on the nucleic acid sequences of, e.g., NS5B, NS5A, or NS3) are well known in the art and can be easily determined, e.g., based on the sequences set forth in SEQ ID NO: 1 and SEQ ID NO:2, which are the nucleic acid and amino acid sequences (respectively) of HCV, genotype Ib complete genome, isolate Con 1.
|0087] Alternatively, mRNA may be amplified before sequencing and/or probing. Such amplification-based techniques are well known in the art and include polymerase chain reaction (PCR), reverse-transcription-PCR (RT-PCR), PCR-enzyme-linked immunosorbent assay (PCR-ELISA), and ligase chain reaction (LCR). Primers and probes for producing and detecting amplified nonstructural gene products (e.g., mRNA or cDNA) may be readily designed and produced without undue experimentation by those of skill in the art based on the nucleic acid sequences of the nonstructural gene. Amplified nonstructural gene products may be directly analyzed, for example, by restriction digest followed by gel electrophoresis; by hybridization to a probe nucleic acid; by sequencing; by detection of a fluorescent, phosphorescent, or radioactive signal; or by any of a variety of well-known methods. In addition, methods are known to those of skill in the art for increasing the signal produced by amplification of target nucleic acid sequences.
Methods for Decreasing the Frequency of Emergence, Decreasing the Level of Resistance, and Delaying the Emergence of a Treatment-Resistant Hepatitis C Viral Infection
|0088) The present invention provides methods for decreasing the frequency of emergence, decreasing the level of resistance, and delaying the emergence of a treatment-resistant hepatitis C viral infection, by, e.g., administering a benzofuran inhibitor (e.g., HCV-796) of hepatitis C virus in combination with an NS3 serine protease inhibitor (e.g., boceprevir) to a subject in need thereof. At least one additional anti-hepatitis C virus agent may also be administered. Benzofuran compounds and additional anti-hepatitis C virus agents are disclosed herein. In some embodiments of the invention, the anti-hepatitis C virus agent is an immunomodulator, particularly an interferon product, or an antiviral agent, particularly a ribavirin product.
Pharmaceutical Compositions
|0089| In some aspects, the invention features methods for decreasing the frequency of emergence, decreasing the level of resistance, or delaying the emergence of a treatment-resistant hepatitis C viral infection. These methods may comprise contacting a population of cells (e.g., by administering to a subject suffering from or at risk for fibrosis or a fibrosis-associated disorder) with an anti-hepatitis C virus agent (e.g., an immunomodulator, particularly an interferon product; an antiviral agent, particularly a ribavirin product; a benzofuran, particularly HCV-796; an NS3 protease inhibitor, particularly boceprevir) in an amount sufficient to decrease the frequency of emergence, decrease the level of resistance, or delay the emergence of a treatment-resistant hepatitis C viral infection.
[0090] Anti-hepatitis C virus agents for decreasing the frequency of emergence, decreasing the level of resistance, or delaying the emergence of a treatment- resistant hepatitis C viral infection may be used as a pharmaceutical composition when combined with a pharmaceutically acceptable carrier. Such a composition may contain, in addition to the anti-hepatitis C virus agent(s) and carrier, various diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials well known in the art. The term "pharmaceutically acceptable" means a nontoxic or relatively nontoxic material that does not interfere with the effectiveness of the biological activity of the active ingredient(s). The characteristics of the carrier will depend on the route of administration, and are generally well known in the art.
(0091 ] The pharmaceutical composition of the invention may be in the form of a liposome in which an anti-hepatitis C virus agent(s) is combined with, in addition to other pharmaceutically acceptable carriers, amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers which exist in aqueous solution. Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithin, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, e.g., in U.S. Patent Nos. 4,235,871 , 4,501 ,728, 4,837,028, and 4,737,323, all of which are incorporated herein by reference in their entireties. [0092) As used herein, the term "therapeutically effective amount" means the amount of each active component of the pharmaceutical composition or method that is sufficient to show a meaningful subject benefit, e.g., amelioration or reduction of symptoms of, prevention of, healing of, or increase in rate of healing of such conditions. When applied to an individual active ingredient, administered alone, the term refers to that ingredient alone. When applied to a combination, the term refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
|0093] In practicing the methods of treatment or use (including embodiments of methods for decreasing the frequency of emergence, decreasing the level of resistance, or delaying the emergence of a treatment-resistant hepatitis C viral infection) of the present invention, a therapeutically effective amount of an anti- hepatitis C virus agent(s) is administered to a subject, e.g., a mammal (e.g., a human). An anti-hepatitis C virus agent(s) may be administered in accordance with the method of the invention either alone or in combination with other therapies as described in more detail herein. When coadministered with one or more agents, an anti-hepatitis C virus agent(s) may be administered either simultaneously with the second agent, or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering an anti-hepatitis C virus agent(s) in combination with other agents. |0094| Administration of an anti-hepatitis C virus agent(s) used in a pharmaceutical composition of the present invention or to practice a method of the present invention may be carried out in a variety of conventional ways, such as oral ingestion, inhalation, or cutaneous, subcutaneous, or intravenous injection. Intravenous administration to the subject is sometimes preferred. When a therapeutically effective amount of an anti-hepatitis C virus agent(s) is administered orally, the binding agent will be in the form of a tablet, capsule, powder, solution or elixir. When administered in tablet form, the pharmaceutical composition of the invention may additionally contain a solid carrier such as a gelatin or an adjuvant. The tablet, capsule, and powder contain from about 5 to 95% binding agent, and preferably from about 25 to 90% binding agent. When administered in liquid form, a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil (albeit keeping in mind the frequency of peanut allergies in the population), mineral oil, soybean oil, or sesame oil, or synthetic oils may be added. The liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol. When administered in liquid form, the pharmaceutical composition contains from about 0.5 to 90% by weight of the binding agent, and preferably from about 1 to 50% of the binding agent.
[0095] When a therapeutically effective amount of an anti-hepatitis C virus agent(s) is administered by intravenous, intramuscular, cutaneous or subcutaneous injection, the binding agent will be in the form of a pyrogen-free, parenterally acceptable aqueous solution. The preparation of such parenterally acceptable protein solutions, having due regard to pH, isotonicity, stability, and the like, is within the skill in the art. A preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection should contain, in addition to a binding agent, an isotonic vehicle such as sodium chloride injection, Ringer's injection, dextrose injection, dextrose and sodium chloride injection, lactated Ringer's injection, or other vehicle as known in the art. The pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additive known to those of skill in the art. |0096) The amount of an anti-hepatitis C virus agent(s) in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments that the subject has undergone. Ultimately, the attending physician will decide the amount of anti-hepatitis C virus agent(s) with which to treat each individual subject. Initially, the attending physician will administer low doses of anti-hepatitis C virus agent(s) and observe the subject's response. Larger doses of anti- hepatitis C virus agent(s) may be administered until the optimal therapeutic effect is obtained for the subject, and at that point the dosage is not generally increased further. It is contemplated that the various pharmaceutical compositions used to practice the method of the present invention should contain about 0.01 μg to about 2000 mg anti-hepatitis C virus agent(s) per kg body weight. Dosing schedules for ribavirin products and interferon products are well known to those of skill in the art and may be found throughout the literature, e.g., in Jen et al. (2002) Clin. Pharmacol. Ther. 72:349-61 , Krawitt et al. (2006) Am. J. Gastroenterol. 101 : 1268-73, Abonyi and Lakatos (2005) Anticancer Res. 25(2B): 1315-20, Jacobson et al. (2005) Am. J. Gastroenterol. 100(1 1):2453-62, and Lurie et al. (2005) Clin. Gastroenterol. Hepatol. 3:610-15. |0097) In one embodiment, pegylated-interferon may be administered at a range of 0.01 μg/kg/dose to 50 μg/kg/dose, e.g., 0.1 μg/kg/dose to 3 μg/kg/dose, one or more times a week. In another embodiment, HCV-796 may be administered in doses at a range of 1 mg to 2000 mg, e.g., 50 mg to 1500 mg, one or more times a day. In another embodiment, boceprevir may be administered in doses at a range of 1 mg to 4000 mg, e.g. 200 mg to 800 mg, three or more times a day. In another embodiment, an interferon product (including pegylated interferon), is administered intramuscularly. In yet another embodiment of the invention, ribavirin is administered orally. In yet other embodiments of the invention, HCV-796 and/or boceprevir are administered orally. |0098| The duration of intravenous therapy using the pharmaceutical composition of the present invention will vary, depending on the severity of the disease being treated and the condition and potential idiosyncratic response of each individual subject. If administered intravenously, it is contemplated that the duration of each application of an anti-hepatitis C virus agent(s) may be in the range of approximately 12 to 24 hours of continuous i.v. administration. Also contemplated is subcutaneous (s.c.) therapy using a pharmaceutical composition of the present invention. These therapies can be administered, e.g., daily, several times a day, weekly, biweekly, or monthly. Typically, anti-hepatitis C viral therapy lasts from 12 to 48 weeks. It is also contemplated that where the anti- hepatitis C virus agent is a small molecule (e.g., for oral delivery), the therapies may be administered daily, twice a day, three times a day, etc. Ultimately the attending physician will decide on the appropriate duration of i.v. or s.c. therapy, or therapy with a small molecule, and the timing of administration of the therapy using the pharmaceutical composition of the present invention. |0099) The polynucleotide and proteins of the present invention are expected to exhibit one or more of the uses or biological activities (including those associated with assays cited herein) identified below. Uses or activities described for proteins, antibodies, or polynucleotides of the present invention may be provided by administration or use of such proteins, or antibodies, or by administration or use of polynucleotides encoding such proteins or antibodies (such as, for example, in gene therapies or vectors suitable for introduction of DNA). [0100] In at least one exemplary embodiment, a pharmaceutical composition comprising a benzofuran inhibitor of an NS5B (e.g., HCV-796) and an inhibitor of NS3 serine protease (e.g., boceprevir) is administered in further combination therapy. Such therapy is useful for decreasing the frequency of emergence, decreasing the level of resistance, and delaying the emergence of a treatment- resistant hepatitis C viral infection. The term "in combination" in this context means that the benzofuran inhibitor and the inhibitor of NS3 protease are given substantially contemporaneously, either simultaneously or sequentially, including in further combination with other agents. If given sequentially, at the onset of administration of a later compound(s), the earlier compound(s) may still be detectable at effective concentrations at the site of treatment. [0101] For example, the combination therapy can include at least one benzofuran inhibitor of an NS5B (e.g., HCV-796) coformulated with, and/or coadministered with, or otherwise administered in combination with, an inhibitor of NS3 (e.g., boceprevir), and additionally at least one other anti-HCV agent. Additional anti- hepatitis C virus agents may include at least one immunomodulator, antiviral, antifibrotics, small interfering RNA compounds, antisense compounds, polymerase inhibitors (such as nucleotide or nucleoside analogs), protease inhibitors or other small molecule anti-HCV agents, immunoglobulins, hepatoprotectants, anti-inflammatory agents, antiviral vaccine, antibiotics, anti- infectives, etc. Such combination therapies may advantageously utilize lower dosages of the administered therapeutic agents, thus avoiding possible toxicities or complications associated with the various monotherapies. [0102] Therapeutic agents used in combination with an anti-hepatitis C virus agent may be those agents that interfere at different stages in the autoimmune and subsequent inflammatory response. In one embodiment, at least one anti- hepatitis C virus agent described herein may be coadministered with at least one benzofuran compound and an inhibitor of NS3 (e.g., boceprevir). The benzofuran compound may include any of those set forth in, e.g., U.S. Provisional Patent App. Nos. 60/735,190 and 60/735,191 , and U.S. Published Patent Application No. 2004/0162318.
|0103) Nonlimiting examples of the agents that can be used in addition to the inhibitor of NS3 and the benzofuran compounds described herein, include, but are not limited to, e.g., interferon products and other immunomodulators, ribavirin products, inhibitors of HCV enzymes, antifibrotics, etc. Such agents include those disclosed in Carroll et al., supra; Dhanak et al., supra; Howe et al. (2004), supra; Love et al., supra; Shim et al, supra; Summa et al., supra; Olsen et al., supra; Nguyen et al., supra; Ludmerer et al., supra; Mo et al., supra; Lu et al., supra; Leyssen et al., supra; Oguz et al., supra; U.S. Patent No. 6,964,979; U.S. Patent Publication Nos. 2006/0063821, 2006/0040944, 2006/0035848, 2005/0159345, 2005/0075309, 2005/0059647, 2005/0049204,2005/0048062, 2005/0031588, 2004/0266723, 2004/0209823, 2004/0077587, 2004/0067877, 2004/0028754 and 2004/0082643; and PCT Publication No. WO 2001/032153. Examples of anti-hepatitis C virus agents include VIRAMIDINE® (Valeant Pharmaceuticals); MERIMEPODIB® (Vertex Pharmaceuticals); mycophenolic acid (Roche); amantadine; additional benzofurans; ACTILON® (Coley); BILN-2061 (Boehringer Ingelheim); Sch-6 (Schering); VX-950 (Vertex . Pharmaceuticals); VALOPICITABINE® (Idenix Pharmaceuticals); JDK-003 (Akros Pharmaceuticals); HCV-796 (Wyeth/ViroPharma); ISlS- 14803 (Isis Pharmaceuticals); ENBREL® (Wyeth); IP-501 (Indevus Pharmaceuticals); ID-6556 (Idun Pharmaceuticals); RITUXIMAB® (Genentech); XLT-6865 (XTL); ANA-971 (Anadys); ANA-245 (Anadys) and TARVACIN® (Peregrine). [0104| Additional anti-hepatitis C virus agents include immunomodulators, e.g., interferons (e.g., IFN α, β, and γ) and interferon products (e.g., pegylated interferons), which includes both natural and recombinant or modified interferons. Examples of interferon products include, but are not limited to, ALBUFERON® (Human Genome Sciences), MULTIFERON® (Viragen), PEG- ALFACON® (Inter-Mune), OMEGA INTERFERON® (Biomedicines), INTRON® A (Schering), ROFERON® A (Roche), INFERGEN® (Amgen), PEG-INTRON® (Schering), PEGASYS® (Roche), MEDUSA INTERFERON® (Flamel Technologies), REBIF® (Ares Serono), and ORAL INTERFERON ALFA® (Amarillo Biosciences). (01051 Additional examples of anti-hepatitis C virus agents include, but are not limited to, agents that may regulate T-cell function (e.g., thymosin alfa- 1 , ZADAXIN® (Sci-Clone)), agents that enhance IFN activation of immune cells (e.g., histamine dihydrochloride, CEPLEME® (Maxim Pharmaceutical)), and interferon products. Additional anti-hepatitis C virus agents also include antiviral agents (e.g., nucleoside analogs), such as ribavirin products, e.g., COPEGUS® (Roche); RIBASPHERE® (Three Rivers Pharmaceuticals); VIRAZOLE® (Valeant Pharmaceuticals); and REBETOL® (Schering).
Characterization of Mutations with the HCV Replicon, and the Effects of Combination Therapies
[0106| There are now more than twenty antiretroviral agents, targeting three different steps in replication, approved for the treatment of human immunodeficiency virus (HIV). Current guidelines suggest an initial antiretroviral therapy consisting of two NIs of the HIV RT, in combination with an NNI or HIV protease inhibitor(s) (Hammer et al. (2006) JAMA 296:827-43. Such combinations provide the best chance of achieving maximal efficiency and curtailing the development of resistance. For HCV, an optimal antiviral regimen is also likely to include several drugs that target different steps in replication. |0107] HCV-796 (an NNI of HCV NS5B) and boceprevir (an inhibitor of the NS3 serine protease) both demonstrated antiviral activity in HCV-infected patients (Villano et al. (2006) 57 th Annual Meeting of American Association for the Study of Liver Diseases, Boston, MA; Zeuzem et al. (2005) American Association for the Study of Liver Disease, San Francisco). In the replicon system, combinations of HCV-796 and boceprevir had an additive inhibitory effect. In addition, replicon variants resistant to one agent were fully susceptible to the other (Howe et al. (2007) 42 nd Annual Meeting of the European Association for the Study of the Liver, Barcelona, Spain. This suggested that in the clinic, the combination of the two compounds might enhance antiviral efficacy and diminish the selection of resistant variants. Combinations of HCV-796 and boceprevir were tested for their ability to generate resistant replicon variants; the susceptibility of these variants to anti-HCV agents of different mechanisms was determined, and the mutations that arose in response to the combination treatment were identified and characterized. 10108) The frequency with which resistant colonies emerged was reduced by a combination of the two compounds (Figure 1), but replicon variants resistant to both compounds could be isolated from cells treated with 40 nM HCV-796 (1000-fold) and either 400 nM (8-fold) or 800 nM (10-fold) boceprevir (Table 1). Cells selected in the presence of 40 nM HCV-796 and 800 nM boceprevir were also resistant to two anthranilate derivatives (Table 2). This cross-resistance is explained by anthranilates and HCV-796 having overlapping binding sites on NS5B. The replicon cells resistant to the combination of HCV-796 and boceprevir, however, were fully sensitive to inhibition by another NNI (HCV-371, a pyranoindole), the NI 2'-C-methylcytidine, Peg-IFN, and inhibitors of Hsp90 that have recently been reported to modulate HCV replication. The replicon cells could be cleared by extended treatment with Peg-IFN (Figure 3). Presumably, therefore, these inhibitors, or mechanistically similar compounds, may diminish the emergence of mutants resistant to both HCV-796 and boceprevir, and increase efficacy in a three-part combination. (0109] Several mutations were identified in the replicon variants selected with HCV-796 and/or boceprevir. A major resistance mutation previously identified for HCV-796, NS5B-C316Y, was identified in several of the resistant replicon populations. This change was previously shown to confer eight-fold reduced susceptibility to HCV-796 in an NS5B enzyme assay, and 166-fold reduced susceptibility in a stable replicon (Howe et al. (2006) 13th International Meeting on Hepatitis C Virus and Related Viruses, Cairns, Australia). When tested in the transient luciferase replicon, NS5B-C316Y conferred a 242-fold increase in resistance to HCV-796 (Table 4). The NS5B-C316Y mutation was associated with a reduced replicative capacity as the mutant was out-competed by the parental replicon when both were introduced into cells (Figure 4D) and the NS5B-C316Y change decreased the efficiency of colony formation by approximately two-fold (Table 4). These findings are consistent a previous report indicating a reduced replicative capacity for this mutant (McCown et al. (2008) Antimicrob. Agents Chemother. 52: 1604-12).
|01101 The NS5B-C445F mutation was detected during selection with anthranilate inhibitors of NS5B (data not shown) and in previous selection experiments with HCV-796 alone (Howe et al. (2006), supra), but was not previously characterized for its effect on susceptibility to HCV-796. In the transient luciferase replicon, NS5B-C445F conferred an eight-fold reduced susceptibility to HCV-796 (Table 4). NS5B-C445F did not have a detectable effect on HCV replication, as it was not out-competed when electroporated together with the parental replicon, nor did it have a significant effect on the efficiency of colony formation. While such a clone was not isolated from the combination-treated replicon cells, it was interesting to see what phenotype a replicon bearing both NS5B-C316Y and -C445F might have. The reduced susceptibility conferred by these mutations was additive, as the EC50 for HCV- 796 on the double mutant was -1800-fold greater than that with the parental replicon (Table 4). This suggests that selection of the NS5B-C445F mutation, together with NS5B-C316Y, would result in a viral variant with high-level resistance to HCV-796. The fitness of this double mutant was not assessed in the competition assay, but it did possess a reduced efficiency of colony formation, similar to that conferred by the -C316Y change alone.
[0111 | A previously described mutation that confers resistance to boceprevir was also identified; NS3-V 17OA had little effect on the catalytic efficiency of the NS3 protease, but did decrease the affinity for the compound (Tong et al., supra). In one report with a strain N replicon, V 170A actually increased replication efficiency (He et al. (2008) Antimicrob. Agents Chemother. 52: 1 101 -10), but little impact on fitness was observed, either by competition with the parent replicon (Figure 4B) or in the colony formation assay (Table 4). NS3-A 156T, which conferred the highest level of resistance to boceprevir in a previous study, was not seen in the combination-treated replicon cells. Long exposure or high concentrations of boceprevir were necessary to induce the appearance of mutations at A 156 (Tong et al., supra). The boceprevir concentrations used in our experiments may have been too low, and the duration of selection too short, to select for A 156T.
[0112] The individual resistance mutations NS5B-C316Y and NS3-V 170A were detected by population sequencing of the NS5B and NS3 genes. To determine if replicons bearing both mutations in the same genome had arisen during the selection process, the entire nonstructural region from the 40/800 combination- resistant replicons was amplified, cloned, and sequenced. The NS3-V 170A mutation was not abundant in these sequences, probably due to the low concentrations of boceprevir used for selection, but a clone was isolated that bore both NS3-V 17OA and NS5B-C316Y. This suggests that these two resistance mutations can be selected together and co-exist in the same genome. A luciferase replicon engineered with both these changes exhibited resistance to both compounds in a transient expression assay. The extent of this resistance was similar to that conferred by the individual mutations to their respective compounds. Together, the data suggest that dually-resistant viral variants bearing both these resistance mutations may arise in response to treatment with the combination of HCV-796 and boceprevir. The fitness of the NS3-V170A and NS5B-C316Y double mutant was debilitated, as it was out-competed by the parental replicon sequence in the competition experiment (Figure 4F) and had a reduced efficiency of colony formation (Table 4).
[0113| Two previously reported adaptive mutations were also identified in many of the selected cell populations (Table 3A). These changes, NS3-Q86R and - E 176G are likely to compensate for debilitated replicon sequences. The cell culture adaptive mutant NS3-E176G generated approximately five times more colonies as compared with the parental replicon. The presence of this mutation confers 4 to 5 fold-reduced susceptibility to HCV-796 and boceprevir (Table 4). NS3-Q86K was also detected (Table 3A). Though not reported previously, this may also have an adaptive phenotype. Similarly, K.583T was found to increase the efficiency of colony formation; another change at this position, K583E, was previously shown to confer adaptation (Table 3A). The substitution of K583T had minimal effect on the drug susceptibility to HCV-796 or boceprevir (Table 4).
[0114| The mutation with the most severe effect on replicon fitness, NS3- V 15,8M, decreased the efficiency of colony formation ~2-fold and transient luciferase expression by 50-fold (Table 4). The NS3-V 158M change was always found in cell cultures that also had the E176G, and sometimes also the -Q86R/K. and K.583T changes (Table 3A), suggesting that adaptive changes were able to compensate for the debilitated V 158M. A significantly resistant phenotype for V 158M for either HCV-796 or boceprevir was not detected, although a ~2-fold decrease in susceptibility to boceprevir was apparent in the transient replication assay. NS3-V158M has not previously been shown to confer resistance to boceprevir, though it is in the proximity of A 156, changes at which confer high levels of resistance to NS3 protease inhibitors. |0115) In addition to the resistance mutations, several other changes were detected in the selected replicon cells. When reintroduced into the parental replicon sequence, neither NS3-V158M nor NS5B-I424V affected susceptibility to HCV-796 or boceprevir, but both had a debilitating effect on replicative capacity. These may be secondary changes that arose after other mutations and may not have such deleterious effects in that context. The interactions of these mutations and other changes remains to be investigated.
(0116| Moreover, no resistant replicon cells could be selected with 80 nM HCV- 796 and either 400 or 800 nM boceprevir. Either (1) mutants resistant to these combinations did not arise or (2) they did arise, but their replication level was insufficient to sustain cell growth in the presence of 1 mg/ml G418. Some apparently resistant colonies were obtained under this G418 concentration in the 80/400 and 80/800 cultures during the colony formation assay (Figure 1). This may be explained by the different selection protocols or the continuous incubation versus trypsinization employed in these experiments - the metabolic state of the cells bearing the replicon can have a major effect on its replication, as replicon RNA levels fall rapidly when cells become confluent (Pietschmann et al. (200I) J Virol. 75: 1252-64).
|0117] The combination of the NNI NS5B polymerase inhibitor, HCV-796, and the NS3 protease inhibitor, boceprevir, decreased the frequency with which resistant variants arose, but that dually resistant viral variants with reduced susceptibility to both agents may be selected if treatment is suboptimal. Such variants maintain their sensitivity to Peg-IFN, however, suggesting that resistance arising in response to an HCV-796 and boceprevir combination would not preclude treatment with the current standard of care. Furthermore, a three-part combination of HCV-796, boceprevir and Peg-IFN may be clinically effective. |0118) The entire contents of all references, patents, and patent applications cited throughout this application are hereby incorporated by reference herein.
EXAMPLES
|0119| The following Examples provide illustrative embodiments of the invention and do not in any way limit the invention. One of ordinary skill in the art will recognize that numerous other embodiments are encompassed within the scope of the invention. Example 1 : Frequency of Selection of Replicons Resistant to Combinations of
HCV-796 and Boceprevir
Example 1.1 : Cells and Materials
|0120) Huh7.5 cells, and Huh7-BB7 cells bearing the Con l strain, genotype Ib subgenomic HCV replicon, and the parental plasmid pHCVreplb.BB7 were licensed from Apath, LLC (St Louis, MO). Cell monolayers were propagated at 37°C in 5% CCb in Dulbecco's minimal essential medium (DMEM; Invitrogen, Carlsbad, CA), supplemented with 10% (v/v) fetal bovine serum (FBS; Hyclone, Logan, UT), penicillin-streptomycin, and nonessential amino acids. This medium was also supplemented with 1 mg/ml Geneticin (G418; Invitrogen) for the Huh7- BB7 cells. Pegylated-interferon (Peg-IFN) was obtained from Schering Corporation (Kenilworth, NJ); 2'-C-methylcytidine from CHEMOS GmbH (Regenstauf, Germany); and 17-dimethylaminoethylamino- 17-demethoxygeldanamycin ( 17-DMAG) from Sigma (St. Louis, MO). All other reagents were obtained from suppliers as indicated.
Example 1.2: Colony Formation Assay
|01211 Huh7-BB7 cells were seeded at a density of 20,000 cells per 100 mm dish and treated with various concentrations of HCV-796 and/or boceprevir in 0.5% (v/v) DMSO in DMEM supplemented with 2% FBS and 1 mg/ml G418. The cells were incubated at 370C, 5% CO2. The medium was removed and replaced with fresh medium supplemented with the appropriate compound concentrations every three or four days. After seven days, the cells were split 1 : 10 into fresh 100 mm dishes and incubated with medium with the appropriate compound concentrations. After twenty days, the medium was removed, the surviving cell colonies were fixed with 7% (w/v) formaldehyde and stained with 1% (w/v) crystal violet in 50% (v/v) ethanol.
Example 1 :3: Results
(0122] To determine if the combination of HCV-796 and boceprevir affected the frequency with which resistant replicons emerged, a genotype I b subgenomic HCV replicon with the neo selectable marker was used, and HCV replicon cells were treated with combinations of the two compounds. To select for replicons resistant to inhibition by these combinations, the medium was supplemented with 1 mg/ml G418. The concentrations of HCV-796 used were 40 nM and 80 nM (approximately ten- and twenty-times the EC50 in a three-day replicon inhibition assay {see Example 3.1), respectively). The concentrations of boceprevir used were 400 nM and 800 nM (approximately two- and four-times the EC50). Combinations hereafter are referred to as x/y for the nM concentrations of HCV-796 / boceprevir (i.e., 40/800 refers to cell populations treated with 40 nM HCV-796 and 800 nM boceprevir). Cell death became apparent after 14 days in culture. After 27 days, the surviving cells were fixed and stained with crystal violet (Figure 1). A confluent cell monolayer was apparent in the DMSO-only, vehicle control (0/0), but selection with increasing HCV-796 or boceprevir concentrations caused fewer cell colonies to survive. The number of colonies was further reduced when the compounds added were in combination. These data suggest that replicon variants resistant to HCV-796 and boceprevir alone and in combination can be isolated. The frequency with which such variants arise, however, is reduced by the combination.
Example 2: Selection of HCV Variants Resistant to the Combination of HCV-796 and Boceprevir
Example 2.1 : Cell Culture and RNA Extraction
|0123] Huh7-BB7 cells were seeded at a density of 7.5 x 105 cells per 25 cm2 tissue-culture flask and cultured in the absence of G418 in DMEM supplemented with 2% FBS, penicillin-streptomycin, 0.5% (v/v) DMSO, and various combinations of HCV-796 and boceprevir, at 37°C and 5% CO2. Each concentration of compound was tested in triplicate. When the cells reached about 80% confluence (about 2-3 days); cells were passaged 1 :3 into fresh medium containing the appropriate concentration of each compound. Each time the cultures were passaged, 105 cells were collected, lysed with 500 μL RLT buffer (RNeasy 96 Kit; Qiagen, Valencia, CA) and stored at -700C until processed. Lysates were thawed, total RNA was extracted using the RNeasy 96 Kit, eluted in nuclease-free water and used for quantitative reverse transcription-polymerase chain reaction (qRT-PCR). To select for resistant replicons, following the two-week treatment period, the cells were passaged in the presence of the appropriate concentrations of compound, but supplemented with G418 to a final concentration of 0.33 mg/ml. Some cell death was observed 7- 10 days following the addition of G418, but the surviving cells were allowed to grow back to confluency. Resistant replicon colonies were selected and enriched by repeating this process, successively increasing the concentration of G418 in the medium to 0.5, 0.75 and 1.0 mg/ml. Subsequently, the selected cell populations were propagated in DMEM supplemented with 2% FBS, the appropriate concentrations of HCV-796 and boceprevir, a final concentration of 0.5% (v/v)DMSO, and 1 mg/ml G418.
Example 2.2: Quantitative Reverse Transcription-Polymerase Chain Reaction [0124| Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed using the ABI Prism 7900HT Sequence Detection System (Applied Biosystems, Foster City, CA), as described previously (Howe et al. (2004), supra). Briefly, the levels of HCV replicon RNA and 18S rRNA were determined in a single-step duplexed reaction using HCV primers and probe against the neomycin phosphotransferase gene and rRNA Pre-Development reagent (Applied Biosystems). The RT reaction was carried out at 48°C for 30 minutes, followed by a denaturation step at 95°C for 10 minutes. The PCR amplification was conducted in 40 cycles, each at 95°C for 15 seconds, followed by 600C for 1 minute. The amount of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) RNA in the total RNA was determined using the GAPDH Pre-Development reagent mix. Total RNA extracted from replicon- bearing cells was used to construct standard curves: HCV RNA copies were quantified by the National Genetics Institute, and total RNA concentration was determined by UV-spectrophotometry. The amount of HCV, 18S rRNA or GAPDH in each sample was determined by comparison to standard curves and was expressed as the number of HCV RNA copies per μg of total RNA (using rRNA as a marker for total RNA measurement) or GAPDH relative to total RNA.
Example 2.3: Results
(0125) To select for resistant variants, replicon cells were cultured in the absence of G418, but in the presence of HCV-796 or boceprevir, alone or in combination. The same compound concentrations were used as for the colony formation assay (see Example 1.2, supra) and three separate cultures were propagated for each of the eight tested conditions. Cell cultures were passaged every two or three days, and fresh medium and compounds were added each time. At every passage, a sample of cells was taken and the HCV RNA and rRNA levels were determined (Figure 2). (01261 Over the treatment period, the control cells (0/0) showed little change in their HCV replicon content. Levels of GAPDH and rRNA also remained approximately constant for each culture over the course of the experiment (data not shown). As expected, treatment with each compound alone caused a dose- and time-dependent reduction in the HCV RNA level (Figure 2). Combination enhanced the magnitude of this reduction; for example, by the second passage, the HCV RNA levels were reduced by approximately 1 log in the 0/800 cells, but by over 3 logs in the 40/800 cells. Following the initial reduction in HCV RNA levels, for all of the tested cultures, levels remained relatively constant over the remaining course of the experiment.
|0127] To select for resistant replicon variants, following six passages (~18 days) in the presence of the compound combinations, but in the absence of G418, the media was supplemented with 333 μg/ml G418, while maintaining the appropriate concentrations of HCV-796 and boceprevir. For the compound- treated cultures, cell death was observed 7-10 days following the addition of G418, but some cells survived and were allowed to grow back to confluence. The selection process was repeated with 0.5, 0.75 and 1 mg/ml G418, each time allowing cell death to occur and any surviving cells to grow back. Under these conditions, cells could be enriched from each of the cultures treated with HCV-796 or boceprevir alone, and from the cultures treated with the 40/400 and 40/800 combinations. The selected cell populations were expanded and subsequently propagated in the presence of the appropriate concentrations of compounds and 1 mg/ml G418.
(0128] No cells survived the selection process from the cultures treated with 80/400 or 80/800, suggesting that the replication level of mutants resistant to these combinations was insufficient to sustain cell growth in the presence of 1 mg/ml G418. Some apparently resistant colonies were obtained under this G418 concentration in the 80/400 and 80/800 cultures during the colony formation assay (Figure 1). This may be explained by the differing selection protocols or the continuous incubation versus trypsinization employed in these experiments - the metabolic state of the cells bearing the replicon can have a major effect on its replication (Pietschmann et al., supra). Example 3: Susceptibility of Replicon Variants Selected with a Combination of HCV-796 and Boceprevir to the Individual Compounds
Example 3.1 : HCV Replicon Inhibition Assay
[0129) The three-day replicon assay for compound inhibition was described previously (Howe et al. (2004), supra). Briefly, cells were seeded at 7000 cells per well of a ninety-six well plate in DMEM with 2% FBS and without G418. HCV-796, boceprevir, and/or other compound(s) under test were solubilized with 100% DMSO, and added to the wells as a ten-point, two- or three-fold dilution series in a final DMSO concentration of 0.5% (v/v). The cells were incubated at 37°C, 5% CO2 for 3 days. Under these conditions, the cells were approximately 25% confluent at the time of seeding, and 80 to 90% confluent after three days. After three days, the medium was removed and total RNA extracted using the RNeasy 96 Kit. The extracted RNA was eluted in 150 μL of nuclease-free water and the amounts of HCV, ribosomal and GAPDH RNAs determined by qRT- PCR (see Example 2.2, supra).
Example 3.2: Results
|0130] The ability of the 40/400 and 40/800 selected cell populations to grow in the presence of both HCV-796 and boceprevir was consistent with the selection of replicon variants with reduced sensitivity to both compounds. To test this, the susceptibility of these cells to HCV-796 and boceprevir individually was determined in a three-day inhibition assay (Table 1). Unselected cells (- / -) and cells treated with DMSO only (0/0) were also tested. No significant effect on the levels of GAPDH RNA or rRNA for any of the cultures was detected (data not shown). The 40/400 and 40/800 cells were approximately 1000-fold less susceptible to HCV-796 than the untreated or 0/0 cells. Similarly, these cultures were approximately 10-fold less susceptible to boceprevir than the untreated or 0/0 cells. No significant difference in sensitivity to boceprevir was noted between the 40/400 and 40/800 cells.
Example 4: Susceptibility of Replicons Resistant to HCV-796 and Boceprevir to
Diverse Anti-HCV Agents
|01311 Multiple classes of HCV inhibitors have been discovered. To evaluate their potential utility against HCV variants resistant to the combination of HCV-796 and boceprevir, several inhibitors with diverse mechanisms were tested in three-day replicon inhibition assays {see Example 3.1 , supra) against the 0/0 and 40/800 cells.
|0132| HCV-371 is a pyranoindole NNI of HCV NS5B that binds to the thumb domain of NS5B and inhibits RdRp activity (Gopalsamy et al. (2004) J. Med. Chem. 47:6603-08; Howe et al. (2006) Antimicrob. Agents Chemother. 50:4103- 13; Howe et al. (2004) Antimicrob. Agents Chemother. 48:4813-21 ). The sensitivities of the 0/0 and 40/800 cells to HCV-371 in a three-day replicon assay were not significantly different (EC50 values of 4832 and 7840 nM, respectively, Table 2), indicating that the 40/800 cell replicons were not cross-resistant to HCV-371. In contrast, the 40/800 cells were much less sensitive (> 15-fold) to inhibition by anthranilate derivatives than were the 0/0 cells. Anthranilate derivatives are also NNIs of HCV NS5B, binding approximately 7.5A from the NS5B active site (Nittoli et al. (2007) J Med. Chem. 50:2108-16). Both 14i and 14j, anthranilate derivatives obtained through optimization of this inhibitor series, showed reduced potency against the 40/800 cells (Table 2). |0133) Inhibitors of the heat shock protein 90 (Hsp90) have recently been shown to be inhibitors of the HCV replicon (Nakagawa et al. (2007) Biochem. Biophys. Res. Commun. 353:882-88; Okamoto et al. (2006) Embo. J. 25:5015-25). Two such inhibitors, geldanamycin and 17-DMAG, were tested against the 0/0 and 40/800 cells. The 40/800 cells were fully susceptible to both of these inhibitors, as there was no significant difference between the susceptibility of the cell lines (Table 2, note that variability of EC50 values in this assay is three- to four-fold). It should be noted that cytotoxicity was apparent for replicon cells treated with both of these Hsp90 inhibitors (data not shown).
[0134) 2'-modified nucleoside analogs inhibit both HCV RdRp activity and the replicon (Carroll et al., supra; Migliaccio et al., supra; Tomassini et al. (2005) Antimicrob. Agents Chemother. 49:2050-58). 2'-C-methylcytidine (NM 107) is the active component of valopcitabine (NM283), a nucleoside analog recently demonstrated to have clinical efficacy. To gain some insight into whether NIs might be effective against HCV variants arising upon selection with the combination of HCV-796 and boceprevir, NM 107 was used to inhibit replicon variants in the 40/800 cells. No significant difference in susceptibility to NM 107 was found between the 0/0 and 40/800 cells. |0135] As Peg-IFN plus ribavirin is the current standard-of-care for treatment.of HCV infection, the ability of Peg-IFN to maintain activity against HCV variants resistant to the combination of HCV-796 and boceprevir was assessed. No significant difference in susceptibility in the three-day replicon assay was found when the 0/0 and 40/800 cells were treated with Peg-IFN (Table 2).
Example 5: PEG-IFN Clearance of HCV Replicon Variants Resistant to the Combination of HCV-796 and Boceprevir
Example 5.1 : Replicon Clearance Assay with PEG-IFN
|0136] The clearance assay was done essentially as described (Lin et al. (2004) Antimicrob. Agents Chemother. 48:4784-92; Lin et al. (2006) Antimicrob. Agents Chemother. 50: 1813-22). The 40/800 combination-selected replicon cells were passaged twice in the absence of G418, then following a third passage, were treated with 0, 1 10, or 1 100 ng/ml Peg-IFN for 30 days in the absence of G418. Confluent monolayers were passaged every 3-4 days. Each time the cells were split, a sample of 105 cells was lysed for qRT-PCR. To allow for receptor recycling and to prevent cell-signaling tolerization, the cultures were seeded into medium without Peg-IFN and incubated for 24 hours, and then Peg-IFN was added (see Blight et al. (2002) / Virol. 76: 13001 -14). After 30 days, the Peg- IFN was withdrawn and 0.25 mg/ml G418 was added to expand cells that had not cleared the replicon. After ~7 days with G418, cell death was observed in several of the cultures. Any surviving cells were permitted to grow back to confluency in the presence of 0.25 mg/ml G418, and the amounts of HCV, ribosomal, and GAPDH were determined by qRT-PCR.
Example 5.2: Results
|0137] To further characterize the response of the HCV-796- and boceprevir- resistant cells to Peg-IFN, the ability of Peg-IFN to clear the replicon from these cells was determined, using a protocol similar to that used to confirm replicon clearance by VX-950 (Lin et al. (2006), supra); Lin et al. (2004), supra). Over a period of 30 days, the 40/800 cells were treated with 0, 1 10 or 1 100 ng/ml Peg- IFN (approximately equivalent to 0, 10x and 10Ox the EC50 determined in the three-day replicon inhibition assay), in the absence of G418. The cells grew normally and were split every 2 or 3 days, and at each passage, a sample of cells was collected and HCV and 18S rRNAs were quantitated. The Peg-IFN treatment was performed with three separate 40/800 cell cultures, in the presence (Figure 3) or absence (data not shown) of 40 nM HCV-796 and 800 nM boceprevir. Three 0/0 cell cultures were similarly treated. After 30 days, the Peg-IFN was withdrawn and 0.25 mg/ml G418 was added to the culture medium to expand any cells that retained the replicon RJSIA. Each untreated cell culture grew normally and, when assayed after 55 and 58 days, contained similar HCV RNA levels as they did at the start of the experiment (Figure 3). Approximately 7 days after withdrawal of Peg-IFN and the addition of G418, cell death was apparent in the cells treated with -10 x EC50 Peg-IFN. Some cells survived this selection, however, and grew back to confluency. When assayed at 55 and 58 days, the HCV RNA level in these cells had returned to that of the original cells. Thus, the replicon had not been cleared from this cell population. In contrast, when Peg-IFN was removed and G418 added to the cells treated with -100 x EC5O Peg-IFN, cell death occurred after 7 days and no cells survived, suggesting that the replicon had been cleared. A similar result was observed for the 40/800 cells when no HCV-796 or boceprevir was added to the culture medium (data not shown). The result was also similar with 0/0 cells, with complete cell death occurring for the 0/0 cells treated with 100 x EC50 Peg-IFN, and with the untreated, and the 10 x EC50 Peg-IFN-treated cells, surviving the selection process and returning to the original HCV RNA levels (Figure 3). Therefore, optimal dosing of Peg-IFN is required to clear HCV replicons regardless of their previous treatment with HCV-796 and boceprevir.
[0138] To summarize, the replicon variants resistant to the combination of HCV-796 and boceprevir were also resistant to the anthranilate derivatives but were susceptible to each of the other tested agents, including the NI (NM 107) and Peg-IFN. The replicon could be cleared from the resistant cells by extended treatment with Peg-IFN.
Example 6: Mapping Amino Acid Changes in Replicons Resistant to HCV-796 and Boceprevir
Example 6.1 : Replicon Sequence Analysis
[0139| Total cellular RNA was extracted from Huh7-BB7 cells using the RNeasy purification system (Qiagen). cDNA of the HCV nonstructural genes were synthesized using the Superscript III One Step RT-PCR system with Platinum Taq High Fidelity enzyme (Invitrogen). RT-PCR was carried out in a 50 μL reaction, containing 0.1 -0.3 μg of total cellular RNA, 200 nM of each forward and reverse primer, 0.4 mM each of dNTP, and 2.4 mM Of MgSO4 in the I x buffer provided in the kit. The reaction was incubated at 55°C for 30 min, 94°C for 2 min, followed by 40 cycles of 94°C for 15 sec, 550C for 30 sec, 68°C for 2 min with a final extension at 68°C for 7 min. The amplicons were evaluated by agarose gel electrophoresis, and purified with QIAquick PCR Purification Kit (Qiagen) before sequencing. Sequencing of the PCR amplicons was performed using the ABI Prism BigDye Terminator Cycle Sequencing Ready Reaction kit v3.0 (Applied Biosystems) according to the manufacturer's instructions. The sequenced products were gel purified using the Performa® Dye Terminator Removal System (Edge BioSystems; Gaithersburg, MD), dried down, denatured with formaldehyde and separated by electrophoresis using an ABI Prism 3700 DNA Sequencer. Sequence data were analyzed using Sequencher v4.0. (0140) To generate single RT-PCR products encompassing NS3 to NS5B, RT was performed with total cellular RNA, oligonucleotide A9412 (SEQ ID NO: 3; 5 '-CAGG ATGGCCTATTGGCCTGG AG-3') and Superscript III reverse transcriptase (Invitrogen) at 55 0C for 1 hr. RNA strands were removed by the addition of RNase H (2U per reaction) and incubation at 37 0C for 20 min. A 6.4 kb product was then amplified according to the manufacturer's instructions with the Expand Long Template PCR System (Roche; Indianapolis, IN) with oligonucleotides 1419F (SEQ ID NO:4; 5'-
GGTCTGTTG AATGTCGTG A AGG A A-3') and 7761 R (SEQ ID NO: 5; 5'- CGTTCATCGGTTGGGG AGTA-3') using Expand Long Template Buffer 1 and 1 μl of the RT reaction. Cycling conditions were as described (Lohmann et al. (200I) J Virol. 75: 1437-49). To avoid potential RT-PCR bias, seven independent PCR reactions were performed, checked by agarose gel electrophoresis, pooled, and cloned using the Zero-Blunt TOPO PCR Cloning kit (Invitrogen). The sequence of inserts was obtained by standard procedures.
Example 6.2: Results
|01411 To identify mutations within the HCV replicon that might be responsible for reduced susceptibility to the combination of HCV-796 or boceprevir, the sequence of the nonstructural genes from the replicons in each of the selected cell lines was determined. RNA was isolated from at least two, independently derived replicon cultures, and RT-PCR products corresponding to NS3/4A, NS4B, NS5A and NS5B were amplified and sequenced. Polymorphic positions were identified by visual appraisal of the sequencing chromatograms at positions that yielded ambiguous amino acid calls.
[0142] Mutations that were present in only one of the cell cultures were interpreted as being sporadic mutations and were not investigated further. Similarly, mutations that were different from the plasmid sequence used to derive the replicon (pHCVrepl b.BB7), but were present in all of the cell cultures were not investigated. No mutations of note were detected in NS4A, NS4B, or in the NS3 cleavage sites, but differences from the originating plasmid sequence, present in more than one cell culture were found in NS3, NS5A and NS5B (Table 3A).
[0143) The primary mutation known to confer resistance to HCV-796 is NS5B- C316Y (Howe et al. (2006), supra). Consistent with this, C316Y was found in cultures that had been selected with HCV-796, either alone or in combination with boceprevir. The changes C316S, C316N, C316F were not observed (previously shown to confer 10-, 26- and 130-fold reduced susceptibilities to HCV-796, respectively). The NS5B amino acids at positions 314, 363, 365 and 414 have been shown to directly interact with HCV-796, and changes at these positions confer varying degrees of resistance to HCV-796. However, no changes at any of these positions was detected in any of the selected cell cultures. |0144) The serine protease domain resides in the N-terminal third of NS3, while the helicase domain constitutes the remainder. Mutations in both protease and helicase domains were identified in the combination-resistant cell populations. The NS3 mutation V 170A is known to confer resistance to boceprevir (Tong et al., supra). This change was detected in 3 of 3 cultures selected with 0/800, and in 1 of 3 selected with 40/800, though not in the 0/400 or 40/400 cells. Thus, boceprevir at 800 nM, but not 400 nM, exerted sufficient pressure for the V 17OA mutation to emerge. Changes at A 156, associated with high-level resistance to NS3 protease inhibitors, were not detected in any of the cultures treated with 400 or 800 nM boceprevir, either alone or in combination with HCV-796, probably due to the low compound concentrations used.
[0145| Two previously reported cell-culture adaptive mutations were found in several of the selected cultures; NS3-Q86R (Blight et al., supra) and -E176G (Krieger et al. (200I ) J Virol. 75:4614-24). These adaptive mutations may compensate for debilitated sequences, restoring replicon fitness and replication capacity. Consistent with such a role, these changes were found in cell cultures selected with boceprevir alone, as well as HCV-796 alone, and in cells selected with both compounds. A mixed population of Q/R at NS3 position 86 was also seen in one of the control, untreated cell cultures. The NS3-Q86K and -K.583T changes not previously reported to be an adaptive mutation were detected in several cultures, though K583E conferred a weakly adapted phenotype (Lohmann et al. (2003), supra; Lohmann et al. (2001 ), supra). The NS3-E176G mutation was not found in the 0/0 cells, but was detected in the majority of the compound- treated replicons, suggesting that it may have been co-selected with resistance mutations that cause a debilitation in replicative capacity. The mutation NS5B- C445F was detected in replicons treated with HCV-796 alone. This change was previously reported as being present in replicons selected with anthranilates or HCV-796 (Howe et al. (2006), supra) but its phenotype was not characterized. |0146| To determine if NS3 and NS5B mutations were present together in the same genome, the entire nonstructural region from the three 40/800 cultures (40/800- A, -B and -C) were' amplified, cloned and sequenced. Five clones from each culture were sequenced. Several sporadic mutations, present in only a single clone, were identified but not investigated further. Amino acid positions identified as being of interest from the population sequencing are shown in Table 3B. The clonal sequencing of the 40/800 replicon cells was generally consistent with the population sequencing, with NS3-V 158M, -E 176G, -G282S and NS5B- C316Y, -P353L and -I424V being notably prevalent among the sequenced clones. The HCV-796 resistance mutation NS5B-C316Y was found in thirteen of the fourteen clones sequenced. Only one clone did not carry this mutation, and this particular clone (40/800-C #2) also carried changes that were not present in any of the other clones, NS5B-C445F, -E440G and -F572L. The boceprevir- resistance mutation NS3-V170A was found in only a single clone from the 40/800 cultures (40/800-C # 1 , Table 3B), which also carried NS5B-C316Y, indicating that these two resistance mutations can coexist in the same replicon genome.
|0147) In summary, amino acid changes previously shown to confer resistance to HCV-796 (NS5B-C316Y) and boceprevir (NS3-V 170A), as well as cell-culture adaptive mutations (NS3-Q86R and -E 176G) and some changes not previously described, were found in the cell populations selected with combinations of HCV-796 and/or boceprevir. In addition to the previously described mutations NS5B-C316Y, NS3-V170A and -E176G, the following mutations were found in more than two of the selected cell cultures and were chosen for further investigation: V 158M and K583T in NS3; I424V and C445F in NS5B.
Example 7: Identification and characterization of mutations responsible for reduced susceptibility to HCV-796 and boceprevir
Example 7.1 : Materials and Methods Example 7.1.1 : Cloning and Mutagenesis
[0148] An HCV replicon expressing a secreted luciferase protein was constructed by replacing the neo gene from the parental pHCVrepl b.BB7 plasmid with the luciferase gene from Gaussia princeps, amplified from pCMV-G-luc (New England Biolabs; Ipswich, MA), to generate the plasmid pHCVrep lb.BB7.G-luc. Following transcription and electroporation of the replicon RNA encoded by this plasmid, the Gaussia luciferase protein was secreted from expressing cells and activity was measured in the culture medium. Mutagenesis was performed using the QuikChange II site-directed mutagenesis kit (Stratagene; La Jolla, CA) following the manufacturer's standard protocols. Mutations were generated in the appropriate shuttle vector pMUT-middle (containing the BsrGI-XhoI fragment from pHCVreplb.BB7, encompassing part of NS3, NS4A, NS4B and most of NS5A) or pMUT-back (containing the Xhol- HindIII site from pHCVrepl b.BB7, with part of NS5A, NS5B and the 3'UTR). Fragments of interest were subcloned back into the appropriate replicon vector, either into pHCVreplb.BB7 for generation of stable cell lines, or into pHCVrepl b.BB7.G-luc for transient expression. The presence of each mutation was confirmed by sequencing of the final replicon plasmids. Amino acid mutations are designated by the single letter amino acid code of the parental sequence, the residue number of the individual protein, and the altered amino acid present in the mutant construct.
Example 7.1.2: RNA Transcription and Electroporation of Cultured Cells |0149) In vitro transcription was performed using the T7 MEGAScript kit (Applied Biosystems), and plasmid DNA templates linearized with Seal. Following treatment with RNase-free DNase to remove template DNA and purification using the RNeasy RNA purification kit (Qiagen), RNA yield was determined by quantification with a UV spectrophotometer, and quality was assessed by agarose gel electrophoresis. Subconfluent monolayers of Huh-7.5 cells grown in 225 cm2 flasks were trypsinized, resuspended in DMEM supplemented with 10% FBS, and a viable cell count was determined by trypan blue exclusion. The cells were washed twice by centrifugation at 250 x g for 5 min and resuspension in room temperature Dulbecco's PBS (D-PBS; 50 ml per flask), then pelleted again and resuspended at a concentration of 1 x 107 cells/ml in Cytomix (120 mM potassium chloride, 0.15 mM calcium chloride, 2 mM EGTA, 5 mM magnesium chloride, 25 mM HEPES, 10 mM potassium phosphate buffer pH 7.6). 4 x 106 cells were transferred to a microfuge tube, and ATP (100 mM in Cytomix) and glutathione (100 mM in water) were added to final concentrations of 2 and 5 mM, respectively. 10 μg of replicon RNA was then added to each tube, and the contents were mixed briefly and transferred to an electroporation cuvette with 0.4 cm gap (Bio-Rad; Hercules, CA). The cells were electroporated using a Bio-Rad Gene Pulser II at 950 μF and 270 V, then immediately transferred to either 45 ml or 30 ml DMEM supplemented with 10% FBS, for colony formation or transient replication assays, respectively. To account for potential variation between in vitro transcribed RNA, each electroporation was performed three-times, on three separate days, each using an independently prepared RNA preparation.
Example 7.1.3: Evaluation of the Efficiency of Replicon Colony Formation [0150) Following electroporation of Huh7.5 cells with RNA generated from pHCVreplb.BB7 templates, a ten-fold serial dilution of the electroporated cells was generated and 15 ml of the 1 : 10, 1 : 100 and 1 :000 dilutions were seeded in 100 mm dishes (~105, 104 and 103 electroporated cells, respectively). To select for replicon-bearing cells, the culture medium was supplemented with G418 at 0.375 mg/ml. To determine the efficiency of colony formation, the medium was removed; the cells were fixed with 7% (w/v) formaldehyde and stained with 1% (w/v) crystal violet in 50% (v/v) ethanol. Cell colonies were counted using the Sorcerer Image Analysis System (Perceptive Instruments Ltd.; Haverhill, UK), and the efficiency of colony formation expressed as colony forming units (cfu) per μg of electroporated RNA.
Example 7.1.4: Transient Replication Assay |0151) Following electroporation of RNA generated from pHCVrep lb.BB7.G-luc templates, 0.1 ml of electroporated cells were seeded per well of a 96-well plate. To follow replication, the cell culture medium was removed at 4, 24, 48, 72 and 96 hours following electroporation, and stored at 4°C until the completion of the experiment. At each time-point following removal of the cell culture medium, except for that at 4 hours, the cells were washed with D-PBS and 0.1 ml of fresh DMEM supplemented with 10% FBS was added to each well. Luciferase activity was measured from 25 μl of culture medium, using the Gaussia luciferase assay kit (New England Biolabs). To calculate the relative fitness of different replicon mutants, the luciferase signal from the sample taken 48 hours post-electroporation was normalized to the luciferase signal 4 hours post-electroporation (to account for electroporation efficiency) and then expressed relative to the parental replicon RNA (relative fitness for the parental RNA is 1.0). To determine the susceptibility of mutant replicons to inhibition by compounds, the medium was removed 48 hours post- electroporation and replaced with DMEM supplemented with 2% FBS and the compound under test. At 72 hours post-electroporation, samples of the cell culture medium was taken and luciferase activity was measured. The EC5O was determined as the compound concentration necessary to inhibit 50% of the luciferase activity determined from untreated cells, following the deduction of background signal.
Example 7.2: Results Example 7.2.1 : Susceptibility
|0152] To determine the phenotype conferred by the mutations found in replicon cells treated with the combination of HCV-796 and boceprevir, each individual mutation was reintroduced into the parental replicon that had the neo gene replaced with luciferase from Gaussia princeps. The susceptibility of each mutant to HCV-796 and boceprevir was tested in a transient expression assay following electroporation of the replicon RNA. The Gaussia luciferase protein was secreted from expressing cells and was assayed in the culture medium 72 hours after the addition of compound. The ECso's for HCV-796 and boceprevir for the parental replicon in the transient assay were comparable to those obtained in the three-day inhibition assay with the stable replicon cells; the EC50 for HCV- 796 in the transient assay was 14 nM, compared to 5 nM for the stable replicon, and the EC50 for boceprevir in the transient assay was 608 nM, compared with 201 nM in the stable (compare Tables 4 & 1).
[0153| In the transient assay, NS5B-C316Y, conferred a 142-fold reduced susceptibility to HCV-796, but had no effect on susceptibility to boceprevir. The NS3-V 170A mutation conferred a five-fold reduced susceptibility to boceprevir, but had no effect on susceptibility to HCV-796. When both primary resistance- mutations, NS3-V 170A and NS5B-C316Y, were introduced together, the double- mutant exhibited reduced susceptibility to both compounds: seven-fold to boceprevir and ~140-fold to HCV-796. The NS5B-C445F mutation conferred a 17-fold reduced susceptibility to HCV-796 but had no effect upon inhibition by boceprevir. The resistance to HCV-796 contributed by NS5B-C316Y and - C445F was additive, as a replicon bearing both mutations had ~1800-fold reduced susceptibility.
|0154] The cell-culture-adaptive mutation, NS3-E176G, showed a slightly reduced susceptibility to inhibition by both HCV-796 (three-fold) and boceprevir (four-fold). This is likely due to an increased replication level and not a specific mechanism of resistance. A similar mechanism may explain the slightly reduced susceptibility to both compounds conferred by NS3-G282S. Three mutations found in the selected replicons did not effect susceptibility to either HCV-796 or boceprevir in the transient assay; NS3-V158M, -K583T and NS5B-I424V. Example 7.2.2: Replicative Fitness
(0155) The replicative fitness of resistant viral variants is likely to be a critical factor determining whether such mutant viruses emerge during drug treatment. Gaussia luciferase-reporter replicons described above was used to determine fitness as has been reported by others (Lu et al. (2004) Antimicrob. Agents Chemother, 48:2260-6; Lin et al. (2005), supra). In these experiments, the NS3- V 158M and NS5B-I424V mutants expressed significantly less luciferase than the parental replicon, but the expression from each of the other mutants was not significantly different from that of the parental sequence (data not shown). The high stability of the Gaussia luciferase protein, compared to the Firefly luciferase used by others, may cause this assay to poorly resolve fitness phenotypes. Instead, other methods to evaluate mutant fitness was used. |0156| Replicative capacity relative to the parental replicon was determined by competition experiments between the parent and mutant replicons. Previous reports used the co-culture of cells bearing parental and mutant replicons to assess relative fitness (Tong et al. (2006) Antiviral Res. 70:28-38; Lahser et al. (2003) Biotechniques 34:26-8). Since this analysis may be complicated by the relative growth rates of the replicon-bearing cell lines, which may be independent of the fitness of the replicon itself, an alternative method was used. Huh-7 cells were electroporated with either the parental replicon, the mutant replicon or with equal amounts of parental and mutant replicon. After G418 selection and expansion (sixteen to twenty days post-electroporation), the NS3 and NS5B genes were amplified and sequenced to determine if the mutant or the parental sequence predominated in the selected cell population (Figures 4A-F). When equal amounts of parental replicon and the cell-culture adaptive mutant NS3- E176G were electroporated, the predominant sequence at NS3-176 after selection was the E 176G mutant (Figure 4C), consistent with its cell-culture adapted phenotype conferring a competitive advantage over the parental sequence. In contrast, when the NS3-V 158M, -V170A and NS5B-C445F mutants were introduced with equal amounts of the parental replicon, the resulting cell populations maintained both parent and mutant sequences (Figures 4A, 4B, & 4E), suggesting that the fitness of these mutants was not significantly impaired and was similar to that of the parental sequence. These mixed replicon populations appeared relatively stable as each carried both parent and the respective mutant sequence five weeks after the initial sequencing. Electroporation of the parent replicon and the NS5B-C316Y mutant yielded a replicon population that was predominantly parental (Figure 4D), suggesting that the NS5B-C316Y change debilitated fitness and as a result, this mutant was out- competed by the parent replicon sequence. Consistent with this, when the NS3- V 170A and NS5B-C316Y double mutant was introduced together with the parental replicon, the resulting cell population predominantly bore the parental sequence at both positions (Figure 4F), providing further evidence for a reduced fitness associated with NS5B-C316Y. The competition experiment was performed three times and each time similar results were obtained, except for one occasion when the NS5B-C445F mutant electroporated alone reverted and possessed a mixed mutant and parental sequence at NS5B-445 (data not shown). (0157J T° obtain a further measure of mutant fitness, the efficiency of colony formation following electroporation was determined (Table 4). The parental replicon had an efficiency of 15 x 103 cfu/μg of RNA. The mutations could be divided into three groups. The first group was those that increased the efficiency of colony formation above that of the parental replicon, including the cell-culture adaptive change NS3-E176G, but also -G282S (36 and 27 x 103 cfu/μg, respectively). The second group of mutations did not significantly alter the efficiency of colony formation and included NS3-V 170A, -K.583T and NS5B- C445F (14, 19 and 12 x 103 cfu/μg). The final group of mutants caused a decrease in the efficiency of colony formation and included NS3-V 158M, NS5B- C316Y and -I424V (5, 7 and 6 x 103 cfu/μg), consistent with these changes debilitating HCV replication.
Table 1: Susceptibility of Replicon Variants Selected with a Combination of HCV-796 and Boceprevir to the Individual Compounds
Cells selected with: Replicon susceptibility:
HCV-796 Boceprevir HCV-796 Fold Boceprevir Fold
(nM) (nM) EC50 ± SD (nM) resistance EC50 ± SD (nM) resistance
4.6 ± 3.7 (M = 3) 201 ± 8.7 (M = 3)
2.4 ± 0.4 (M = 3) 165 ± 25 (M = 3)
40 400 2459 ± 601 (M = 3) 1025 1328 ± 305 (M = 4)
40 800 3368 ± 1068 (M = 3) 1403 1577 ± 598 (M = 4) 10
Replicon-bearing cell populations, selected under the indicated treatments, were tested for their susceptibility to HCV-796 or boceprevir in a three-day inhibition assay. The mean EC50 ± standard deviation is indicated from n independent determinations. Fold resistance relative to the DMSO-only, vehicle-control treated culture (0/0) is shown.
Table 2: Susceptibility of Replicons Resistant to a Combination of HCV-796 and Boceprevir to Different Anti-HCV Compounds
40/800 selected
0/0 selected cells cells
Fold
Compound Class
EC50 (nM or ng/ml for resistance
EC50 (nM or ng/ml Peg-IFN) for Peg-IFN)
Geldanamycin Hsp90 inhibitor 0.25 ± 0.01 (n - 3) 1.2 ± 0.65 (n = 3) 5
17-DMAG Hsp90 inhibitor 1.2 ± 0.9 (n = 3) 3.1 ± 1.2 (π = 3) 3
HCV-371 Pyranoindole 4832 ± 1077 (n = 5) 7840 ± 2145 (π = 2) 2
14i' Anthranilate 1308 ± 267 (n = 3) > 20,000 (n = 3) > 15
14j Anthranilate 499 ± 269 (n = 3) > 15,000 (π = 3) > 30
2'-C- methylcytidine Nucleoside 1143 ± 177 (n = 5) 1623 ± 736 (n = 4)
(NM107)
, . 14.0 ± 11.7 ng/ml 16.9 ± 4.4 ng/ml
Inducer of innate a a
Peg-IFN immunity
(n = 3) (n = 3)
Replicon cell populations, selected DMSO-only (0/0) or 40 nM HCV-796 and 800 nM boceprevir (40/800), were tested for their susceptibility to miscellaneous anti-HCV inhibitors in a three-day inhibition assay. The mean EC5O ± S. D. is indicated from n independent determinations. EC50 values are shown in nM for each compound, except for Peg-IFN, in ng/ml. Fold resistance relative to the DMSO-only, vehicle-control treated culture is shown. = from Nittoli et al. (2007) J. Med. Chem. 50:2108- 16.
Table 3 A: Population sequence analysis of nonstructural genes from cells selected with combinations of HCV-796 and/or boceprevir
Figure imgf000064_0001
RNA from multiple independently selected replicon cultures (A, B or C) was extracted and genes for the nonstructural proteins NS3/NS4A, NS4B, NS5A and NS5B were amplified and sequenced. Amino acid numbering within NS3, NS5A and NS5B, the predicted amino acids present in the parental Ib, pBB7 plasmid and polyprotein numbering according to the Conl sequence (accession # AJ238799) is shown (see also SEQ ID NOs: 1 and 2). Grey cells = not performed.
Table 3B: Clonal sequence analysis of nonstructural genes from cells selected with combinations of HCV-796 and/or boceprevir
Figure imgf000065_0001
RNA from independently selected replicon cultures (0/0-A or 40/800-A, -B or -C) was extracted and cDNA encoding the nonstructural coding region was amplified and cloned. Five different clones derived from each selected culture were sequenced (#1 -5). Only amino acid positions noted as being of interest from the population sequencing are shown. Amino acid numbering within NS3 and NS5B, the predicted amino acids present in the parental pBB7 plasmid and polyprotein numbering according to the Conl sequence (accession # AJ238799) is shown.
Table 4: Characterization of individual mutations
HCV-796 Boceprevir Efficiency of colony
Mutatιon(s) Proteιn(s) EC50 ± S D Fold EC50 ± S D. Fold formation ± S D
(nM) resistance (nM) resistance (103cf_7μg)
14 ± 7
Parental n/a 1 608 ± 255 1 150 ± 129 (n = 12) (n= 12) (/7 = 11)
9 + 4
V158M NS3 1 377 + 211 1 48 ±47 (1 = 6) (π = 6) (1 = 7)
13 ± 4
V 170A NS3 1 3170± 1110
5 140 ± 136
</? = 9) (" = 9) (i = 8)
38 ± 23 2152 ± 1028 362 ± 257
E176G NS3 3 4 (π = 9) (n = 9) (i= 7)
22 1937 ± 182 269 ± 193
G282S NS3 2 3
(n = 2) (n = 3) (i = 5)
15 ± 9
K583T NS3 1 738 ± 395 1 187 ± 160
(π = 3) (i = 3) (i = 5)
1936 ± 779 781 ± 504
C316Y NS5B 142 1 71 ±61 <i = 9) (1 = 9) (n = 8)
I424V NS5B 13 ± 3 1 647 ± 105 1 59 + 74
(n = 3) (i = 3) (π = 8)
C445F NS5B 114 ±26 795 ± 473
8 1 123 ± 100 (1= 9) (i = 9) (1 = 6)
1335 ± 995 4362 ± 573 83 ±66
V170A/C316Y NS3/NS5B 95 7 (π = 3) (i = 3) (i = 3)
25680 ± 6020 821 ± 363 59±37
C316Y/C445F NS5B/NS5B 1834 1 (n = 6) (i = 6) (1 = 3)
NS5B 0
PoI - - - - -
(1 = 3)
The susceptibility of replicon mutants to HCV-796 or boceprevir was determined using a transient luciferase replicon. The EC50 and the fold resistance compared to the parental replicon sequence are indicated. The efficiency of colony formation was determined following electroporation of Huh7.5 cells with replicon RNA and selection with G418. The efficiency of colony formation was determined for each mutant replicon in three separate electroporations on different days, with independently derived RNA preparations. Mean efficiency of colony formation ± S. D. is shown. A replication defective RNA (Pol -) is shown as a negative control.

Claims

WHAT IS CLAIMED IS:
1. A method of decreasing the frequency of emergence of a treatment- resistant hepatitis C viral infection, comprising administering an inhibitor of a hepatitis C vims NS5B polymerase in combination with an inhibitor of a hepatitis C vims NS3 serine protease to a subject in need thereof.
2. A method of delaying the emergence of a treatment-resistant hepatitis C viral infection, comprising administering an inhibitor of a hepatitis C vims NS5B polymerase in combination with an inhibitor of a hepatitis C vims NS3 serine protease to a subject in need thereof.
3. A method of decreasing the level of resistance of a treatment-resistant hepatitis C viral infection, comprising administering an inhibitor of a hepatitis C vims NS5B polymerase in combination with an inhibitor of a hepatitis C vims NS3 serine protease to a subject in need thereof.
4. The method as in any one of claims 1-3. further comprising administering at least one additional anti-hepatitis C vims agent.
5. The method of claim 4. wherein the at least one additional anti-hepatitis C vims agent is an immunomodulator.
6. The method of claim 4. wherein the at least one additional anti-hepatitis C vims agent is a ribavirin product.
7. The method of claim 4. wherein the at least one additional anti-hepatitis C vims agent is selected from the group consisting of those set forth in Table 2.
8. The method as in any one of claims 1-3. wherein the inhibitor of a hepatitis C vims NS5B polymerase is HCV 796.
9. The method as in any one of claims 1-3. wherein the inhibitor of a hepatitis C vims NS3 serine protease is boceprevir.
10. A method of decreasing the emergence of an HCV 796-resistant and/or boceprevir-resistant hepatitis C viral infection, comprising administering HCV 796 in combination with boceprevir to a subject in need thereof.
11. A method of decreasing the emergence of an HCV 796-resistant and/or boceprevir-resistant hepatitis C viral infection, comprising administering HCV 796 in combination with boceprevir. either before or after administration of at least one additional anti-hepatitis C vims agent to a subject in need thereof.
12. The method of claim 11. wherein the at least one additional anti-hepatitis C vims agent is an immunomodulator.
13. The method of claim 11. wherein the at least one additional anti-hepatitis C vims agent is a ribavirin product.
14. The method of claim 11. wherein the at least one additional anti-hepatitis C vims agent is selected from the group consisting of those set forth in Table 2.
15. A method of identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the individual at a first time point; and
(b) determining the amino acid sequence of the nonstructural gene in a sample from the individual at a second time point. wherein a change in the amino acid sequence of the nonstructural gene in the sample from the individual at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the individual at the first time point, indicates a decreased likelihood that the individual will respond to an anti-hepatitis C viral therapy.
16. A method of identifying an individual with a decreased likelihood of responding to an anti-hepatitis C viral therapy, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the individual; and
(b) comparing the amino acid sequence of the nonstructural gene in the sample from the individual to the amino acid sequence in a reference sample. wherein a change in the amino acid sequence of the nonstructural gene in the sample from the individual, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, indicates a decreased likelihood that the individual will respond to an anti-hepatitis C viral therapy.
17. A method for monitoring the course of treatment of a hepatitis C viral infection in a subject, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject;
(b) administering a benzofuran compound and an inhibitor of the NS3 serine protease to the subject; and
(c) determining the amino acid sequence of the nonstructural gene in a sample from the subject following administration of the benzofuran compound and the inhibitor of the NS3 serine protease to the subject. wherein a change in the amino acid sequence of the nonstructural gene in a sample from the subject following administration of the benzofuran compound and the inhibitor of the NS3 serine protease, in comparison to the amino acid sequence of the nonstructural gene in a sample from the subject prior to said administration, provides a negative indication of the effect of the treatment of the hepatitis C viral infection in the subject.
18. A method for monitoring the course of treatment of a hepatitis C viral infection in a subject, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject;
(b) administering HCV 796 and boceprevir to the subject; and (c) determining the amino acid sequence of the nonstructural gene in a sample from the subject following administration of HCV 796 and boceprevir. wherein a change in the amino acid sequence of the nonstructural gene in a sample from the subject following administration of HCV 796 and boceprevir. in comparison to the amino acid sequence of the nonstructural gene in a sample from the subject prior to said administration, provides a negative indication of the effect of the treatment of the hepatitis C viral infection in the subject.
19. A method for monitoring the course of treatment of a hepatitis C viral infection in a subject, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject;
(b) administering HCV 796. boceprevir. and at least one additional anti- hepatitis C agent to the subject; and
(c) determining the amino acid sequence of the nonstructural gene in a sample from the subject following administration of HCV 796. boceprevir. and at least one additional anti-hepatitis C agent to the subject. wherein a change in the amino acid sequence of the nonstructural gene in a sample from the subject following administration of HCV 796. boceprevir and at least one additional anti-hepatitis C agent, in comparison to the amino acid sequence of the nonstructural gene in a sample from the subject prior to said administration, provides a negative indication of the effect of the treatment of the hepatitis C viral infection in the subject.
20. The method of claim 19. wherein the at least one additional anti-hepatitis C vims aaent is an immunomodulator.
21. The method of claim 19. wherein the at least one additional anti-hepatitis C vims agent is a ribavirin product.
22. The method of claim 19. wherein the at least one additional anti-hepatitis C vims agent is selected from the group consisting of those set forth in Table 2.
23. A method for prognosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject at a first time point; and
(b) determining the amino acid sequence of the nonstructural gene in a sample from the subject at a second time point. wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the subject at the first time point, indicates an increased likelihood that the subject will develop a treatment- resistant hepatitis C viral infection.
24. A method for prognosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; and
(b) comparing the amino acid sequence of the nonstructural gene in the sample from the subject to the amino acid sequence of the nonstructural gene in a reference sample. wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, indicates an increased likelihood that the subject will develop a treatment-resistant hepatitis C viral infection.
25. A method for monitoring a hepatitis C viral infection in a subject, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject at a first time point; and
(b) determining the amino acid sequence of the nonstructural gene in a sample from the subject at a second time point. wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the subject at the first time point, provides an indication that the hepatitis C viral infection has changed in severity.
26. A method for monitoring a hepatitis C viral infection in a subject, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; and
(b) comparing the amino acid sequence of the nonstructural gene in the sample from the subject to the amino acid sequence of the nonstructural gene in a reference sample. wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, provides an indication that the hepatitis C viral infection has changed in severity.
27. A method for diagnosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising:
(a) determining the amino acid sequence of an HCV nonstructural gene in a sample from the subject at a first time point; and
(b) determining the amino acid sequence of the nonstructural gene in a sample from the subject at a second time point. wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject at the second time point, in comparison to the amino acid sequence of the nonstructural gene from the subject at the first time point, indicates an increased likelihood that the subject has developed or is developing a treatment-resistant hepatitis C viral infection.
28. A method for diagnosing the development of a treatment-resistant hepatitis C viral infection in a subject, comprising: (a) detemiining the amino acid sequence of an HCV nonstructural gene in a sample from the subject; and
(b) comparing the amino acid sequence of the nonstructural gene in the sample from the subject to the amino acid sequence of the nonstructural gene in a reference sample. wherein a change in the amino acid sequence of the nonstructural gene in the sample from the subject, in comparison to the amino acid sequence of the nonstructural gene in the reference sample, indicates an increased likelihood that the subject has developed is developing a treatment-resistant hepatitis C viral infection.
29. The method as in any one of claims 15-19 and 23-28. wherein the change in the amino acid sequence of the nonstructural gene is an amino acid change selected from the group consisting of those set forth in Table 3A.
30. The method of claim 29. wherein the change in the amino acid sequence of the nonstructural gene is an amino acid change selected from the group consisting of C316Y. V 170A. Q86R. and E176G.
31. The method as in any one of claims 15-19 and 23-28. wherein the nonstructural gene is selected from the group consisting of NS3. NS5A. and NS5B.
32. The method of claim 31. wherein the nonstructural gene is NS5B.
33. The method of claim 32. wherein NS5B is derived from a hepatitis C virus genotype selected from the group consisting of genotype Ia. genotype Ib. genotype 2. genotype 3. genotype 4. genotype 5. and genotype 6.
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