WO2006109196A2 - Modeles de souris transgeniques du virus de l'hepatite c (vhc) et identification des therapies pour le vhc - Google Patents

Modeles de souris transgeniques du virus de l'hepatite c (vhc) et identification des therapies pour le vhc Download PDF

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WO2006109196A2
WO2006109196A2 PCT/IB2006/001668 IB2006001668W WO2006109196A2 WO 2006109196 A2 WO2006109196 A2 WO 2006109196A2 IB 2006001668 W IB2006001668 W IB 2006001668W WO 2006109196 A2 WO2006109196 A2 WO 2006109196A2
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inhibitor
hcv
protein
mouse
genetically modified
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WO2006109196A3 (fr
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Matti Sallberg
Lars Frelin
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Tripep AB
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Tripep AB
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/8509—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells for producing genetically modified animals, e.g. transgenic
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00—Genetically modified animals
    • A01K2217/05—Animals comprising random inserted nucleic acids (transgenic)
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00—Animals characterised by species
    • A01K2227/10—Mammal
    • A01K2227/105—Murine
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2267/00—Animals characterised by purpose
    • A01K2267/03—Animal model, e.g. for test or diseases
    • A01K2267/0337—Animal models for infectious diseases
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/24011—Flaviviridae
    • C12N2770/24211—Hepacivirus, e.g. hepatitis C virus, hepatitis G virus
    • C12N2770/24222—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes

Definitions

  • aspects of the invention concern the use of genes encoding the hepatitis C virus (HCV) nonstructural proteins (NS3/4A) to create transgenic mice, which can be used to identify compounds that inhibit HCV infection.
  • Embodiments include the exogenous nucleic acids used to create NS3/4A-containing transgenic mice, the exogenous peptides encoded by said nucleic acids, genetically modified mice containing said compositions, methods of using said genetically modified mice to identify compositions that treat or prevent HCV infection and pharmaceuticals and dietary supplements that comprise an inhibitor of a kinase (e.g., a p38 Map kinase) or an inhibitor of nuclear factor kappa B (NFKB), which are useful for subjects infected with HCV or subjects at risk of becoming infected with HCV.
  • a kinase e.g., a p38 Map kinase
  • NFKB nuclear factor kappa B
  • the HCV genome is approximately 9.4 kb in length, and encodes at least ten polypeptides. (Kato, Microb. Comp. Genomics, 5:129-151 (2000)).
  • the genomic RNA is translated into one single polyprotein that is subsequently cleaved by viral and cellular proteases to yield the functional polypeptides.
  • the polyprotein is cleaved to three structural proteins (core protein, El and E2), to p7 of unknown function, and to six nonstructural (NS) proteins (NS2, NS3, NS4A/B, NS5A/B).
  • NS3 encodes a serine protease that is responsible for some of the proteolytic events required for virus maturation (Kwong et al, Antiviral Res., 41 :67-84 (1999)) and NS4A acts as a co-factor for the NS3 protease.
  • NS3 further displays NTPase activity, and possesses RNA helicase activity in vitro. (Kwong et al, Curr. Top. Microbiol. Immunol, 242:171-96 (2000)).
  • HCV infection typically progresses from an acute to a chronic phase.
  • Acute infection is characterized by high viral replication and high viral load in liver tissue and peripheral blood. (Id. at 1041-42.)
  • the acute infection is cleared by the patient's immune defense system in roughly 20-40% of the infected individuals; in the other 60-80% the virus establishes a chronic, persistent infection. (Lawrence, Adv. Intern. Med., 45:65-105 (2000)).
  • chronic phase replication takes place in the liver and the virus is readily detected in peripheral blood.
  • the infected host mounts both a humoral and a cellular immune response against the HCV virus but in most cases the response fails to prevent establishment of the chronic disease.
  • the infected patient produces antiviral antibodies including neutralizing antibodies to the envelope proteins El and E2.
  • This antibody response is sustained during chronic infection.
  • the liver is also infiltrated by both CD8+ and CD4+ lymphocytes.
  • infected patients produce interferons as an early response to the viral infection. (Id. at 1045). It is likely that the vigor of the initial immune response against the infection determines whether the virus will be cleared or whether the infection will progress to a chronic phase. (Pape et al, J. Viral. Hepat., 6 Supp. 1:36-40 (1999)).
  • HCV hepatitis C virus
  • NS3 nonstructural protein 3
  • NS4A nonstructural protein 4A
  • HCV NS3/4A transgenic mice created, as described herein, have a reduced sensitivity or an increased resistance to TNF-alpha, as compared to wild-type mice of the same variety that have not been genetically modified to contain NS3/4A. That is, some of the genetically modified mice, created as described herein, survive contact with an amount of TNF-alpha that is lethal to wild-type mice of the same variety.
  • mice created as described herein also revert to a TNF-alpha sensitive phenotype when said mice are contacted with a p38 MAP kinase inhibitor, such as SB203580 or SB202190.
  • SB203580 blocks p38 MAPK it may also block other kinases such as protein kinase receptor interacting protein-2 (RIP2; also known as RIP-like interacting CLARP kinase, RICK; or CARD containing interleukin-1 beta converting enzyme associated kinase, CARDIAK) (Argast GM, Fausto N, and Campbell.
  • RIP2 protein kinase receptor interacting protein-2
  • RICK RIP-like interacting CLARP kinase
  • CARDIAK interleukin-1 beta converting enzyme associated kinase
  • mice created as described herein which have a reduced sensitivity or increased resistance to TNF-alpha, can be induced to become as sensitive to TNF-alpha as a wild-type mouse of the same variety by contacting the genetically modified mouse with an inhibitor of p38 MAP kinase and/or other sensitive kinases.
  • Genetically modified mice that express NS3/4A are used as models for HCV infection and provide an in vivo system for the analysis and testing of compounds that inhibit HCV replication and/or HCV infection.
  • signal molecules and secretory signals can be included on said nucleic acid constructs used to create said genetically modified mice so as to facilitate the analysis and testing of said compounds for anti-HCV activity.
  • the genetically modified mice, created as described herein are contacted with a compound and an indicator of HCV infection, such as expression of NS3, NS3 protease activity, or TNF-alpha sensitivity is analyzed.
  • HCV replication e.g., inhibitors of NS3 expression or protease activity or compounds that restore TNF-alpha sensitivity
  • identified compounds e.g., p38 MAP kinase inhibitors such as, SB203580 or SB202190
  • pharmaceuticals and/or dietary supplements which can be provided to HCV infected individuals or individuals at risk of becoming infected with HCV. That is, aspects of the invention described herein concern the use of p38 MAP kinase inhibitors such as, SB203580 or SB202190, to prepare a medicament for the treatment and/or prevention of HCV infection and methods of using said medicaments in HCV treatment or prophylactic methods.
  • some embodiments relate to a transgenic non-human mammal (e.g., a rodent such as, a mouse) containing an exogenous DNA sequence stably integrated in its genome, wherein said exogenous DNA sequence comprises a mouse major urinary promoter (MUP) operably linked to an HCV NS3 gene.
  • the genetically modified non-human mammal can comprise an allele comprising an HCV NS3 gene and an HCV NS4A gene.
  • the non- human mammal preferably expresses HCV NS3 and/or NS4A proteins in the liver.
  • the NS3 gene and the NS4A genes are codon optimized.
  • the only hepatitis C virus genes in the allele consist of a NS3/4A gene.
  • the NS3 and NS4A genes that are inserted into mice can be codon optimized for mice or humans. Codon-optimized sequences can be generated by software, for example, DNABUILDER.
  • NS3/4A cleavage site nucleic acid and amino acid constructs can be created so as to create secretion dependent indicators of NS3 protease activity.
  • These indicators (PADSI, for Protease Activity Dependent Secreted Indicators) can be used to monitor the activity of a NS3 protease in vivo by looking for the presence or absence of detectable markers (indicators) in various localities in an organism.
  • a method of identifying a compound that inhibits hepatitis C virus replication is provided.
  • a genetically modified mouse created as described above is contacted with a test compound, and a marker for the inhibition of HCV replication (e.g., protease activity or TNF-alpha sensitivity) is analyzed.
  • the marker for the inhibition of HCV is identified by analyzing a liver cell or liver tissue of the mouse contacted with the test compound and analyzing a liver cell or liver tissue of a second mouse, which was not contacted with the test compound.
  • the NS3 protein that is expressed in said transgenic mice is detectable via a western blot. In some embodiments, the NS3 protein that is expressed in said transgenic mice is restricted to expression in the cytoplasm of hepatocytes. In some embodiments, the genetically modified mouse has a liver with a significantly increased weight relative to a mouse without NS3 protein expression. In some embodiments, the genetically modified mouse has a lower number of nuclei per unit area in its liver tissue relative to a mouse without NS3 protein being expressed in the mouse.
  • the genetically modified mouse created as described herein, comprises an altered intrahepatic distribution of immune cells, hi some embodiments, the genetically modified mouse has a reduced number of intra-hepatic inflammatory foci than a mouse that does not comprise an NS3 and/or NS4A gene (e.g., a wild-type mouse). In some embodiments, the frequency of such foci occurring in the genetically modified mouse is reduced as compared to that of a non-transgenic mouse that does not contain the NS3 and/or NS4A genes. In some embodiments the frequency is reduced at least two fold or at least four fold.
  • the genetically modified mouse has a reduced number of intra- hepatic inflammatory foci, as compared to a non-transgenic mouse that does not comprise a an NS3 and/or NS4A gene.
  • the liver in the genetically modified mouse has a NS3/4A protein distribution and tissue localization consistent with HCV infection (e.g., protein expression in the liver).
  • the liver in the mouse having an allele with an NS3 and NS4A gene has an altered hepatic distribution of immune cells.
  • NS3 and/or NS4A protein expression is restricted to hepatocytes.
  • NS3 and/or NS4A protein expression in said genetically modified mice is in the hepatic venules and protal tracts.
  • the amount of NS3 protein that is expressed in said genetically modified mice is an amount that is sufficient for detection by immuno histochemistry (e.g., expression in at least 1% of the hepatocytes of the mouse).
  • the genetically modified mice comprise an amount of hepatocytes that express NS3 and/or NS4A , which is at least, more than, or equal to 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%,
  • a genetically modified mouse with a persistent expression of NS3 and/or NS4A proteins is provided.
  • the only HCV proteins produced by the mouse are NS3 and/or NS4A proteins.
  • the amount of persistent NS3 protein produced is detectable and limited to liver cells.
  • the term "persistent" means an expression of NS3 and/or NS4A that lasts for more than 1 week, 2 weeks, 3 weeks, 1 month, two months, three onths, four months, five months, six months, sevem months, eight months, nine months ten months, eleven months, one year, 13 months, fourteen months, fifteen months, sixteen months, seventeen months, or eighteen months.
  • a composition for analyzing compounds for their ability to inhibit the activity of a protease comprises a NS3 gene, a gene encoding a detectable marker attached to the NS3 gene, a NS3/4A cleavage site, and a secretory gene encoding a secretory protein signal. Cleavage of the NS3/4A cleavage site results in a change in localization of the detectable marker.
  • a nucleic acid encoding a PADSI protein comprises a nucleic acid section encoding a NS3 protein, a nucleic acid section encoding a cleavage site protein, a nucleic acid section encoding a secretory protein signal, and a nucleic acid section encoding a detectable marker.
  • the nucleic acid sections are associated together so that their translation results in a single contiguous protein and cleavage of the cleavage site results in a change in localization of the detectable maker.
  • a PADSI protein that comprises a NS3 protein segment, a cleavage site segment, a secretory protein signal segment, and a detectable marker segment.
  • the segments are associated in one contiguous piece and cleavage of the cleavage site results in a change in localization of the detectable maker.
  • the cleavage of the protein cleavage site results in the separation of the secretory protein signal and the detectable marker from the NS3 protein segment.
  • the cleavage of the cleavage site results in an increase in a presence of the detectable marker in a venous blood of an organism.
  • the NS3 protein is not autocatalytic for the cleavage of the cleavage site.
  • a nucleic acid encoding a PADSI protein comprises a nucleic acid section encoding a cleavage site, a nucleic acid section encoding a secretory protein signal, and a nucleic acid section encoding a detectable marker.
  • the cleavage site section, detectable marker, and secretory protein signal are associated together so that their translation results in a single contiguous protein. Cleavage of the cleavage site results in a change in localization of the detectable maker.
  • the compositions above further comprise a nucleic acid section encoding a NS3 protein.
  • a PADSI protein that comprises a cleavage site segment, a secretory protein signal segment, and a detectable marker segment is provided.
  • the cleavage site segment and the secretory protein signal segment are associated in one contiguous piece, and cleavage of the cleavage site results in a change in localization of the detectable marker.
  • the protein further comprises a NS3 protein segment.
  • the cleavage site is positioned between the secretory protein signal and the detectable marker.
  • the constructs described above are incorporated into a transgenic organism (e.g., a mouse). Accordingly, cleavage at the protease cleavage site results in two separate protein segments such that one segment comprises the secretory protein signal and the other section comprises the detectable marker. In some embodiments of the previous aspects, the cleavage of the cleavage site segment results in the retention of the marker protein in a cell in which the PADSI is located.
  • the detectable marker is selected from the group consisting of: beta galactosidase, l ⁇ c Z, Green Fluorescent Protein, and Luciferase.
  • the secretory signal is from an IG kappa sequence.
  • the cleavage site is selected from the group consisting of NS4A/4B, NS4B/5A, NS5A/5B, NS2/3, andNS3/4.
  • the change in localization is between the cells in which the uncleaved PADSI protein is located and the venous blood.
  • a system for determining a NS3 protease inhibitor comprises a PADSI nucleic acid.
  • the PADSI nucleic acid comprises a nucleic acid encoding a secretory section connected to a nucleic acid encoding a cleavage site, which is connected to a nucleic acid encoding a detectable marker and a transgenic organism.
  • the transgenic organism produces NS3.
  • the transgenic organism further comprises the NS4A gene.
  • the PADSI nucleic acid is capable of being administered to the transgenic organism via a virus.
  • a system for determining a NS3 protease inhibitor comprises a PADSI protein that comprises a secretory protein signal connected to a NS3/4A cleavage site which in rum is connected to a detectable marker and a transgenic organism containing NS3/4A.
  • the transgenic organism produces the NS3 protease.
  • the PADSI protein is administered to the transgenic organism in a viral vector and the transgenic organism is a transgenic mouse.
  • a system for determining a NS3 protease inhibitor comprises a PADSI nucleic acid.
  • the PADSI nucleic acid comprises a nucleic acid encoding a NS3 protein connected to a nucleic acid encoding a NS3/4A cleavage site that in turn is connected to a nucleic acid encoding a detectable marker and a nucleic acid encoding a secretory protein signal.
  • the PADSI nucleic acid is expressed in an organism that is transgenic for the PADSI nucleic acid.
  • a system for determining a NS 3 protease inhibitor comprises a PADSI protein.
  • the PADSI protein comprises a NS3 protein connected to a NS3/4A cleavage site that in turn is connected to a detectable marker and a secretory protein signal.
  • the PADSI protein is in an organism that is transgenic for the PADSI nucleic acid.
  • the detectable marker is detectable in venous blood.
  • the detectable marker is detectable via fluorescence.
  • the detectable marker is luciferase.
  • a method of identifying a protease inhibitor comprises determining an initial level of detectable marker in the venous blood of one of the genetically modified mice described herein, contacting a candidate protease inhibitor to the mouse, determining the level of detectable marker in the venous blood of the mouse.
  • a change in the level of detectable marker indicates the presence of a protease inhibitor.
  • the PADSI protein comprises a NS3 protein connected to a NS3/4A cleavage site.
  • the NS3/4A cleavage site is connected to a secretory signal, the secretory signal is, in turn, connected to a detectable marker.
  • a decrease in the amount of detectable marker in the venous blood of the organism indicates the presence of a protease inhibitor.
  • the PADSI protein comprises a secretory signal connected to a NS3 cleavage site that in turn is connected to a marker protein.
  • the transgenic mouse is a NS3/4A-containing transgenic mouse. Cleavage of the NS3 cleavage site results in the marker protein remaining in a cell and, thus, an increase in the detectable marker in the venous blood indicates the presence of a protease inhibitor.
  • the detection of the detectable marker is accomplished fluorescently.
  • the detection of the detectable marker is accomplished on the outside of the transgenic mouse's body.
  • a protease inhibitor detected by any of the above methods is formulated into a pharmaceutical or dietary supplement.
  • a genetically modified mouse that comprises a NS3 gene and a NS4A gene displays an increased resistance to an adverse effect of an application of TNF- alpha to the genetically modified mouse compared to a standard resistance of a wild-type mouse to the application of TNF-alpha.
  • the adverse effect is death of the mouse.
  • the adverse effect is death of a plurality of cells (e.g., death of liver cells).
  • the term "TNF-alpha sensitivity" refers amount of cell death (e.g., liver cell death) in an animal after contact with TNF-alpha.
  • the term “TNF-alpha sensitivity” refers to death of the animal.
  • the genetically modified mice created as described herein have a reduced TNF-alpha sensitivity as compared to a wild-type mouse of the same variety, which can be that the genetically modified mouse comprising NS3/4A exhibits less cell death (e.g., liver cell death) than a wild-type mouse of the same variety or that the NS3/4A-containing transgenic mouse survives contact with an amount of TNF-alpha that is lethal to a wild-type mouse of the same variety.
  • the genetically modified mouse comprising NS3/4A exhibits less cell death (e.g., liver cell death) than a wild-type mouse of the same variety or that the NS3/4A-containing transgenic mouse survives contact with an amount of TNF-alpha that is lethal to a wild-type mouse of the same variety.
  • a method for screening for an inhibitor of suppressor of cytokine signaling- 1 (SOCSl) inhibitor comprises providing a candidate SOCSl inhibitor to a transgenic mouse, created as described herein, providing a lethal amount of TNF-alpha to the transgenic mouse, determining the impact of TNF-alpha on said transgenic mouse, comparing the impact of TNF-alpha administration on said transgenic mouse with the impact of TNF-alpha administration on a control mouse (e.g., a wild-type mouse of the same variety), and selecting an inhibitor of SOCSl based on the observation that the impact of TNF-alpha on the transgenic mouse in the presence of the candidate inhibitor is approximately the same as the impact of TNF-alpha on the control mouse.
  • SOCSl suppressor of cytokine signaling- 1
  • the impact of TNF-alpha is ascertained by analyzing the amount of cell death in the mouse, which can include an analysis of the liver cells or livers of the mice, such as, a measurement of liver cell death. In some embodiments, the amount of cell death is measured by determining survival of the mouse after contact with TNF-alpha.
  • a method of identifying a p38 MAP kinase inhibitor or a NF- IdB inhibitor comprises providing a candidate p38 inhibitor or a NF- kB inhibitor to a transgenic mouse created as described herein, providing an amount of TNF- alpha to said transgenic mouse, determining a first amount of cell death resulting from the contact of TNF-alpha to the transgenic mouse, comparing the first amount of cell death with a standard amount of cell death due to the contact of the amount of TNF-alpha to a control mouse (e.g., a wild-type mouse of the same variety), and selecting an inhibitor of p38 or NF- IcB based on the fact that the first amount of cell death and the standard amount of cell death are about the same.
  • a control mouse e.g., a wild-type mouse of the same variety
  • a method for preventing, treating, or ameliorating an HCV related symptom in a patient comprises identifying a subject having an HCV related symptom and providing said identified subject a compound identified in by the methods described herein.
  • the compound is a p38 inhibitor.
  • the HCV treatment is a SOCSl inhibitor.
  • the p38 inhibitor functions by preventing the phosphorylation of p38 kinase.
  • the p38 inhibitor is selected from the group consisting of of SB 203580, SB 202190, KN62, UO 126, PD 98059, Wortmannin, rapamycin, Ro 31-8220, Bis-1, Go 6976, UCNOl, Indirubin-3'-monoxime, kenpaullone, alsterpaullone, PPl, PP2, SU 6656, SP 600125, ML-9, PD 169316, p38 MAP Kinase inhibitor, SB202190 hydrochloride, SB 203580 hydrochloride, SB 203580 Iodo, SC68376, SKF-86002, ZM 3363772, Anti-p38/HOG-l antibody, and anti- p38 MAP Kinase antibody.
  • the p38 inhibitor is SB203580. In some embodiments, the p38 inhibitor is SB202190. In some embodiments, the HCV treatment is selected from the group that consists of: a SOCSl inhibitor, an IFR3 enhancer, type-1 IFN, typel/II hepatic DC, STATl activator, STAT2 activator, siRNA to SOCSl, siRNA to ⁇ 38, siRNA to PP2A, a blocking antibody to SOCSl, a blocking antibody to p38, a blocking antibody to PP2A, an activating antibody to IFR3, an activating antibody to STATl, an activating antibody to STAT2, and a PP2A inhibitor.
  • a SOCSl inhibitor an IFR3 enhancer, type-1 IFN, typel/II hepatic DC
  • STAT2 activator siRNA to SOCSl
  • siRNA to ⁇ 38 siRNA to PP2A
  • a blocking antibody to SOCSl a blocking antibody to p38
  • the compound is an inhibitor of PP2A and it lowers the activity of PP2A in a NS3/4A transgenic mouse to a level similar to that of an activity of PP2A in a wild type mouse.
  • the compound is an inhibitor of SOCSl and it lowers the activity of SOSCl in a NS3/4A transgenic mouse to a level similar to that of an activity of SOCSl in a wild type mouse.
  • the compound is an enhancer of the IFR3 activity and it increases the activity of IFR3 in a NS3/4A transgenic mouse to a level similar to that of an activity of IFR3 in a wild type mouse.
  • the enhancer of IFR3 activity functions by phosphorylating IFR3.
  • a dietary supplement comprising one or more of the aforementioned compounds is provided to a subject (e.g., an individual identified as having HCV) for the purpose of improving the general health or welfare of said subject, improving the immune system function or function of the liver.
  • a subject e.g., an individual identified as having HCV
  • some embodiments include methods of improving the general health or welfare of a subject, methods of improving the function of the immune system, or methods of improving the function of the liver by providing a subject in need (e.g., a subject infected with HCV) with a dietary supplement comprising any one or more of the compounds described above, or Kunitz trypsin inhibitor (KTI) and a Bowman-Birk trypsin inhibitor (BBI), soy bean extract, grape seed extract, quercitin, flavinoids, carotenoids, brassica extract, phytoestrogens, or troglitazone.
  • KTI Kunitz trypsin inhibitor
  • BBI Bowman-Birk trypsin inhibitor
  • KTI Kunitz trypsin inhibitor
  • BBI Bowman- Birk trypsin inhibitor
  • soy bean extract grape seed extract
  • quercitin flavinoids
  • carotenoids carotenoids
  • brassica extract phytoestrogens
  • troglitazone for the preparation of a dietary supplement for the improvement of the general health or welfare of a subject (e.g., an HCV infected subject), the improvement of the immune system of a subject (e.g., an HCV infected subject), or the improvement of the function of the liver of a subject (e.g., an HCV infected subject) are embodiments.
  • aspects of the invention also include methods of treating or preventing HCV infection comprising identifying a subject in need of a compound that inhibits proliferation or replication of HCV, and providing said subject a Kunitz trypsin inhibitor (KTI) and a Bowman-Birk trypsin inhibitor (BBI), soy bean extract, grape seed extract, quercitin, flavinoids, carotenoids, brassica extract, phytoestrogens, or troglitazone.
  • KTI Kunitz trypsin inhibitor
  • BBI Bowman-Birk trypsin inhibitor
  • Particularly preferred embodiments include a genetically modified mouse comprising a reduced sensitivity to TNF-alpha, as compared to a wild-type mouse of the same variety and an exogenous nucleic acid construct that comprises a promoter operably linked to a gene encoding a hepatitis C virus (HCV) nonstructural protein 3 (NS3).
  • the genetically modified mouse can further comprise a gene encoding a HCV nonstructural protein 4A (NS4A).
  • the genetically modified mice described above have the proviso that said genetically modified mice do not comprise an HCV core protein, structural protein El (El), structural protein E2 (E2), nonstructural protein 2 (NS2), nonstructural protein 4B (NS4B), nonstructural protein 5A (NS 5A), or nonstructural protein 5B (NS5B).
  • the genetically modified mice described above comprise a promoter that is a mouse major urinary promoter (MUP).
  • MUP mouse major urinary promoter
  • the genetically modified mice described above have an exogenous nucleic acid construct that further comprises a nucleic acid encoding a NS3 protease cleavage site.
  • the genetically modified mice described above have a nucleic acid that encodes an NS3 protease cleavage site that is joined to said NS3 gene. In some embodiments, the genetically modified mice described above have an exogenous nucleic acid construct that further comprises a nucleic acid encoding a secretory signal. In some embodiments, the genetically modified mice described above comprise an exogenous nucleic acid construct that further comprises a nucleic acid encoding a signal molecule. In some embodiments, the genetically modified mice described above comprise an NS3 gene that is codon optimized. In some embodiments, the genetically modified mice described above comprise an NS4A gene that is codon optimized.
  • the genetically modified mice described above have an increased sensitivity to TNF-alpha after contact with an inhibitor of a p38 MAP kinase, as compared to a genetically modified mouse, created as described herein, that has not been contacted with said inhibitor.
  • the inhibitor is SB203580.
  • the genetically modified mice described above comprise at least 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2,
  • the genetically modified mice described above comprise more than 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3,
  • the genetically modified mice described above comprise between about 0.1 - 1.0, 0.5 - 1.5, 1.0 - 2.0, 1.5 - 2.5, 2.0 - 3.0, 2.5 - 3.5, 3.0 - 4.0, 3.5 - 4.5, 4.0 - 5.0, 4.5 - 5.5, 5.0 - 6.0, 5.5 - 6.5, 6.0 - 7.0, 6.5 - 7.5, 7.0 - 8.0, 7.7 - 8.5, 8.0 - 9.0, 8.5 - 9.5, 9.0 - 10.0 micrograms NS3 protein per gram of liver tissue.
  • aspects of the invention relate to an isolated totipotent mouse cell comprising an exogenous nucleic acid construct that comprises a mouse major urinary promoter (MUP) operably linked to a gene encoding an hepatitis C virus (HCV) nonstructural protein 3 (NS3).
  • the isolated totipotent mouse cell further comprises a nonstructural protein 4A (NS4A).
  • N4A nonstructural protein 4A
  • Some embodiments include the isolated totipotent mouse cell as described above, with the proviso that said isolated totipotent cell does not comprise an HCV core protein, structural protein El (El), structural protein E2 (E2), nonstructural protein 2 (NS2), nonstructural protein 4B (NS4B), nonstructural protein 5 A (NS 5A), or nonstructural protein 5B (NS 5B).
  • a method of using a genetically modified mouse to identify a compound that inhibits HCV replication comprises providing a genetically modified mouse, created as described herein; contacting said genetically modified mouse with a compound; and analyzing the expression of NS3, NS3 protease activity, or the sensitivity of said genetically modified mouse to TNF- alpha, after contact with said compound, whereby said compound that inhibits HCV replication is identified by the ability of said compound to inhibit expression of NS3, inhibit protease activity of NS3, or restore TNF-alpha sensitivity in said genetically modified mouse.
  • a pharmaceutical or dietary supplement comprising the compound identified by the method above is also an embodiment.
  • the compound is a p38 MAP kinase inhibitor or a NF-IcB inhibitor.
  • the compound is SB203580 or SB202190.
  • a method of inhibiting HCV infection comprises identifying a subject infected with HCV; and providing said subject a composition comprising a p38 MAP kinase inhibitor or a NF-IcB inhibitor.
  • the p38MAP kinase inhibitor is selected from the group consisting of SB 203580, SB 202190, KN62, U0126, PD 98059, Wortmannin, rapamycin, Ro 31-8220, Bis-1, Go 6976, UCNOl, Indirubin-3'-monoxime, kenpaullone, alsterpaullone, PPl, PP2, SU 6656, SP 600125, ML-9, PD 169316, p38 MAP Kinase inhibitor, SB202190 hydrochloride, SB 203580 hydrochloride, SB 203580 Iodo, SC68376, SKF-86002, ZM 3363772, Anti-p38/HOG-l antibody, and anti
  • the inhibitor is SB203580 or SB202190.
  • the inhibitor is a suppressor of cytokine signaling-1 (SOCSl).
  • the method further comprises measuring the inhibition of HCV in said subject. Accordingly, aspects of the invention concern the use of a p38 MAP kinase inhibitor for the preparation of a medicament for the treatment or prevention of HCV infection.
  • the p38 inhibitor is SB203580 or SB202190.
  • a use of a NF-IcB inhibitor is provided for the preparation of a medicament for the treatment, prevention, and/or ameliorating a condition associated with HCV infection.
  • the use further comprises a p38 inhibitor in the preparation of the medicament.
  • the NF-IcB inhibitor is selected from the group consisting of: Withaferin A; Sulfasalazine; PPM- 18 (2-Benzoylamino-l,4- naphthoquinone); Oridonin; Parthenolide; NF-kB Activation Inhibitor; NF-IcB SN50 (AAVALLPAVLLALLAPVQRKRQKLMP SEQ ID NO: 74), Cell-Permeable Inhibitor Peptide; NF-IcB Activation Inhibitor; NEMO-Binding Domain Binding Peptide (DRQIKIWFQNRRMKWKKTALDWSWLQTE SEQ ID NO: 75); Kamebakaurin; Acetyl-- 11-keto-b-Boswellic Acid; Andrographolide; BAY 11-7082 ((E)3-[(4- Methylphenyl)sulfonyl]-2-propen
  • the non-steroidal anti inflammatory drug is selected from the group consisting of: ibuprofen (2-(isobutylphenyl)-propionic acid); methotrexate (N-[4-(2,4 diamino 6-pteridinyl-methyl]methylamino]benzoyl)-L-glutamic acid); aspirin (acetylsalicylic acid); salicylic acid; diphenhydramine (2-(diphenylmethoxy)-NN- dimethylethylamine hydrochloride); naproxen (2-naphthaleneacetic acid, 6-methoxy-9- methyl-, sodium salt, (-)); phenylbutazone (4-butyl-l,2-diphenyl-3,5-pyrazolidinedione); sulindac-(2)-5-fuoro-2-methyl-l-[[p-(methylsulfinyl)phenyl]methylene-]-lH- indene
  • methotrexate N
  • a method of treating, inhibiting, preventing, and/or ameliorating a condition associated with HCV infection comprises identifying a subject infected with HCV and providing said subject a composition comprising a NF-IcB inhibitor. In some embodiments, the method further comprises providing said subject a second composition comprising a p38 inhibitor. In some embodiments, the NF-kB and p38 inhibitors are a same composition.
  • the NF-IcB inhibitor is selected from the group consisting of: Withaferin A; Sulfasalazine; PPM- 18 (2-Benzoylamino-l,4- naphthoquinone); Oridonin; Parthenolide; NF-kB Activation Inhibitor; NF-IcB SN50 (AAVALLPAVLLALLAPVQRKRQKLMP SEQ ID NO: 74), Cell-Permeable Inhibitor Peptide; NF-kB Activation Inhibitor; NEMO-Binding Domain Binding Peptide (DRQIKIWFQNRRMKWKKTALDWSWLQTE SEQ ID NO: 75); Kamebakaurin; Acetyl- 11-keto-b-Boswellic Acid; Andrographolide; BAY 11-7082 ((E)3-[(4- Methylphenyl)sulfonyl]-2-propenenit
  • the non-steroidal anti inflammatory drug is selected from the group consisting of: ibuprofen (2- (isobutylphenyl)-propionic acid); methotrexate (N-[4-(2,4 diamino 6-pteridinyl- methyl]methylamino]benzoyl)-L-glutamic acid); aspirin (acetylsalicylic acid); salicylic acid; diphenhydramine (2-(diphenylmethoxy)-NN-dimethylethylamine hydrochloride); naproxen (2-naphthaleneacetic acid, 6-methoxy-9-methyl-, sodium salt, (-)); phenylbutazone (4-butyl- l,2-diphenyl-3,5-pyrazolidinedione); sulindac-(2)-5-fuoro-2-methyl-l-[[p-
  • FIGURE 1 is a graph demonstrating the antibody titer in H-2 d mice against NS3 as a function of time after the first intra muscular immunization.
  • Diamonds denote antibody titer in mice immunized with NS3/4A-pVAX and squares denote antibody titer in mice immunized with NS 3 -p V AX.
  • FIGURE 2A is a bar graph demonstrating NS3-specific responses.
  • FIGURE 2B is a bar graph demonstrating NS3-specific IgG subclasses.
  • FIGURE 3 is a bar graph demonstrating CTL precursor frequency for wtNS3, wtNS3/4A and coNS3/4A.
  • FIGURE 4A is a graph demonstrating the priming, following a single immunization, of in vitro detectable CTLs in H-2b mice by gene gun immunization of the various constructs.
  • FIGURE 4B is a graph demonstrating the priming, following two immunizations, of in vitro detectable CTLs in H-2b mice by gene gun immunization of the various constructs.
  • FIGURE 5 shows the in vivo protection conferred by one gene gun immunization of NS3/4A-pVAXl (4 ⁇ g) or MSLFl -p VAXl (4 ⁇ g).
  • Mice were immunized with the respective plasmid and 14 days later the mice were challenged with an NS3/4A expressing SP2/0 cell line (approximately 10 6 cells/mouse). Tumor size was then measured through the skin daily following day 6 post-challenge and the data plotted.
  • FIGURE 6 shows the in vivo protection conferred by two gene gun immunizations of NS3/4A-pVAXl (4 ⁇ g) or MSLFl-pVAXl (4 ⁇ g).
  • Mice were immunized with the respective plasmid at weeks zero and week four and, 14 days after the last immunization, the mice were challenged with an NS3/4A expressing SP2/0 cell line (approximately 10 6 cells/mouse). Tumor size was then measured through the skin daily following day 6 post-challenge and the data plotted.
  • FIGURE 7 shows the in vivo protection conferred by three gene gun immunizations of NS3/4A-pVAXl (4 ⁇ g) or MSLFl-pVAXl (4 ⁇ g).
  • Mice were immunized with the respective plasmid at weeks zero, week four, and week eight and, 14 days after the last immunization, the mice were challenged with an NS3/4A expressing SP2/0 cell line (approximately 10 6 cells/mouse). Tumor size was then measured through the skin daily following day 6 post-challenge and the data plotted.
  • FIGURE 8A is a graph demonstrating the percentage of specific CTL-mediated lysis of SP2/0 target cells as a function of the effector to target ratio.
  • Phosphate Buffered Saline (PBS) was used as a control immunogen.
  • FIGURE 8B is a graph demonstrating the percentage specific CTL-mediated lysis of SP2/0 target cells as a function of the effector to target ratio. Plasmid NS3/4A-pVAX was used as the immunogen.
  • FIGURE 9A is a graph demonstrating the specificity of protection for the constructs.
  • FIGURE 9B is a graph demonstrating the in vivo functional effector cell population.
  • FIGURE 1OA is a graph demonstrating the ability of an immunogen to prime HCV NS3/4A-specific tumor inhibiting responses after a single immunization. As a negative control the mean data from the group immunized with the empty pVAX plasmid were plotted in the graph.
  • FIGURE 1OB is a graph demonstrating the ability of an immunogen to prime HCV NS3/4A-specif ⁇ c tumor inhibiting responses after a single immunization. As a negative control the mean data from the group immunized with the empty pVAX plasmid were plotted in the graph.
  • FIGURE 1OC is a graph demonstrating the ability of an immunogen to prime HCV NS3/4A-specific tumor inhibiting responses after a single immunization. As a negative control the mean data from the group immunized with the empty pVAX plasmid were plotted in the graph.
  • FIGURE 1OD is a graph demonstrating the ability of an immunogen to prime HCV NS3/4A-specific tumor inhibiting responses after a single immunization. As a negative control the mean data from the group immunized with the empty pVAX plasmid were plotted in the graph.
  • FIGURE 1OE is a graph demonstrating the ability of an immunogen to prime HCV NS3/4A-specific tumor inhibiting responses after a single immunization. As a negative control the mean data from the group immunized with the empty pVAX plasmid were plotted in the graph.
  • FIGURE 1OF is a graph demonstrating the ability of an immunogen to prime HCV NS3/4A-specific tumor inhibiting responses after a single immunization. As a negative control the mean data from the group immunized with the empty pVAX plasmid were plotted in the graph.
  • FIGURE 1OG is a graph demonstrating the ability of an immunogen to prime HCV NS3/4A-specific tumor inhibiting responses after a single immunization. As a negative control the mean data from the group immunized with the empty pVAX plasmid were plotted in the graph.
  • FIGURE 1OH is a graph demonstrating the ability of an immunogen to prime HCV NS3/4A-specif ⁇ c tumor inhibiting responses after a single immunization. As a negative control the mean data from the group immunized with the empty pVAX plasmid were plotted in the graph.
  • FIGURE HA is a graph of the efficiency of different plasmids in priming tumor- inhibiting immune responses with a single monthly immunization.
  • FIGURE HB is a graph of the efficiency of different plasmids in priming tumor- inhibiting immune responses with two monthly immunizations.
  • FIGURE HC is a graph of the efficiency of different plasmids in priming tumor- inhibiting immune responses with three monthly immunizations.
  • FIGURE 12 is a graph demonstrating the effect of therapeutic vaccination with the coNS3/4A plasmid using a gene gun.
  • FIGURE 13A is a sequence displaying key residues and relevant binding areas of the NS3 protein.
  • FIGURE 13B is a sequence displaying key residues and relevant binding areas of the NS4A protein.
  • the arrow shows the NS3/4A cleavage site (i.e., TJ.STW).
  • FIGURE 14A is a schematic representation of the linearized fragment (pMUP- NS3/4A) used for microinjection to produce the transgenic mice.
  • FIGURE 14B is a schematic representation of the linearized fragment of a PADSI construct (pMUP-NS3 -cleavage site-secretory signal-signal molecule) used for the detection of protease inhibitors.
  • FIGURE 14C is a schematic representation of the linearized fragment of an alternative PADSI construct (pMUP-NS3 -cleavage site-secretory signal-signal molecule) used for the detection of protease inhibitors.
  • FIGURE 14D is a diagram of the sequences of one embodiment of FIGURE 14C
  • FIGURE 15 is a chart that lists the NS3 protein expression levels in male transgenic mice.
  • FIGURE 16A is a graph showing the weight comparison of female NS3/4A- transgenic- and non-trans genie mice.
  • FIGURE 16B is a graph showing the weight comparison of male NS3/4A-transgenic- and non-transgenic mice.
  • FIGURE 17A is a bar graph comparing the intra hepatic immune cells of wild-type mice and NS3/4A transgenic mice.
  • FIGURE 17B is a bar graph comparing the various subtypes of hepatic DCs in wild- type and NS3/4A transgenic mice.
  • FIGURE 18 A is a graph showing the extent of CCU-induced liver damage in wild- type and NS3/4A transgenic mice.
  • FIGURE 18B is a graph showing the extent of LPS-induced liver damage in wild- type and NS3/4A transgenic mice.
  • FIGURE 18C is a graph showing the extent of FAS-induced liver damage in wild- type and NS3/4A transgenic mice.
  • FIGURE 18D is a graph showing the extent of TNF-alpha-induced liver damage in wild-type and NS3/4A transgenic mice.
  • FIGURE 18E shows the results of a Western blot that compares the expression levels of various proteins in wild-type mice and NS3/4A transgenic mice following treatment with LPS.
  • FIGURE 18F shows the results of a Western blot that compares the expression levels of various proteins in wild-type mice and NS3/4A transgenic mice following treatment with alpha-IFN.
  • FIGURE 18G shows the results of a Western blot that compares the expression levels of various proteins in wild-type mice and NS3/4A transgenic mice following treatment with gamma-IFN.
  • FIGURE 19A is a graph showing the percent survival of wild-type mice andNS3/4A transgenic mice after administration of TNF-alpha .
  • FIGURE 19B is a graph showing the percent survival of NS3/4A transgenic mice after administration of TNF-alpha in the presence or absence of a p38 MAP kinase inhibitor.
  • FIGURE 19C is a graph showing the percent survival of wild-type mice after administration of TNF-alpha in the presence or absence of a p38 Map kinase inhibitor.
  • FIGURE 20 is a flow chart showing various pathways involved with FAS, TNF- alpha, LPS, and IFN-alpha signal transduction. Protein-protein interactions are shown using arrows (denoting activating interactions) or bars (denoting inhibiting interactions).
  • FIGURE 21 A is a depiction of a western blot comparing the levels of NF-IcB in wild type mice and NS3/4A transgenic mice.
  • FIGURE 2 IB is a depiction of a western blot comparing the levels of NF-kB and caspase-3 in the cytoplasm and nucleus of liver cells between NS3/4A-Tg and wild-type mice at various time points following the administration of TNF-a/D-Gal treatment. Levels of clkB-a were also examined.
  • FIGURE 21C is a depiction of a western blot comparing cIAP and TRAF2 and levels between NS3/4A-Tg and non-Tg mice at various time points following the administration of TNF-a/D-Gal treatment.
  • FIGURE 2 ID depicts TUNEL staining of hepatocytes from a NS3/4A-Tg mouse and non-Tg mouse following treatment with TNF-a/D-Gal. The staining identifies those cells from each mouse with fragmented DNA.
  • FIGURE 22A is a graph showing the effect of an adjuvant with 100 micrograms of coNS3/4A.
  • FIGURE 22B is a graph showing the effect of an adjuvant with 10 micrograms of coNS3/4A.
  • FIGURE 22C is a graph showing the effect of an adjuvant with 1 microgram of coNS3/4A.
  • mice comprising an exogenous nucleic acid construct that comprises a hepatitis C virus (HCV) nonstructural protein 3 (NS3) and nonstructural protein 4A (NS4A) have been created.
  • HCV hepatitis C virus
  • NS3 and/or NS4A proteins in the liver (e.g., 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2,
  • the HCV NS3/4A transgenic mice created, as described herein, also have a reduced sensitivity or an increased resistance to TNF-alpha, as compared to wild-type mice of the same variety that have not been genetically modified to contain NS3/4A. That is, some of the NS3/4A- containing genetically modified mice survive a lethal dose of TNF-alpha but said transgenic mice revert to a TNF-alpha sensitive phenotype in the presence of a p38 MAP kinase inhibitor, such as SB203580 or SB202190.
  • a p38 MAP kinase inhibitor such as SB203580 or SB202190.
  • some of the genetically modified mice created as described herein which have a reduced sensitivity or increased resistance to TNF- alpha, can be induced to become as sensitive to TNF-alpha as a wild-type mouse of the same variety by contacting the genetically modified mouse with an inhibitor of p38 MAP kinase (or an inhibitor of NF-kB).
  • the genetically modified mice that express NS3/4A are used as models for HCV infection and provide an in vivo system for the identification of compounds that inhibit HCV replication and/or HCV infection.
  • signal molecules e.g., luciferase, lac z, or green fluorescent protein
  • secretory signals e.g., IG kappa
  • the genetically modified mice, created as described herein are contacted with a compound and the expression of NS3, NS3 protease activity, or TNF-alpha sensitivity is analyzed.
  • HCV replication e.g., inhibitors of NS3 expression or protease activity or compounds that restore TNF-alpha sensitivity
  • identified compounds e.g., p38 MAP kinase inhibitors such as, SB203580 or SB202190 or NF-kB inhibitors
  • pharmaceuticals and/or dietary supplements which can be provided to HCV infected individuals or individuals at risk of becoming infected with HCV.
  • aspects of the invention described herein concern the use of p38 MAP kinase inhibitors such as, SB203580 or SB202190, or NF-kB inhibitors to prepare a medicament for the treatment and/or prevention of HCV infection and methods of using said medicaments in HCV treatment or prophylactic methods.
  • p38 MAP kinase inhibitors such as, SB203580 or SB202190, or NF-kB inhibitors to prepare a medicament for the treatment and/or prevention of HCV infection and methods of using said medicaments in HCV treatment or prophylactic methods.
  • NF-kB inhibitors NF-kB inhibitors
  • a new isolate of HCV was identified and a nucleic acid encoding NS3/4A was cloned and sequenced (SEQ. ID. NO. 1). (See EXAMPLE 1).
  • a Genebank search revealed that the cloned sequence had the greatest homology to HCV sequences but was only 93% homologous to the closest HCV relative (accession no. AJ 278830).
  • a truncated mutant of the novel NS3/4A peptide and NS3/4A mutants, which lack a proteolytic cleavage site, (as well as corresponding nucleic acids) were also created.
  • mice immunized with the NS3/4A enhanced mRNA amplification construct were found to prime NS3-specific CTLs more effectively and exhibit better in vivo tumor inhibiting immune responses than mice immunized with wild-type NS3/4A containing constructs.
  • the NS3/4A peptide (SEQ. ID. NO.: 36) encoded by the codon-optimized nucleic acid sequence was 98% homologous to HCV-I and contained a total of 15 different amino acids.
  • the codon optimized nucleic acid (MSLFl or coNS3/4A) (SEQ. ID. NO.: 35) was found to be more efficiently translated in vitro than the native NS3/4A and mice immunized with the coNS3/4 containing construct generated significantly more NS3/4A specific antibodies than mice immunized with a wild-type NS3/4A containing construct.
  • mice immunized with the coNS3/4A containing construct were found to prime NS3-specific CTLs more effectively and exhibit better in vivo tumor inhibiting immune responses than mice immunized with wild-type NS3/4A containing constructs. ⁇ See EXAMPLES 3-16).
  • nucleic acid embodiments include nucleotides encoding the HCV peptides described herein (SEQ. ID. NOs.: 2-11 or SEQ. ID. NO.: 36) or a fragment thereof ⁇ e.g., SEQ. ID. NOs.: 14 and 15) containing any number of consecutive amino acids between at least 25-100 ⁇ e.g., 25, 35, 45, 55, 65, 75, 85, 95, or 100 amino acids in length).
  • Some embodiments for example include genomic DNA, RNA, and cDNA encoding these HCV peptides.
  • the HCV nucleotide embodiments not only include the DNA sequences shown in the sequence listing ⁇ e.g., SEQ. ID. NO.: 1 or SEQ. ID.
  • nucleotide sequences encoding the amino acid sequences shown in the sequence listing ⁇ e.g., SEQ. ID. NOs.: 2-11 or SEQ. ID. NO.: 36) and any nucleotide sequence that hybridizes to the DNA sequences shown in the sequence listing under stringent conditions ⁇ e.g., hybridization to filter-bound DNA in 0.5 M NaHPO 4 , 7.0% sodium dodecyl sulfate (SDS), 1 mM EDTA at 50°C) and washing in 0.2 X SSC/0.2% SDS at 5O 0 C and any nucleotide sequence that hybridizes to the DNA sequences that encode an amino acid sequence provided in the sequence listing (SEQ. ID.
  • nucleic acid embodiments of the invention also include fragments, modifications, derivatives, and variants of the sequences described above. Desired embodiments, for example, include nucleic acids having at least 100 consecutive nucleotides of one of the novel HCV sequences or a sequence complementary thereto and preferred fragments include at least 200 consecutive nucleotides of a nucleic acid encoding the NS3/4A molecule of SEQ. ID. NO.: 2 or SEQ. ID. NO.: 36 or a mutant NS3/4A molecule of SEQ. ID. NOs.: 3- 13 or a sequence complementary thereto.
  • nucleic acid embodiments described herein can have any number of consecutive nucleotides between about 30 to approximately 2112 consecutive nucleotides of SEQ. ID. NO.: 1 or SEQ. ID. NO.: 35.
  • Some DNA fragments include nucleic acids having at least, more than, or equal to 30, 30-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500 - 600, 600-700, 700-800, 800-900, 900-1000, 1000-1500, 1500-2079, or 1500- 2112 consecutive nucleotides of SEQ. ID. NO.: 1 or SEQ. ID. NO.: 35 or a complement thereof.
  • nucleic acid embodiments can also be altered by substitution, addition, or deletion so long as the alteration does not significantly affect the structure or function (e.g., ability to serve as an immunogen) of the HCV nucleic acid.
  • Due to the degeneracy of nucleotide coding sequences for example, other DNA sequences that encode substantially the same HCV amino acid sequence as depicted in SEQ. ID. NOs.: 2-13 or SEQ. ID. NO.: 36 can be used in some embodiments. These include, but are not limited to, nucleic acid sequences encoding all or portions of HCV peptides (SEQ. ID.
  • nucleic acid embodiments of the invention are said to be comprising, consisting of, or consisting essentially of nucleic acids encoding any one of SEQ. ID. NOs.: 2-27 or SEQ. ID. NO.: 36 in light of the modifications above.
  • probes that complement these molecules can be designed and manufactured by oligonucleotide synthesis.
  • Desirable probes comprise a nucleic acid sequence of (SEQ. ID. NO.: 1) that is unique to this HCV isolate. These probes can be used to screen cDNA from patients so as to isolate natural sources of HCV, some of which may be novel HCV sequences in themselves. Screening can be by filter hybridization or by PCR, for example.
  • the labeled probe preferably contains at least 15-30 base pairs of the nucleic acid sequence of (SEQ. ID. NO.: 1) that is unique to this NS3/4A peptide.
  • the hybridization washing conditions used are preferably of a medium to high stringency.
  • the hybridization can be performed in 0.5M NaHPO 4 , 7.0% sodium dodecyl sulfate (SDS), 1 mM EDTA at 42 0 C overnight and washing can be performed in 0.2X SSC/0.2% SDS at 42°C.
  • SDS sodium dodecyl sulfate
  • washing can be performed in 0.2X SSC/0.2% SDS at 42°C.
  • HCV nucleic acids can also be isolated from patients infected with HCV using the nucleic acids described herein. ⁇ See also EXAMPLE 1). Accordingly, RNA obtained from a patient infected with HCV is reverse transcribed and the resultant cDNA is amplified using PCR or another amplification technique.
  • the primers are preferably obtained from the NS3/4A sequence (SEQ. ID. NO.: 1).
  • RT-PCR Reverse Transcriptase Asymmetric Gap Ligase Chain Reaction
  • RT-AGLCR Reverse Transcriptase Asymmetric Gap Ligase Chain Reaction
  • RNA is isolated, following standard procedures.
  • a reverse transcription reaction is performed on the RNA using an oligonucleotide primer specific for the most 5' end of the amplified fragment as a primer of first strand synthesis.
  • the resulting RNA/DNA hybrid is then "tailed" with guanines using a standard terminal transferase reaction.
  • the hybrid is then digested with RNAse H, and second strand synthesis is primed with a poly-C primer.
  • primers on either side of the sequence to be amplified are added to a suitably prepared nucleic acid sample along with dNTPs and a thermostable polymerase, such as Tag polymerase, Pfu polymerase, or Vent polymerase.
  • a thermostable polymerase such as Tag polymerase, Pfu polymerase, or Vent polymerase.
  • the nucleic acid in the sample is denatured and the primers are specifically hybridized to complementary nucleic acid sequences in the sample.
  • the hybridized primers are then extended. Thereafter, another cycle of denaturation, hybridization, and extension is initiated. The cycles are repeated multiple times to produce an amplified fragment containing the nucleic acid sequence between the primer sites.
  • PCR has further been described in several patents including US Patents 4,683,195, 4,683,202 and 4,965,188, all of which are expressly incorporated by reference in their entireties.
  • the primers are selected to be substantially complementary to a portion of the nucleic acid sequence of (SEQ. ID. NO.: 1) that is unique to this NS3/4A molecule, thereby allowing the sequences between the primers to be amplified.
  • primers can be any number between at least 16-20, 20-25, or 25-30 nucleotides in length.
  • Tm melting temperature
  • the formation of stable hybrids depends on the melting temperature (Tm) of the DNA.
  • Tm depends on the length of the primer, the ionic strength of the solution and the G+C content. The higher the G+C content of the primer, the higher is the melting temperature because G:C pairs are held by three H bonds whereas A:T pairs have only two.
  • the G+C content of the amplification primers described herein preferably range between 10% and 75 %, more preferably between 35% and 60%, and most preferably between 40% and 55 %.
  • the appropriate length for primers under a particular set of assay conditions can be empirically determined by one of skill in the art.
  • amplified segments carrying nucleic acid sequence encoding HCV peptides can range in size from at least about 25 bp to the entire length of the HCV genome. Amplification fragments from 25-1000 bp are typical, fragments from 50-1000 bp are preferred and fragments from 100-600 bp are highly preferred. It will be appreciated that amplification primers can be of any sequence that allows for specific amplification of the NS3/4A region and can, for example, include modifications such as restriction sites to facilitate cloning.
  • the PCR product can be subcloned and sequenced to ensure that the amplified sequences represent the sequences of an HCV peptide.
  • the PCR fragment can then be used to isolate a full length cDNA clone by a variety of methods or can be used to create the exogenous nucleic acid constructs described herein.
  • the amplified fragment can be labeled and used to screen a cDNA library, such as a bacteriophage cDNA library.
  • the labeled fragment can be used to isolate genomic clones via the screening of a genomic library.
  • an expression library can be constructed utilizing cDNA synthesized from, for example, RNA isolated from an infected patient. In this manner, HCV gene products can be isolated using standard antibody screening techniques in conjunction with antibodies raised against the HCV gene product.
  • Embodiments of the invention also include (a) DNA vectors that contain any of the foregoing nucleic acid sequence and/or their complements (i.e., antisense); (b) DNA expression vectors that contain any of the foregoing nucleic acid sequences operatively associated with a regulatory element that directs the expression of the nucleic acid; and (c) genetically engineered host cells that contain any of the foregoing nucleic acid sequences operatively associated with a regulatory element that directs the expression of the coding sequences in the host cell.
  • These recombinant constructs are capable of replicating autonomously in a host cell. Alternatively, the recombinant constructs can become integrated into the chromosomal DNA of a host cell.
  • Such recombinant polynucleotides typically comprise an HCV genomic or cDNA polynucleotide of semi-synthetic or synthetic origin by virtue of human manipulation. Therefore, recombinant nucleic acids comprising these sequences and complements thereof that are not naturally occurring are provided.
  • nucleic acids encoding an HCV peptide or nucleic acids having sequences that complement an HCV gene as they appear in nature can be employed, they will often be altered, e.g., by deletion, substitution, or insertion, and can be accompanied by sequence not present in humans.
  • regulatory elements include, but are not limited to, inducible and non-inducible promoters, enhancers, operators and other elements known to those skilled in the art that drive and regulate expression.
  • Such regulatory elements include, but are not limited to, MUP, the cytomegalovirus hCMV immediate early gene, the early or late promoters of SV40 adenovirus, the lac system, the trp system, the TAC system, the TRC system, the major operator and promoter regions of phage A, the control regions of fd coat protein, the promoter for 3-phosphoglycerate kinase, the promoters of acid phosphatase, and the promoters of the yeast-mating factors.
  • HCV peptide-encoding nucleic acid sequences and their complementary sequences can be engineered so as to modify their processing or expression.
  • the HCV nucleic acids described herein can be combined with a promoter sequence and/or ribosome binding site, or a signal sequence can be inserted upstream of HCV peptide-encoding sequences so as to permit secretion of the peptide and thereby facilitate harvesting or bioavailability.
  • a given HCV nucleic acid can be mutated in vitro or in vivo, to create and/or destroy translation, initiation, and/or termination sequences, or to create variations in coding regions and/or form new restriction sites or destroy preexisting ones, or to facilitate further in vitro modification.
  • Any technique for mutagenesis known in the art can be used, including but not limited to, in vitro site-directed mutagenesis. (Hutchinson et al., J. Biol. Chem., 253:6551 (1978)).
  • the nucleic acids encoding the HCV peptides, described above, can be manipulated using conventional techniques in molecular biology so as to create recombinant constructs that express the HCV peptides.
  • nucleic acids encoding other proteins or domains of other proteins can be joined to nucleic acids encoding an HCV peptide so as to create a fusion protein.
  • Nucleotides encoding fusion proteins can include, but are not limited to, a full length NS3/4A sequence (SEQ. ID. NO.: 2 or SEQ. ID. NO.: 36), mutant NS3/4A sequences (e.g., SEQ. ID. NOs.: 3-11) or a peptide fragment of an NS3/4A sequence fused to an unrelated protein or peptide, such as for example, polyhistidine, hemagglutinin, an enzyme, fluorescent protein, or luminescent protein, as discussed below.
  • the embodied HCV peptides or derivatives thereof include but are not limited to, those containing as a primary amino acid sequence all of the amino acid sequence substantially as depicted in the Sequence Listing (SEQ. ID. NOs.: 2-11 and SEQ. ID. NO.: 36) and fragments of SEQ. ID. NOs.: 2-11 and SEQ. ID. NO.: 36 that are at least four amino acids in length (e.g., SEQ. ID. NOs.: 14-16) including altered sequences in which functionally equivalent amino acid residues are substituted for residues within the sequence resulting in a silent change.
  • HCV peptides can be, for example, at least about 30-704 amino acids in length (e.g., any number between 25-30, 30-40, 40-50, 50-100, 100-150, 150- 250, 250-500 or 500-704 amino acids in length).
  • Preferred peptides include a functional NS3 protease.
  • Embodiments also include HCV peptides that are substantially identical to those described above. That is, HCV peptides that have one or more amino acid residues within SEQ. ID. NOs.: 2-11 and SEQ. ID. NO.: 36 and fragments thereof that are substituted by another amino acid of a similar polarity that acts as a functional equivalent, resulting in a silent alteration. Further, the HCV peptides can have one or more amino acid residues fused to SEQ. ID. NOs.: 2-11 and SEQ. ID. NO.: 36 or a fragment thereof so long as the fusion does not significantly alter the structure or function (e.g., immunogenic properties or protease activity) of the HCV peptide.
  • HCV peptides that are substantially identical to those described above. That is, HCV peptides that have one or more amino acid residues within SEQ. ID. NOs.: 2-11 and SEQ. ID. NO.: 36 and fragments thereof that are substituted by another amino acid of a
  • Substitutes for an amino acid within the sequence can be selected from other members of the class to which the amino acid belongs.
  • the non-polar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine.
  • the polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine.
  • the positively charged (basic) amino acids include arginine, lysine, and histidine.
  • the negatively charged (acidic) amino acids include aspartic acid and glutamic acid.
  • the aromatic amino acids include phenylalanine, tryptophan, and tyrosine. Accordingly, the peptide embodiments of the invention are said to be consisting essentially of SEQ. ID. NOs.: 2-27 and SEQ. ID. NO.: 36 in light of the modifications described above.
  • HCV peptides described herein can be prepared by chemical synthesis methods (such as solid phase peptide synthesis) using techniques known in the art such as those set forth by Merrifield et al., J. Am. Chem. Soc. 85:2149 (1964), Houghten et al., Proc. Natl. Acad. ScL USA, 82:51:32 (1985), Stewart and Young (Solid phase peptide synthesis. Pierce Chem Co., Rockford, IL (1984), and Creighton, 1983, Proteins: Structures and Molecular Principles, W. H. Freeman & Co., N.Y. Such polypeptides can be synthesized with or without a methionine on the amino terminus. Chemically synthesized HCV peptides can be oxidized using methods set forth in these references to form disulfide bridges.
  • HCV peptides described herein can be chemically synthesized, it can be more effective to produce these polypeptides by recombinant DNA technology.
  • Such methods can be used to construct expression vectors containing the HCV nucleotide sequences described above, for example, and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination.
  • RNA capable of encoding an HCV nucleotide sequence can be chemically synthesized using, for example, synthesizers. See, for example, the techniques described in Oligonucleotide Synthesis, 1984, Gait, M. J. ed., IRL Press, Oxford.
  • HCV peptides e.g., totipotent cells
  • cell lines that have been engineered to express the embodied HCV peptides.
  • some cells are made to express the HCV peptides of SEQ. ID. NOs.: 2-11 and SEQ. BD. NO.: 36 or fragments of these molecules (e.g., SEQ. ID. NOs.: 14-26), preferably fragments that contain a functional NS3 protease.
  • Suitable expression systems include, but are not limited to, microorganisms such as bacteria (e.g., E. coli or B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing HCV nucleotide sequences; yeast (e.g., Saccharomyces, Pichi ⁇ ) transformed with recombinant yeast expression vectors containing the HCV nucleotide sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing the HCV sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing HCV sequences; or mammalian cell systems (e.g., E. coli or B. subtilis) transformed with recombinant bacter
  • a number of expression vectors can be advantageously selected depending upon the use intended for the HCV gene product being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of pharmaceutical compositions of HCV peptide or for raising antibodies to the HCV peptide, for example, vectors which direct the expression of high levels of fusion protein products that are readily purified can be desirable.
  • vectors include, but are not limited, to the E.
  • coli expression vector pUR278 (Ruther et al., EMBO J., 2: 1791 (1983), in which the HCV coding sequence can be ligated individually into the vector in frame with the lacZ coding region so that a fusion protein is produced; pIN vectors (Inouye & Inouye, Nucleic Acids Res., 13:3101-3109 (1985); Van Heeke & Schuster, J. Biol. Chem., 264:5503-5509 (1989)); and the like.
  • the pGEX vectors can also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST).
  • fusion proteins are soluble and can be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione.
  • the PGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety.
  • Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes.
  • the virus grows in Spodoptera frugiperda cells.
  • the HCV coding sequence can be cloned individually into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter). Successful insertion of an HCV gene coding sequence will result in inactivation of the polyhedrin gene and production of non-occluded recombinant virus, ⁇ i.e., virus lacking the proteinaceous coat coded for by the polyhedrin gene).
  • the HCV nucleotide sequence of interest can be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite leader sequence.
  • This chimeric gene can then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g., region El or E3) will result in a recombinant virus that is viable and capable of expressing the HCV gene product in infected hosts.
  • a non-essential region of the viral genome e.g., region El or E3
  • Specific initiation signals can also be required for efficient translation of inserted HCV nucleotide sequences. These signals include the ATG initiation codon and adjacent sequences.
  • exogenous translational control signals including, perhaps, the ATG initiation codon
  • the initiation codon can be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert.
  • exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc. (See Bittner et al., Methods in Enzymol, 153:516-544 (1987)).
  • a host cell strain can be chosen, which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products are important for the function of the protein.
  • Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed.
  • eukaryotic host cells that possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product can be used.
  • mammalian host cells include, but are not limited to, CHO 3 VERO, BHK, HeLa, COS, MDCK, 293, 3T3, and WI38.
  • HCV peptides described above can be engineered.
  • host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker.
  • appropriate expression control elements e.g., promoter, enhancer sequences, transcription terminators, polyadenylation sites, etc.
  • engineered cells are allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media.
  • the selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn are cloned and expanded into cell lines. This method is advantageously used to engineer cell lines which express the HCV gene product.
  • a number of selection systems can be used, including but not limited to the herpes simplex virus thymidine kinase (Wigler, et al., Cell 11:223 (1977), hypoxanthine-guanine phosphoribosyltransferase (Szybalska & Szybalsld, Proc. Natl. Acad. ScL USA 48:2026 (1962)), and adenine phosphoribosyltransferase (Lowy, et al., Cell 22:817 (1980)) genes can be employed in tk ⁇ , hgprf or aprf cells, respectively.
  • antimetabolite resistance can be used as the basis of selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler, et al., Proc. Natl. Acad. Sd. USA 77:3567 (1980); O'Hare, et al., Proc. Natl. Acad. Sd. USA 78:1527 (1981)); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, Proc. Natl. Acad. Sci. USA 78:2072 (1981)); neo, which confers resistance to the aminoglycoside G-418 (Colberre-Garapin, et al., J. MoI. Biol. 150:1 (1981)); and hygro, which confers resistance to hygromycin (Santerre, et al., Gene 30:147 (1984)).
  • sequences, constructs, vectors, clones, and other materials comprising the embodied HCV nucleic acids and peptides can be in enriched or isolated form.
  • enriched means that the concentration of the material is many times its natural concentration, for example, at least about 2, 5, 10, 100, or 1000 times its natural concentration, advantageously 0.01%, by weight, preferably at least about 0.1% by weight.
  • Enriched preparations from about 0.5% or more, for example, 1%, 5%, 10%, and 20% by weight are also contemplated.
  • isolated requires that the material be removed from its original environment (e.g., the natural environment if it is naturally occurring).
  • a naturally-occurring polynucleotide present in a living animal is not isolated, but the same polynucleotide, separated from some or all of the coexisting materials in the natural system, is isolated. It is also advantageous that the sequences be in purified form.
  • the term "purified” does not require absolute purity; rather, it is intended as a relative definition. Isolated proteins have been conventionally purified to electrophoretic homogeneity by Coomassie staining, for example. Purification of starting material or natural material to at least one order of magnitude, preferably two or three orders, and more preferably four or five orders of magnitude is expressly contemplated.
  • Embodiments of the invention also include NS3/4A fusion proteins or nucleic acids encoding these molecules. For instance, production and purification of recombinant protein may be facilitated by the addition of auxiliary amino acids to form a "tag".
  • tags include, but are not limited to, His-6, Flag, Myc and GST. The tags may be added to the C-terminus, N-terminus, or within the NS3/4A amino acid sequence.
  • Further embodiments include NS3/4A fusion proteins with amino or carboxy terminal truncations, or internal deletions, or with additional polypeptide sequences added to the amino or carboxy terminal ends, or added internally.
  • NS3/4A fusion proteins or truncated or mutated versions thereof, where the residues of the NS3/4A proteolytic cleavage site have been substituted.
  • substitutions include, but are not limited to, sequences where the Pl' site is a Ser, GIy, or Pro, or the Pl position is an Arg, or where the P8 to P4' sequence is Ser-Ala- Asp-Leu-Glu-Val-Val-Thr-Ser-Thr-Trp-Val (SEQ. ID. NO.: 15).
  • a fusion protein containing NS3/4A, as described herein, can be readily purified by utilizing an antibody specific for the fusion protein being expressed.
  • a system described by Janknecht et al. allows for the ready purification of non-denatured fusion proteins expressed in human cell lines. (Janknecht, et al., Proc. Natl. Acad. Sd. USA 88: 8972-8976 (1991)).
  • the gene of interest is subcloned into a vaccinia recombination plasmid such that the gene's open reading frame is translationally fused to an amino-terminal tag consisting of six histidine residues. Extracts from cells infected with recombinant vaccinia virus are loaded onto Ni 2+ nitriloacetic acid-agarose columns and histidine-tagged proteins are selectively eluted with imidazole-containing buffers.
  • More embodiments concern an immunogen comprising the NS3/4A fusion protein, or a truncated, mutated, or modified version thereof, capable of eliciting an enhanced immune response against NS3.
  • the immunogen can be provided in a substantially purified form, which means that the immunogen has been rendered substantially free of other proteins, lipids, carbohydrates or other compounds with which it naturally associates.
  • Some embodiments comprise at least one of the HCV nucleic acids or HCV peptides (e.g., SEQ. ID. NOs.: 1-27, 35, or 36) joined to a support.
  • these supports are manufactured so as to create a multimeric agent.
  • These multimeric agents provide the HCV peptide or nucleic acid in such a form or in such a way that a sufficient affinity to the molecule is achieved.
  • a multimeric agent having an HCV nucleic acid or peptide can be obtained by joining the desired molecule to a macromolecular support.
  • a “support” can be a termed a carrier, a protein, a resin, a cell membrane, a capsid or portion thereof, or any macromolecular structure used to join or immobilize such molecules.
  • Solid supports include, but are not limited to, the walls of wells of a reaction tray, test tubes, polystyrene beads, magnetic beads, nitrocellulose strips, membranes, microparticles such as latex particles, animal cells, Duracyte®, artificial cells, and others.
  • an HCV nucleic acid or peptide can also be joined to inorganic carriers, such as silicon oxide material (e.g., silica gel, zeolite, diatomaceous earth or aminated glass) by, for example, a covalent linkage through a hydroxy, carboxy or amino group and a reactive group on the carrier.
  • silicon oxide material e.g., silica gel, zeolite, diatomaceous earth or aminated glass
  • the macromolecular support has a hydrophobic surface that interacts with a portion of the HCV nucleic acid or peptide by a hydrophobic non- covalent interaction.
  • the hydrophobic surface of the support is a polymer such as plastic or any other polymer in which hydrophobic groups have been linked such as polystyrene, polyethylene or polyvinyl.
  • HCV nucleic acid or peptide can be covalently bound to carriers including proteins and oligo/polysaccarides (e.g. cellulose, starch, glycogen, chitosane, the gal antigen, Gal alpha (1,3) Gal beta, or animated sepharose).
  • proteins and oligo/polysaccarides e.g. cellulose, starch, glycogen, chitosane, the gal antigen, Gal alpha (1,3) Gal beta, or animated sepharose.
  • a reactive group on the molecule such as a hydroxy or an amino group, is used to join to a reactive group on the carrier so as to create the covalent bond.
  • Additional multimeric agents comprise a support that has other reactive groups that are chemically activated so as to attach the HCV nucleic acid or peptide.
  • cyanogen bromide activated matrices epoxy activated matrices, thio and thiopropyl gels, nitrophenyl chloroformate and N-hydroxy succinimide chlorformate linkages, or oxirane acrylic supports are used. (Sigma).
  • Carriers for use in the body are desirably physiological, non-toxic and preferably, non-immunoresponsive.
  • Suitable carriers for use in the body include poly-L-lysine, poly-D, L-alanine, liposomes, capsids that display the desired HCV peptide or nucleic acid, and Chromosorb ® (Johns-Manville Products, Denver Co.).
  • Ligand conjugated Chromosorb ® (Synsorb-Pk) has been tested in humans for the prevention of hemolytic-uremic syndrome and was reported as not presenting adverse reactions. (Armstrong et al. J. Infectious Diseases 171:1042-1045 (1995)).
  • a naked carrier i.e., lacking an attached HCV nucleic acid or peptide
  • a "prodrug-type” therapy is envisioned in which the naked carrier is administered separately from the HCV nucleic acid or peptide and, once both are in the body of the organism, the carrier and the HCV nucleic acid or peptide are assembled into a multimeric complex.
  • linkers e.g., " ⁇ linkers” engineered to resemble the flexible regions of ⁇ phage
  • linkers e.g., " ⁇ linkers” engineered to resemble the flexible regions of ⁇ phage
  • the determination of an appropriate length of linker that allows for an optimal cellular response or lack thereof, can be determined by screening the HCV nucleic acid or peptide with varying linkers in the assays detailed in the present disclosure.
  • a composite support comprising more than one type of HCV nucleic acid or peptide is also envisioned.
  • a "composite support” can be a carrier, a resin, or any macromolecular structure used to attach or immobilize two or more different HCV nucleic acids or peptides.
  • linkers such as ⁇ linkers
  • the determination of an appropriate length of linker that allows for an optimal cellular response or lack thereof, can be determined by screening the HCV nucleic acid or peptide with varying linkers in the assays detailed in the present disclosure.
  • the multimeric and composite supports discussed above can have attached multimerized HCV nucleic acids or peptides so as to create a "multimerized- multimeric support" and a “multimerized-composite support", respectively.
  • a multimerized ligand can, for example, be obtained by coupling two or more HCV nucleic acids or peptides in tandem using conventional techniques in molecular biology.
  • the multimerized form of the HCV nucleic acid or peptide can be advantageous for many applications because of the ability to obtain an agent with a higher affinity, for example.
  • linkers or spacers, such as flexible ⁇ linkers, between the individual domains that make-up the multimerized agent can also be advantageous for some embodiments.
  • ⁇ linkers of an appropriate length between protein binding domains can encourage greater flexibility in the molecule and can overcome steric hindrance.
  • the insertion of linkers between the multimerized HCV nucleic acid or peptide and the support can encourage greater flexibility and limit steric hindrance presented by the support.
  • the determination of an appropriate length of linker can be determined by screening the HCV nucleic acids or peptides in the assays detailed in this disclosure.
  • Embodiments also include vaccine compositions and immunogen preparations comprising the NS3/4A nucleic acids or peptides as described herein and, optionally, an adjuvant (e.g., ribavirin).
  • the constructs described herein are useful for the identification of HCV protease inhibitors. There are many different methods by which one can detect the cleavage or absence of cleavage of the NS3/4A protein, and thereby, determine whether or not any given compound possesses the abiilty to inhibit the NS3 protease.
  • the NS3/4A construct contains a secretory sequence connected to a signal molecule (detectable marker, indicator, or other similar item), and thus is refered to as a PADSI (protease activity dedependent secreted indicator) construct.
  • the indicator is a secreted indicator whose level of secretion is dependent upon protease activity.
  • protease inhibitor-based constructs are directed to NS3 proteases, NS3/4A or sections or derivatives thereof and, optionally, may be associated with detectable markers and secretory signals.
  • the activity of protease inhibitors can be monitored through the relative presence or absence of the detectable marker outside a cell harboring the construct (e.g., in the blood of a transgenic organism), and optionally the amount of secreted marker can be compared to the amount of marker retained in the cells (e.g., in the liver cells of a transgenic organism).
  • venous or venous blood
  • venous blood the terms are not meant to denote any particular limitation as far blood from veins, arteries, or other blood flow systems. Rather, all that is meant by the term “venous,” unless otherwise specifically denoted herein, is that the marker, for example, is outside the cell harboring the construct.
  • venous can include any solution, at any point in an organism, whether it be aterial, venous, or otherwise.
  • the PADSI construct is not the entire NS3/4A protein, but comprises a minimal NS3/4A cleavage (proteolytic) site. Any amount of the cleavage site can be used, as long as the section can be cleaved by an NS3 or NS3/4A protein. Additionally, the section of protein encoding for the cleavage site should not be so large as to allow for self cleavage (in embodiments where this is not desired). However, as will be appreciated by one of skill in the art, the entire NS3/4A complex could be used as part of the construct, as long as it cannot cleave itself; thus, NS3 protease inactive variants may also be used.
  • the PADSI proteins include NS3/4A variants that are NS3 protease inactive.
  • the NS3/4A section of the PADSI protein will not autocatalytically cleave the NS3/4A peptide bond.
  • Such a variant PADSI protein is useful as a means of controlling when the NS3 protease cleaves the NS3/4A peptide bond. While the variant NS3/4A will not cleave its own bond, an active NS3 or NS3/4A protein can still act upon the NS3/4A variant in order to cleave the bond.
  • the variants can be made in a variety of ways.
  • Guidance can be provided by the crystal structures of the NS3/4A complexes.
  • Guidance can also be found in FIGURE 13A and FIGURE 13B, which show the active-site residues of NS3 (*), His-1083, Asp-1107, and Ser-1165, for example. Substitutions at these sites will result in the prevention of cleavage at NS3/4A, NS4A/4B, NS4B/5A, and NS5A/B (see, for example, Tomei et al., J. Virol.
  • the variant PADSI protein is not only unable to cleave the NS3/4A peptide bond, but the NS3 and NS4A proteins will not associate with each other, apart from through the peptide bond.
  • these molecules may be especially useful for high throughput (HTP) screening as large numbers of possible candidate protease inhibitors may be added either simultaneously or sequentially at high rates and the NS3/4A PADSI proteins are amenable to the identification of protease inhibitors in a HTP format. While one of ordinary skill in the art will recognize that these proteins can be applied to many HTP systems, systems that readily allow the visualization of changes in the amount of detectable marker (e.g., a fluorescence marker) inside and/or outside of a cell are particularly useful. For example, chip based technology where the PADSI proteins are readily observable when they are attached to a fixed surface may be particularly useful.
  • detectable marker e.g., a fluorescence marker
  • the PADSI proteins may be expressed in cells and the cells themselves may serve as a fixed platform overwhich candidate protease inhibitors can be applied.
  • some embodiments include codon optimized sequences and, as discussed further below, these constructs can be used in transgenic mice. The next section describes several negative PADSI constructs that can be used to identify protease inhibitors.
  • FIGURE 14B A schematic of a negative PADSI construct is shown in FIGURE 14B, which can be compared to other constructs shown in FIGURES 14A and 14C.
  • the construct is called a negative PADSI because the absence of the detectable marker outside of a cell harboring the PASDSI contract (e.g., the venous blood of a transgenic organism) indicates that the candidate protease inhibitor is effective.
  • this construct has a NS3 section, a cleavage site section, a secretory signal, and a signal molecule (detectable marker). Cleavage at the cleavage site results in the separation of the secretory signal peptide from the signal molecule (detectable marker).
  • the signal molecule which is attached to a secretory signal, is able to leave the cell harboring the PADSI construct (e.g., if the construct is expressed in a transgenic organism, the construct may enter the venous blood where it can be detected).
  • cleavage of the PADSI fusion protein will result in the distribution of the signal molecule to areas outside of the cell but in the presence of a protease inhibitor, the signal molecule is retained in the cells harboring the PADSI construct.
  • the PADSI constructs need not fluoresce. That is, in some embodiments, the detectable marker is GFP, Luciferase, or Beta-gal, or any other detectable marker known to those of skill in the art.
  • the PADSI construct encodes a fusion protein comprising NS3 connected to a protease cleavage site, which can optionally be connected to the first approximately 5-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-50, or 50 or more consecutive amino acids of NS4A.
  • a secretory sequence Connected to the 3 prime section of this optional part of the nucleic acid encoding NS4A is a secretory sequence, which is further connected to a signal molecule sequence (e.g., a detectable marker).
  • a signal molecule sequence e.g., a detectable marker
  • the PADSI is a positive PADSI construct.
  • the presence of the detectable marker in the venous blood or outside the cell that harbors the construct will be a positive indication that the candidate protease inhibitor can prevent (e.g., reduce) cleavage of the NS3/4A molecule at the protease cleavage site.
  • An example of a construct for a positive PADSI is shown in FIGURE. 14C and an example of the sequences selected for such a construct are shown in FIGURE 14D.
  • the positive PADSI construct described in FIGURE 14C comprises a secretory signal sequence, a NS3-specific proteolytic site, and a marker protein, which are connected in the depicted manner or some equivalently functional manner.
  • This construct can be delivered to a cell (e.g. a liver cell in a mouse) that is already expressing a NS3 or an NS3/4A construct such that liberated NS3 can cleave the positive PADSI construct and thereby release the detectable marker allowing secretion outside of the cell (e.g., into the blood of the mouse).
  • Delivery of the positive PADSI construct or a positive PADSI protein may be by injection, transfection, or transduction. In the presence of a protease inhibitor, however, cleavage of the NS3-specific proteolytic site is prevented, marker protein and secretory signal sequence is not released and the fusion protein is retained within the cell (e.g., within the liver cells of a mouse).
  • the amount of detectable marker present outside of the cell harboring the construct e.g., in the venous blood of a NS3/4A transgenic organism that receives the positive PADSI construct
  • a greater amount of marker protein outside of the cell harboring the PADSI construct indicates a a more efficient protease inhibitor.
  • cleaved marker may exit cell, even in the absence of a protease inhibitor.
  • changes in the relative amounts of the detectable marker can indicate the activity of a protease inhibitor.
  • any significant change in the amount of a detectable marker inside or outside of a cell harboring the PADSI construct can be sufficient.
  • a detectable marker either external to the original host cell (e.g., venous blood) or internal to the original host cell, can indicate that the candidate agent is an efficient protease inhibitor.
  • a change in amount of marker detected is expressed as a ratio between the amount of detectable marker observed in the cell harboring the PADSI construct (e.g., liver cell of a transgenic organism) and the amount of detectable marker observed outside the cell harboring the PADSI construct (e.g., in the venous blood of the transgenic organism).
  • venous blood is meant is that the detectable marker is on the opposite side of the cell membrane of the cell containing the construct or the PADSI protein.
  • Expression data e.g., expression levels and ratios
  • a particular candidate HCV inhibitor e.g., a candidate protease inhibitor
  • a media e.g., on a hard drive of a computer
  • databases containing this information for a plurality of candidate HCV inhibitors can be assembled.
  • patterns of structure/function indicia can be recorded and, accordingly, candidate compounds can be assembled into groups that share similar structure/function indicia.
  • Approaches in rational drug design can then be used to generate new candidate agents, which can be analyzed in the assays described herein, the data recorded and assembled into databases, and the process can be repeated. In this manner, an evolutionary approach to identify agents that inhibit HCV replication and infection can be employed based on an itterative or cyclical development process.
  • the MUP promoter shown in FIGURE 14B is a tissue-specific promoter in that it expresses a construct in the liver of an organism.
  • Other tissue secific promoters, constitutive promoters and inducible promoters can be used with embodiments described herein, as well.
  • the MUP promoter is used to drive expression of one of the PADSI constructs, however, the construct is expressed in liver cells.
  • a change in the localization of the fluorescence, from the liver to the venous blood, or vice versa can faciltates identification of protease inhibitors.
  • the entire NS3 protein is encoded by the nucleic acid construct. This allows the NS3 protein to cleave the NS3/4A cleavage site.
  • variants of particular NS3 proteins such as nonenzymatic variants, may be used for the NS3 section of the construct.
  • PADSI refers to a construct that contains a minimal NS3 cleavage site (e.g., comprising at least the "TS" motif).
  • cleavage domains that can be used in the embodiments described herein can comprise CMSADLEVVTSTWVLVGGVL SEQ. ID. No. 45 or fragments thereof that comprise the (TS) cleavage site, such as, MSADLEVVTSTWVLVGGVL, SEQ. ID. No. 46, SADLEVVTSTWVLVGGVL, SEQ. ID. NO. 47, ADLEVVTSTWVLVGGVL, SEQ.
  • Preferred cleavage domains to be incorporated in embodiments described herein comprise LEWTSTWVL, SEQ. ID. No. 70, EVVTSTWVL, SEQ. ID. No. 71, or VVTSTWVL, SEQ. ID. No. 72.
  • NS3/4A cleavage site is included in the construct.
  • part of the NS4A orNS3 nucleic acid section is also incorporated in the construct.
  • a nucleic acid encoding 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive amino acids of any one of the peptides above or CMSADLEVVTSTWVLVGGVL, SEQ. ID. No. 73, or a fragment of NS3/4A that comprises the cleavage site (TS) may be included in the nucleic acid construct.
  • More of the NS4A protein may be included, as long as it does not interfere with the desired effects of the secretory signal and the signal molecule.
  • Other cleavage sites may also be used if the protease acitivity of those sites is of interest.
  • secretory signal Any type of secretory signal may be used, as long as it is sufficient to move the signal molecule out of the cell.
  • An example of a secretory signal includes Ig kappa.
  • the secretory signal is located close to the end of the cleaved NS3/4A product, thus allowing the secretory signal and the signal molecule attached to it to more readily diffuse out of the cell.
  • Examples of possible signal molecules include green fluorescent protein (GFP), Luciferase and Beta-galactosidase.
  • GFP green fluorescent protein
  • Luciferase Luciferase
  • Beta-galactosidase Several such signal sequences are known in the art, however. Exemplary sequences include, but are not limited to, GenBank Accession numbers, U49181 (luciferase), U73901 (GFP), and sequences in U.S. Pat.
  • the PADSI nucleic acids and proteins described above can be used to detect whether or not a candidate protease inhibitor is functioning to stop the activity of the NS3 protease in vivo.
  • a MUP promoter-driven construct When a MUP promoter-driven construct is expressed in an animal, such as a transgenic mouse, the resulting protein product may comprise a NS3 protein with a cleavage site, connected to a secretory signal and a signal molecule.
  • NS3 will cleave the cleavage site, allowing the secretory signal and signal molecule to be released from the NS3, allowing the signal molecule to leave the hepatocytes and to diffuse to the venous blood.
  • the signal molecule when a protease inhibitor is absent in the animal, the signal molecule is present in the venous blood. In the presence a protease inhibitor, however, cleavage is prevented and the signal molecule remains localized within the hepatocytes. Therefore, by monitoring the presence or absence of a signal molecule in the venous blood , one is able to determine if, and to what degree, the candidate protease inhibitors are able to prevent cleavage of NS3/4A. One may look in other areas as well as the venous blood, in particular when other tissue-specific promoters are used.
  • any location outside of the cells that produced the PADSI protein will indicate the level of activity of the NS3/4A protease and the protease inhibitor.
  • the luciferase marker is used with the constructs above, which allows one to analyze protease activity in vivo using whole animal screening, in addition to the blood analysis mentioned above. Accordingly, in some embodiements, when luciferase is detected in the animal outside of the liver or outside of liver cells, the protease is not inhibited by the candidate protease inhibitor and when the luciferase remains localized to the liver, then the protease inhibitor is effective at disrupting cleavage of NS3/4A.
  • Several options are available with the systems described herein.
  • the NS3 PADSI construct can be expressed in its proper cell type, (liver cells) so that candidate inhibitors must be able to inhibit protease activity in the infected cell type and under physiological conditions. Additionally, there is an internal control for signal, because all of the PADSI mice will exhibit the signal molecule and it is only the localization of the signal molecule that changes. Additionally, if the signal molecule is fluorescent (e.g., luciferase), one may simply look for fluorescence in the blood of the mouse (e.g., whole animal screening) and no sample need be withdrawn from the organism.
  • the above constructs are adapted so that they can be used to detect the cleavage of other HCV peptides, such as NS4B and NS5. The following section provides more detail on the transgenic organisms described herein.
  • HCV gene products described herein can be expressed in plants, insects, and animals so as to create a transgenic organism.
  • Desirable transgenic plant systems having an HCV peptide include Arabadopsis, maize, and Chlamydomonas.
  • Desirable insect systems having an HCV peptide include, but are not limited to, D. melanogaster and C. elegans.
  • Animals of any species including, but not limited to, amphibians, reptiles, birds, mice, hamsters, rats, rabbits, guinea pigs, pigs, micro-pigs, goats, dogs, cats, and non-human primates, e.g., baboons, monkeys, and chimpanzees can be used to generate transgenic animals having an embodied HCV molecule.
  • These transgenic organisms desirably exhibit germline transfer of HCV peptides described herein.
  • Any technique known in the art is preferably used to introduce the HCV transgene into animals to produce the founder lines of transgenic animals or to knock out or replace existing HCV genes.
  • Several methods to produce transgenic animals liave become conventional in the-art. Such techniques also include, but are not limited to pronuclear microinjection (Hoppe, P. C. and Wagner, T. E., 1989, U.S. Pat. No. 4,873,191; and U.S. Pat. No. 4,736,866, issued April 12, 1998 to Leder); retrovirus mediated gene transfer into germ lines (Van der Putten et al., Proc. Natl. Acad. ScL, USA 82:6148-6152 (1985)) and U.S. Pat. Pub.
  • the transgenic organism is created by microinjection. Once a construct is decided upon, it will be inserted into a cell. Each construct must first be in the linear form to be inserted into the cell. Therefore, if the construct has been inserted into a vector, linearization is accomplished by digesting the DNA with a suitable restriction endonuclease selected to cut only within the vector sequence and not within the construct sequence. For insertion, the construct is added to the ES cells under appropriate conditions for the insertion method chosen, as is known to the skilled artisan. For example, if the ES cells are to be electroporated, the ES cells and construct DNA are exposed to an electric pulse using an electroporation machine and following the manufacturer's guidelines for use.
  • each construct can be introduced simultaneously or one at a time.
  • the cells can be inserted into an embryo. Insertion may be accomplished in a variety of ways known to the skilled artisan, however a preferred method is by microinjection. For microinjection, about 10-30 cells are collected into a micropipet and injected into embryos that are at the proper stage of development to permit integration of the foreign ES cell containing the construct into the developing embryo. For instance, the transformed ES cells can be microinjected into blastocytes. The suitable stage of development for the embryo used for insertion of ES cells is very species dependent, however for mice it is about 3.5 days. The embryos are obtained by perfusing the uterus of pregnant females. Suitable methods for accomplishing this are known to the skilled artisan, and are set forth by, e.g., Bradley et al. (1986) Current Topics in Devel. Biol. 20:357-371.
  • preferred embryos are male.
  • the preferred embryos also have genes coding for a coat color that is different from the coat color encoded by the ES cell genes.
  • the offspring can be screened easily for the presence of the construct by looking for mosaic coat color (indicating that the ES cell was incorporated into the developing embryo).
  • the embryo selected will carry genes for black or brown fur.
  • the embryo may be implanted into the uterus of a pseudopregnant foster mother for gestation. While any foster mother may be used, the foster mother is typically selected for her ability to breed and reproduce well, and for her ability to care for the young. Such foster mothers are typically prepared by mating with vasectomized males of the same species.
  • the stage of the pseudopregnant foster mother is important for successful implantation, and it is species dependent. For mice, this stage is about 2-3 days pseudopregnant.
  • Offspring that are born to the foster mother may be screened initially for mosaic coat color where the coat color selection strategy (as described above, and in the appended examples) has been employed.
  • DNA from tail tissue of the offspring may be screened for the presence of the construct using Southern blots and/or PCR as described above. Offspring that appear to be mosaics may then be crossed to each other, if they are believed to carry the construct in their germ line, in order to generate homozygous animals. Homozygotes may be identified by Southern blotting of equivalent amounts of genomic DNA from mice that are the product of this cross, as well as mice that are known heterozygotes and wild type mice.
  • Northern blots can be used to probe the mRNA for the presence or absence of transcripts encoding either the gene, the marker gene, or both.
  • Western blots can be used to assess the level of expression of the NS3/4A gene in various tissues of the offspring by probing the Western blot with an antibody against the NS3/4A protein, or an antibody against the marker gene product, where this gene is expressed.
  • in situ analysis such as fixing the cells and labeling with antibody
  • FACS fluorescence activated cell sorting
  • the discussion below and the examples that follow describe the creation of a NS3/4A HCV transgenic mouse. (See EXAMPLES 18-36).
  • the NS3/4A transgenic mouse was created without the Cre/Lox-P system.
  • the transgenic mouse, created by the methods described herein was found to produce both the NS3 and NS4A proteins. Furthermore, the proteins are produced in these mice in surprisingly large amounts, making the NS3 readily identifiable. Additionally, the transgenic mice created as described herein exhibit an HCV appropriate phenotype that is not so overwhelming so as to endanger the life of the model organism, namely livers with increased weight and a lower number of nuclei per area unit indicating enlarged cells.
  • the NS3/4A transgenic mice display a reduced likelihood of having intra-hepatic inflammatory foci and other phenotypes as will be discussed infra. While NS3/4A expression may not appear to cause a prominent phenotype in the liver of these mice, expression of NS3/4A protein does alter the intrahepatic distribution of immune cells in these animals. These phenotypes and others as described below provide evidence that the present description teaches the first successful transgenic HCV model.
  • a genetically modified non-human mammal that comprises an allele that comprises a gene from a hepatitis C virus.
  • the hepatitis C virus gene can be codon optimized.
  • the genetically modified non-human mammal further comprises a NS3 gene, hi some embodiments, the genetically modified non- human mammal further comprises a NS4A gene.
  • the genetically modified non-human mammal comprises both a NS3 gene and a NS4A gene.
  • the genetically modified non-human mammal has the further proviso that no other hepatitis C virus gene is in an allele of the non-human mammal, apart from the group that consists of: aNS3 gene aNS4A gene, and a combination of the two genes.
  • a vector that comprises a mouse major urinary promoter and at least one hepatitis C virus gene is provided.
  • the hepatitis C virus gene is selected from the group that consists of: NS3, NS4A, and a combination of NS3 and NS4A.
  • a vector that comprises a promoter and a codon optimized hepatitis C virus gene is provided.
  • the codon optimized hepatitis C virus gene is selected from the group that consists of: a NS4A gene, a NS3 gene, and a combination of a NS4A gene and a NS3 gene.
  • a vector that comprises a hepatitis C virus gene and a Semliki forest virus replicon is provided.
  • the hepatitis C virus gene is selected from the group that consists of: a NS4A gene, a NS3 gene, and a combination of a NS4A gene and a NS3 gene.
  • one aspect of the present invention relates to a transgenic non-human mammal (e.g., a mouse) comprising an exogenous DNA sequence stably integrated in its genome, wherein said exogenous DNA sequence comprises a mouse major urinary promoter (MUP) operably linked to an HCV NS3 gene and a method of making said genetically modified non-human mammal, as described herein.
  • a transgenic non-human mammal e.g., a mouse
  • said exogenous DNA sequence comprises a mouse major urinary promoter (MUP) operably linked to an HCV NS3 gene and a method of making said genetically modified non-human mammal, as described herein.
  • MUP mouse major urinary promoter
  • the genetically modified mouse is created by providing a construct that comprises a mouse major urinary promoter (MUP)operably linked to an HCV NS3 gene, transferring said construct to a totipotent cell, and transferring said totipotent containing said construct to a pseudo pregnant mouse, whereby said pseudo pregnant mouse gives birth to the genetically modified mouse describe herein.
  • the totipotent cell is a fertilized oocyte.
  • the totipotent cell is an embryonic stem cell.
  • the totipotent cell is a stem cell and in some embodiments the totipotent cell is a cell of a blastocyst.
  • the construct used in the method of making a genetically modified non-human mammal further comprises an NS4A gene operably linked to said MUP promoter.
  • the construct further comprises a nucleic acid encoding a NS3 protease cleavage site.
  • said nucleic acid encoding saidNS3 protease cleavage site is joined to saidNS3 gene.
  • saidNS3 protease cleavage site is joined to said NS4A gene.
  • said construct further comprises a secretory signal joined to said NS3 gene and said NS3 protease cleavage site.
  • said construct further comprises a signal molecule joined to said secretory signal, said NS3 gene, and said NS3 protease cleavage site.
  • the transgenic non-human mammal containing an exogenous DNA further comprises an HCV NS4A gene operably linked to said MUP promoter.
  • the transgenic non-hur ⁇ an mammal containing an exogenous DNA further comprises a nucleic acid encoding a NS3 protease cleavage site.
  • the transgenic non-human mammal containing an exogenous DNA wherein said nucleic acid encoding said NS3 proteose cleavage site is joined to said NS3 gene.
  • the present invention relates to a transgenic non-human mammal containing an exogenous DNA wherein said nucleic acid encoding said NS3 protease cleavage site is joined to said NS4a gene.
  • the invention relates to a transgenic non- human mammal containing an exogenous DNA as described above further comprising a nucleic acid encoding a secretory signal joined to the NS3 gene and the NS3 protease cleavage site.
  • the transgenic non-human mammal containing an exogenous DNA as described above further comprising further comprises a signal molecule joined to the secretory signal, the NS3 gene and the NS3 protease cleavage site.
  • any of the genes described above are codon optimized for expression in a non-human mammal, in particular mice or humans.
  • the NS3 gene is codon optimized for expression in humans.
  • the NS3 gene and the NS4A gene are codon optimized for expression in humans.
  • transgenic non-human mammal accoding to the present invention comprising a phenotype of survival after contact with an amount of TNF- alpha that is lethal for a wild type non-human mammal of the same variety.
  • said transgenic non-human mammal further comprises a phenotype of reversion to TNF-alpha sensitivity after contact with an inhibitor of p38 MAP kinase (and/or an inhibitor of NF-kB).
  • said inhibitor is SB203580.
  • Some embodiments concern a transgenic non-human mammal accoding to the present invention comprising a phenotype of a reduced amount of intra-heptic CD4+ T cells, as compared to a non-human mammal of the same variety. Some embodiments concern a a transgenic non-human mammal accoding to the present invention comprising a phenotype of a reduced amount of type I and II dendritic cells, as compared to a non-human mammal of the same variety.
  • a genetically modified mouse that comprises an allele that comprises a NS3 gene and a NS4A gene that allow the genetically modified mouse to express a NS3 protein and a NS4A protein.
  • the NS3 protein produced by a liver of a genetically modified non human mammal is produced in an amount between about 0.1 to about 8 micrograms per gram of liver tissue, such as between 0.1 to 7 micrograms, between 0.1 to 6 micrograms, between 0.1 to 5 micrograms, between 0.1 to 4 micrograms between 0.1 to 3 micrograms, between 0.1 to 3 micrograms, between 0.1 to 2 micrograms, between 0.1 to 1 micrograms, between 1 to 7 micrograms, between 2 to 7 micrograms, between 3 to 7 micrograms, between 4 to 7 micrograms, between 5 to 7 micrograms, between 6 to 7 micrograms, between 7 to 8 micrograms.
  • the NS3 protein produced by a liver of a genetically modified liver tissue such as between 0.1 to 7 microgram
  • the NS3 protein expressed is detectable via a western blot. In some embodiments, the NS3 protein expressed is restricted to expression in the cytoplasm of hepatocytes. In some embodiments, the genetically modified mouse has a liver with a significantly increased weight relative to a mouse without NS3 protein being expressed in the mouse. In some embodiments, the genetically modified mouse has a lower number of nuclei per area unit in its liver tissue relative to a mouse without NS3 protein being expressed in the mouse.
  • Some embodiments concern a nucleic acid construct, the protein capable of being encoded by the nucleic acid construct, and/or a transgenic organism, such as a non-human mammal, expressing or that comprises any of the above.
  • the protease whose activity is being monitored is the NS3 protease
  • the protein being cleaved is the NS3/4A cleavage site, or sections thereof.
  • the construct comprises a nucleic acid that encodes a NS3 peptide, comprising the NS3/4A cleavage site, joined to a secretory signal, which is attached to a signal molecule (e.g., an indicator molecule or marker protein).
  • a signal molecule e.g., an indicator molecule or marker protein.
  • FIGURE 14B a fusion protein, as depicted in FIGURE 14B, is created.
  • the resulting fusion peptide will cleave itself, via the NS3 protein, at the NS3/4A cleavage site. This cleavage will allow the signal molecule to be secreted out of a cell that harbors the fusion peptide (e.g., into the bloodstream of a transgenic organism harboring the construct).
  • NS3 when a protease inhibitor is present, NS3 will not cleave the fusion peptide and the detectable marker (also known as a signal molecule, indicator, or marker protein) will not be secreted.
  • detectable marker also known as a signal molecule, indicator, or marker protein
  • PADSI Protease Activity Dependent Secreted Indicators
  • a PADSI is called a negative PADSI, as it is the absence (or relative absence) of the indicator outside of the cell harboring the construct (e.g., in the venous blood) that indicates an active protease inhibitor.
  • the presence of the indicator in the venous blood (or outside of the cell) will indicate the presence of an effective protease inhibitor.
  • the construct may be that described in FIGURE 14C.
  • the construct comprises a secretory signal attached to a NS3/4A proteolytic site that is attached to a marker protein (signal molecule, indicator, detectable marker or similar term). This construct is then placed into a system that has, or can have, active NS3 present.
  • a transgenic non-human mammal discussed herein expressing the NS3/4A construct can be used.
  • the fusion peptide in the absence of inhibitor, the fusion peptide will be cleaved by NS3 and secretion of the marker protein into the blood stream will occur.
  • a protease inhibitor is present, cleavage will not occur and fluorescence in the blood stream will not be observed.
  • This embodiment is termed a positive PADSI, as the presence of fluorescence, in the venous blood, indicates the presence of an active protease inhibitor.
  • the presence or absence of an indicator need not be binary and any statistically significant change can indicate the presence of an inhibitor.
  • these constructs may be expressed in vivo and the presence or absence of the detectable marker (indicator) in the venous blood can be determined without drawing blood from the non-human mammal.
  • a transgenic non-human mammal that expresses NS3 can be provided a positive PADSI construct that will express the NS3/4A cleavage site along with the secretory signal and the detectable marker.
  • the PADSI construct is only expressed in the liver. In the absence of any NS3 protease inhibitor, the positive PADSI construct will be cleaved keeping the indicator inside the cell and allowing the secretory signal to leave the cell.
  • the venous blood of the organism will not have a significant amount of marker.
  • a NS3 protease inhibitor is added, cleavage of the NS3/4A cleavage site will not occur, allowing the secretory signal to pull the detectable marker out of the cell, into the venous blood.
  • any section of the non-human mammal that allows one to monitor the detectable marker in the venous blood through the skin of the non-human mammal can be observed to determine the activity associated with the protease inhibitor.
  • a similar in vivo approach may be applied with the negative PADSI constructs, in which case, one correlates the absence of an indicator with the level of activity of the protease inhibitor.
  • these PADSI constructs indicate acitivity based upon secretion and one is not limited to examination in transgenic non-human mammal. That is, various in vivo and in vitro tests may also be applied. For example, as mentioned supra, any time the indicator is detected outside of a eel harboring the construct, one can determine the activity of a candidate protease inhibitor. Additionally, viruses or other systems can be used to induce an organism to express the NS3 protein.
  • transgenic non-human mammal expressing the combination of NS3/NS4A fusion protein.
  • the nucleic acids described above can be used to generate model HCV transgenic non-human mammal.
  • the nucleic acids were expressed stably and at high levels in transgenic mice. These mice exhibited livers with increased weight and a lower number of nuclei per area unit indicating enlarged cells. Additionally, the presence of intra-hepatic inflammatory foci were less common in the NS3/4A transgenic mice. As such, these transgenic mice are useful as, among other things, model organisms for HCV analysis.
  • a transgenic mouse comprises the wild-type NS3/4A gene.
  • a transgenic mouse comprises the codon optimized NS3/4A gene.
  • the transgenic non-human mammal displays a biochemical phenotype.
  • the transgenic mice can display an increased level of suppressor of cytokine activation- 1 (SOCSl), increased immunity or resistance to TNF-alpha or TNF- alpha-induced lethality, and/or lower IRF-3 levels.
  • SOCSl suppressor of cytokine activation- 1
  • More embodiments concern methods of treating or preventing HCV replication and infection by providing molecules that modulate the expression, phosphorylation, or activity of these proteins or proteins that are members of a phosphorylation cascade involving p38 MAP kinase or cascades involving or influencing NF-kB.
  • NS3/4A complex interferes with TNF receptor signalling in a p38 MAPK dependent way and in a NF-kB dependent way. This was demonstrated by showing that a NS3/4A transgenic phenotype, e.g., resistance to TNF ⁇ induced cytotoxicity, was revereted to wild-type by providing an inhibitor of p38 MAP kinase (and/or NF-IcB) signaling.
  • a TNF-a signal transduction cascade involving NS3/4A was unknown. Further, these' findings provide evidence that molecules that directly or indirectly inhibit p38 MAP kinase (or NF-IcB) signaling can inhibit HCV replication and infection. Enhancers of inhibitors of NF-kB can also be used to inhibit HCV replication and/or infection.
  • the NS3/4A-transgenic mice described in the examples herein also provide a new and rapid way to identify inhibitors of p38 MAP kinase and NF-kB (including activators of NF-kB inhibitors) and thereby identify HCV therapeutics.
  • an amount of TNF-alpha that is lethal to a wild-type mouse is provided to a NS3/4A transgenic mouse.
  • an amount of a candidate agent is then provided to the transgenic mouse and a reversion to TNF-alpha sensitivity (e.g., death or damage of the mouse) indicates that the candidate inhibits HCV replication and infection
  • a transgenic non-human mammal comprises a PADSI NS3/4A protein or nucleic acid emcoding said protein and this transgenic non-human mammal is used to identify HCV protease inhibitors.
  • a PADSI NS3/4A protein for example, one may, determine if a candidate protease inhibitor inhibits, reduces or prevents NS3/4A protease activity in vivo by observing the fluorescence of the tissue of the mouse when candidate protease inhibitor compounds are provided.
  • various candidate NS3 protease inhibitors can be administered to the transgenic mouse and the presence of the detectable marker in the venous blood is detected through the surface of the organism via a CCD.
  • a decrease in the level of detectable marker will indicate that one of the candidate protease inhibitors is actually an effective protease inhibitor is described in the Examples. Accordingly, novel protease inhibitors can be identified.
  • the following section provides more detail on the NS3/4A transgenic mice described herein.
  • NS3/4A transgenic mice (“NS3/4A-Tg") created as described herein were found to exhibit several characteristics associated with an impaired immunity. It was observed, for example, that NS3/4A-Tg mice had a reduced number of spontaneously appearing intra-hepatic inflammatory foci. Accordingly, the immune cells present in the liver were further analyzed. In a first set of experiments, flow cytometry was used to analyze the percent of non-parenchymal immune cell populations in the liver and this analysis revealed that the NS3/4A-Tg mice had a minute increase in intra-hepatic NK cells but a marked reduction in CD4+ T cells (see EXAMPLE 31, FIGURE 17A).
  • the observed lack of inflammatory foci in the NS3/4A-Tg mice detected by histology may be a result of the reduced amount of CD4+ T cells.
  • This reduced amount of intra-hepatic CD4+ T cells was confirmed by analysing the presence of different intra-hepatic immune markers using an RNAse protection assay ("RPA").
  • RPA RNAse protection assay
  • CDl Ic positive dendritic cell (DC) populations in the transgenic mouse livers It has recently been shown that three to four distinct DC populations can be detected in the mouse liver (Jomantaite, I. et al., Hepatic dendritic cell subsets in the mouse. Eur J Immunol 34:355-365 (2004); Lian, Z.X. et al., Heterogeneity of dendritic cells in the mouse liver: identification and characterization of four distinct populations, J Immunol 170:2323-2330 (2003)).
  • the CDl Ic+ hepatic DCs can be divided into three distinct populations by quantifying the surface expression of CDlIb, MHC-II, and Ly6C/G.
  • CDl lc+/CDl lb-/MHC-IIint/Ly6C/G+ population also termed type I/II, similar in phenotype and function to plasmacytoid DCs of a lymphoid origin (Colonna et al., Nat Immunol, 5:1219-1226 (2004)), was significantly reduced in the NS3/4A-Tg livers as compared to wild-type mice (see FIGURE 17B, EXAMPLE 31).
  • This DC population is a major producer of type-I IFN and a reduction of this cell type impairs the intra-hepatic immune response to viral pathogens.
  • NS3/4A transgenic mice were also examined to determine if they exhibited a functional impairment of the intra-hepatic immunity. Groups of transgenic and non- transgenic mice were treated with several different agents that are known to cause immune mediated liver damage and the results were recorded.
  • the NS3/4A-transgenic mice were contacted with CCl 4 and it was observed that the NS3/4A-Tg mice exhibited a reduced sensitivity to toxic liver damage, as compared to wild-type mice, (see EXAMPLE 33, FIGURE 18A). While CCl 4 initially causes toxic liver damage, a large part of the following inflammatory response is mediated through TNF- ⁇ (see Morio et al., Distinct roles of tumor necrosis factor-alpha and nitric oxide in acute liver injury induced by carbon tetrachloride in mice, Toxicol Appl Pharmacol, 172:44-51 (2001); Simeonova, P.P. et al, The role of tumor necrosis factor-alpha in liver toxicity, inflammation, and fibrosis induced by carbon tetrachloride, Toxicol Appl Pharmacol 177:112-120 (2001)).
  • TLR TOLL-like receptor
  • Soluble TNF- ⁇ acts through the TNF receptor 1 (TNFRl), or p55, a receptor that is expressed on adult murine hepatocytes.
  • TNF receptor 1 TNF receptor 1
  • p55 TNF receptor 1
  • TNF-alpha regulates mouse fetal hepatic maturation induced by oncostatin M and extracellular matrices, Hepatology, 40:527-536 (2004).
  • TNFRl TNF receptor 1
  • p55 a receptor that is expressed on adult murine hepatocytes.
  • TNF- ⁇ mediated TNFRl activation leads either directly to apoptosis through caspases, or to activation of the transcriptional complex IKK/NF-kB (see FIGURE 20).
  • TRAF2/RIP in turn activates ASK-I, which signals through either the JNK or the p38 MAP kinases (hereinafter "p38").
  • TLR4 Activation of TLR4 leads to signalling either through MyD88 or through an MyD88-independent pathway.
  • TLR4 mainly acts through TNF-alpha by IKK/NF-kB activation through MyD88 signalling, whereas TLR4-induced IFN signalling is mediated through the MyD 88 -independent pathway and IRF3.
  • the IFN-signalling pathways were then evaluated to determine if they were affected in the NS3/4A-transgenic mice. Following IFN ⁇ treatment, it was noted that nuclear IRF3 levels were reduced in the NS3/4A-Tg mice (see EXAMPLE 34), which confirms previous in vitro observations, (see Foy, E. et al., Regulation of Interferon Regulatory Factor-3 by the Hepatitis C Virus Serine Protease, Science (2003)). It was again noted that the NS3/4A- transgenic mice had increased basal levels of SOCSl, and that IFN ⁇ treatment induced increased levels of SOCSl, as compared to non-transgenic mice (see EXAMPLE 34).
  • TNF- ⁇ sensitivity of the NS3/4A-transgenic mice and wild-type mice was compared. Injections of TNF- ⁇ (5 ⁇ g/kg) killed 80% of the non-transgenic mice within 24 hours, however, all NS3/4A-Tg mice survived this lethal TNF- ⁇ dose. (See EXAMPLE 35, FIGURE 19A; p ⁇ 0,05, Fisher's exact test). Since TNFRl signalling is mediated through both the MKK4/7 and JNK, or the MKK3/6 and p38 pathways, the effect of p38 inhibitors on the NS3/4A-transgenic was investigated.
  • NS3/4A induces and/or activates nuclear factor kappa-B (NF-kB).
  • NS3/4A-Tg mice were further examined to determine the identity of proteins that NS3/4A may be acting through or with. It was found that the induction and/or activation of NF-kB may explain why the MUP-NS3/4A-Tg mice are resistant to TNF-a mediated liver disease (see EXAMPLE 40 below).
  • wild type and NS3/4A-Tg mice were treated with TNF-alpha and D-galactose amine. While TNF-alpha/D-gal treatment of wild type mice failed to effectively activate or increase the level of NF-IdB, MUP-NS3/4A-Tg mice showed the presence of a strong NF-kB band.
  • RIP2 protein kinase receptor interacting protein-2
  • RICK protein kinase receptor interacting protein-2
  • CARDIAK interleukin-1 beta converting enzyme associated kinase
  • NS3/4A-mediated protection of hepatocytes to TNF-alpha- mediated liver disease is, at least in part, due to an increase in NF-kB levels and/or activation, which can be effectively inhibited by the p38 inhibitor SB203580.
  • the data provides evidence thatNS3, and HCV in general, causes an increase in the level of NF-IcB in a subject. This, in turn, is reflected in the phenotype of a subject infected with HCV. As such, preventing the elevation of NF-kB activity can be an effective way to treat an HCV infected individual or to ameliorate a condition associated with HCV infection.
  • NF-kB inhibitors can be used in some embodiments to treat or prevent HCV infection and/or to ameliorate a condition associated with HCV infection.
  • NF-kB activity there are a variety of mechanisms through which one can influence NF-kB activity.
  • inhibitors prevent NF-IcB from functioning on its target. This can be achieved in a variety of ways. For example, in many cells, NF-kB is often associated with an inhibitory compound, such as I ⁇ B ⁇ , IicB ⁇ , I ⁇ B ⁇ , plO5, and plOO.
  • compounds that maintain the presence of these NF-IcB inhibitors or compounds that elevate the level of these compounds in a subject or compounds that prevent these NF-IcB inhibitors from dissociating can all be useful in inhibiting the activity of NF-kB and thereby inhibiting the proliferation/replication of HCV and/or ameliorate a condition associated with HCV infection.
  • preventing changes that occur downstream due to the elevation in NF-kB activity can also be an effective way to treat an HCV infected individual or to ameliorate a condition associated with HCV infection. The following discussion describes some of those downstream changes and mechanisms. As with directly preventing elevations in NF-IcB activity, preventing or reducing the subsequent changes can also be an effective way to treat an HCV infected individual or to ameliorate a condition associated with HCV infection.
  • IkB inhibitory IkappaB
  • aspects of the invention include moleucles that upregulate production of these NF-kB inhibitors (e.g., nucleic acids encoding one or more IkBs or fragments thereof at least or equal to 50, 100, 150, or 200 consecutive nucleotides).
  • NF-kB inhibitors e.g., nucleic acids encoding one or more IkBs or fragments thereof at least or equal to 50, 100, 150, or 200 consecutive nucleotides.
  • molelcules that inhibit phosphorylation of the IkBs or phosphorylation defective HcBs, which do not disassociate from NF-IcB are also embodiments (e.g., nucleic acids that encode an IkB or a fragment thereof at least or equal to 50, 100, 150, or 200 consecutive nucleotides or a peptide encoded by said nucleic acids, wherein said nucleic acids and the peptides encoded by said nucleic acids comprise a mutation that prevents phosphorylation, such as a mutation at Ser 32 and/or Ser 36 or at the codons encoding said amino acids).
  • Activation occurs via phosphorylation of IkB-a at Ser32 and Ser36, followed by ubiquitination and proteasome-mediated degradation, resulting in the release and nuclear translocation of active NF-kB (See, Finco, T.S. et al. (1994) Proc. Natl. Acad. Sci. USA 91, 11884-11888; Brown, K. et al. (1995) Science 267, 1485-1488; Brockman, J.A. et al. (1995) MoI. Cell. Biol. 15, 2809-2818; Traenclcner, E.B. et al. (1995) EMBO J. 14, 2876-2883; and Chen, ZJ. et al.
  • IkB-a phosphorylation, and resulting ReI- dependent transcription are activated by a highly diverse group of extracellular signals, including inflammatory cytokines, growth factors and chemokines.
  • Kinases that phosphorylate IkB at these activating sites have been identified (See, Karin, M. and Ben- Neriah, Y. (2000) Annu. Rev. Immunol. 18, 621-663). Accordingly, aspects of the invention concern inhibitors of kinases that phosphorylate IkB, which can be used to treat or prevent HCV infection.
  • IKK The multisubunit IkappaB kinase (IKK), which is responsible for inducible IkB phosphorylation, is a point of convergence for most NF-kB-activating stimuli. Accordingly, aspects of the invention concern inhibitors of IKK, which can be used in some of the HCV therapeutics described herein.
  • IKK contains two catalytic subunits, IKKalpha and IKKbeta, both of which are able to correctly phosphorylate IkappaB. Because phosphorylation of IkB- a at Ser32 is essential for release of active NF-IcB, phosphorylation at this site is an excellent marker of NF-kappaB activation. (See, Baeuerle, P.A. and Baltimore, D.
  • IKK phosphorylation of IlcB-beta occurs at Serl9 and Ser23, while IkB-epsilon can be phosphorylated at Serl8 and Ser22. (See, Shirane, M. et al. (1999) J. Biol. Chem. 274, 28169-28174).
  • compositions that inhibt phosphorylation of Ser 19 and 23 of IkB-beta are embodiments.
  • inhibt phosphorylation of Ser 19 and 23 of IkB-beta e.g., nucleic acids enocoding IlcB-beta that contains a mutation at Ser 19 and/or 23 or a fragment thereof at least or equal to 50, 100, 150, or 200 consecutive nucleotides, which includes said mutation and peptides encoded by said nucleic acids
  • compositions that inhibt phosphorylation of Ser 18 and Ser 22 of IkB-epsilon are embodiments.
  • IkB-a appears to be expressed at the same levels between Tg and non-Tg mice. This suggests that one of the other IkBs may be of more direct importance in the HCV response. However, as noted herein, IkB-a can be effective in treating HCV, as it can reduce the amount of NF-IcB present in the nucleus.
  • Each of the IkBs contain at least one, if not numerous copies of a 30-33 amino acid sequence, called ankyrin repeats. These ankyrin repeats can be used to identify other HcB or independently as useful pepetides. The ankyrin repeats are believed to interact with the RHD region of the NF-kB protein, thereby preventing the NF-kB from nuclear translocation. Thus, in some embodiments, ankyrin repeats, or molecules containing them, can be used to suppress the translocation of NF-kB protein and thereby inhibit HCV replication and infection.
  • some embodiments comprise HCV therapeutics that comprise an ankyrin repeat and methods of treating or preventing HCV replication or infection by providing an ankyrin repeat to a subject in need of a molecule that inhibits HCV replication or infection (e.g., a subject identified as having HCV infection or a subject identified as being at risk of acquiring an HCV infection).
  • a subject identified as having HCV infection or a subject identified as being at risk of acquiring an HCV infection e.g., a subject identified as having HCV infection or a subject identified as being at risk of acquiring an HCV infection.
  • a subject identified as having HCV infection or a subject identified as being at risk of acquiring an HCV infection e.g., a subject identified as having HCV infection or a subject identified as being at risk of acquiring an HCV infection.
  • activators of any inhibitors of NF-IcB are contemplated for various methods and compositions.
  • Such compounds can increase the amount of the inhibitors (e.g., IkB) or
  • translocation inhibitors a subset of general inhibitors of NF-kB.
  • the use of translocation inhibitors can be a valuable method of treating, preventing, and/or ameliorating a condition associated with HCV.
  • the NF-kB must undergo acetylation to become fully active.
  • p65 is acetylated by p300 and CBP acetyltransferases. Acetylation appears to occur at lysine 218, 221, and 310.
  • the therapeutic compounds for use in the manufacture of a medicament for the potpose of treating or preventing HCV infection or otherwise ameliorating a condition associated with HCV infection include molecules that inhibit acetylation of NF-IcB.
  • Such compounds can generally be described as "acetylation inhibitors," a subset of general inhibitors of NF-IcB.
  • the preferred method or compound involves an acetylation inhibitor.
  • histone deacetylase 3 HDAC3
  • HDAC3 histone deacetylase 3
  • NF-kB which will allow IkB to bind to NF-IcB, allowing for its transport out of the nucleus
  • Compounds that increase the concentration or activity of deacetylases can be inhibitors of NF-kB and, according to the teachings provided herein, can be used in anti-HCV pharmaceuticals and methods of making such pharmaceuticals for the purpose of treating or preventing HCV infection and/or ameliorating a condition associated with HCV infection.
  • NF-IcB inhibitor including, but not limited to, a deacetylase, I ⁇ B ⁇ , I ⁇ B ⁇ , IicB ⁇ , plO5, or plOO or a derivative thereof, whereby a subject that is identified as having HCV infection is provided an amount of said inhibitor that is sufficient to reduce the proliferation of HCV and/or ameliorate a condition associated with HCV infection.
  • any of the compounds, molecules, mechanisms, or steps discussed in this section can be targeted or used to reduce the effect of the elevated NF-kB activity found in an HCV infection.
  • these all can represent methods and compositions for the treatment and prevention and/or amelioration of a condition associated with HCV.
  • the inhibitors are dominant negative forms of NF-kB that prevent native or active NF-IdB from having an effect in a subject.
  • the inhibitors block proteins that activate NF-kB.
  • the inhibitors block RIP2, a kinase that activates NF-IcB.
  • the inhibitors bind directly to NF-kB or otherwise interact with NF-kB preventing it from exerting an effect in the subject.
  • the protein or small molecule, antibody, etc.
  • the inhibitor can directly bind to the DNA binding site involved in an NF-kB-mediated event.
  • the inhibitor can bind directly to the binding site of the DNA to be transcribed, for example.
  • it is not critical exactly what the mechanism is by which NF-kB is inhibited.
  • the NF-IcB inhibitor can act on different levels, and need not directly act on NF-kB itself, the term can encompass a variety of molecule that act on a variety of targets.
  • some embodiments concern anti-HCV pharmaceuticals that comprise an NF-kB inhibitor.
  • the use of any of the compounds that can treat or prevent HCV infection in a medicament is also an embodiment.
  • Methods of using these pharmaceuticals to treat or prevent HCV infection and/or to ameliorate a malady associated with HCV infection are also embodiments.
  • a subject in need of a compound that inhibits HCV infection and/or ameliorates a condition associated with HCV infection is provided an amount of an NF-kB inhibitor sufficient to inhibit proliferation/replication of HCV and/or an amount sufficient to ameliorate a condition associated with HCV infection.
  • the class of NF-kB inhibitors can include kinase inhibitors, DNA binding inhibitors, dominant negative inhibitors, "NF-IcB HcB inhibitors" (e.g., inhibitors of NF-IcB that work through DcB inhibitors), "NF-IcB HcB release inhibitors” (e.g., inhibitors of NF-kB that work through preventing the release of IkB); "NF-kB IkB degradation inhibitors” (e.g., inhibitors of NF-IcB that work through preventing the degradation of IkB), or generally, NF-IcB translocation inhibitors, NF-kB acetylation inhibitors, etc.
  • NF-IcB HcB inhibitors e.g., inhibitors of NF-IcB that work through DcB inhibitors
  • NF-IcB HcB release inhibitors e.g., inhibitors of NF-kB that work through preventing the release of IkB
  • any inhibitor of NF-kB e.g., any composition that lessens the activity of the final fully active form of NF-kB
  • any inhibitor of NF-kB can be used in the pharmaceuticals and methods described herein.
  • NF-IcB inhibitors that can be used in the embodiements described herein including, but not limited to, Withaferin A, e.g., from Withania somnifera; Sulfasalazine; PPM- 18 (2-Benzoylamino-l,4-naphthoquinone); Oridonin, e.g., from R.
  • Withaferin A e.g., from Withania somnifera
  • Sulfasalazine Sulfasalazine
  • PPM- 18 (2-Benzoylamino-l,4-naphthoquinone
  • Oridonin e.g., from R.
  • Parthenolide e.g., from Tanacetum parthenium; NF-kB Activation Inhibitor; NF- kB SN50, (AAVALLPAVLLALLAPVQRKRQKLMP SEQ ID NO: 74): Cell-Permeable Inhibitor Peptide; InSolutionTM NF-kB Activation Inhibitor; NEMO-Binding Domain Binding Peptide, (DRQIKIWFQNRRMKWKKTALD WSWLQTE SEQ ID NO: 75) e.g., Cell-Permeable; Kamebakaurin, e.g., from Isodon japonicus; Acetyl- 11-keto-b-Boswellic Acid, e.g., from Boswellia serrata; Andrographolide; BAY 11-7082; InSolutionTM BAY 11- 7082 ((E)3-[(4-Methylphen
  • NF-IcB inhibitors Many of these examples are known in the art as compounds of the class of NF-IcB inhibitors and are discussed in greater detail in "The Ubiquitin-Proteasome Pathway: a link with NF-kB Activation" by Chandra Mohan, EMD Biosciences Inc., pages 20-22 of which are herein incorporated by reference. Additionally, ⁇ N-I ⁇ B ⁇ ( ⁇ N-IkB-a or "super-repressor,” for example, as discussed in Chaisson et al., J. Clin. Investigation, 110:193-202, 2002), gliotoxin, anti-inflamatories, and aspirin can also be used as NF-IcB inhibitors.
  • parthenolide also known as partenolid and partenolide
  • IKKBeta HcB kinase Beta
  • IKKBeta Inhibition of IKKBeta prevents the phosphorylation of IkB, which is the inhibitory complex associated with NF-kB in the cytoplasm (preventing its entry into the cytoplasm), as described in Kwolc et al., Chemistry and Biology, 8:759 (2001) (herein incorporated by reference in its entirety).
  • 1) parthenolide, 2) another inhibitor of IKKBeta that prevents the phosphorylation of IkB, or 3) another compound that prevents a) the phosphylation of IkB or b) its dissociation from NF-IcB is contemplated and can be used to treat HCV or the related complications.
  • activators of inhibitors of NF-kB can also be used in the treatment of HCV, for both methods of treatments and compositions of treatment.
  • compounds and methods that address different steps of the process are used at the same time or in the same treatment for a more beneficial result.
  • the NF-kB inhibitors encompass compounds or methods that activate NF-IcB inhibitors.
  • compounds that increase the amount of IkB, such as additional HcB; prevent the degradation of IkBs or their dissociation from NF-kB; or variants of IkBs that will not dissociate from NF-kB can be encompassed with compounds that are activators of NF-kB inhibitors.
  • increasing the amount or effectiveness of an inhibitor of NF-IcB, especially an inhibitor, which prevents nuclear translocation can be included as a method of activating NF-kB inhibitors.
  • any of the compounds that alter the activity of NF-IcB, or an upstream or downstream component of it, which has been altered by the presence of NS3/4A can be used in the treatment, prevention, etc., of HCV infection.
  • Such compounds can be broadly refered to as "NF-IcB cascade inhibitors.”
  • Such compounds are not only involved in the NF-IcB cascade that is altered by the presence of NS3/4A but also result in the correction of the cascade so that a wild-type phenotype is observed.
  • the above compounds, as well as, the following compounds provide examples of NF-kB cascade inhibitors.
  • compounds that block inhibitors of caspases, or compounds that block inhibitors of apoptosis can be used to treat, prevent and/or ameliorating a condition associated with HCV infection.
  • compounds that block the inhibitor of apoptosis protein would be included as relevant as a NF-kB inhibitor.
  • the IAP family includes c-IAP-1, c-IAP-2, XIAP, Surivivin, Livin, and NAIP. Suppression of any of these can be useful in the treatment and prevention of HCV.
  • the IAP proteins function through direct interactions to inhibit the activity several caspases, including caspase-3, caspase-7, and caspase-9.
  • caspase-3 is relevant in HCV infections and that compounds or methods that stimulate or increase the activity of caspase-3 (activators of caspase-3, additional caspase-3, activated caspase-3, etc.) can be useful in the treatment and prevention of HCV. Additional information regarding these compounds can be found in Kasof, G.M. and Gomes, B.C. (2001) J. Biol. Chem. 276, 3238-3246 and Deveraux, Q. L. et al. (1997) Nature 388, 300-304.
  • a compound that prevents the IAP proteins from interacting with caspase-3 can be an inhibitor that would be relevant in relation to HCV infection.
  • One example of such a compound can include an antibody that binds to the IAP protein so as to prevent the IAP protein from binding to caspase-3.
  • A20 is a cytokine-induced primary response gene that encodes a protein that inhibits apoptosis.
  • A20 does not seem to demonstrate a major difference in expression levels between NS3/4A mouse livers and non-Tg mouse livers. Additionally, A20 does not, at present, appear to display a major difference between NS3/4A-Tg and non-Tg mice (data not shown).
  • Bcl-2 family members Other relevant regulators of apoptosis are the Bcl-2 family members. Again, compounds which block or prevent the inhibition of apoptosis can be useful as NF-IdB inhibitors and/or used in the treatment and prevention and/or amelioration of a condition associated with HCV.
  • the Bcl-2 family is divided into three subgroups based on their structure. Members of the first subgroup, represented by Bcl-2 and Bcl-xL, have an anti- apoptotic function. Members of the second subgroup, represented by Bax and Bak, as well as members of the third subgroup such as Bid and Bad, are pro-apoptotic molecules.
  • the pro-apoptotic molecules can be enhanced in their activity for the treatment of HCV, while the anti-apoptotic molecules can be suppressed in their activity for the treatment of HCV.
  • TRAFs TNF receptor-associated factors
  • TRAFs are a family of multifunctional adaptor proteins that bind to surface receptors and recruit additional proteins, forming multiprotein signaling complexes capable of promoting cellular responses (See, Arch, R. H. et al. (1998) Genes Dev. 12, 2821-2830; Chung, J. Y. et al. (2002) J. Cell Sci. 115, 679-688; and Bradley, J.R. and Pober, J.S. (2001) Oncogene 20, 6482-6491).
  • TRAF domain which mediates interactions with associated proteins.
  • the first TRAFs identified, TRAFl and TRAF2 interacts with the cytoplasmic domain of TNF-receptor 2 (TNFRII) (See, Rothe, M. et al. (1994) Cell 78, 681-692). At least six TRAFs have been identified (TRAF 1-6), and they have been found to act as adaptor proteins for a wide range of cell surface receptors, participating in the regulation of cell survival, proliferation, differentiation and stress responses.
  • TRAF2 interacts with surface receptors including TNFRII, CD27, CD30, CD40, 4-1BB, Ox40, HVEM/ATAR and LMP-I (See, Arch, R.
  • TRAF2 also associates with a large number of intracellular proteins, including TRADD, FADD, I-TRAF/TANK, TRIP, A20, c-IAPl and 2, Casper, RIP, and NIK, which help to regulate cell survival.
  • TRAF2 plays an important role in TNF-mediated activation of NF-IcB and the MAPK/ JNK kinase pathway (See, Yeh, W. C. et al. (1997) Immunity 7, 715-725; Reinhard, C. et al. (1997) EMBO J. 16, 1080-1092; and Rothe, M. et al. (1995) Science 269, 1424-1427).
  • TRAF2 displayed no major difference between NS3/4A-Tg and non-Tg mice.
  • the inhibitors can be reversible or irreversible inhibitors of NF-kB activity, or the compounds can influence any or all of the activation related steps required for full NF-IdB activity (meaning transcription, not simply separation of the inhibitory compound (IkB) and acetylation of the complex.)
  • the inhibitors share structural similarities with any of the above compounds.
  • the inhibitors are highly specific and only detectably inhibit NF-kB activity.
  • the inhibitor suppresses NF-kB activity without inhibiting JNK activity.
  • the NF-IcB inhibitors that are used in the pharmaceuticals or methods described herein are anti-inflammatory compounds such as non-steroidal antiinflammatory drugs, in particular Cox-2 inhibitors. That is, aspects of the invention concern methods of treating or preventing HCV infection and/or ameliorating a condition associated with HCV infection comprising providing a therapeutically effective amount of an NSAID 5 for example one or more of the following compunds: wherein said non-steroidal anti inflammatory drug (NSAID) is selected from the group consisting of ibuprofen (2- (isobutylphenyl)-propionic acid); methotrexate (N-[4-(2,4 diamino 6-pteridinyl- methyl]methylamino]benzoyl)-L-glutamic acid); aspirin (acetylsalicylic acid); salicylic acid; diphenhydramine (2-(diphenylmethoxy)-NN-dimethylethylamine hydrochloride); naproxen (2-
  • NF-kBs there are a variety of "NF-kBs," any and all of which can be relevant to various instant embodiments.
  • NF-kB when used alone, is meant to denote NF-IdB free of IkB.
  • activated or inactivated NF-kB can also be used to describe the various states in which NF-kB can exist (e.g., bound to the inhibitor or acetylated).
  • NF-kB, or the NF-IcB complex has at least a p65 and a p50; a c-Rel and p50; a p65 and p52; or a ReIB and a p52 protein.
  • the NF-IcB family includes NF-IcBl (p50/pl05), NF-kB2 (p52/pl00), ReIA (p65), ReIB, and c-Rel.
  • the members of this family can be identified by a highly conserved ReI homology domain (RHD), which functions in DNA binding, dimerazation, and interaction with HcB.
  • RHD ReI homology domain
  • Inhibitors to any and all of these can be useful for the treatment and prevention of HCV.
  • inhibitors to the activity and levels of p65/p52 duplex are especially relevant.
  • at least p65 is part of the NF-kB.
  • p65 and especially nuclear p65, demonstrates a correlation between non-Tg and NS3/4A-Tg mice in response to TNF-a/D-Gal exposure, suggesting that it plays a role in HCV infection.
  • more than one inhibitor is combined for the treatment (either in the adminstration to a subject or combined in a pill or other form to administer to a subject).
  • different inhibitors are used in combination.
  • an inhibitor of p38 can be combined with an inhibitor of NF-kB.
  • inhibitors of p38, NF-IcB, and RIP2 can all be used in combination.
  • the inhibitor is a single inhibitor that works on multiple proteins or manners at the same time. For example, SB203580 not only inhibits p38, but it also inhibits RIP2.
  • any inhibitor can readily be tested through the use of the NS3/4A-Tg mouse disclosed herein.
  • any compound, method of treatment, etc., that results in the NS3/4A mice returning to their wild-type, TNF- alpha sensitive state can be an adequate inhibitor or method.
  • the present mouse model is predictive of the response of other organisms, especially other mammals, such as humans. Accordingly, as will be appreciated by one of skill in the art, the presently disclosed use of the mouse model for the identification of p38 inhibitors can also be used to identify NF-IcB inhibitors that inhibit the proliferation/replication of HCV and/or ameliorate a condition associated with HCV infection.
  • this model can be useful for the in vivo study of inhibitors of both p38 and NF-kB.
  • the model can be used to find more effective inhibitors of p38 and/or NF-kB.
  • the mouse model can be used to identify inhibitors that are relatively specific to those pathways that are influenced by HCV and NS3/4A in particular.
  • inhibitors such as SB203580, which influence multiple levels (e.g., NF-IdB and p38) can be used.
  • Some embodiments concern a method of identifying a compound that inhibits hepatitis C virus replication, proliferation, or infection. Some methods comprise the steps of providing a genetically modified non-human mammal described herein, contacting a test compound to the non-human mammal, and analyzing the presence or absence of a marker that indicates that the compound inhibits hepatitis C virus replication, proliferation, or infection in a human. Accordingly, a reduction in the presence of the marker identifies the compound as one that inhibits hepatitis C virus replication, proliferation, or infection.
  • the reduction in hepatitis C virus replication is identified by comparing the liver or cell thereof of the non-human mammal treated with the test compound to a liver or cell thereof of a second non-human mammal.
  • the second non-human mammal can be a wild-type mouse or an NS3/4A-Tg mouse that was not treated with the test compound.
  • a method of using the genetically modified non-human mammal e.g., a NS3/4A-Tg mouse
  • said method comprises providing the genetically modified non-human mammal, created as described herein, contacting said genetically modified non-human mammal with a candidate molecule, and determining whether said molecule inhibits the activity of NS3, whereby said molecule that inhibits HCV replication is identified by the ability of said molecule to inhibit the activity of NS3.
  • said genetically modified non-human mammal further comprises a nucleic acid encoding a signal molecule, a secretory signal, and an NS3 protease cleavage site.
  • said signal molecule is luciferase.
  • said determining step is performed by analyzing the presence or absence of the signal molecule outside a liver cell. In yet other embodiments, said determining step is performed by analyzing the presence or absence of the signal molecule inside a liver cell. The methods described abovel can be used to analyze various candidate compounds so as to identify molelcules that inhibit p38 MAP kinase or a NF-kB.
  • kinase inhibitors in particular p38 kinase inhibitors or a NF-kB inhibitor
  • a composition e.g., pharmaceutical or dietary supplement
  • said compositions can be provided to a subject in need of an agent that inhibits HCV replication and infection or an agent that otherwise improves the health or wellness of the subject (e.g., improves the function of the liver or immune system).
  • the inhibition of HCV replication in said subject is measured before and/or after providing said composition.
  • kinase inhibitor e.g., a p38 kinase inhibitor
  • NF-kB inhibitor e.g., a NF-kB inhibitor
  • the data provided herein demonstrate that the NS3//NS4A-transgenic mice can be used as a rapid in vivo model to screen for inhibitors of HCV (e.g., inhibitors of the p38 MAP kinase).
  • HCV e.g., inhibitors of the p38 MAP kinase
  • any compound or treatment that results in the NS3/4A transgenic mice exhibiting a wild-type phenotype e.g., susceptibility to TNF-alpha induced cell death
  • aspects of the present invention relate to methods of using the genetically modified non-human mammals (e.g., mice) to identify a molecule that inhibits HCV replication, wherein said methods comprise providing the genetically modified non human mammal created as described herein, contacting said genetically modified non-human mammal with a molecule; and determining whether said molecule increases the sensitivity of said genetically modified non-human mammal to TNF-alpha (e.g., TNF-alpha-induced cell death).
  • said molecule is a p38 MAP kinase inhibitor (or a NF-kB inhibitor).
  • said inhibitor is selected from the group consisting of SB 203580, SB 202190, KN62, U0126, PD 98059, Wortmannin, rapamycin, Ro 31-8220, Bis-1, Go 6976, UCNOl 5 Indirubin-3'-monoxime, kenpaullone, alsterpaullone, PPl, PP2, SU 6656, SP 600125, ML-9, PD 169316, p38 MAP Kinase inhibitor, SB202190 hydrochloride, SB 203580 hydrochloride, SB 203580 Iodo, SC68376, SKF-86002, ZM 3363772, Anti- p38/HOG-l antibody, and anti-p38 MAP Kinase antibody.
  • said molecule is SB203580. In another presently preferred embodiment said molecule is SB202190. In more embodiments, said molecule is selected from the group consisting of a SOCSl inhibitor, an IFR3 enhancer, type-1 IFN, typel/II hepatic DC, STATl activator, STAT2 activator, siRNA to SOCSl, siRNA to p38, siRNA to PP2A, a blocking antibody to SOCSl, a blocking antibody to p38, a blocking antibody to PP2A, an activating antibody to IFR3, an activating antibody to STATl, an activating antibody to STAT2, and a PP2A inhibitor. In still more embodiments, said molecule is a suppressor of cytokine signaling- 1 (SOCSl) inhibitor.
  • SOCSl cytokine signaling- 1
  • kinase inhibitors in particular p38 kinase inhibitors or NF-kB inhibitors
  • a composition e.g., pharmaceutical or dietary supplement
  • said compositions can be provided to a subject in need of an agent that inhibits HCV replication and infection or an agent that otherwise improves the health or wellness of the subject (e.g., improves the function of the liver or immune system).
  • the inhibition of HCV replication in said subject is measured before and/or after providing said composition.
  • kinase inhibitor e.g., a p38 kinase inhibitor
  • NF-IcB inhibitor e.g., a NF-IcB inhibitor
  • mice can be used as a rapid in vivo model to screen inhibitors of the p38 MAP kinase or for NF-kB inhibitors. Additionally, the mice can be used as a rapid in vivo system to screen candidate treatments directed to HCV. For example, any compound or treatment that results in the NS3/4A transgenic mice exhibiting a wild-type phenotype (e.g., susceptibility to TNF-alpha induced cell death) can also be a candidate compound for HCV prevention and/or treatment, as the compound will have displayed the ability to prevent an NS3/4A-based disruption in vivo.
  • a wild-type phenotype e.g., susceptibility to TNF-alpha induced cell death
  • a NS3/4A transgenic mouse can be used to screen candidate inhibitors of p38 MAP kinase and/or NF-kB inhibitors.
  • the present NS3/4A-Tg mice demonstrate an increased or high resistance to cell death mediated by TNF- alpha.
  • NS3/4A transgenic mice that receive TNF-alpha have a much lower risk of death or cell damage than wild-type mice. It appears that this interaction occurs through p38 and/or NF-kB, as the inhibition of p38 and/or NF-kB results in NS3/4A transgenic mice exhibiting wild-type sensitivity to TNF-alpha (e.g., cell death and mouse death).
  • a compound administered to a NS3/4A transgenic mouse e.g., a candidate p38 inhibitor or NF-kB inhibitor
  • a wild-type lethal amount of TNF-alpha that results in the NS3/4A transgenic mouse dying indicates that the candidate molecule is an effective inhibitor of p38 activity (e.g., SB203580) and also a compound that can be formulated into an anti-HCV pharmaceutical.
  • wild-type lethal amount can be used to describe the amount of a substance that would typically kill, or measurably increase the risk of death, of a wild-type mouse or cell, but not necessarily kill aNS3/4A transgenic mouse or cell. This amount can be an LD 5 O- based amount, where half of the population of wild-type mice would be dead, or it can be based on some other expected amount' of death (e.g., the 80% death induced by TNF-alpha, as described above). The exact percent or risk of death need not be limited to any set amount, as long as a difference in the expected percent dead and the actual percent dead can be observed.
  • control lethal amount denotes the amount required to kill a certain percentage of a control animals, i.e., the animal need not be a wild-type mouse.
  • wild-type lethal substance denotes that a wild-type mouse can die from the administration of the substance to the mouse, while implying that a transgenic mouse (e.g., NS3/4A-Tg) would not have the same risk of death from the same amount of the substance.
  • positive controls are run with the above test to make certain that the candidate compound is not lethal for other reasons.
  • a wild-type mouse can be provided the candidate compound to make certain it is not acting through other mechanisms.
  • the positive indication of a candidate p38 inhibitor (or a candidate NF-IcB inhibitor) can vary, and can include, for example, mouse death, or cell death.
  • the NS3/4A transgenic mouse has a consistent and steady level of TNF-alpha in its system so that it can be used continuously to test for candidate composistions.
  • NS3/4A-Tg mice exhibit a resistance to TNF-alpha relative to wild type mice is one phenotype of the NS3/4A-Tg mice.
  • phenotypes described herein as well e.g., increased SOCSl levels
  • these other phenotypes are examined, instead of analyzing TNF-alpha mediated cell death.
  • phenotypes are generally termed “NS3/4A phenotypes.”
  • the compounds that are administered to the mouse to induce phenotypes are termed “NS3/4A phenotype inducing substances.”
  • TNF-alpha is one example of a NS3/4A phenotype inducing substance, as administration of TNF-alpha to the mouse results in a phenotype (e.g., reduced likelihood of cell and mouse death).
  • a phenotype e.g., reduced likelihood of cell and mouse death.
  • phenotypes other than cell death or phenotypes other than those relating to TNF-alpha can be observed.
  • the phenotype observed is an activity level of various proteins in a pathway, for example, as shown above.
  • a phenotype can be an elevated activity of a protein in a NS3/4A Tg can be used as a phenotype.
  • Activity can encompass the kinetic rates associated with how quickly an enzyme may catalyze a reaction, which can be altered through events such as phosphorylation.
  • Activity can also encompass the absolute level or amount of the protein present in a system. If intended to be separated, the terms can be denoted as enzymatic activity and protein expression respectively or other similar such terms.
  • HCV treatments can encompass both a method of treating HCV and a composition for treating HCV (e.g., a medicament).
  • HCV treatments can prevent the onset of symptoms or infection.
  • HCV treatments can also reduce symptoms associated with the disease, as well as reverse the course of the HCV infection.
  • Regimens for treating or preventing HCV can vary dramatically. However, in light of the present disclosure, the identification and analysis of other kinase modulatory molecules that reduce HCV replication and infection are straightforward.
  • compounds that revert a NS3/4A phenotype of the NS3/4A transgenic mouse to a wild-type phenotype can be used to identify molecules for incorporation into a HCV medicament that if formulated for human administration (e.g., prepared according to cGMP standards).
  • a HCV treatment need not completely remove all symptoms or aspects of HCV infection. In some embodiments, only some of the symptoms are reduced, such as a reduced amount of protein expressed in a patient who is receiving the treatment. In other embodiments, all of the symptoms are eliminated. In other embodiments, even the proteins associated with the HCV virus itself are eliminated.
  • the treatments e.g., methods or medicaments
  • the treatments can only reduce the risk of infection by some percent, for example, more than zero to 1, 1-10, 10-20, 20-30, 30-50, 50-60, 60-70, 70-80, 80-90, 95-99, and 99-100 percent reduction in risk of infection.
  • the treatments only delay the onset of initial or additional symptoms.
  • a “candidate” HCV treatment, p38 inhibitor, NF-kB inhibitor etc. denotes that the compound or method may be useful in the treatment or prevention of HCV, NF-IcB, or p38 activity.
  • a “treatment,” etc., when not modified by the term “candidate,” denotes that the composition or method does alter the symptoms of HCV, inhibit p38 activity, inhibit NF-IcB activity, etc.
  • compounds that are treatments can also have other adverse side effects or be less effective in certain patients; however, such adjustments only require routine modifications and testing, as the risk of adverse side effects is common to almost all forms of medication.
  • FIGURE 20 Particular guidance for testing, characterizing, and using the candidate HCV treatments is provided herein in the description and in the Examples. Additional guidance is provided in FIGURE 20. In particular, compounds that have previously been known to alter the indicated pathways for NS3/4A activity can be tested in the methods provided herein. Additionally, FIGURE 20 can also be used to determine steps at which NS3/4A can act and thus provide guidance to one of skill in the art as to which later steps in the cascade should be activated to compensate for the inhibition or stimulation induced by NS3/4A. Additional pathways known to one of skill in the art can also be examined. These pathways have been discussed above. Additionally, it is believed that NS3/4A can have multiple influences.
  • NS3/4A can impair IFN ⁇ signalling through IRF3 in vivo, possibly through SOCSl. Additionally, NS3/4A can cause resistance to TNF- ⁇ mediated apoptosis due to p38, which up-regulates PP2A, which in turn blocks TNFRl -signalling through the MKK4-JNK pathway. This pathway is demonstrated in Avdi et al. (J. of Biol. Chem., 277:40687-40696 (2002)) involving TNF-alpha, p38 MAP kinase, and PP2A and can also be used to determine possible proteins that are of interest in preventing or treating HCV.
  • the balance between TNFRl signalling through the pro- apoptotic MKK4/7-JNK, and the anti-apoptotic MKK3/6-p38 MAPK pathways can be disturbed.
  • the TNF- ⁇ resistant phenotype of the NS3/4A-Tg mice can be due to a p38- mediated activation of PP2A that blocks JNK-induced apoptosis.
  • the pathway can involve the NF-IcB proteins. Such pathways are known in the art.
  • the pathways, and for example, the relevant targets to manipulate include IkBs, the NF-kBs themselves, the kinases for the IkBs, the enzymes for the acetylation of the NF-IcBs, and the proteins that remove or assist in removing NF-IcBs from the nucleus.
  • relevant proteins and pathways can be found in Chandra et al., "The Ubiquitin-Proteasome Pathway: A link with NF-kB Activation" (Calbiochem) and "Biologies, In Focus: NF-kB, A Therapeutic Target for Inflammation and Cancer” VoI 30, No. 1, 2004. These theories are not intended to limit the scope of the various embodiments.
  • revert to wild-type it is meant that a NS3/4A phenotype in a NS3/4A transgenic is made more similar to the wild-type phenotype. In some embodiments, reverting to a wild- type phenotype indicates that a HCV treatment has been identified.
  • a NS3/4A phenotype is a characteristic that the NS3/4A transgenic exhibits that the wild-type does not exhibit, e.g, a different level of SOCSl expression or an immunity to TNF-alpha induced death). Many such differences are noted above and in the figures and any of these differences can be used as a phenotype.
  • the above disclosed screening methods and the transgenic organisms described herein can also be used to screen for candidate HCV treatments, as compounds that are effective in reversing the phenotype in the transgenic mice can also reverse the phenotype of HCV in HCV infected organisms.
  • the above compositions and methods applicable to p38 inhibition (or NF-IcB inhibition) can be useful for HCV prevention and treatment.
  • SB203580, or analogs thereof can be used as an inhibitor of p38 (or NF-IcB) and to treat or prevent HCV.
  • compositions that may be used with the embodiments described herein include, but are not limited to: antisense RNA, siRNA to p38 MAP kinase (or NF-kB), SB 203580, SB 202190, KN62, U0126, PD 98059, Wortmannin, rapamycin, Ro 31-8220, Bis-1, Go 6976, UCNOl 3 Indirubin-3'-monoxime, kenpaullone, alsterpaullone, PPl, PP2, SU 6656, SP 600125, ML-9, PD 169316, p38 MAP Kinase inhibitor, SB202190 hydrochloride, SB 203580 hydrochloride, SB 203580 Iodo, SC68376, SKF-86002, ZM 3363772, Anti-p38/HOG-l antibody, and anti-p38 MAP Kinase antibody, as well as, any inhibitors obtained by the identification methods disclosed herein.
  • the HCV treatment relates to the readjustment of a protein or enzyme that is altered in the NS3/4A transgenic mouse, as described herein (e.g., SOCSl).
  • More examples of compounds that can be used to inhibit proliferation of HCV in an afflicted subject include, but are not limited to, a SOCSl inhibitor, an IFR3 enhancer, type-1 IFN, typel/II hepatic DC 5 STATl activator, STAT2 activator, siRNA to SOCSl, antisense RNA, miRNA and siRNA to p38 (or NF-IcB) or to PP2A, a PP2A inhibitor, an inhibiting antibody (e.g., it acts as an inhibitor for the protein to which it binds) for any of the above inhibitors, and an activating antibody (e.g., it acts as an enhancer or activates the protein to which it binds) for any of the above activators.
  • a SOCSl inhibitor an IFR3 enhancer
  • type-1 IFN typel/II hepatic DC 5 STATl activator
  • STAT2 activator siRNA to SOCSl
  • antisense RNA miRNA and siRNA to p38 (or
  • any compound that alters, modifies, or modulates any of the activities of a molecule depicted in FIGURE 20 may be formulated into an anti-HCV pharmaceutical for human administration.
  • additional screening steps can be performed.
  • the compound can be tested to make certain that it does not induce death in wild-type mice.
  • the compound can be analyzed to determine its effectiveness in preventing or treating HCV or HCV related symptoms in an HCV infected subject (e.g., a human).
  • the general method for screening for candidate p38 (or NF-IcB) inhibitors can also be used to screen for agents to treat or prevent HCV.
  • the procedure is similar to that described in the Examples.
  • Agents that make a NS3/4A mouse react to TNF-alpha in the same manner that a wild-type mouse reacts to TNF-alpha are selected as HCV treatments. These selected treatments can then be examined with more traditional and routine techniques known to one of skill in the art to determine how effective they are in preventing or treating HCV.
  • candidate HCV treatments can include any compound that results in the reversion of the phenotype to a wild-type phenotype.
  • a HCV treatment can function at a level beneath a p38 kinase (or NF-kB), for example by inhibiting later steps in a pathway.
  • NS3/4A model system rather than a NS3/4A transgenic mouse, another NS3/4A model system is used.
  • a cell culture is used instead of an entire organism.
  • a cell expressing NS3/4A protein is administered a wild-type lethal amount of TNF-alpha, alternatively, the cells may create their own TNF-alpha.
  • candidate p38 (or NF-kB) inhibitors are applied to the cells. Cells will primarily die if the candidate p38 (or NF-kB) inhibitor is a p38 (or NF-IcB) inhibitor (assuming the candidate inhibitor does not kill the wild-type cells when it is administered to the wild-type cells alone).
  • the cells are liver cells.
  • the cells are any type of cell that can express NS3/4A as desired.
  • the testing is done in a mouse, but the mouse is not a traditional transgenic mouse.
  • the mouse is a transient transgenic. That is, one or more of the constructs described herein is provided to said mouse (e.g., an NS3/4A expression construct containing a signal sequence and a secretory sequence is provided by injection).
  • an NS3/4A-containing construct containing a signal sequence and a secretory sequence is provided by injection.
  • compositions, cells, and transgenic NS3/4A mice described above are used to determine the pathways in a cell that are influenced or impacted by NS3/4A expression.
  • an inhibitor to any of the other proteins involved in the cascade e.g., those shown in FIGURE 20
  • any compound to a given protein that reverts the NS3/4A phenotype (e.g., TNF-alpha resistance) to the wild-type phenotype (e.g., TNF-alpha susceptibility) will demonstrate that the protein is influenced by the presence of NS3/4A.
  • the entirety of the pathway(s) that NS3/4A impacts can readily be elucidated by the routine application of the present teachings.
  • EXAMPLE 39 provides a demonstration of this embodiment.
  • the present invention also relates to approaches to identify other proteins involved in the NS3/4A phenotype.
  • alternative inhibitors or enhancers i.e., SOCSl
  • SOCSl alternative inhibitors or enhancers
  • the various proteins are tested until the precise protein that interacts with NS3/4A is identified. This protein is then used as a target for development of a HCV treatment.
  • HCV treatments based on these proteins can be readily developed.
  • SOCSl siRNA or microRNA can be administered.
  • SOCSl will be shown to be involved in the NS3/4A phenotype. This also would mean that SOCSl would be a target for HCV treatments (e.g., SOCSl antibodies, competitive binders, etc.).
  • a method in which one uses a composition that reverses an altered activity level induced by NS3/4A, as shown in FIGURE 20.
  • This can be directly, for instance by preventing an interaction between NS3/4A, for example through an antibody.
  • Antibodies that bind to the proteins identified in FIGURE 20 as possibly interacting directly with NS3/4A can be made.
  • this could be through altering the activity of another protein either above or below the protein that interacts with NS3/4A.
  • it could be achieved by preventing the activation of a precursor or preventing the over-activation or uneractivation of later steps in the cascade.
  • Guidance and description of which step(s) is provided in FIGURE 20 and in the discussion and Examples.
  • FIGURE 20 displays the order and interaction between the various proteins. Arrows indicate activation, while flat bars indicate inhibition.
  • NS3/4A results in an inhibition of a particular enzyme
  • a method or composition that activates or stimulates later steps in that same cascade can be useful for inhibiting HCV.
  • One application of this method in the treatment of HCV is described in the Examples below.
  • the transgenic animals used are NS3/4A transgenic mice. In some embodiments, the transgenic animals used are coNS3/4A transgenic mice. In some embodiments, the transgenic animals used are positive or negative PADSI NS3/4A transgenic mice. In some embodiments, the transgenic animals used are variant positive or negative PADSI NS3/4A transgenic mice. In some embodiments, the transgenic animals used are variant positive or negative PADSI coNS3/4A transgenic mice. In some embodiments, any of the transgenic animals described above may be used as models for isolating candidate protease inhibitors.
  • the transgenic animal displays a visible phenotype indicating that the organism is producing NS3/4A proteins.
  • the transgenic organism displays an enlarged liver.
  • the transgenic organism displays a form of steatosis.
  • Detection of whether or not the candidate protease inhibitor functions as a protease inhibitor can be performed by many different methods. For example, since the transgenic animal described above displays a phenotype that is similar to a human infected with HCV, similar phenotypes may be used to determine if the transgenic animal. Additionally, as the cleaving of the NS3/4A peptide bond is required for the cleaving of several other protein products of the HCV protein, one may detect the activity of the NS3/4A protease by detecting the amount of cleaved NS3/4A peptide in the transgenic organism.
  • cleaved products may be tested for other cleaved products as well, such as 4A/4B, 4B/5A, and 5A/5B, for example.
  • these cleaved products are detected by using antibodies directed to each half of the protein product, as described in the Examples.
  • the transgenic organism has other genes in its alleles.
  • the transgenic organism is only transgenic for the NS3 protease and for the NS4A enhancer.
  • the other proteins to be cleaved may be added before, simultaneously, or after the addition of the candidate protease inhibitor to the transgenic organism. By doing this, one knows precisely how much initial protein material one has and what form it is in.
  • the NS4A/4B, 4B/5A, and 5A/5B can also be added by viral vector.
  • the transgenic organism contains the NS3/4A gene
  • the proteolytic activity of NS3/4A on its own NS3/4A peptide bond requires no additional genes.
  • the PADSI constructs need not be fluorescent.
  • Beta-galactosidase can be used as a marker for protease activity.
  • multiple transgenic organisms are tested in each set of experiments. This may be done in order for enough sample to be isolated at each stage of the experiment, especially in situations in which organism sacrifice may be required in order to obtain enough sample.
  • multiple candidate compounds are administered at one time in a pool of candidate compounds. A positive response will result in subfractions of the pool being administered to determine which compounds are responsible for the inhibition of the protease activity.
  • a successful protease inhibitor will be one which shows any decrease in the amount of cleaved product examined.
  • a candidate protease inhibitor will be considered a protease inhibitor if it reduces the amount of cleaved protein product by at least or more than 1%, 2%, 3%, 4-5%, 6-10%, 11-20%, 20-30%, 30- 40%, 40-50%, 50-60%, 60-70%, 70-80%, 90-95%, 95-96%, 97%, 98%, 99%, 99-100%.
  • a candidate protease inhibitor will be considered a protease inhibitor if it displays an ability to decrease the amount of proteolytic activity, and causes little harm to the transgenic organism.
  • "little harm" is a relative term, thus, a candidate protease inhibitor that causes less harm to an organism than an HCV infection would cause is considered a protease inhibitor.
  • little harm means that the protease inhibitor causes less or the same amount of harm to a patient as compared to other similar drugs relating to HCV treatments.
  • the harm caused can be severe, such as resulting in tissue and cell death, but the damage is limited to areas that are infected with the HCV.
  • the protease inhibitor identified using the methods described herein may be used to treat HCV or prevent HCV from spreading in an organism.
  • treat what is meant is that when the protease inhibitor is administered in an effective dose to a patient, an effect caused by HCV is reduced.
  • the physical manifestations of HCV are reduced by the application of the protease inhibitor.
  • the amount of cleaved protein product from HCV proteins is reduced.
  • the rate of cleaving of the proteins of the HCV is reduced. Treatment does not require the elimination of all symptoms or the prevention of all proteolytic activity.
  • the protease inhibitor can be used to reduce the symptoms or the amount of HCV present in a host.
  • the protease inhibitor can be used to help ameliorate the symptoms and problems associated with HCV infection.
  • a transgenic organism that has the ability to produce a PADSI protein is used to screen candidate inhibitors for their ability to inhibit protease activity. In some embodiments, this is done within an organism that is transgenic for the PADSI construct. However, the organism need not be transgenic for the PADSI construct itself.
  • a mouse that is transgenic for the NS3/4A construct can be used as a host " and the PADS! construct can be delivered to the host's liver at a desired time and with the appropriate promoter, or directly in protein form.
  • the blood of a negative PADSI transgenic organism is examined to determine if a detectable marker, which is released from hepatocytes via NS3 and/or NS3/4A protease activity, is present in nonhepatocytes.
  • a detectable marker which is released from hepatocytes via NS3 and/or NS3/4A protease activity
  • the presence of the signal molecule in nonhepatocyte cells can indicate that the NS3/4A complex (or NS3, as appropriate) is still proteolytically active.
  • the inhibitor will reduce the amount of signal molecule (the secreted indicator) present in nonhepatocytes.
  • the presence of a protease inhibitor will be demonstrated by the fact that there is a greater amount of signal molecule in the hepatocytes than in the venous blood.
  • the presence of an inhibitor will be demonstrated by the fact that there is a reduction in the amount of signal molecule present in nonhepatocytes. Any significant amount of reduction will be sufficient, for example, reductions to 99, 99-90, 90-70, 70-50, 50-30, 30-10, 10-5, 5-1, or less will be sufficient to demonstrate that there is a protease inhibitor in the transgenic organism.
  • Methods of detecting the signal peptide are known in the art and will vary based upon the particular peptide and the amount of signal molecule one starts with, among other factors. For example, if the signal molecule is fluorescent, then fluorescent measurements can be made. For example, venous blood, can be taken, or whole body screening can be performed. In the later, where there are sufficient signal molecules present (or, as appropriate, absent), fluorescent readings through the skin can be possible without withdrawing a blood sample from the transgenic organism.
  • the mice are not killed in order to determine if the candidate protease inhibitor is effective.
  • the level of signal molecule, or secreted indicator is determined by non-invasive means. Any suitable method may be used.
  • a CCD may be used to detect the presence of the signal molecule in various tissue, as demonstrated by Wu et al., (MoI. Ther., 4:297-306, (2001)), herein incorporated by reference in its entirety.
  • the CCD is positioned for detection of the signal molecule anywhere that fluorescence of venous blood is detectable through the surface of the organism.
  • the signal molecule will be present in nonhepatocytes, e.g., the blood, unless an effective protease inhibitor is administered to the mouse, at which point the signal molecule will be relatively limited to the cells that create the PADSI.
  • a CCD at the surface of the organism's skin will be able to detect the presence of the signal molecule in nonhepatocytes, which will be indicative of a lack of a protease inhibitor.
  • the CCD will also be able to detect the absence of the signal molecule at the surface of the organism's skin, thus indicating the presence of a protease inhibitor.
  • methods of delivery of protease inhibitors are tested.
  • the level of signal molecule in the venous blood will decrease (or increase as appropriate) when the inhibitor makes it into the hepatocytes, one can monitor the effectiveness of the delivery method as a function of the absence of signal molecule in the blood.
  • delivery compositions for protease inhibitors are tested.
  • one may administer a known protease inhibitor with a variety of different delivery compounds.
  • One possible example of a delivery composition would be an antibody targeted to hepatocytes, which may improve the delivery of the protease inhibitor to the hepatocytes.
  • the positive PADSI construct is used to screen for protease inhibitors.
  • the procedure can involve the same constructs described above for the positive PADSI constructs, the same NS3/4A transgenic mouse described herein, and the same detection procedures described above.
  • One difference between the method of screening with this PADSI mouse and the above method involving a negative PADSI mouse is that in analyzing the amount of detectable marker present in the venous blood of the mouse, or external to the liver cells, that an increase in the amount of detectable marker in the venous blood will indicate that the candidate protease inhibitor is functioning as a protease inhibitor.
  • the positive PADSI construct can be used to screen for NS3 protease inhibitors.
  • a PADSI construct as shown in FIGURE 14C, is created.
  • the detectable marker is luciferase.
  • a NS3 transgenic mouse is created, as described herein. The amount of detectable marker in the blood system of the transgenic mouse is detected.
  • the positive PADSI construct is delivered, through approaches known in the art, to the transgenic mouse so that there are positive PADSI protein constructs in the liver cells of the NS3 transgenic mouse.
  • the NS3/4A cleavage site may contain different amounts of the NS3 protein or the NS4A protein, as long as the NS3 protein is not autocatalytic under normal circumstance. Thus, in one embodiment, an entire NS3 protein is used, although it is catalytically inactive.
  • the section below describes the manufacture of compositions that comprise the HCV nucleic acids, HCV peptides, NS3 protease inhibitors, kinase inhibitors, and compounds identified by the methods described herein.
  • the NS3 protease inhibiting agents identified by the methods described herein can be suitable for incorporation into pharmaceuticals or dietary supplements that treat or prevent HCV replication or infection in subjects or improve the general health and welfare of subjects infected with HCV.
  • the active ingredients described herein can be processed in accordance with conventional methods to produce medicinal agents and dietary supplements for administration to subjects, e.g., mammals including humans.
  • the active ingredients can be incorporated into a pharmaceutical or dietary supplement product with and without modification.
  • the manufacture of pharmaceuticals or dietary supplement that deliver the compounds of this invention by several routes are aspects of the invention.
  • DNA, RNA, and viral vectors having sequence encoding the NS3 protease modulators or kinase inhibitors are used with embodiments.
  • Nucleic acids encoding NS3 protease modulators or kinase inhibitors can be administered alone or in combination with other active ingredients.
  • compositions described herein are also useful as immunogens, which can be administered alone or in conjunction with an adjuvant.
  • Preferred embodiments include compositions that comprise one or more of the nucleic acids and/or peptides described above with or without an adjuvant ⁇ e.g., ribavirin, see e.g., U.S. Pat. No. 6,680,059, herein expressly incorporated by reference in its entirety). That is, some of the compositions described herein are prepared with or without an adjuvant and comprise, consist, or consist essentially of a NS3/4A peptide (SEQ. ID. NO.: 2 or SEQ. ID.
  • nucleic acid encoding one or more of these molecules e.g., SEQ. ID. NO.: 35 or a fragment thereof that is any number of consecutive nucleotides between at least 30-2112 (e.g., 30-50, 50-100, 100-200, 200-500, 500-1000, 1000-1500, 1500-2079, or 1500- 2112 consecutive nucleotides in length).
  • compositions are prepared with or without an adjuvant and comprise, consist, or consist essentially of one or more of the NS3/4A mutant peptides (SEQ. ID. NOs.: 3-13) and fragments thereof that are any number of consecutive amino acids between at least 30-500 (e.g., 30-50, 50-70, 70-90, 90-150, 150- 200, 200-500, amino acids in length).
  • Embodiments of the invention also include methods of making and using the compositions above. Some methods involve the making of nucleic acids encoding NS3/4A, codon-optimized NS3/4A, mutant NS34A, fragments thereof that are any number of consecutive nucleotides between at least 30-100 (e.g., 30-40, 40-50, 50-60, 60-75, 75-90, or 90-2000, or more consecutive nucleotides in length), peptides corresponding to said nucleic acids, constructs comprising said nucleic acids, and cells containing said compositions.
  • nucleic acids encoding NS3/4A, codon-optimized NS3/4A, mutant NS34A, fragments thereof that are any number of consecutive nucleotides between at least 30-100 (e.g., 30-40, 40-50, 50-60, 60-75, 75-90, or 90-2000, or more consecutive nucleotides in length), peptides corresponding to said nucleic acids, constructs comprising said
  • Preferred methods concern the making of vaccine compositions or immunogenic preparations that comprise, consist, or consist essentially of the newly discovered NS3/4A fragment, codon-optimized NS3/4A, or an NS3/4A mutant (e.g., a truncated mutant or a mutant lacking a proteolytic cleavage site), or a fragment thereof or a nucleic acid encoding one or more of these molecules, as described above.
  • Preferred fragments for use with the methods described herein include SEQ. ID. NOs.: 12-27 and fragments of SEQ. ID. NO.: 35 that contain at least 30 consecutive nucleotides.
  • compositions described above can be made by providing an adjuvant (e.g., ribavirin), providing an HCV antigen (e.g., a peptide comprising an HCV antigen such as (SEQ. ID. NOs.: 2-11 or 36) or a fragment thereof such as, SEQ. ID. NOs.: 12-26 or a nucleic acid encoding one or more of said peptides), and mixing said adjuvant and said antigen so as to formulate a composition that can be used to enhance or facilitate an immune response in a subject to said antigen.
  • an adjuvant e.g., ribavirin
  • HCV antigen e.g., a peptide comprising an HCV antigen such as (SEQ. ID. NOs.: 2-11 or 36) or a fragment thereof such as, SEQ. ID. NOs.: 12-26 or a nucleic acid encoding one or more of said peptides
  • the compounds of this invention can be employed in admixture with conventional excipients, i.e., pharmaceutically acceptable organic or inorganic carrier substances suitable for parenteral, enteral (e.g., oral) or topical application that do not deleteriously react with the pharmacologically active ingredients of this invention.
  • conventional excipients i.e., pharmaceutically acceptable organic or inorganic carrier substances suitable for parenteral, enteral (e.g., oral) or topical application that do not deleteriously react with the pharmacologically active ingredients of this invention.
  • Suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, gum arabic, vegetable oils, benzyl alcohols, polyetylene glycols, gelatine, carbohydrates such as lactose, amylose or starch, magnesium stearate, talc, silicic acid, viscous paraffin, perfume oil, fatty acid monoglycerides and diglycerides, pentaerythritol fatty acid esters, hydroxy methylcellulose, polyvinyl pyrrolidone, etc.
  • auxiliary agents e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, flavoring and/or aromatic substances and the like that do not deleteriously react with the active compounds.
  • the effective dose and method of administration of a particular formulation having a a compound described herein can vary based on the individual needs of the patient and the treatment or preventative measure sought. Efficacy and toxicity of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED50 (the dose therapeutically effective in 50% of the population).
  • ED50 the dose therapeutically effective in 50% of the population.
  • NS3 protease inhibiting agents identified by the in vitro or in vivo screens discussed above can be administered to the transgenic mouse models described above and the effect on the HCV phenotype in the mouse can be determined. The data obtained from these assays is then used in formulating a range of dosage for human use.
  • the dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with no toxicity. The dosage varies within this range depending upon type of compound, the dosage form employed, sensitivity of the patient, and the route of administration.
  • Normal dosage amounts of a composition described herein may vary from approximately 1 to 100,000 micrograms, up to a total dose of about 10 grams, depending upon the route of administration. Desirable dosages include 250 ⁇ g, 500 ⁇ g, lmg, 50mg, lOOmg, 150mg, 200mg, 250mg, 300mg, 350mg, 400mg, 450mg, 500mg, 55Omg, 600mg, 650mg, 700mg, 750mg, 800mg, 850mg, 900mg, Ig, l.lg, 1.2g, 1.3g, 1.4g, 1.5g, 1.6g, 1.7g, 1.8g, 1.9g, 2g, 3g, 4g, 5, 6g, 7g, 8g, 9g, and 1Og.
  • the dose of the composition preferably produces a tissue or blood concentration or both from approximately 0.1 ⁇ M to 50OmM. Desirable doses produce a tissue or blood concentration or both of about 1 to 800 ⁇ M. Preferable doses produce a tissue or blood concentration of greater than about 10 ⁇ M to about 500 ⁇ M.
  • Preferable doses are, for example, the amount of composition required to achieve a tissue or blood concentration or both of lO ⁇ M, 15 ⁇ M, 20 ⁇ M, 25 ⁇ M, 30 ⁇ M, 35 ⁇ M, 40 ⁇ M, 45 ⁇ M, 50 ⁇ M, 55 ⁇ M, 60 ⁇ M, 65 ⁇ M, 70 ⁇ M, 75 ⁇ M, 80 ⁇ M, 85 ⁇ M, 90 ⁇ M, 95 ⁇ M, lOO ⁇ M, HO ⁇ M, 120 ⁇ M, 130 ⁇ M, 140 ⁇ M, 145 ⁇ M, 150 ⁇ M, 160 ⁇ M, 170 ⁇ M, 180 ⁇ M, 190 ⁇ M, 200 ⁇ M, 220 ⁇ M, 240 ⁇ M, 250 ⁇ M, 260 ⁇ M, 280 ⁇ M, 300 ⁇ M, 320 ⁇ M, 340 ⁇ M, 360 ⁇ M, 380 ⁇ M, 400 ⁇ M, 420 ⁇ M, 440 ⁇ M, 460 ⁇ M, 480 ⁇ M, and 500 ⁇ M.
  • a constant infusion of a composition described herein can also be provided so as to maintain a stable
  • the exact dosage is chosen by the individual physician in view of the patient to be treated. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Additional factors that can be taken into account include the severity of the fertility defect, age of the patient, age, and weight of the patient; diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. Short acting pharmaceutical compositions are administered daily whereas long acting pharmaceutical compositions are administered every 2, 3 to 4 days, every week, or once every two weeks. Depending on half-life and clearance rate of the particular formulation, the pharmaceutical compositions of the invention are administered once, twice, three, four, five, six, seven, eight, nine, ten or more times per day.
  • Routes of administration of the pharmaceuticals and dietary supplements of the invention include, but are not limited to, transdermal, parenteral, gastrointestinal, transbronchial, and transalveolar.
  • Transdermal administration is accomplished by application of a cream, rinse, gel, etc. capable of allowing the pharmacologically active compounds to penetrate the skin.
  • Parenteral routes of administration include, but are not limited to, electrical or direct injection such as direct injection into a central venous line, intravenous, intramuscular, intraperitoneal, intradermal, or subcutaneous injection.
  • Gastrointestinal routes of administration include, but are not limited to, ingestion and rectal.
  • Transbronchial and transalveolar routes of administration include, but are not limited to, inhalation, either via the mouth or intranasally.
  • compositions described herein that are suitable for transdermal administration include, but are not limited to, pharmaceutically acceptable suspensions, oils, creams, and ointments applied directly to the skin or incorporated into a protective carrier such as a transdermal device ("transdermal patch").
  • transdermal patch a transdermal device
  • suitable creams, ointments, etc. can be found, for instance, in the Physician's Desk Reference.
  • suitable transdermal devices are described, for instance, in U.S. Patent No. 4,818,540 issued April 4, 1989 to Chinen, et al.
  • compositions described herein that are suitable for parenteral administration include, but are not limited to, pharmaceutically acceptable sterile isotonic solutions.
  • Such solutions include, but are not limited to, saline and phosphate buffered saline for injection into a central venous line, intravenous, intramuscular, intraperitoneal, intradermal, or subcutaneous injection.
  • compositions described herein that are suitable for transbronchial and transalveolar administration include, but not limited to, various types of aerosols for inhalation.
  • Devices suitable for transbronchial and transalveolar administration of these are also embodiments.
  • Such devices include, but are not limited to, atomizers and vaporizers.
  • Many forms of currently available atomizers and vaporizers can be readily adapted to deliver compositions having the pharmacologically active compounds of the invention.
  • compositions described herein that are suitable for gastrointestinal administration include, but are not limited to, pharmaceutically acceptable powders, pills or liquids for ingestion and suppositories for rectal administration. Due to the ease of use, gastrointestinal administration, particularly oral,is a preferred embodiment.
  • compositions described herein are administered with an adjuvant.
  • adjuvants include, but are not limited to, ribavirin, Freund's, mineral gels such as aluminum hydroxide, and surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol.
  • BCG ⁇ Bacillus Calmette-Guerin) and Corynebacterium parvum are also potentially useful adjuvants.
  • a compound with an increased ability to induce an immune response is contemplated.
  • an adjuvant ⁇ e.g., ribavirin
  • an HCV antigen ⁇ e.g., a peptide comprising an HCV antigen such as a NS3/4A protein ⁇ e.g., SEQ. ID. NOs.: 2-11 or 36) or a fragment thereof such as, SEQ. ID. NOs.: 12-26 or a nucleic acid encoding one or more of said peptides
  • an adjuvant ⁇ e.g., ribavirin
  • an HCV antigen e.g., a peptide comprising an HCV antigen such as a NS3/4A protein ⁇ e.g., SEQ. ID. NOs.: 2-11 or 36
  • a fragment thereof such as, SEQ. ID. NOs.: 12-26 or a nucleic acid encoding one or more of said peptides
  • a method of treatment, using the NS3/4A constructs described herein and an adjuvant is contemplated.
  • the expression construct for NS3/4A is introduced into the subject in a mixture of adjuvant ⁇ e.g., ribavirin) or in conjunction with an adjuvant ⁇ e.g., ribavirin).
  • the adjuvant ⁇ e.g., ribavirin is administered shortly after the expression construct at the same site.
  • RNA encoding the HCV polypeptide antigen of interest is provided to the subject in a mixture with ribavirin or in conjunction with an adjuvant ⁇ e.g., ribavirin).
  • Ribavirin is a synthetic guanosine analog that has been used to inhibit RNA and DNA virus replication.
  • Ribavirin has been shown to be a competitive inhibitor of inositol mono-phosphate (IMP) dehydrogenase (IMPDH), which converts IMP to IMX (which is then converted to GMP).
  • IMP inositol mono-phosphate
  • IMPDH inositol mono-phosphate
  • IMX IMX
  • De Clercq Anti viral Agents: characteristic activity spectrum depending on the molecular target with which they interact. Academic press, Inc., New York-N.Y., pp. 1-55 (1993). Intracellular pools of GTP become depleted as a result of long term ribavirin treatment.
  • Ribavirin has been shown to inhibit functional humoral immune responses (Peavy et al., J. Immunol, 126:861-864 (1981); Powers et al., Antimicrob. Agents. Chemother., 22:108-114 (1982)) and IgE-mediated modulation of mast cell secretion. (Marquardt et al., J. Pharmacol. Exp. Therapeutics, 240:145-149 (1987)).
  • an amount of adjuvant that is effective to enhance an immune response to an antigen in an animal can be considered to be an any amount that is sufficient to achieve a blood serum level of antigen approximately 0.25 - 12.5 ⁇ g/ml in the animal, preferably, about 2.5 ⁇ g/ml.
  • the amount of adjuvant is determined according to the body weight of the animal to be given the vaccine. Accordingly, the amount of adjuvant in a particular formulation can be any amount between about 0.1 - 6.0 mg/kg body weight.
  • some embodiments have an amount of adjuvant that corresponds to any amount between 0.1 - 1.0 mg/kg, 1.1 - 2.0 mg/kg, 2.1 - 3.0 mg/kg, 3.1 - 4.0 mg/kg, 4.1 - 5.0 mg/kg, 5.1, and 6.0 mg/kg body weight of an animal. More conventionally, some of the compositions described herein contain any amount between about 0.25 mg - 2000 mg of adjuvant.
  • some embodiments have approximately 250 ⁇ g, 500 ⁇ g, 1 mg, 25 mg, 50 mg, 100 mg, 150 mg, 200 mg, 250 mg, 300 mg, 350 mg, 400 mg, 450 mg, 500 mg, 550 mg, 600 mg, 650 mg, 700 mg, 750 mg, 800 mg, 850 mg, 900 mg, 1 g, 1.1 g, 1.2 g, 1.3 g, 1.4 g, 1.5 g, 1.6 g, 1.7 g, 1.8 g, 1.9 g, and 2 g of adjuvant.
  • the exact amount of adjuvant and/or HCV antigen is chosen by the individual physician in view of the patient to be treated. Further, the amounts of adjuvant can be added in combination to or separately from the same or equivalent amount of antigen and these amounts can be adjusted during a particular vaccination protocol so as to provide sufficient levels in light of patient-specific or antigen- specific considerations.
  • patient-specific and antigen-specific factors that can be taken into account include, but are not limited to, the severity of the disease state of the patient, age, and weight of the patient, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy.
  • a pharmaceutical composition for treating a patient infected by a hepatitis C virus comprising a compound that intereferes with the effects related to expression of NS3 in a genetically modified non-human mammal described above.
  • an anti-HCV pharmaceutical formulated for human administration comprising a p38 MAP kinase inhibitor (or NF-kB inhibitor).
  • said p38 (or NF-kB) inhibitor is SB203580.
  • Some embodiments relate to a method of making the anti-HCV pharmaceutical comprising providing a p38 MAP kinase (or NF-kB) inhibitor and formulating said ⁇ 38 MAP kinase inhibitor for human administration.
  • said p38 MAP kinase inhibitor is SB203580.
  • Some embodiments relate to a method of using the anti-HCV pharmaceutical to inhibit HCV replication comprising identifying a subject in need of a compound that inhibits HCV; and providing said subject a p38 MAP kinase (or NF-kB) inhibitor.
  • said p38 (or NF-kB) inhibitor is SB203580.
  • the inhibition of HCV in said subject is measured.
  • the NS3/4A sequence was amplified from the serum of an HCV-infected patient (HCV genotype Ia) using the Polymerase Chain Reaction (PCR). Total RNA was extracted from serum, and cDNA synthesis and PCR were performed according to standard protocols (Chen M et al., J. Med. Virol. 43:223-226 (1995)). The cDNA synthesis was initiated using the antisense primer "NS4KR" (5'-CCG TCT AGA TCA GCA CTC TTC CAT TTC ATC-3' (SEQ. ID. NO.: 28)).
  • a 2079 base pair DNA fragment of HCV corresponding to amino acids 1007 to 1711, which encompasses the NS3 and NS4A genes, was amplified.
  • a high fidelity polymerase (Expand High Fidelity PCR, Boehringer- Mannheim, Mannheim, Germany) was used with the "NS3KF" primer (5'-CCT GAA TTC ATG GCG CCT ATC ACG GCC TAT-3' (SEQ. ID. NO.: 29) and the NS4KR primer.
  • the NS3KF primer contained a EcoRI restriction enzyme cleavage site and a start codon and the primer NS4KR contained a Xbal restriction enzyme cleavage site and a stop codon.
  • the amplified fragment was then sequenced (SEQ. ID. NO.: 1). Sequence comparison analysis revealed that the gene fragment was amplified from a viral strain of genotype Ia. A computerized BLAST search against the Genbank database using the NCBI website revealed that the closest HCV homologue was 93% identical in nucleotide sequence.
  • the amplified DNA fragment was then digested with EcoRI and Xbal, and was inserted into a pcDNA3.1/His plasmid (Invitrogen) digested with the same enzymes.
  • the NS3/4A-pcDNA3.1 plasmid was then digested with EcoRI and Xba I and the insert was purified using the QiaQuick kit (Qiagen, Hamburg, Germany) and was ligated to a EcoRI/Xba I digested pVAX vector (Invitrogen) so as to generate the NS3/4A-pVAX plasmid.
  • the rNS3 truncated mutant was obtained by deleting NS4A sequence from the NS3/4A DNA. Accordingly, the NS3 gene sequence of NS3/4A-pVAX was PCR amplified using the primers NS3KF and 3'NotI (5'-CCA CGC GGC CGC GAC GAC CTA CAG-3' (SEQ. ID. NO.: 30)) containing EcoRI and Not I restriction sites, respectively. The NS3 fragment (1850 bp) was then ligated to a EcoRI and Not I digested pVAX plasmid to generate the NS 3 -p V AX vector. Plasmids were grown in TOPlO E. coli cells (Invitrogen). The plasmids were sequenced and were verified by restriction cleavage and the results were as to be expected based on the original sequence.
  • Table 1 describes the sequence of the proteolytic cleavage site of NS3/4A, referred to as the breakpoint between NS3 and NS4A. This wild-type breakpoint sequence was mutated in many different ways so as to generate several different NS3/4A breakpoint mutants. Table 1 also identifies these mutant breakpoint sequences.
  • the fragments listed in Table 1 are preferred immunogens that can be incorporated with or without an adjuvant (e.g., ribavirin) into a composition for administration to an animal so as to induce an immune response in said animal to HCV.
  • an adjuvant e.g., ribavirin
  • the NS3/4A-pVAX plasmid was mutagenized using the QUICKCHANGETM mutagenesis kit (Stratagene), following the manufacturer's recommendations.
  • the plasmid was amplified using the primers 5'- CTGGAGGTCGTCACGCCTACCTGGGTGCTCGTT-S' (SEQ. ID. NO.: 31) and 5'- ACCGAGCACCCAGGTAGGCGTGACGACCTCCAG-3' (SEQ. ID. NO.: 32) resulting in NS3/4A-TPT-pVAX.
  • the plasmid was amplified using the primers 5'-CTGGAGGTCGTCCGCGGTACCTGGGTGCTCGTT-S ' (SEQ. ID. NO.: 33) and 5'-ACCGAGCACCCAGGTACC-GCGGACGACCTCCAG-S ' (SEQ. ID. NO.: 34) resulting in NS3/4A-RGT-pVAX. All mutagenized constructs were sequenced to verify that the mutations had been correctly made. Plasmids were grown in competent TOPlO E. coli. The following section describes the codon opitimzation of the NS3/4A gene.
  • the sequence of the previously isolated and sequenced unique NS3/4A gene (SEQ. ID. NO.: 1) was analyzed for codon usage with respect to the most commonly used codons in human cells. A total of 435 nucleotides were replaced to optimize codon usage for human cells. The sequence was sent to Retrogen Inc. (6645 Nancy Ridge Drive, San Diego, CA 92121) and they were provided with instructions to generate a full-length synthetic codon optimized NS3/4A gene. The codon optimized NS3/4A gene had a sequence homology of 79% within the region between nucleotide positions 3417-5475 of the HCV-I reference strain. A total of 433 nucleotides differed. On an amino acid level, the homology with the HCV-I strain was 98% and a total of 15 amino acids differed.
  • the plasmid DNA used for in vivo injection was purified using Qiagen DNA purification columns, according to the manufacturers instructions (Qiagen GmbH, Hilden, FRG). The concentration of the resulting plasmid DNA was determined spectrophotometrically (Dynaquant, Pharmacia Biotech, Uppsala, Sweden) and the purified DNA was dissolved in sterile phosphate buffer saline (PBS) at concentrations of 1 mg/ml.
  • PBS sterile phosphate buffer saline
  • the wild type sequence for the NS3/4A fragment is NS3/4A-pVAX.
  • the NS3/4A breakpoint is identified by underline, wherein the Pl position corresponds to the first Thr (T) and the Pl ' position corresponds to the next following amino acid the NS3/4A-pVAX sequence.
  • the NS3 protease cleaves between the Pl and Pl' positions.
  • HepG2 cells were plated into 25 cm 2 wells (0.5 x 10 6 ) in DMEM medium the day before transfection. Two ⁇ g of each plasmid DNA construct (wtNS3/4A and coNS3/4A) was transfected into HepG2 cells using Fugene 6 Transfection Reagent (Roche). After transfection, the HepG2 cells were incubated for 24- 48hrs.
  • Cell lysates were analysed by immunoprecipitation followed by SDS-PAGE.
  • transient transfected HepG2 cells were lysed in RIPA buffer (0,15M NaCl, 5OmM Tris, 1% Triton-X 100, 1% Na-deoxycholate and 1% SDS).
  • the cell lysates were immunoprecipitated with protein A sepharose and anti-NS3 polyclonal antibody overnight at 4 0 C.
  • the washed pellets were re-suspended in SDS sample buffer, heated at 100°C for 5 minutes prior to SDS- PAGE analysis on 4-12% Bis-Tris gel (Invitrogen) and electrotransferred onto Nitrocellulose membranes.
  • the expression constructs described in Example 1 were purified using the Qiagen DNA purification system, according to the manufacturer's instructions and the purified DNA vectors were used to immunize groups of four to ten Balb/c mice.
  • the plasmids were injected directly into regenerating tibialis anterior (TA) muscles as previously described (Davis et al., Human Gene Therapy 4(6):733 (1993)).
  • mice were injected intramuscularly with 50 ⁇ l/TA of 0.0 ImM cardiotoxin (Latoxan, Rosans, France) in 0.9% sterile NaCl. Five days later, each TA muscle was injected with 50 ⁇ l PBS containing either rNS3 or DNA.
  • Inbred mouse strains C57/BL6 (H-2b), Balb/C (H-2d), and CBA (H-2k) were obtained from the breeding facility at M ⁇ llegard Denmark, Charles River Uppsala, Sweden, or B&K Sollentuna Sweden. All mice were female and were used at 4-8 weeks of age. For monitoring of humoral responses, all mice received a booster injection of 50 ⁇ l /TA of plasmid DNA every fourth week. In addition, some mice were given recombinant NS3 (rNS3) protein, which was purified, as described herein. The mice receiving rNS3 were immunized no more than twice. All mice were bled twice a month.
  • rNS3 recombinant NS3
  • Enzyme immunosorbent assays were used to detect the presence of murine NS3-specific antibodies. These assays were performed essentially as described (Chen et al., Hepatology 28(1): 219 (1998), herein expressly incorporated by reference in its entirety). Briefly, rNS3 was passively adsorbed overnight at 4 0 C to 96-well microtiter plates (Nunc, Copenhagen, Denmark) at 1 ⁇ g/ml in 50 mM sodium carbonate buffer (pH 9.6). The plates were then blocked by incubation with dilution buffer containing PBS, 2% goat serum, and 1% bovine serum albumin for one hour at 37°C.
  • mice immunized with NS3/4A-pVAX had developed NS3 antibodies, whereas one out of five immunized with NS3-pVAX had developed antibodies (FIGURE 1).
  • mice immunized with NS3/4A-pVAX had developed high levels (>10 4 ) of NS3 antibodies (mean levels 10800 ⁇ 4830) and one had a titer of 2160.
  • NS3-pVAX developed NS3 antibodies, none of them developed levels as high as that produced by the NS3/4A-pVAX construct (mean levels 1800 ⁇ 805).
  • the antibody levels elicited by the NS3/4A fusion construct were significantly higher than those induced by NS3-pVAX at six weeks (mean ranks 7.6 v.s 3.4, p ⁇ 0.05, Mann- Whitney rank sum test, and p ⁇ 0.01, Students t- test).
  • immunization with either NS3-pVAX or NS3/4A-pVAX resulted in the production of NS3 -specific antibodies, but the NS3/4A containing construct was a more potent immunogen.
  • the following example describes a similar experiment that compared the immunogenicity of NS3/4A- ⁇ VAX and MSLFl -p VAX.
  • MSLFl gene was found to be more immunogenic than the native NS3/4A gene since NS3 -specific antibodies were significantly higher in mice immunized with the MSLFl- pVAX construct at two weeks after the second and third immunization (TABLE 2). These results confirmed that MSLFl-pVAX was a more potent B cell immunogen than NS3/4A- pVAX. In the next example, the intrinsic immunogenicity of the NS3 genes was examined.
  • mice were immunized with the wtNS3/4A, coNS3/4A DNAs, or wtNS3/4A ⁇ SFV vectors.
  • Doses of 4 ⁇ g DNA were administered using the gene gun and doses of 10 7 SFV particles were injected subcutaneously (s.c).
  • the mice were boosted after four weeks.
  • the mice immunized with the wtNS3/4A-SFV developed antibodies already after the first injection indicating a potent immunogenicity (see FIGURES 2A and 2B).
  • mice immunized with the coNS3/4A or wtNS3/4A-SFV vectors had developed mean antibody levels over 10 3 . (See FIGURES 2A and 2B).
  • none of the mice immunized with the wtNS3/4A plasmid had developed detectable NS3-specif ⁇ c antibodies at six weeks.
  • both codon optimization and mRNA amplification by SFV resulted in an increased B cell immunogenicity of the NS3/4A gene.
  • ThI T helper 1
  • Th2-skewing of the T cell response primed by wtNS3/4A, coNS3/4A, and wtNS3/4A-SFV immunizations the levels of NS3- specif ⁇ c IgGl (Th2) and IgG2a (ThI) antibodies were analyzed (see FIGURES 2A and 2B).
  • mice immunized with rNS3 with or without adjuvant were always ⁇ 1 regardless of the murine haplotype (Sallberg M et al., J Gen Virol, 77:2721-2728 (1996)), signaling a Th2-dominated response Schirmbeck R., et al., Intervirology, 44:115-123 (2001).
  • mice immunized Lm. with the wtNS3, wtNS3/4A DNA, or coNS3/4A plasmids had ThI -skewed Th-cell responses evidenced by IgG2a/IgGl ratios of > 1.
  • codon optimization did not change the IgG subclass distribution.
  • the subclass ratio indicated a mixed Thl/Th2 response.
  • EXAMPLE 6 To test if the enhanced immunogenicity of NS3/4A could be solely attributed to the presence of NS4A, or if the NS3/4A fusion protein in addition had to be cleaved at the NS3/4A junction, another set of experiments were performed. In a first experiment, the immunogenicity of the NS3-pVAX, NS3/4A-pVAX, and mutant NS3/4A constructs were compared in Balb/c mice. Mice were immunized on week 0 as described above, and, after two weeks, all mice were bled and the presence of antibodies to NS3 at a serum dilution of 1:60 was determined (TABLE 3). Mice were bled again on week 4.
  • the mutant constructs for example, the NS3/4A-TGT- ⁇ VAX vector was comparable to the NS3-pVAX vector (4/10 vs. 0/10; NS, Fisher's exact test).
  • the NS3/4A-pVAX vector was more potent than the mutant constructs.
  • HCV hepatocellular carcinoma
  • EXAMPLE 7 This example demonstrates the effect of codon optimization and mRNA amplification on priming NS3-specific cytoxic T lymphocytes (CTLs).
  • CTLs NS3-specific cytoxic T lymphocytes
  • the CTL priming event is enhanced by codon optimization or mRNA amplification of the NS3/4A gene.
  • the difference was less clear when using the NS3/4A-expressing EL-4 cells presumably since this assay is less sensitive.
  • all NS3/4A vectors seemed to prime NS3-specific CTLs with a similar efficiency. (See FIGURE 4B).
  • the NS3/4A-containing vectors were clearly more efficient in priming NS3-specif ⁇ c CTLs as compared to the plasmid containing only the wtNS3 gene.
  • codon optimization or mRNA amplification of the NS3/4A gene seems to allow for a more rapid priming of NS3-specific CTLs.
  • an in vivo tumor growth assay was performed.
  • an SP2/0 tumor cell line (SP2/0-Agl4 myeloma cell line (H-2 d )) stably transfected with the NS3/4A gene was made.
  • the SP2/0 cells were maintained in DMEM medium supplemented with 10% fetal calf serum (FCS; Sigma Chemicals, St.
  • the pcDNA3.1 plasmid containing the NS3/4A gene was linearized by BgIII digestion. A total of 5 ⁇ g linearized plasmid DNA was mixed with 60 ⁇ g transfection reagent (Superfect, Qiagen, Germany) and the mixture was added to a 50% confluent layer of SP2/0 cells in a 35 mm dish. The transfection procedure was performed according to manufacturer's protocol.
  • Transfected cells were cloned by limiting dilution and selected by addition of 800 ⁇ g geneticin (G418) /ml complete DMEM medium after 14 days.
  • a stable NS3/4A-expressing SP2/0 clone was identified using PCR and RT-PCR and/or a capture EIA using a monoclonal antibody to NS3. All EIAs for the detection of murine NS3 antibodies were essentially performed as follows. In brief, rNS3 (recombinant NS3 protein produced in E.
  • CoIi dialyzed overnight against PBS, and sterile filtered
  • the plates were then blocked by incubation with dilution buffer containing PBS, 2% goat serum, and 1% bovine serum albumin for one hour at +37°C.
  • Serial dilutions of mouse sera starting at 1:60 were then incubated on the plates for one hour.
  • Bound murine serum antibodies were detected by an alkaline phosphatase conjugated goat anti-mouse IgG (Sigma cell products, Saint Louis, Missouri USA) followed by addition of the substrate pNPP (1 tablet/5ml of IM Diethanolamin buffer with 0.5 mM MgC12). The reaction was stopped by addition of IM NaOH. Absorbance was then read at 405 nm.
  • mice The in vivo growth kinetics of the SP2/0 and the NS3/4A-SP2/0 cell lines were then evaluated in Balb/c mice. Mice were injected subcutaneously with 2 x 10 6 tumor cells in the right flank. Each day the size of the tumor was determined through the skin. The growth kinetics of the two cell lines was comparable. The mean tumor sizes did not differ between the two cell lines at any time point, for example. ⁇ See TABLE 4).
  • mice immunized with the NS3/4A constructs had developed a T-cell response against NS3.
  • NS3-sp2 NS3-spNS3 1.750 0.58 0.584
  • NS3-sp2 4 9.750 24.917 4.992 2.496 NS3-spNS3 3 8.000 1.000 1.000 0.57
  • mice were immunized with PBS, rNS3, a control DNA, or the NS3/4A construct, and tumor sizes were determined, as described above.
  • the NS3/4A construct was able to elicit a T-cell response sufficient to cause a statistically significant reduction in tumor size (See TABLE 6).
  • the example below describes more experiments that were performed to determine whether the reduction in tumor size can be attributed to the generation of NS3-specific T- lymphocytes.
  • mice immunized with the NS3/4A-pVAX plasmid the growth of NS3/4A-SP2/0 tumor cells was significantly inhibited as compared to growth of the non-transfected SP2/0 cells. (See TABLE 7).
  • NS3/4A- pVAX immunization elicits CTLs that inhibit growth of cells expressing NS3/4A in vivo.
  • mice were immunized with different immunogens (4 ⁇ g of plasmid) using a gene gun at weeks zero, four, eight, twelve, and sixteen. Two weeks after the last immunization approximately 1 x 10 6 NS3/4A-expressing SP2/0 cells were injected s.c into the right flank of the mouse. The kinetics of the tumor growth was then monitored by measuring the tumor size through the skin at days seven, 11, and 13. The mean tumor sizes were calculated and groups were compared using the Mann- Whitney non-parametric test. At day 14 all mice were sacrificed.
  • mice were immunized three times with lOO ⁇ g NS3/4A-pVAX Lm. Two weeks after the last injection the mice were sacrificed and splenocytes were harvested. Re- stimulation cultures with 3 x 10 6 splenocytes and 3 x 10 6 NS3/4A-SP2/0 cells were set.
  • NS3/4A-SP2/0 or SP2/0 cells were used as targets. Percent specific lysis was calculated as the ratio between lysis of NS3/4A-SP2/0 cells and lysis of SP2/0 cells. Mice immunized with NS3/4A-pVAX displayed specific lysis over 10% in four out of five tested mice, using an effector to target ratio of 20:1 ⁇ See FIGURE 8A and 8B).
  • in vitro stimulation was carried out for five days in 25 -ml flasks at a final volume of 12 ml, containing 5U/ml recombinant murine IL-2 (mIL-2; R&D Systems, Minneapolis, MN).
  • the restimulation culture contained a total of 4O x 10 6 immune spleen cells and 2 x 10 6 irradiated (10,000 rad) syngenic SP2/0 cells expressing the NS3/4A protein.
  • mIL-2 murine IL-2
  • the restimulation culture contained a total of 4O x 10 6 immune spleen cells and 2 x 10 6 irradiated (10,000 rad) syngenic SP2/0 cells expressing the NS3/4A protein.
  • a standard 5 Cr-release assay was performed. Effector cells were harvested and a four-hour Cr assay was performed in 96-well U-bottom plates in a total volume of 200 ⁇ l.
  • a total of 1 x 10 6 target cells was labeled for one hour with 20 ⁇ l of 51 Cr (5 mCi/ml) and then washed three times in PBS. Cytotoxic activity was determined at effectortarget (E: T) ratios of 40:1, 20:1, and 10:1, using 5 x 10 3 51 Cr-labeled target cells/well.
  • spleenocytes were harvested from C57BL/6 mice 12 days after peptide immunization and were resuspended in RPMI 1640 medium supplemented with 10% FCS, 2 niM L-Glutamine, 1OmM HEPES, 100 U/ml Penicillin and 100 ⁇ g/ml Streptomycin, ImM non-essential amino acids, 50 ⁇ M ⁇ -mercaptoethanol, ImM sodium pyruvate.
  • In vitro stimulation was carried out for five days in 25ml flasks in a total volume of 12ml, containing 25 x 10 6 spleen cells and 25 x 10 6 irradiated (2,000 rad) syngeneic splenocytes.
  • the restimulation was performed in the presence of 0.05 ⁇ M NS3/4A H-2D b binding peptide (sequence GAVQNEVTL SEQ. ID. NO.: 37) or a control peptide H-2D b peptide (sequence KAVYNFATM SEQ. ID. NO.: 38).
  • a 51 Cr-release assay was performed.
  • RMA-S target cells were pulsed with 50 ⁇ M peptide for 1.5 hrs at +37°C prior to 51 Cr- labelling, and then washed three times in PBS. Effector cells were harvested and the four hour 51 Cr assay was performed as described.
  • Cytotoxic activity was determined at the E:T ratios 60:1, 20:1, and 7:1 with 5 x 10 3 51 Cr-labeled target cells/well. By these assays, it was determined that the coNS3/4A gene primed higher levels of in vitro lytic activity compared to the NS3/4A-pVAX vector. (See FIGURE 4A and FIGURE 4B). Similar results were obtained with both the peptide coated H-2b expressing RMA-S cells and NS3/4A-expressing EL-4 cells.
  • the cells were then washed twice in FACS buffer and resuspended in 100 ⁇ l FACS buffer containing 10 ⁇ l/lOO ⁇ l PE conjugated Rat- ⁇ Mouse IgGl secondary antibody and incubated on ice for 30 minutes. The cells were then washed twice in FACS buffer and incubated with l ⁇ g/10 6 cells of FITC conjugated ⁇ -mouse CD8 antibody for 30 minutes. The cells were then washed twice in FACS buffer and resuspended in 0.5 ml FACS buffer containing 0.5 ⁇ g/ml of PI. Approximately 200,000 events from each sample were acquired on a FACS Calibur (BDB) and dead cells (PI positive cells) were excluded from the analysis.
  • BDB FACS Calibur
  • the advantage of quantifying specific CTLs by FACS analysis is that it bypasses the possible disadvantages of in vitro expansion of CTLs in vitro prior to analysis.
  • Direct ex-vivo quantification of NS3-specific CTLs using NS3-peptide loaded divalent H-2D b :Ig fusion protein molecules revealed that the codon optimized MSLF-I gene primed a effectively primed NS3 -specific CTLs already after two immunizations, whereas the original NS3/4A gene did not.
  • the optimized MSLF-I gene effectively primes NS3-specific CTLs that are of higher frequency and of better functionality by all parameters tested, as compared to the original NS3/4A gene.
  • the following example demonstrates which population of cells is the protector population.
  • This example demonstrates a method by which one may determine which population of cells is the major protector population.
  • CD4+ or CD8+ T cells of splenocytes from coNS3/4A plasmid immunized H-2 b mice indicated that CD8+ T cells were the major effector cells in the 51 Cr-release assay.
  • CD4+ or CD8+ T cells were depleted in mice immunized with the coNS3/4A plasmid one week prior to, and during, challenge with the NS3/4A-EL-4 tumor cell line. Analysis by flow cytometry revealed that 85% of CD4+ and CD8+ T cells had been depleted, respectively.
  • NS3/4A- specific CD8+ CTLs are the major protective cell at the effector stage in the in vivo model for inhibition of tumor growth.
  • the following example demonstrates the benefit of codon optimization in vivo.
  • This example demonstrates the effect of codon optimization and mRNA amplification on priming in vivo functional NS3-specific CTLs.
  • the tumor challenge model was used to evaluate how effective the different immunogens were in priming a protective immunity against growth of NS3/4A-EL-4 tumor cells in vivo. To ensure that the effectiveness of the priming event was studied, all mice were immunized only once. Vectors containing NS3/4A were able to rapidly prime protective immune responses as compared to the immunized with the empty pVAX plasmid (p ⁇ 0.05, ANOVA; FIGURE 10). However, this was dependent on NS4A but independent on either codon optimization or mRNA amplification and indicates that C57BL/6 mice are easily protected against tumor growth using genetic immunization.
  • the next example examines the prerequisites for priming of CD8+ CTL.
  • This example demonstrates how to evaluate the effect of therapeutic immunization after the injection of tumor cells.
  • Groups of 10 C57BL/6 mice were challenged with 10 6 NS3/4A-EL-4 tumor cells.
  • One group was immunized transdermally with of 4 ⁇ g coNS3/4A at six days, and another group at 12 days, after tumor challenge.
  • both groups had significantly smaller tumors as compared to the nonimmunized control group (p ⁇ 0.01, respectively, ANOVA; FIGURE 12).
  • gene gun immunization with the coNS3/4A plasmid is an effective therapeutic vaccine.
  • the next example describes some of the peptide embodiments in greater detail.
  • NS3/4A-pVAX, MSLF 1-p VAX, and the NS3/4A mutant constructs, described in Example 1 the plasmids were transcribed and translated in vitro, and the resulting polypeptides were visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE).
  • SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis
  • the in vitro analysis revealed that all proteins were expressed to high amounts from their respective expression constructs.
  • the rNS3 construct (NS3-pVAX vector) produced a single peptide of approximately 61IcDa
  • the mutant constructs e.g., the TGT construct (NS3/4A-TGT-pVAX) and the RGT construct (NS3/4A-RGT-pVAX)
  • the cleaved product produced from the expressed NS3/4A peptide was approximately 61 kDa, which was identical in size to the rNS3 produced from the NS3-pVAX vector.
  • the amount of input DNA was serially diluted prior to addition to the assay.
  • Serial dilutions of the plasmids revealed that the coNS3/4A plasmid gave stronger bands at higher dilutions of the plasmid than the wild-type NS3/4A plasmid, providing evidence that in vitro transcription and translation was more efficient from the coNS3/4A plasmid.
  • the NS3/4A- pVAX and coNS3/4A plasmids were then analyzed for protein expression using transiently transfected Hep-G2 cells. Similar results were obtained in that the MSLF-I gene provided more efficient expression of NS3 than the native NS3/4A gene.
  • NS3/4A complementary DNA (cDNA) clone from a HCV genotype 1 infected patient was isolated as described in Lazdina et al. (2001).
  • a fragment containing the MUP promoter (Held et al. 1989) and NS3/4A ⁇ Hindlll to EcoRI) was excised and cloned into the pVAXl (Invitrogen, San Diego) expression vector.
  • pMUP-NS3/4A (illustrated in FIGURE 14A).
  • the entire pMUP-NS3/4A-BGH polyadenylation signal construct was sequenced prior to microinjection to confirm correct sequence.
  • the purified transgene construct was microinjected into fertilized oocytes from C57BL/6 (H-2 b ) x CBA (H-2 k ) mice, see FIGURE 14.
  • Potential founder mice were analyzed for the presence of transgene by polymerase chain reaction (PCR) and Southern blot of genomic tail DNA.
  • PCR polymerase chain reaction
  • specific outer primers were used; for example, sense primer (5'-CCT GAA TTC ATG GCG CCT ATC ACG GCC TAT-3') (SEQ ID. NO.: 41) and antisense primer (5'-CCG TCT AGA TCA GCA CTC TTC CAT TTC ATC-3') (SEQ ID.
  • mice were born from mothers implanted with microinjected oocytes.
  • Tail DNA from the founder mice was screened for the presence of the NS3/4A transgene by PCR and Southern blot.
  • Six founder mice were identified by screening, all having the full- length NS3/4A fragment as determined by PCR.
  • the full-length amplification of NS3/4A from transgenic mice tail DNA was determined by PCR. The appropriate bands appeared for the transgenic mouse and positive control. No bands were observed for the negative control or a non-transgenic mouse EXAMPLE 19
  • This example provides a method for the visualization of genomic DNA, as described above.
  • a Southern blot analysis of genomic DNA isolated from mouse tails was performed.
  • lO ⁇ g DNA was immobilized onto un-charged nylon membranes using a Bio-Dot apparatus (Bio-Rad Laboratories, Hercules, CA).
  • a lkb gel-purified fragment of the NS3/4A DNA was labeled with [ ⁇ - 32 P]dATP by random priming procedure and used as a probe.
  • the probe was hybridized with the membrane at 68°C overnight and washed stringently.
  • the genomic NS3/4A DNA was visualized by exposure of the membrane to X-ray film (Hyper f ⁇ lm-MP, Amersham) for 12-72 hours.
  • Six founder mice were identified by the above method
  • Organ samples (lOOmg) were homogenized and analyzed by inimunoprecipitation followed by SDS-PAGE.
  • organ homogenates were lysed in ImL radioimmune precipitation assay (RIPA) buffer (0.15M NaCl, 5OmM Tris, 1% Triton-X 100, 1% Na-deoxycholate and 1% SDS).
  • the homogenates were immunoprecipitated with protein A sepharose and anti-NS3 or anti-NS4A polyclonal antibody overnight at 4°C.
  • NS3/4A protein was re-suspended in SDS sample buffer, heated at 100°C for 5 minutes prior to SDS-PAGE analysis on 4-12% Bis-Tris gel (Invitrogen) and electrotransferred onto Nitrocellulose membranes.
  • Detection of NS3/4A protein was done according to manufacturer's protocol by using a chemiluminiscence-linked Western blot kit (WesternBreeze; Invitrogen).
  • NS3/4A protein expression was detected and quantified as a chemiluminiscent signal by using an NS3- or NS4A-specif ⁇ c polyclonal antibody. Chemiluminiscent signals were detected by the GeneGnome (Syngene, Cambridge, UK).
  • the characterization of the NS3 protein expression included comparing the detection of NS3 protein in liver homogenates from transgenic mice with a molecular weight marker, (Magic Mark, Invitrogen) and Western blot analysis of immunoprecipitated HepG2 cells transient transfected with the codon optimised NS3/4A gene, and a non-transgenic littermate.
  • a band for NS3 was detected only in transgenics and, a similar NS3 band, was detected from the codon optimized NS3/4A transfected HepG2 cells.
  • NS3 protein expression was detected only in total protein preparations from livers of one out of the six transgenic mice lineages.
  • NS3 protein expression was examined in different tissues of transgenic and non-transgenic mice by immunoprecipitation and Western blot. Liver, kidney, and spleen from a NS3/4A transgenic mouse was compared with the liver, kidney and spleen of a non- transgenic mouse. The only sample with an appropriately sized band for NS3 was found in the liver sample from the NS3/4A transgenic mouse, as well as the positive controls, such as HepG2 cells transfected with the coNS3/4A gene, and a recombinant NS3 protein.
  • the full-length wtNS3/4A gene was detected in DNA from transgenic mouse livers by PCR. BHK-2 cells were transiently transfected with the codon optimized NS3/4A gene and a MOCK transfected control, as well as nontransgenic mice. Thus, this is the first transgenic mouse with a detectable expression of the HCV NS3 protein.
  • transgene expression was restricted to the liver and was not detectable in other tissues, such as spleen, kidney, lungs, heart, brain and skin. This is consistent with the expected expression pattern of the MUP promoter.
  • Non-transgenic mice were consistently negative for NS3 in all total protein preparations. Thus, the transgenic mice have a NS 3 protein expression restricted to the liver.
  • NS3 protein expression was detected in both transgenic males and females by Western blot, despite the fact that expression levels are usually higher in males due the sex hormone regulated MUP promoter. (See Pang PS., et al., Embo J, 21:1168-1176 (2002)). Out of the 67 male transgenic mice tested, 43 mice (64%) were found to express NS3 . Out of the 50 female transgenic mice that were tested, only 16% were found to express NS3. A wide range of protein expression among males was observed, which is consistent with observations from other transgenic mice that contain transgenes driven by the MUP promoter.
  • FIGURE 15 is a chart quantifying NS3 protein expression levels in male transgenic mice. The amount NS3 protein in lOOmg of liver tissue was quantified from 44 individual transgenic mice, as described herein.
  • NS3 Expression levels of NS3 were also quantified from HepG2, HeLa, and BHK-21 cells that were transiently transfected with the expression plasmids wild-type (wt) NS3/4A-pVAXl or codon-optimized (co) NS3/4A- pVAXl.
  • the wtNS3/4A dot represents a mean value + SD of nine different quantifications of NS3 protein after transient transfection and the coNS3/4A dot represents a mean value ⁇ SD of 14 different quantifications.
  • the amount of rNS3 protein used to generate the standard curve was 5 ⁇ g, l ⁇ g, 0.1 ⁇ g, 0.05 ⁇ g, and 0.0 l ⁇ g.
  • This example provides a method by which mouse sera can be tested biochemically.
  • Transgenic- and non-transgenic mice were bled retro-orbitally and sera was tested for alanine aminotransferase (ALT) and blood glucose levels. Serum was stored at -20 0 C until tested. ALT values were measured using the Modular P equipment (Roche Diagnostics GmbH, Mannheim, Germany). Blood glucose levels were measured in serum from mice by using the Accu-Check ® Sensor equipment (Roche Diagnostics). Serum from venous blood was used to analyse the ALT and glucose levels in female and male transgenic and non-transgenic mice. No consistent differences in ALT levels between the different groups were observed, indicating that the NS3/4A protein does not induce a spontaneous liver damage (TABLE 11).
  • the serum glucose levels were found to be equal in transgenic and non- transgenic mice.
  • intra-hepatic expression of the NS3/4A protein did not affect ALT or glucose levels in all of the transgenic mice.
  • both serum levels of ALT and glucose were comparably small in the present study. Statistical differences were observed in subgroups regarding both ALT and glucose values.
  • This example provides a method by which a histological analysis of a sample may be prepared.
  • Mice were sacrificed and liver tissue was placed in formalin or OCT cryostat embedded compound (Tissue-Tek, Torrance, CA, USA) and immediately snap-frozen in liquid nitrogen and then stored at -80 0 C.
  • Formalin fixed liver samples were paraffin embedded, and sectioned.
  • Four ⁇ m thick liver sections were mounted on slides and stained with Hematoxylin-Eosin dye. Liver sections were also stained with Periodic Acid Schiff s (PAS) for detection of basal membranes and glycogen accumulation, and by Sirius red staining for visualization of fibrosis.
  • PAS Periodic Acid Schiff s
  • Frozen liver sections (four to seven ⁇ m thick) were stained using Oil red O to visualize lipid droplets and estimate the degree of macro- and micro steatosis. The different staining types were done according to standard procedures. All sections were analysed by a liver pathologist who was blinded to the status of the animal. Sections from different tissues were analysed blindly by a mouse pathologist to identify possible transgene-related changes outside the liver. The NS3 protein was visualized using an anti-human NS3 antibody.
  • the NS3 protein was only found in hepatocytes from NS3/4A transgenic mice. NS3 expression was consistently perinuclear and cytoplasmic. The immunohistochemical detection of HCV NS3 protein in liver was readily observable. Liver from a 17 months old transgenic mouse and an aged matched non-transgenic mouse was formalin fixed, sectioned, and stained using an anti-human NS3 antibody as described herein. Sections were photomicrographs obtained with a magnification of xlOO , x200, and x400. NS3 staining was perinuclear and cytoplasmic, and localized to the hepatocytes..
  • NS3/4A-expression in the transgenic mice has a distribution and localization of the protein fully consistent with infected humans.
  • the following example demonstrates how one can determine the percentage of hepatocytes expressing NS3 protein at detectable levels.
  • the percentage of hepatocytes expressing the NS3 protein was determined by immunohistochemistry and calculated by examination of an average of 40 randomly chosen fields (400 x magnification) in sections positively stained for NS3. Calculation of standardized surface areas indicated that approximately 1% of the hepatocytes expressed the NS3 protein at high enough levels to allow for detection by immunohistology.
  • mice that are transiently transfected with the above proteins or constructs are useful controls for analyzing or even performing some of the herein described technques. The following example demonstrates one such transfection procedure.
  • HepG2, HeLa or BHK-21 cells were transiently transfected by a standard protocol. Accordingly, cells were plated into 25cm 2 wells (0.5 x 10 6 ) in DMEM medium the day before transfection. Two ⁇ g of each plasmid DNA construct was transfected into HepG2, HeLa or BHK-21 cells using Fugene 6 Transfection Reagent (Roche). After transfection, the HepG2, HeLa or BHK-21 cells were incubated for 24-48hrs. Cell lysates were prepared and NS3/4A protein expression was detected by chemiluminiscence with NS3- or NS4A-specific hyperimmune sera. The following example demonstrates a method of determining the significance of a given observed change.
  • This example demonstrates a method by which the results of the present embodiments may be analyzed to determine if a particular change in protease activity is significant. Fisher's exact test was used for frequency analysis and Student's t-test and Mann- Whitney U-test were used for comparing values from two groups. For calculations of repeated measurements the area under the curve (AUC) and analysis of variance (ANOVA) was used. The calculations were performed using the Macintosh version of the StatView software (version 5.0). The following example demonstrates some of the observed characteristics of the NS3/4A transgenic mice.
  • FIGURE 16 is graphs showing the weight comparison of female NS3/4A-transgenic- and non-transgenic mice (FIGURE 16A) and male NS3/4A-transgenic- and non-transgenic mice (FIGURE 16B). Each dot represents a group of mice (one to seven mice). A total number of 33 female and 38 male NS3/4A-transgenic mice were weighed and 10 female and 14 male non-transgenic mice were weighed during the first five months after birth. Transgenic- and non-transgenic mouse weight in female and male groups were compared statistically using area under the curve (AUC) and analysis of variance (ANOVA).
  • AUC area under the curve
  • ANOVA analysis of variance
  • liver weight, as well as the percent liver weight of total body weight was significantly higher in the young transgenic mice (1-3 months old) as compared to age matched controls (males and females together; p ⁇ 0.01; FIGURE 16 and TABLE 11.
  • the slight increase in liver weight was statistically different in young male mice but not in female mice, indicating that the increase is related to the expression levels of NS3/4A.
  • the livers from NS3/4A transgenic were slightly enlarged.
  • transgenic- and non-transgenic liver sections By staining the transgenic- and non-transgenic liver sections with glycogen and lipid-specific dyes (PAS and Oil red O;) it was found that the vacuoles in hepatocytes were filled with lipids. Liver sections were stained with Hematoxylin and Eosin and liver sections were stained with Oil red O according to standard procedures for visualization. However, transgenic and non-transgenic liver sections were stained for presence of NS3 protein by immunohistochemistry, as described herein. Sections were from 1 to 3 months old and >17 months old , with a magnification of xlOO and x400. By the histological examination, it was found that both macrovesicular and microvesicular steatosis appeared and increased with age.
  • glycogen and lipid-specific dyes PAS and Oil red O;
  • liver weight and percent liver weight of total body weight were small, albeit statistically significant, between the transgenic- and non-transgenic groups. Thus, it is possible that the absence of a correlation was due to this minor increase in size to a histologically visible pathology or anomaly (TABLE 12). It cannot be excluded that the NS3/4A transgenic mice develop slightly enlarged livers due to a very mild steatosis, undetectable by histology, but that increases the size of the hepatocytes. The increased liver size may also be due to accumulation of glycogen within the hepatocytes. Regardless of the reason for the mild hepatomegaly it is clear that the hepatic NS3/4A-ex ⁇ ression does not result in overt liver pathology.
  • NS3/4A does not cause an immediately detectabe overt spontaneous liver disease.
  • NS3/4A-transgenic mice began to loose hair within two months of age. A histological analysis of the skin revealed a destruction of hair follicles. This destruction appeared at the same time and was of the same magnitude in males and females. NS3/4A expression was not detected in any skin sample, however, even in mice that were characterized as having high levels of NS3 expression in the liver.
  • the following example provides a method for analyzing histological sections for the frequency of occurrence of inflamatory foci. Histological sections from transgenic and non- trans genie mouse livers were analysed at 1-3 and >17 months of age. The initial histological examination of hematoxylin and eosine stained sections revealed that vacuoles were present in the hepatocytes from both transgenic and non-transgenic mice. The cause of these vacuoles could either be fat or glycogen deposition. It is well known that inflammatory foci spontaneously appear in laboratory mice.
  • mice expressing the full HCV genome have a defective immune response to hepatic infection.
  • the presently observed reduction of inflammatory foci in the NS3/4A transgenic mice livers provides more evidence that the intra-hepatic immune defense system is compromised in the presence of HCV proteins.
  • the following example demonstrates that the NS3/4A transgenics have enlarged livers due to the presence of larger cells.
  • the number of nuclei in the transgenic livers was statistically lower as compared to non-transgenic livers, indicating the presence larger cells (p ⁇ 0,01; TABLE 12).
  • the number of nuclei was lower in transgenic males as compared to transgenic females (70,l ⁇ 14 v.s. 80,4 ⁇ 13; p ⁇ 0,05, Student's t-test), and a similar difference was not seen when comparing non- transgenic males and females.
  • This example discloses the preparation of liver and spleen leukocytes.
  • the male NS3/4A-transgenic (i.e., "NS3/4A-Tg") or wild-type (i.e., "Wt") mice (6-12 weeks old) were killed by CO 2 inhalation and their abdomens opened.
  • the spleens were excised and placed in 5 ml of serum free AIM-V medium (Gibco-BRL).
  • a 10 ml syringe conected to a 25 G needle was then gently inserted into the portal vein and the liver were perfused with 5-7 ml of PBS (pH 7.4, 20 0 C) until the the liver turn pale, whereafter it was excised and weighed.
  • liver tissue was taken for Western blot analysis and immunohistochemistry.
  • the remaining liver tissue was placed in 5 ml of serum free AIM-V medium.
  • Single cell suspension of the spleen was obtained by crushing the organ in medium.
  • the red blood cells of the spleen were lysed by addition of Red blood lysis buffer (Sigma). Cells were then washed and resuspended in 5 ml of medium. The number of cells was determined by trypan blue dye exclusion.
  • the liver cell suspension was prepared by crushing the organ in medium.
  • the cell suspensions were then passed through a 70 ⁇ m cell strainer (Falcon). The liver cells were then centrifuged for 15 minutes at 200 xg.
  • the supernatant was discarded and the cell pellet was resuspended in 80% isotonic Percoll solution (Amerham- Biosciences) and overlaid with a 40% Percoll solution.
  • the cells were then centrifuged for 20 minutes at 300xg. The cells located at the interphase were collected, washed in medium and thereafter counted by Trypan blue dye exclusion. The spleen cells and liver cells were then processed for flow cytometry as described below.
  • EXAMPLE 31 This example describes the flow cytometry staining and analysis of the above samples. Spleen and liver cells were incubated for 20 min with Fc block (anti-CD 16/CD32 clone 2.4G2). The cells were then incubated for 30 minutes on ice with fluorochrome or biotin-conjugated mAbs. After washing, cells stained with biotinylated antibodies were exposed to streptavidin conjugated phycoerythrin (PE) for 30 minutes on ice.
  • PE streptavidin conjugated phycoerythrin
  • anti- CD16/CD32 clone 2.4G2 anti- CD16/CD32 clone 2.4G2; FITC conjugated anti-CD3 (145-2C11), anti-CDllc (HL3); PE conjugated anti-NKl.l (PK136); Biotin conjugated anti-MHC class I-A/I-E (2G9), anti-CD4 (RM4-5); PerCP-Cy5.5 conjugated anti-CDllb (Ml/70), anti-CD19 (1D3); APC conjugated anti ⁇ CD45 (Ly-5, 30- FIl), anti-Ly 6C/G (RB6-8C5), anti-CD8 (53-6.7).
  • Appropriate isotype controls (all from BD Biosciences) were used to check for background staining and for setting gates.
  • FACS data were aquired on a FACSCalibur (BD Biosciences) and data analysed with CellQuest software (BD Biosciences). The results are shown in FIGURE 17A. As can be seen from the results, there is a larger number of CD4+ T cells in the NS3/4A trangenic mice than in the wild-type mice.
  • RNA levels in a cell were assessed for the composition of the various subsets, using the antibodies discussed above.
  • FIGURE 17B NS3/4A transgenic mice had significantly less type I/II cells.
  • the following example describes a method for analyzing RNA levels in a cell.
  • the example describes an Rnase Protection Assay (RPA).
  • RPA Rnase Protection Assay
  • Total RKA was extracted from NS3/4A-Tg and wt-mice liver homogenates using TRIzol Reagent (Gibco-BRL) according to the manufacturers protocol. After the total RNA extraction, the RNA was further purified by the use of RNeasy columns (Qiagen) to yield a higher purity of the RNA. All RNA samples used in the Rnase Protection Assay had an A 260 / 280 ratio of > 1.9. Twenty micrograms of total RNA was assayed with the Multi-probe Rnase Protection Assay (RPA) system using Probe template set mCD-1 according to the manufacturers recommendations (BD Biosciences, Pharmingen, San Diego).
  • RPA Multi-probe Rnase Protection Assay
  • Rnase-protected probes were purified by phenol-extraction and resolved on a 4.75% denaturating polyacrylamide gel together with non-protected probe and then subjected to autoradiography. Using the undigested probes as markers, a standard curve of migration distance versus nucleotide lengths was plotted. This standard curve was used to identify the "Rnase protected" fragment lengths. The results of these experiments revealed that the amount of CD4+ cells was reduced in NS3/4A transgenic mice compared to wild-type mice.
  • This Example describes several of the approaches used to induce hepatic injury in the NS3/4A-Tg mice and the techniques used to analyze the data.
  • All NS3/4A-Tg or wild-type (Wt) mice used in these experiments were male and/or females between 6-12 weeks old. All groups of mice contained five to ten mice. Comparisons were done in age matched animals, excluding an age dependent difference when comparing groups.
  • Serum from individual mice was collected at various time intervals (12, 24, 48, and 72 hours) after CCl 4 -treatment by retro-orbital bleeding. Serum alanine aminotransferase (ALT) values were measured to evaluate the extent of liver injury.
  • LPS lipopolysaccharide
  • D-GaI D-galactosamine
  • LPS/D-Gal was diluted/dissolved in lOO ⁇ L pyrogen-free PBS and administered i.p. as a single dose to NS3/4A-Tg and Wt mice. Each mouse was treated with 0.1 ⁇ g (5 ⁇ g/kg) LPS (Sigma) and 20mg D-GaI (Sigma) per mouse.
  • Serum from individual mice was collected at various time intervals (2, 6, 12, 24 and 48 hours) after LPS/D-Gal-treatment by retro-orbital bleeding. Serum ALT values were measured to evaluate the extent of liver injury.
  • Alpha-mouse FAS monoclonal antibody (Jo2) treatment involved Jo2 monoclonal antibody that was diluted in 200 ⁇ L pyrogen-free PBS and administered intravenously (Lv.) to NS3/4A-Tg and Wt mice. Each mouse was treated with 2 ⁇ g (O.lmg/kg) Jo2 monoclonal antibody (BD Pharmingen).
  • Serum from individual mice was collected at various time intervals (2, 6, 12, 24, and 48 hours) after Jo2 monoclonal antibody-treatment by retro-orbital bleeding.
  • Serum ALT values were measured to evaluate the extent of liver injury.
  • rm TNF- ⁇ tumor necrosis factor- ⁇
  • D-GaI D-GaI
  • rm TNF- ⁇ /D-Gal was diluted/dissolved in lOO ⁇ L pyrogen-free PBS containing lmg/mL bovine serum albumin (BSA; Sigma) and administered Lp. as a single dose to NS3/4A-Tg and Wt mice.
  • BSA bovine serum albumin
  • Each mouse was treated with 0.1 ⁇ g (5 ⁇ g/kg), 0.3 ⁇ g (15 ⁇ g/kg) or 0.4 ⁇ g (20 ⁇ g/kg) TNF- ⁇ (BD Pharmingen) and 20mg D- GaI (Sigma) per mouse.
  • FIGURES 18A-D The results of the experiments above are presented in FIGURES 18A-D.
  • the amount of liver damage in the wild-type mice in response to CCL 4 , LPS, and TNF- alpha treatment was significantly higher than the amount of damage seen in the NS3/4A transgenic mice livers.
  • the damage due to FAS treatment was approximately equivalent between wild-type and NS3/4A transgenics, however.
  • the following Example describes how to determine proteins or pathways through which NS3/4A can interact to result in a phenotype or a disease symptom.
  • This Example describes a method for analyzingr the role of LPS in IFN-Induced Jak- STAT Signalling.
  • aged-matched male NS3/4A-Tg and wild-type mice (6-12 weeks old) were used.
  • Groups of 6 mice were either left un-treated, injected Lp. with: LPS (0,2 ⁇ g/mouse)/D-Gal (20mg/mouse), recombinant murine IFN ⁇ (rmlFN ⁇ ; 1000 U/g mouse body weight; Sigma), or recombinant murine IFN ⁇ (rmlFN ⁇ ; lO ⁇ g/mouse; Sigma).
  • the mice were sacrified 20, 40, and 80 minutes after injections.
  • Whole cell extracts, cytoplasmic and nuclear extracts were prepared from liver cells as described below. Whole liver cell extracts and cytoplasmic/nuclear cell extracts were obtained from the same liver lobe throughout all experiments.
  • liver cell extracts were generated by homogenizing the liver tissue sample in RIPA buffer (0,15M NaCl, 5OmM Tris, 1% Triton-X 100, 1% Na-deoxycholate, 1% SDS, 0,2mM PMSF, ImM Na 3 VO 4 , and 0,5mM DTT). The homogenates were then incubated on ice for 20 minutes and centrifuged 12,000xg for 2 minutes. The supernatant was collected and stored at -8O 0 C until used in Western blot analysis.
  • Cytoplasmic/nuclear extracts were generated by a short homogenization on ice of the liver tissue sample in buffer A (1OmM HEPES-KOH pH 7.9, 1.5mM MgCl 2 , 1OmM KCl, 0,2mM PMSF, ImM Na 3 VO 4 , and 0,5mM DTT).
  • the homogenates were the incubated on ice for 10 minutes, and then subsequently centrifuged for 2 minutes, 14.000xg at 4 0 C.
  • the supernatant, containing the cytoplasmic cell fraction was collected and stored at -80 0 C until used in Western blot analysis. The remaining pellet was washed once with PBS containing ImM Na 3 VO 4 .
  • the pellet was re-suspended in buffer C (2OmM HEPES-KOH pH 7.9, 1.5mM MgCl 2 , 42OmM NaCl, 0.2mM EDTA pH 8.0, 25% Glycerol, 0,2mM PMSF, ImM Na 3 VO 4 , and 0,5mM DTT) by vortexing.
  • the homogenate was incubated on ice for 30 minutes, then centrifuged for 2 minutes, 14.000xg at 4 0 C.
  • the supernatant, containing the nuclear cell fraction was collected and stored at -8O 0 C until used in Western blot analysis.
  • the whole cell extract were immunoprecipitated and analysed by Western blot. For detections of IFN- induced signalling molecules; a total of 60 ⁇ g cytoplasmic or nuclear protein per sample was loaded onto a 4-12% SDS-PAGE gel.
  • Membranes were probed with ⁇ -STATl (BD Biosciences), ⁇ -STAT2, ⁇ -STATlpTyr (Upstate, Waltham, USA), ⁇ -STAT2pTyr, ⁇ -SOCSl (Imgenex, San Diego, USA), ⁇ -IRF-3, ⁇ -TC-PTP, ⁇ -PP2Ac, and Histone 2B. Proteins were detected using HRP-conjugated secondary antibodies and visualized using a chemiluminescent detection kit (ECL Plus, Amersham Biosciences).
  • This Example discloses a method for administering and testing a p38 inhibitor, SB203580.
  • This protocol can be used to test various candidate compounds to identify molelcules that inhibit p38 MAP ldnase.
  • These compounds and other kinase inhibitors, in particular a p38 kinase inhibitor can be incorporated into a pharmaceutical that is formulated for human administration and said pharmaceuticals can be provided to a subject in need of an agent that inhibits HCV replication and infection.
  • the inhibition of HCV replication in said subject is measured before and/or after providing said ldnase inhibitor.
  • kinase inhibitor e.g., a p38 ldnase inhibitor
  • SB203580 (Calbiochem) was dissolved/diluted in sterile dH 2 O and administered to mice intra orally (Lo.). NS3/4A-Tg and Wt mice were pre-treated with 0.5mg (25mg/kg) SB203580 thirty minutes prior to challenge with rm TNF- ⁇ /D-Gal. Animals were followed for survival after TNF- ⁇ /D-Gal-treatment and observed at different time intervals (6, 9, 24, 48, 72, 96, and 120 hours) after treatment. The results are provided in FIGURES 19A through 19C.
  • mice almost completely lacked the spontaneous inflammatory foci. This indicated that the hepatic expression of NS3/4A interferes with the hepatic immunity.
  • An extensive analysis of the intra-hepatic immune cell population revealed that the livers from the NS3/4A-Tg mice had reduced amounts of CD4+ T cells and plasmacytoide-like DCs. This is consistent with the absence of inflammatory foci and indicated that these mice have a functional deficit in the hepatic immunity.
  • Transgenic mice were then treated with different agents that activate the hepatic immunity by different signal transduction pathways.
  • the HCV NS3/4A complex is involved in interfering with the hepatic immunity on many levels.
  • the HCV NS3/4A complex alters the hepatic subsets of CD4+ T cells and DCs.
  • these findings are consistent with the previously observed inhibition of IFN- signalling in vitro and in vivo.
  • the NS3/4A-transgenic mice also have an impaired functionality of the hepatic immunity mainly related to a reduced response to TNF- ⁇ -mediated signalling pathways.
  • NS3/4A can either up-regulate signalling through the MKK3/6-p38 pathway, inhibit signalling through the FADD or JNK pathways, or operate through both pathways.
  • NS3/4A can also proteolytically cleave one or more proteins related to signalling, or that the NS3/4A helicase/NTPase activity may interefere with the kinases, or other signal molecules.
  • the p38 inhibitor can also affect the NS3/4A complex. A summary of some of these pathaways, and how NS3/4A can interact with these pathways in light of the current data is presented in FIGURE 20.
  • a general method for screening for agents that block p38 can be similar to that employed in Example 35, above.
  • a candidate p38 inhibitor (agent, medicament, treatment, etc.) is administered to a NS3/4A transgenic mouse.
  • the NS3/4A transgenic mouse is provided a wild-type lethal amount of TNF-alpha.
  • an amount is a dose sufficient to kill 50% of the wild-type mice receiving it.
  • Indication of a successful p38 inhibitor can be observed via observing the entire mouse ⁇ i.e., mouse death will demonstrate a ⁇ 38 inhibitor), or, alternatively, on the level of tissue or cell death (via the procedures described above, for example).
  • a wild-type mouse is administered the candidate ⁇ 38 inhibitor to make certain that the candidate p38 inhibitor is killing the NS3/4A-Tg mouse in a manner relating to an effect from the NS3/4A protein expressed.
  • the candidate p38 inhibitor when applied to a wild-type mouse in amounts sufficient to reduce p38 activity, will not kill the wild-type mouse.
  • a positive control with SB203580 and two negative controls, using TNF-alpha in a wild-type mouse and in a NS3/4A transgenic mouse can be used for comparisons as well, especially if protein levels are to be compared.
  • the next Example discusses how the general method above can be used for discovering agents or drugs that treat or prevent HCV. EXAMPLE 38
  • the general method for screening for candidate p38 inhibitors can also be used to screen for agents to treat or prevent HCV.
  • the procedure is similar to that described in the Examples above.
  • Agents that make a NS3/4A mouse react to TNF-alpha in the same manner that a wild-type mouse reacts to TNF-alpha are selected as HCV treatments. These selected treatments can then be examined with more traditional and routine techniques known to one of skill in the art to determine how effective they are in preventing or treating HCV.
  • candidate HCV treatments can include any compound that results in the reversion of the phenotype to a wild-type phenotype.
  • a HCV treatment can function at a level beneath a p38 kinase, for example by inhibiting later steps in a pathway.
  • This Example demonstrates how other proteins involved in the NS3/4A phenotype can be elucidated.
  • the method is similar to Example 35 above, except an alternative inhibitor or enhacer to a different protein (e.g., SOCSl) is administered.
  • SOCSl a different protein
  • NS3/4A-Tg and Wt mice are administered SOCSl siRNA prior to challenge with rm TNF- ⁇ /D-Gal. Animals are followed for survival after TNF- ⁇ /D-Gal-treatment and observed at different time intervals (6, 9, 24, 48, 72, 96, and 120 hours) after treatment. Additional amounts of SOCSl siRNA can be administered to the animals.
  • TNF-alpha can typically induce death in wild-type mice and will not be able to do so for the NS3/4A transgenics at a similar dose.
  • the addition of the SOCSl siRNA to the transgenic mice makes the NS3/4A transgenic mice again susceptible to the death inducing properties of TNF-alpha.
  • NF-kB is another protein that is involved in the NS3/4A phenotype.
  • NS3/4A induces and/or activates nuclear factor kappa-B directly and/or indirectly.
  • the TNF-a-resistance of the MUP-NS3/4A-Tg mice was found to be reversible by a simultaneous treatment with the p38 inhibitor SB203580 (FIGURES 19A- 19C).
  • SB203580 p38 inhibitor SB203580
  • the protection of hepatocytes by NS3/4A to TNF-alpha- mediated liver disease is due to an increase in NF-kB levels or activation, which can effectively be inhibited using SB203580, demonstrating that this inhibitor and other NF-IcB inhibitors can be used ot treat or prevent or otherwise ameliorate a condition associated with HCV infection.
  • a patient at risk of HCV symptoms is identified by routine methods ⁇ e.g., external symptoms, blood tests, lifestyle, etc.).
  • the patient is administered an amount of an HCV treatment, as identified above, based on the particular patient and the severity of the HCV symptoms.
  • the patient's HCV related symptoms are reduced.
  • the reduction of viral lode or another indicator for HCV infection is measured.
  • a patient in need of treatment of symptoms is identified by routine methods.
  • the patient is administered an amount of a p38 inhibitor, as identified above, based on the particular patient and the severity of the HCV symptoms.
  • the patient's HCV related symptoms are reduced.
  • the reduction of viral lode or another indicator for HCV infection is measured.
  • a patient in need of treatment of HCV s is identified by routine methods, as above.
  • the patient is administered an amount of a SOCSl inhibitor, as identified above, based on the particular patient and the severity of the HCV symptoms.
  • the patient's HCV related symptoms are reduced.
  • the reduction of viral lode or another indicator for HCV infection is measured.
  • EXAMPLE 44 A patient in need of treatment of HCV related complications is identified by routine methods. The patient is administered an amount of SB203580, based on the particular patient and the severity of the HCV symptoms. Following a repeated course of treatment, if required, the patient's HCV related symptoms are reduced. In some applications, the reduction of viral lode or another indicator for HCV infection is measured. The next example describes a method for identifying agents that block NF-kB activity.
  • This example demonstrates a general method for screening for agents that block NF- kB activity, which can be similar to that employed in Example 35, above.
  • a candidate NF-kB inhibitor agent, medicament, treatment, etc.
  • the NS3/4A transgenic mouse is provided an amount of TNF-alpha that is lethal to a wild-type mouse.
  • an amount of TNF-alpha that is lethal to a wild-type mouse is a dose that is sufficient to kill 50% of the wild-type mice receiving the compound.
  • Identification of an NF-IcB inhibitor is made by observing a change in the mouse ⁇ e.g., mouse death will demonstrate that an NF- kB inhibitor has been identified), or, alternatively, on the level of tissue or cell death (via the procedures described above, for example).
  • a wild-type mouse is provided the candidate NF-kB inhibitor to confirm that the candidate NF-kB inhibitor is mediating the observed change (e.g., death) in the NS3/4A-Tg mouse.
  • a positive control with SB203580 and two negative controls, using TNF-alpha in a wild-type mouse and in a NS3/4A transgenic mouse can be used for comparison, as well, especially if protein levels are to be analyzed.
  • the following example provides one possible use of the identified compound.
  • a patient in need of of an agent that inhibits the proliferation/replication of HCV and/or an agent that ameliorates a condition associated with HCV infection is identified by routine methods (e.g., diagnostic or clinical determination).
  • the identified patient is provided an amount of a NF-IcB inhibitor, as identified above, based on the particular patient and the severity of the HCV symptoms.
  • the patient's HCV related symptoms are reduced.
  • the reduction of viral load or another indicator for HCV infection or a condition associated with HCV infection is measured. The following three examples provide more evidence that other NF-kB inhibitors could be used to treat or prevent HCV infection.
  • a patient in need of an agent that inhibits the proliferation/replication of HCV and/or an agent that ameliorates a condition associated with HCV infection is identified by routine methods (e.g., diagnostic or clinical determination).
  • the identified patient is provided an amount of parthenolide, based on the particular patient and the severity of the HCV symptoms.
  • the patient's HCV related symptoms are reduced.
  • the reduction of viral load or another indicator for HCV infection or a condtion associated with HCV infection is measured.
  • a patient in need of an agent that inhibits the proliferation/replication of HCV and/or an agent that ameliorates a condition associated with HCV infection is identified by routine methods (e.g., diagnostic or clinical determination).
  • the identified patient is provided an amount of aspirin, based on the particular patient and the severity of the HCV symptoms. Following a repeated course of treatment, if required, the patient's HCV related symptoms are reduced. In some applications, the reduction of viral load or another indicator for HCV infection or a condtion associated with HCV infection is measured.
  • an effective amount of an anti-inflamatory is provided.
  • an effective amount of a non-steroidal anti inflammatory drug is provided.
  • a patient in need of an agent that inhibits the proliferation/replication of HCV and/or an agent that ameliorates a condition associated with HCV infection is identified by routine methods (e.g., diagnostic or clinical determination).
  • the identified patient is provided an amount of an activator of an inhibitor of NF-kB, based on the particular patient and the severity of the HCV symptoms.
  • the patient's HCV related symptoms are reduced.
  • the reduction of viral load or another indicator for HCV infection or a condtion associated with HCV infection is measured.
  • An effective amount of the compound to be applied can be determined by administering an amount that is less than a lethal amount to a patient in increasing amounts until a reduction in viral load or another indicator of HCV infection is reduced.
  • the following example further examines NF-kB involvement in the NS3/4A-Tg mouse model and the mechanism by which NF-kB activity can be modulated. That is, EXAMPLES 50-52 demonstrate that HCV NS3/4A increases the levels of cytoplasmic and, perhaps more importantly, nuclear NF-kB, which in turn protects the hepatocytes against the pro-apoptotic effects conferred by TNF-a/D-Gal. This protection can occur through NF-kB 's ability to reduce the levels of caspase-3, an enzyme responsible for DNA fragmentation in apoptosis.
  • This example provides evidence that wild-type and the NS3/4A transgenics differ in that the NS3/4A transgenics have elevated levels of NF-kB (p65 in particular) compared to non-Tg mice in response to TNF-a/D-Gal treatement. Moreover, the difference in the levels of nuclear NF-IcB between NS3/4A-Tg mice and the non-Tg mice is very large, suggesting that nuclear tanslocation can be an important step in this process.
  • the NF-IcB signalling pathway is a survival signalling pathway. This pathway was studied in wildtype (non-Tg) and NS3/4A-Tg mice. Mice were treated with 0.3 ⁇ g TNF- a/20mg D-GaI and livers were removed at 0, 30, 60, 120, 240, 480 minutes. Liver homogenates were analyzed for the presence of cytoplasmic NF-IcB and IkB-a, and nuclear NF-kB.
  • NS3/4A-Tg livers have higher basal levels of cytoplasmic NF-kB. Additionally, within 30 minutes of TNF-a activation, cytoplasmic IkB-a (clkB-a or clkB-alpha) disappears in both NS3/4A-Tg and wt (non-Tg) livers. Each lane represents one mouse liver. Simultaneously, nuclear NF-kB appears in the NS3/4A-Tg, but not in non-Tg, livers. Thus, TNF-a/D-Gal activation results in nuclear NF-kB in the NS3/4A-Tg but not in the non-Tg mice.
  • compositions or methods that inhibit the translocation of NF-kB to the nucleus would appear to make the NS3/4A-Tg mouse the same as the wild-type mice.
  • this particular difference (nuclear translocation) between the NS3/4A-Tg mice and the non-Tg mice can be targeted to prevent or treat HCV infection.
  • compositions and methods that prevent the translocation of NF-kB to the nucleus can be used to treat or prevent HCV related symptoms and issues according to the present NS3/4A-Tg model.
  • IkB-a seems to be present in similar levels between NS3/4A-Tg and non-Tg mice. This can mean that another inhibitory complex (e.g., a different IkB) is complexed with the p65 subunit, for example, IkB-b.
  • another inhibitory complex e.g., a different IkB
  • IkB-b another inhibitory complex
  • HcB is not ideally correlated between the NS3/4A-Tg results and the non-Tg results does not mean that a particular HdB could not be used in the treatment or prevention of HCV.
  • IkB-a even though it does not demonstrate the trends demonstrated by NF-kB, can still be used to sequester or block NF-IdB from entering the nucleus, although other forms of IkB can be more effective. Additionally, this result demonstrates that the other IkB(s) can be relevant in preventing the effects of NF-IdB (and thus serve as a treatment for HCV) as long as they can prevent NF-IcB from entering the nucleus. Additional examples of such inhibitors include translocation inhibitors in general and cIAP. The following example examines possible subsequent downstream genes and proteins that can be acted upon by NF-kB.
  • This example demonstrates how one can determine the identity of additional genes that NF-IcB can operate on in this HCV model pathway. Additionally, this example demonstrates that a variety of NF-kB activated genes do not appear to be significantly regulated in the NS3/4A-Tg model. Finally, this example demonstrates that caspase-3, one NF-IcB regulated gene, is differentially expressed between the NS3/4A-Tg and the non-Tg.
  • the activation of nuclear NF-IcB results in activation of anti-apoptotic genes, for example, A20, cIAP, XIAP, suvivin, HSP27, and HSP90.
  • To determine which anti-apoptotic pathways were activated by the nuclear NF-IcB western blots were obtained to determine cIAP, TRAF-2, and caspase-3 levels following the administration of TNF-a/D-Gal.
  • the samples tested were from liver extracts. The results were analyzed at 30, 120, and 480 minutes. The results are shown in FIGURE 21B and FIGURE 21C. It was found that cIAP and TRAF-2 levels were comparable in non-Tg and the NS3/4A-Tg mice (FIGURE 21C). This raises the possibility that these molecules may not directly be involved in the resistance to TNF-a/D-Gal in the NS3/4A-Tg mice.
  • caspase-3 levels were comparable in the NS3/4A-Tg and the non-Tg livers (in response to the addition of TNF-a/D- Gal)
  • a more detailed analysis revealed that there was a significant difference between caspase-3 levels in the NS3/4A-Tg and non-Tg mice (FIGURE 21B).
  • the western blot results for caspase-3 in FIGURE 2 IB demonstrate that the NS3/4A-Tg mouse livers clearly had reduced levels of caspase-3 compared to the non-Tg mouse livers.
  • this difference in caspase-3 levels is not only present in the cytoplasm, but is also present in the nucleus as well.
  • the level of caspase-3 increases in the system over time, in response to TNF-a/D-Gal treatment.
  • the greatest levels of caspase-3 are shown at 240 and 480 minutes.
  • the amount of caspase-3 is observably greater in the non-Tg mice than in the NS3/4A-Tg mice.
  • the difference between the amount of cytoplasmic caspase-3 in the NS3/4A-Tg and non-Tg mice is very large.
  • caspase-3 its activity, and those compounds and methods that regulate caspase-3 activity can be used to treat and prevent HCV infection.
  • compounds that increase the amount of active caspase-3 (such as additional caspase-3 or caspase-3 activators) can be used to treat and prevent HCV infection.
  • additional caspase-3 or caspase-3 activators can be used to treat and prevent HCV infection.
  • caspase-3 can undergo other forms of regulation downstream of activation.
  • additional compounds, which can enhance caspase-3 activity or block inhibitors of caspase-3 can be used to treat HCV. This can also be due to the lower level of caspase-3 in the NS3/4A-Tg.
  • FIGURE 21D The greater the amount of staining that appears in a sample, the greater the amount of fragmented DNA in the sample.
  • FIGURE 21D As shown in FIGURE 21D, 480 minutes after the addition of TNF-a/D-Gal, the number of TUNEL positive cells were lower in the NS3/4A-Tg mice compared to the non-Tg mice. This also applied to the results obtained after 240 minutes (data not shown). Thus, there is less DNA fragmentation in NS3/4A-Tg mice compared to non-Tg mice, supporting the above discussed results and theories.
  • EXAMPLE 52 demonstrates that the lower level of activated caspase-3 shown in EXAMPLE 51 is an accurate reflection of what is occurring in the NS3/4A-Tg system.
  • compounds that increase caspase-3 activity e.g., as described above and including caspase-3 or activated caspase-3) can be used to treat and /or prevent HCV.
  • Apaf-1 (apoptotic protease activating factor- 1); ⁇ -(trichloromethyl)-4- pyridineethanol (PETCM); Ac-YVAD-AFC, N-Acetyl-Tyr-Val-Ala-Asp-(7-ammo-4- trifluoromethylcoumarin) (SEQ ID NO: 76); cas ⁇ ase-1; caspase-11; granzyme B; caspase-10 can be useful compounds for the treatment or prevention of HCV.
  • Compounds and methods that restore DNA fragmentation in the NS3/4A-Tg mouse livers, to a level comparable to that observed in the non-Tg mouse livers, can be used for the treatment of HCV.
  • EXAMPLES 50 through 52 demonstrate that NS3/4A-Tg mice have higher basal levels of cytoplasmic NF-kB. Furthermore, TNF-a/D-Gal activation leads to a rapid degradation of IkB-a and liberation of NF-kB, allowing NF-kB to enter the nucleus in the NS3/4A-Tg but not the non-Tg mice. However, the level of IkB-alpha was similar between NS3/4A-Tg and non-Tg mice. This suggests that the phenotype can be due to the excess level of NF-kB present in the NS3/4A-Tg.
  • the molecule that is responsible for keeping NF-kB out of the nucleus is an IkB that is not IkB- alpha.
  • other IkBs can be responsible for the phenotype.
  • any IkB can be used in the treatment of HCV, as long as it prevents NF-kB from entering the nucleus.
  • the nuclear NF-IcB present in the NS3/4A-Tg mice, likely results in a resistance to pro-apoptotic molecules, for example, through a decrease in the amount of active caspase-3, a result that is directly demonstrated in FIGURE 2 IB and further supported by a reduction in DNA fragmentation in the NS3/4A-Tg hepatocytes (FIGURE 21D).
  • pro-apoptotic molecules for example, through a decrease in the amount of active caspase-3
  • FIGURE 2 IB and further supported by a reduction in DNA fragmentation in the NS3/4A-Tg hepatocytes
  • HCV NS3/4A increases the levels of cytoplasmic and, perhaps more importantly, nuclear NF-kB, which in turn protects the hepatocytes against the pro-apoptotic effects conferred by TNF-a/D-Gal, which can occur through a reduction in the levels of caspase-3.
  • compounds that restore the level of cytoplasmic NF-IcB closer to a wild-type level can prevent or treat HCV infection.
  • the next example describes more transgenic organisms that contain the costructs described herein.
  • PADSI NS3/4A complementary DNA (cDNA) clone from a HCV genotype Ib infected patient will be isolated as described in Lazdina et al. (2001).
  • the PADSI NS3/4A (PADSI NS3/4A) gene fragment, corresponding to the amino acids 1026 to 1711 encompassing the NS3 and NS4A as well as a luciferase gene connected to a secretory signal will be attached to the end of the NS3/4A construct at the cleavage site. This will be inserted into the BamHI and EcoRI sites of pMUP-1 IAS plasmid. A fragment containing the MUP promoter (Held et al.
  • NS3/4A ⁇ Hindlll to EcoRI will be excised and cloned into the pVAXl (Invitrogen, San Diego) expression vector.
  • pVAXl Invitrogen, San Diego
  • the MUP promoter, PADSI NS3/4A fragment, and BGH polyadenylation signal will be excised from the pVAXl vector to generate the transcriptional unit to be used for microinjection, designated pMUP-PADSI NS3/4A (illustrated in FIGURE 14B).
  • the entire pMUP-PADSI NS3/4A-BGH polyadenylation signal construct will be sequenced prior to microinjection to confirm correct sequence.
  • the purified transgene construct will be microinjected into fertilized oocytes from C57BL/6 (H-2 b ) x CBA (H-2 k ) mice. Potential founder mice will be analyzed for the presence of transgene by polymerase chain reaction (PCR) and Southern blot of genomic tail DNA.
  • PCR polymerase chain reaction
  • specific outer primers will be used; for example, sense primer (5'-CCT GAA TTC ATG GCG CCT ATC ACG GCC TAT-3'; SEQ ID. NO.: 41) and antisense primer (5'-CCG TCT AGA TCA GCA CTC TTC CAT TTC ATC-3) (SEQ ID.
  • mice will be expressing luciferase, detection of incorporation of the gene can be done by probes for luciferase, or by looking for fluorescence at the luciferase emission spectra.
  • detection of incorporation of the gene can be done by probes for luciferase, or by looking for fluorescence at the luciferase emission spectra.
  • FIGURE 14B A PADSI construct as shown in FIGURE 14B is created.
  • the detectable marker is luciferase.
  • a transgenic mouse expressing the PADSI construct is then generated.
  • the amount of detectable marker in the blood system of the transgenic mouse is detected.
  • various candidate NS3 protease inhibitors are administered to the transgenic mouse and the presence of the detectable marker in the venous blood is detected through the surface of the organism via a CCD.
  • a decrease in the level of detectable marker will indicate that one of the candidate protease inhibitors is actually an effective protease inhibitor.
  • EXAMPLE 55 This example describes how the positive PADSI construct can be used to screen for NS3 protease inhibitors.
  • a PADSI construct as shown in FIGURE 14C, is created. In particular, the construct shown in FIGURE 14D is used. The detectable marker is luciferase.
  • a NS3 transgenic mouse is created, as described herein. The amount of detectable marker in the blood system of the transgenic mouse is detected. Then, the positive PADSI construct is delivered, through approaches known in the art, to the transgenic mouse so that there are positive PADSI protein constructs in the liver cells of the NS3 transgenic mouse.
  • This example demonstrates the effectiveness of the adjuvant ribavirin in reducing the size of a tumor when combined with the codon optimized form of the NS3/4A peptides.
  • the effectiveness of ribavirin on coNS3/4A in mice was also examined through a tumor challenge model. Either 100, 10, or 1 micrograms of coNS3/4A were injected into sets of 10 Balb/c mice. In each set, some mice were immunized with coNS3/4A alone, some were immunized with 3 mg ribavirin and coNS3/4A, and some were not immunized at all.
  • mice Two weeks after the single immunization the mice were challenged with 1 million NS3/4A-expressing SP2/0 cells. Tumor size was then measured following this challenge to determine how well the initial immunization primed the immune system against cells expressing coNS3/4A.
  • FIGURES 22A-C the presence of ribavirin dramatically increased the effectiveness of the initial immunization. Additionally, it did so in a coNS3/4A dose dependent manner as low doses of the coNS3/4A construct displayed little effect (as shown in FIGURE 22C), while large doses of coNS3/4A, with the same amount of ribavirin, showed substantially great effect (as shown in FIGURES 22B and 22C).

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Abstract

L'invention porte sur la découverte de nouvelles compositions NS3/4A présentant de meilleures capacités d'expression. Les réalisations de l'invention comprennent des compositions NS3/4A optimisées par le codon et des compositions ayant le réplicon du virus de la forêt de Semliki. D'autres réalisations comprennent des organismes transgéniques contenant ces compositions NS3/4A, sur les méthodes d'utilisation de ces souris transgéniques pour cribler et raffiner des médicaments et sur les médicaments raffinés selon ses méthodes. Des réalisations additionnelles comprennent des molécules dépendant de l'activité des protéases et qui peuvent indiquer la présence ou l'absence d'un inhibiteur de protéases.
PCT/IB2006/001668 2005-02-04 2006-02-03 Modeles de souris transgeniques du virus de l'hepatite c (vhc) et identification des therapies pour le vhc Ceased WO2006109196A2 (fr)

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Cited By (6)

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WO2008150899A1 (fr) * 2007-05-29 2008-12-11 Emory University Thérapies combinées pour le traitement du cancer et des maladies inflammatoires
WO2012038950A1 (fr) 2010-09-20 2012-03-29 Ramot At Tel-Aviv University Ltd. Complexes de toxine activables comprenant un peptide inhibiteur clivable
WO2012176149A1 (fr) * 2011-06-23 2012-12-27 Panmed Ltd. Traitement du virus de l'hépatite c
WO2013147649A3 (fr) * 2012-03-29 2013-12-05 ХОЛИН, Максим Николаевич Inhibiteurs de la voie de signalisation pi3k/akt/ikk/nf-kb, leurs sels pharmaceutiquement acceptables et compositions les comprenant pour la prévention et le traitement de maladies virales
US8987302B2 (en) 2010-06-24 2015-03-24 Panmed Ltd. Treatment of hepatitis C virus related diseases using hydroxychloroquine or a combination of hydroxychloroquine and an anti-viral agent
CN117085007A (zh) * 2023-09-28 2023-11-21 南通大学 冬凌草甲素在制备预防或治疗雄性少弱精症药物中的应用

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IT1299134B1 (it) * 1998-02-02 2000-02-29 Angeletti P Ist Richerche Bio Procedimento per la produzione di peptidi con proprieta' inibitrici della proteasi ns3 del virus hcv, peptidi cosi' ottenibili e peptidi
WO1999061039A2 (fr) * 1998-05-22 1999-12-02 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Nouvelle composition de modulation de la mort cellulaire ischemique
SE9904177D0 (sv) * 1999-11-18 1999-11-18 Astra Ab Novel compounds
JP2004000179A (ja) * 2002-03-29 2004-01-08 Toray Ind Inc Ｃ型慢性肝炎、肝硬変、肝癌病態を呈するモデル動物及びその作製方法
TWI344959B (en) * 2003-04-02 2011-07-11 Nat Health Research Institutes Treatment of hepatitis c virus infection with sesquiterpene lactones

Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008150899A1 (fr) * 2007-05-29 2008-12-11 Emory University Thérapies combinées pour le traitement du cancer et des maladies inflammatoires
US8987302B2 (en) 2010-06-24 2015-03-24 Panmed Ltd. Treatment of hepatitis C virus related diseases using hydroxychloroquine or a combination of hydroxychloroquine and an anti-viral agent
WO2012038950A1 (fr) 2010-09-20 2012-03-29 Ramot At Tel-Aviv University Ltd. Complexes de toxine activables comprenant un peptide inhibiteur clivable
US9321847B2 (en) 2010-09-20 2016-04-26 Ramot At Tel Aviv University Ltd. Activatable toxin complexes comprising a cleavable inhibitory peptide
WO2012176149A1 (fr) * 2011-06-23 2012-12-27 Panmed Ltd. Traitement du virus de l'hépatite c
US8912141B2 (en) 2011-06-23 2014-12-16 Panmed Ltd. Treatment of hepatitis C virus
WO2013147649A3 (fr) * 2012-03-29 2013-12-05 ХОЛИН, Максим Николаевич Inhibiteurs de la voie de signalisation pi3k/akt/ikk/nf-kb, leurs sels pharmaceutiquement acceptables et compositions les comprenant pour la prévention et le traitement de maladies virales
CN117085007A (zh) * 2023-09-28 2023-11-21 南通大学 冬凌草甲素在制备预防或治疗雄性少弱精症药物中的应用

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