Reporter gene system for use in cell-based assessment of inhibitors of the hepatitis C virus protease

Abstract

A cell-based assay system in which the detection of the reporter gene activity, or secreted alkaline phosphatase (SEAP), is dependent upon the protease activity of the Hepatitis C virus NS3 gene product. This system can be used to assess the activity of candidate protease inhibitors in a mammalian cell-based assay system. The assay system is simpler than previously described assays due to the use of SEAP which allows the reporter gene activity to be quantified by measuring the amount of secreted gene product in the cell media by monitoring the conversion of luminescent or calorimetric alkaline phosphatase substrate.

Description

TECHNICAL AND INDUSTRIAL APPLICABILITY OF INVENTION

[0002] A cell-based assay system in which the detection of reporter gene activity (secreted alkaline phosphatase or SEAP) is dependent upon active Hepatitis C virus (HCV) NS3 protease. The assay system is useful in the in vitro screening, in a mammalian cell-based assay, of potential protease inhibiting molecules useful in the treatment of HCV. The advantages of using SEAP over more routinely used reporter genes such as beta-galactosidase or luciferase, is that a cell lysis step is not required since the SEAP protein is secreted out of the cell. The absence of a cell lysis step decreases intra- and inter-assay variability as well as makes the assay easier to perform then earlier assays.

BACKGROUND OF THE INVENTION

[0003] HCV is one of the major causes of parenterally transmitted non-A, non-B hepatitis worldwide. HCV is now known as the etiologic agent for Non-A Non-B hepatitis throughout the world. Mishiro et al., U.S. Pat. No. 5,077,193; Mishiro et al., U.S. Pat. No. 5,176,994; Takahashi et al, U.S. Pat. No. 5,032,511; Houghton et al., U.S. Pat. Nos. 5,714,596 and 5,712,088; as well as (M. Houghton, Hepatitis C Viruses, p.1035-1058 in B. N. Fields et al.(eds.), Field's Virology (3d. ed. 1996). HCV infection is characterized by the high rate (>70%) with which acute infection progresses to chronic infection (Alter, M. J. 1995. Epidemiology of hepatitis C in the west. Sem. Liver Dis. 15:5-14.). Chronic HCV infection may lead to progressive liver injury, cirrhosis, and in some cases, hepatocellular carcinoma. Currently, there are no specific antiviral agents available for the treatment of HCV infection. Although alpha interferon therapy is often used in the treatment of HCV-induced moderate or severe liver disease, only a minority of patients exhibit a sustained response Saracco, G. et al., J. Gastroenterol. Hepatol. 10:668-673 1995. Additionally, a vaccine to prevent HCV infection is not yet available and it remains uncertain whether vaccine development will be complicated by the existence of multiple HCV genotypes as well as viral variation within infected individuals Martell, M. et al., J. Virol. 66:3225-3229 1992; Weiner, et al., Proc. Natl. Acad. Sci. 89:3468-3472 1992. The presence of viral heterogeneity may increase the likelihood that drug resistant virus will emerge in infected individuals unless antiviral therapy effectively suppresses virus replication. Most recently, several of the HCV encoded enzymes, specifically the NS3 protease and NS5B RNA polymerase, have been the focus of intensive research, in vitro screening, and/or rational drug design efforts.

[0004] HCV has been classified in the flavivirus family in a genus separate from that of the flaviviruses and the pestiviruses. Rice, C. M., in B. N. Fields and P. M. Knipe (eds.), Virology, 3rd edn., p. 931-959;1996 Lippincott-Raven, Philadelphia, Pa. Although the study of HCV replication is limited by the lack of an efficient cell-based replication system, an understanding of replicative events has been inferred from analogies made to the flaviviruses, pestiviruses, and other positive strand RNA viruses. The HCV virus has a 9.4 kb single positive-strand RNA genome encoding over 3,000 amino acids. The genome expresses over 10 structural and non-structural proteins. Post-translational processing of the viral genome requires cleavage by two proteases. As in the pestiviruses, translation of the large open reading frame occurs by a cap-independent mechanism and results in the production of a polyprotein of 3010-3030 amino acids. Proteolytic processing of the structural proteins (the nucleocapsid protein or core (C)) and two envelope glycoproteins, E1 and E2 is accomplished by the action of host cell signal peptidases. Santolini, E., et al., J. Virol. 68:3631-3641, 1994; Ralston, R., et al., J. Virol. 67:6753-6761 1993. Cleavage of the nonstructural proteins (NS4A, NS4B, NS5A, and NS5B) is mediated by the action of the NS2/3 protease or the NS3 protease. Grakoui, A. et al., J. Virol. 67:2832-2843 1993; Hirowatari, Y., et al., Anal. Biochem. 225:113-120 1995; Bartenschlager, R. et al., J. Virol. 68:5045-5055 1994; Eckart, M. R., et al., Biochem. Biophys. Res. Comm. 192:399-406 1993; Grakoui, A., et al., J. Virol. 67:2832-2843 1993; Tomei, L., et al., J. Virol. 67:4017-40261993; NS4A is a cofactor for NS3 and NS5B is an RNA dependent RNA polymerase. Bartenschlager, R. et al., (1994); Failla, C.,et al., J. Virol. 68:3753-3760 1994; Lin, C. et al., Proc. Natl. Acad. Sci. 92:7622-7626 1995; Behrens, S. -E., et al., EMBO J. 15:12-22 1996. Functions for the NS4B and NS5A proteins have yet to be defined.

[0005] The NS2/3 is a metalloprotease and has been shown to mediate cleavage at the 2/3 junction site Grakoui, et al. (1993); Hijikata, M., et al., J. Virol. 67:4665-4675 1993. In contrast, the NS3 protease is required for multiple cleavages within the nonstructural segment of the polyprotein, specifically the 3/4A, 4A/4B, 4B/5A, and 5A/5B junction sites Bartenschlager et al. (1993); Eckart, M. R., et al., Biochem. Biophys. Res. Comm. 192:399-406 1993; Grakoui et al. (1993); Tomei et al. (1994). More recently, it is thought that the NS2/3 protease might actually be part of the HCV NS3 protease complex even though they have two functionally distinct activities. Although NS3 protease is presumed to be essential for HCV viability, definitive proof of its necessity has been hampered by the lack of an infectious molecular clone that can be used in cell-based experiments. However, recently two independent HCV infectious molecular clones have been developed and have been shown to replicate in chimpanzees. Kolykhalov, A. A., et al., Science 277:570-574 1997; Yanagi, M., et al., Proc. Natl. Acad. Sci. 94:8738-8743 1997. The requirement for NS3 in the HCV life cycle may be validated in these clones by using oligo nucleotide-mediated site directed mutagenesis to inactivate the NS3 catalytic serine residue and then determining whether infectious virus is produced in chimpanzees. Until these experiments are performed, the necessity of NS3 is inferred from cell-based experiments using the related yellow fever (YFV) and bovine viral diarrhea (BVDV) viruses. Mutagenesis of the YFV and BVDV NS3 protease homologs has shown that NS3 serine protease activity is essential for YFV and BVDV replication. Chambers, T. J., et al., Proc. Natl. Acad. Sci. 87:8898-8902 1990; Xu, J., et al., J. Virol. 71:5312-5322 1997.

[0006] In general, when investigators screen potential anti-viral compounds for inhibitory activity, it usually involves initial in vitro testing of putative enzyme inhibitors followed by testing the compounds on actual infected cell lines and animals. It is obvious that working with live virus in large scale screening activities can be inherently dangerous and problematic. While final testing of putative inhibitors in infected cells and animals is still necessary for preclinical drug development, for initial screening of candidate molecules, such work is cost-prohibitive and unnecessary. Furthermore, the inability to grow HCV in tissue culture in a reproducible quantitative manner prevents the evaluation of potential antiviral agents for HCV in a standard antiviral cytopathic effect assay. In response to this real need in the industry, development of non-infectious, cell-based, screening systems is essential.

[0007] For example, Hirowatari, et al. developed a reporter assay system, inter alia, that involves the transfection of mammalian cells with two eukaryotic expression plasmids. Hirowatari, et al., Anal. Biochem. 225:113-120 1995. One plasmid has been constructed to express a polyprotein that encompasses the HCV NS2-NS3 domains fused in frame to an NS3 cleavage site followed by the HTLV-1 TAX1 protein. A second plasmid has been constructed to have the expression of the chloramphenicol acetyltransferase (CAT) reporter gene under the control of the HTLV-1 LTR. Thus when COS cells are transfected with both plasmids, NS3-mediated cleavage of the TAX1 protein from the NS2-NS3-TAX1 polyprotein allows the translocation of TAX1 to the nucleus and subsequent activation of CAT transcription from the HTLV-1 LTR. CAT activity can be measured by assaying the acetylation of 14C-chloramphenicol through chromatographic or immunological methods. In the CAT assay generally, cell extracts are incubated in a reaction mix containing 14C- or 3H-labeled chloramphenicol and n-Butyryl Coenzyme A. The CAT enzyme transfers the n-butyryl moiety of the cofactor to chloramphenicol. For a radiometric scintillation detection (LSC) assay, the reaction products are extracted with a small volume of xylene. The n-butyryl chloramphenicol partitions mainly into the xylene phase, while unmodified chloramphenicol remains predominantly in the aqueous phase. The xylene phase is mixed with a liquid scintillant and counted in a scintillation counter. The assay can be completed in as little as 2-3 hours, is linear for nearly three orders of magnitude, and can detect as little as 3×10−4 units of CAT activity. CAT activity also can be analyzed using thin layer chromatography (TLC). This method is more time-consuming than the LSC assay, but allows visual confirmation of the data.

[0008] Similarly, the other patents of Houghton, et al., U.S. Pat. No. 5,371,017, U.S. Pat. No. 5,585,258, U.S. Pat. No. 5,679,342 and U.S. Pat. No..5,597,691 or Jang et al. WO 98/00548 all disclose a cloned NS3 protease or portion fused to a second gene encoding for a protein which a surrogate expression product can be detected for example, in the '017 patent of Houghton, b-galactosidase, superoxide dismutase, ubiquitin or in Jang, the expression is measured by the proliferation of poliovirus in cell culture) and its use for candidate screening. It is unclear in the Houghton, et al. patents, however, whether the protease described in the specification is the NS2/3 metalloprotease or NS3 serine protease. Although the serine protease is claimed, the experimental data show putative cleavage of the N-terminal SOD fusion partner at the NS2/3 junction, a function which recently has been deemed to be the domain of the NS2/3 metalloprotease (Rice, C. M., et al., Proc. Nat. Acad. Sci. 90:1 0583-10587 (1993)). Furthermore, an active soluble NS3 serine protease is not disclosed in the Houghton, et al. patents, but a insoluble protein derived from E. coli inclusion bodies and which was N-terminally sequenced. For purposes of the present invention the term “NS2 protease” will refer to the enzymatic activity associated with the NS2/3 metalloprotease as defined by Rice et al., and the term “NS3 protease” will refer to the serine protease located within the NS3 region of the HCV genome.

[0009] De Francesco et al., U.S. Pat. No. 5,739,002, also describes a cell free in vitro system for testing candidates which activate or inhibit NS3 protease by measuring the amount of cleaved substrate. Hirowatari et al. (1995) discloses another HCV NS3 protease assay, however, it differs from the present invention in several aspects, including the reporter gene, the expression plasmid constructs, and the method of detection. Recently, Cho et al. describe a similar SEAP reporter system for assaying HCV NS3 protease which also differs in its structure and function from the present invention. Cho et al., J. Virol. Meth. 72:109-115 1998. Also of interest is a NS3 protease assay system developed by Chen et al. in WO 98/37180. In the Chen et al. application, a fusion protein is described which uses NS3 protease polypeptide or various truncation analogs fused to the NS4A polypeptide or various truncation analogs and is not autocleavable. The fusion protein is then incubated with known substrates with or without inhibitors to screen for inhibitory effect.

[0010] There are a number of problems inherent in all the abovementioned assay systems. For example, the reporter gene product or analyte is many steps removed from the initial NS3 protease cleavage step, the cells used in the assay system are prokaryotic or Yeast based and must be lysed before the reporter gene product can be measured, and the surrogate marker is proliferation of live virus. All of these problems are overcome in the present invention as summarized below.

SUMMARY OF INVENTION

[0011] The present invention describes a reporter gene system for use in the cell based assessment of inhibitors of the HCV protease. Applicants point out that throughout the description of this invention, the reference to specific non-structural (NS) regions or domains of the HCV genome are functional definitions and correspond approximately to the defined sequence locations described by C. M. Rice and others. The present invention discloses the co-transfection of a target cell line with a viral vector which has been engineered to express from the T7 RNA polymerase promoter and a recombinant plasmid or viral vector which has been engineered to express a polyprotein that includes NS3 HCV serine protease and the secreted human placental alkaline phosphatase (SEAP) gene (Berger et al. 1988) under control of the T7 promoter. The present invention was designed to have a linkage between the detection of reporter gene activity and NS3 serine protease activity through construction of a segment of the HCV gene encoding the NS2-NS3-NS4A-NS4B′-sequence linked to the SEAP reporter.

[0012] Detection of NS3 protease activity is accomplished by having the release and hence, the subsequent detection, of the SEAP reporter gene to be dependent upon NS3 serine protease activity. In a preferred embodiment, the target cell line is first infected with a viral vector that expresses the T7 RNA polymerase followed by either co-infection with a second viral vector that encodes the NS3 HCV protease/SEAP polyprotein, or transfection with a plasmid that contains the same NS3/SEAP gene elements.

[0013] The SEAP enzyme is a truncated form of human placental alkaline phosphatase, in which the cleavage of the transmembrane domain of the protein allows it to be secreted from the cells into the surrounding media. SEAP activity can be detected by a variety of methods including, but not limited to, measurement of catalysis of a fluorescent substrate, immunoprecipitation, HPLC, and radiometric detection. The luminescent method is preferred due to its increased sensitivity over colorimetric detection methods, and such an assay kit is available from Tropix®. The advantages of using SEAP over more routinely used reporter genes such as beta-galactosidase or luciferase, is that a cell lysis step is not required since the SEAP protein is secreted out of the cell. The absence of a cell lysis step decreases intra- and inter-assay variability as well as makes the assay easier to perform then earlier assays in the prior art. When both the T7 promoter and NS3/SEAP constructs are present, SEAP can be detected in the cell medium within the usual viral assay timeframe of 24-48 hours, however, the timeframe should not be read as a limitation because it is theoretically possible to detect the SEAP in the media only a few hours after transfection. The medium can then be collected and analyzed. Various examples illustrating the use of this composition and method will be detailed below.

BRIEF DESCRIPTION OF THE DRAWINGS

[0014] FIG. 1 illustrates schematically the Vaccinia Virus NS3/SEAP System gene construct.

[0015] FIG. 1B illustrates schematically the Plasmid/Vaccinia Virus NS3/SEAP assay.

[0016] FIG. 2 illustrates schematically how the assay operates.

[0017] FIG. 3 illustrates schematically the DI/DR Assay.

[0018] FIGS. 4A and 4B shows the SEAP activity dose response curve for a representative plasmid/virus assay.

[0019] FIG. 5 shows an experimental 96 well plate diagram for the SEAP protocol on Day 1 in Example 3.

[0020] FIG. 6 shows an experimental 96 well plate diagram for the SEAP protocol on Day 2 in Example 3.

[0021] FIG. 7 shows SEAP activity and Cytotoxicity data for Example 4.

[0022] FIG. 8 shows a summary of DI/DR assay data.

[0023] FIG. 9 illustrates the experimental plate set-up for Example 2.

DETAILED DESCRIPTION OF A PREFERRED EMBODIMENT OF THE INVENTION

[0024] The practice of this invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA manipulation and production, virology and immunology, which are within the skill of the art. Such techniques are explained fully in the literature: Sambrook, Molecular Cloning; A Laboratory Manual, Second Edition (1989); DNA Cloning, Volumes I and II (D. N. Glover, Ed. 1985); Oligonucleotide Synthesis (M. J. Gait, Ed. 1984); Nucleic Acid Hybridization (B. D. Hames and S. I. Higgins, Eds. 1984); Transcription and Translation (B. D. Hames and S. I. Higgins, Eds. 1984); Animal Cell Culture (R. I. Freshney, Ed. 1986); Immobilized Cells and Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide to Molecular Cloning (1984); Gene Transfer Vectors for Mammalian Cells (J. H. Miller and M. P. Calos, Eds. 1987, Cold Spring Harbor Laboratory); Methods in Enzymology, Volumes 154 and 155 (Wu and Grossman, and Wu, Eds., respectively), (Mayer and Walker, Eds.) (1987); Immunochemical Methods in Cell and Molecular Biology (Academic Press, London), Scopes, (1987), Expression of Proteins in Mammalian Cells Using Vaccinia Viral Vectors in Current Protocols in Molecular Biology, Volume 2 (Frederick M. Ausubel, et al., Eds.)(1991). All patents, patent applications and publications mentioned herein, both supra and infra, are hereby incorporated by reference.

[0025] Both prokaryotic and eukaryotic host cells are useful for expressing desired coding sequences when appropriate control sequences compatible with the designated host are used. Among prokaryotic hosts, E. coli is most frequently used. Expression control sequences for prokaryotes include promoters, optionally containing operator portions, and ribosome binding sites. Transfer vectors compatible with prokaryotic hosts are commonly derived from, for example, pBR322, a plasmid containing operons conferring ampicillin and tetracycline resistance, and the various pUC vectors, which also contain sequences conferring antibiotic resistance markers. These plasmids are commercially available. The markers may be used to obtain successful transformants by selection. Commonly used prokaryotic control sequences include the β-lactamase (penicillinase) and lactose promoter systems (Chang et al, Nature (1977) 198:1 056), the tryptophan (trp) promoter system (Goeddel et al, Nuc Acids Res (1980) 8:4057) and the lambda-derived PL promoter and N gene ribosome binding site (Shimatake et al, Nature (1 981) 292:128) and the hybrid tac promoter (De Boer et al, Proc Nat Acad Sci USA (1983) 292:128) derived from sequences of the trp and lac UV5 promoters. The foregoing systems are particularly compatible with E. coli; if desired, other prokaryotic hosts such as strains of Bacillus or Pseudomonas may be used, with corresponding control sequences.

[0026] Eukaryotic hosts include without limitation yeast and mammalian cells in culture systems. Yeast expression hosts include Saccharomyces, Klebsiella, Picia, and the like. Saccharomyces cerevisiae and Saccharomyces carlsbergensis and K. lactis are the most commonly used yeast hosts, and are convenient fungal hosts. Yeast-compatible vectors carry markers which permit selection of successful transformants by conferring prototrophy to auxotrophic mutants or resistance to heavy metals on wild-type strains. Yeast compatible vectors may employ the 2 μ origin of replication (Broach et al, Meth Enzymol (1983) 101:307), the combination of CEN3 and ARS1 or other means for assuring replication, such as sequences which will result in incorporation of an appropriate fragment into the host cell genome. Control sequences for yeast vectors are known in the art and include promoters for the synthesis of glycolytic enzymes (Hess et al, J Adv Enzyme Reg (1968) 7:149; Holland et al, Biochem (1978), 17:4900), including the promoter for 3-phosphoglycerate kinase (R. Hitzeman et al, J Biol Chem (1980) 255:2073). Terminators may also be included, such as those derived from the enolase gene (Holland, J Biol Chem (1981) 256:1385).

[0027] Mammalian cell lines available as hosts for expression are known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC), including HeLa cells, Chinese hamster ovary (CHO) cells, baby hamster kidney (BHK) cells, BSC 1 cells, CV1 cells, and a number of other cell lines. Suitable promoters for mammalian cells are also known in the art and include vital promoters such as that from Simian Virus 40 (SV40) (Fiers et al, Nature (1978) 273:113), Rous sarcoma virus (RSV), adenovirus (ADV), and bovine papilloma virus (BPV). Mammalian cells may also require terminator sequences and poly-A addition sequences. Enhancer sequences which increase expression may also be included, and sequences which promote amplification of the gene may also be desirable (for example methotrexate resistance genes). These sequences are known in the art.

[0028] Vectors suitable for replication in mammalian cells are known in the art, and may include vital replicons, or sequences which insure integration of the appropriate sequences encoding HCV epitopes into the host genome. For example, another vector used to express foreign DNA is Vaccinia virus. In this case the heterologous DNA is inserted into the Vaccinia genome and transcription can be directed by either endogenous vaccinia promoters or exogenous non-vaccinia promoters (e.g. T7 retroviral promoter) known to those skilled in the art, depending on the characteristics of the constructed vector. Techniques for the insertion of foreign DNA into the vaccinia virus genome are known in the art, and may utilize, for example, homologous recombination. The heterologous DNA is generally inserted into a gene which is non-essential to the virus, for example, the thymidine kinase gene (tk), which also provides a selectable marker. Plasmid vectors that greatly facilitate the construction of recombinant viruses have been described (see, for example, Mackett et al, J Virol (1984) 49:857; Chakrabarti et al, Mol Cell Biol (1985) 5:3403; Moss, in GENE TRANSFER VECTORS FOR MAMMALIAN CELLS (Miller and Calos, eds., Cold Spring Harbor Laboratory, N.Y., 1987), p. 10). Expression of the HCV polypeptide then occurs in cells or animals which are infected with the live recombinant vaccinia virus.

[0029] In order to detect whether or not the HCV polypeptide is expressed from the vaccinia vector, BSC 1 cells may be infected with the recombinant vector and grown on microscope slides under conditions which allow expression. The cells may then be acetone-fixed, and immunofluorescence assays performed using serum which is known to contain anti-HCV antibodies to a polypeptide(s) encoded in the region of the HCV genome from which the HCV segment in the recombinant expression vector was derived.

[0030] Other systems for expression of eukaryotic or vital genomes include insect cells and vectors suitable for use in these cells. These systems are known in the art, and include, for example, insect expression transfer vectors derived from the baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV), which is a helper-independent, viral expression vector. Expression vectors derived from this system usually use the strong viral polyhedron gene promoter to drive expression of heterologous genes. Currently the most commonly used transfer vector for introducing foreign genes into AcNPV is pAc373 (see PCT WO89/046699 and U.S. Ser. No. 7/456,637). Many other vectors known to those of skill in the an have also been designed for improved expression. These include, for example, pVL985 (which alters the polyhedron start codon from ATG to ATT, and introduces a BamHI cloning site 32 bp downstream from the ATT; See Luckow and Summers, Virol (1989) 17:31). AcNPV transfer vectors for high level expression of non-fused foreign proteins are described in co-pending applications PCT WO89/046699 and U.S. Ser. No. 7/456,637. A unique BamHI site is located following position-8 with respect to the translation initiation codon ATG of the polyhedron gene. There are no cleavage sites for SmaI, PstI, BglII, XbaI or SstI. Good expression of non-fused foreign proteins usually requires foreign genes that ideally have a short leader sequence containing suitable translation initiation signals preceding an ATG start signal. The plasmid also contains the polyhedron polyadenylation signal and the ampicillin-resistance (amp) gene and origin of replication for selection and propagation in E. coli.

[0031] Methods for the introduction of heterologous DNA into the desired site in the baculovirus virus are known in the art. (See Summer and Smith, Texas Agricultural Experiment Station Bulletin No. 1555; Smith et al, Mol. Cell Biol. (1983) 3:2156-2165; and Luckow and Summers, Virol. (1989) 17:31). For example, the heterologous DNA can be inserted into a gene such as the polyhedron gene by homologous recombination, or into a restriction enzyme site engineered into the desired baculovirus gene. The inserted sequences may be those which encode all or varying segments of the polyprotein, or other orfs which encode viral polypeptides. For example, the insert could encode the following numbers of amino acid segments from the polyprotein: amino acids 1-1078; amino acids 332-662; amino acids 406-662; amino acids 156-328, and amino acids 199-328.

[0032] The signals for post-translational modifications, such as signal peptide cleavage, proteolytic cleavage, and phosphorylation, appear to be recognized by insect cells. The signals required for secretion and nuclear accumulation also appear to be conserved between the invertebrate cells and vertebrate cells. Examples of the signal sequences from vertebrate cells which are effective in invertebrate cells are known in the art, for example, the human interleukin-2 signal (IL2s) which signals for secretion from the cell, is recognized and properly removed in insect cells.

[0033] Transformation may be by any known method for introducing polynucleotides into a host cell, including, for example packaging the polynucleotide in a virus and transducing a host cell with the virus, and by direct uptake of the polynucleotide. The transformation procedure used depends upon the host to be transformed. Bacterial transformation by direct uptake generally employs treatment with calcium or rubidium chloride (Cohen, Proc. Nat. Acad. Sci. USA (1972) 69:21 10; T. Maniatis et at, “Molecular Cloning; A Laboratory Manual” (Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 1982). Yeast transformation by direct uptake may be carried out using the method of Hinnen et al, Proc. Nat. Acad. Sci. USA (1978) 75:1929. Mammalian transformations by direct uptake may be conducted using the calcium phosphate precipitation method of Graham and Van der Eb, Virol. (1978) 52:546, or the various known modifications thereof. Other methods for introducing recombinant polynucleotides into cells, particularly into mammalian cells, include dextran-mediated transfection, calcium phosphate mediated transfection, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the polynucleotides into nuclei.

[0034] Vector construction employs techniques which are known in the art. Site-specific DNA cleavage is performed by treating with suitable restriction enzymes under conditions which generally are specified by the manufacturer of these commercially available enzymes. In general, about 1 mg of plasmid or DNA sequence is cleaved by 1 unit of enzyme in about 20 mL buffer solution by incubation for 1-2 hr at 37° C. After incubation with the restriction enzyme, protein is removed by phenol/chloroform extraction and the DNA recovered by precipitation with ethanol. The cleaved fragments may be separated using polyacrylamide or agarose gel electrophoresis techniques, according to the general procedures described in Meth. Enzymol. (1980) 65:499-560.

[0035] Sticky-ended cleavage fragments may be blunt ended using E. coli DNA polymerase I (Klenow fragment) with the appropriate deoxynucleotide triphosphates (dNTPs) present in the mixture. Treatment with S1 nuclease may also be used, resulting in the hydrolysis of any single stranded DNA portions.

[0036] Ligations are carried out under standard buffer and temperature conditions using T4 DNA ligase and ATP; sticky end ligations require less ATP and less ligase than blunt end ligations. When vector fragments are used as part of a ligation mixture, the vector fragment is often treated with bacterial alkaline phosphatase (BAP) or calf intestinal alkaline phosphatase to remove the 5′-phosphate, thus preventing re-ligation of the vector. Alternatively, restriction enzyme digestion of unwanted fragments can be used to prevent ligation. Ligation mixtures are transformed into suitable cloning hosts, such as E. coli, and successful transformants selected using the markers incorporated (e.g., antibiotic resistance), and screened for the correct construction.

[0037] Synthetic oligonucleotides may be prepared using an automated oligonucleotide synthesizer as described by Warner, DNA (1984) 3:401. If desired, the synthetic strands may be labeled with 32P by treatment with polynucleotide kinase in the presence of 32P-ATP under standard reaction conditions.

[0038] DNA sequences, including those isolated from cDNA libraries, may be modified by known techniques, for example by site directed mutagenesis (see e.g., Zoller, Nuc. Acids Res. (1982) 10:6487). Briefly, the DNA to be modified is packaged into phage as a single stranded sequence, and converted to a double stranded DNA with DNA polymerase, using as a primer a synthetic oligonucleotide complementary to the portion of the DNA to be modified, where the desired modification is included in the primer sequence. The resulting double stranded DNA is transformed into a phage-supporting host bacterium. Cultures of the transformed bacteria which contain copies of each strand of the phage are plated in agar to obtain plaques. Theoretically, 50% of the new plaques contain phage having the mutated sequence, and the remaining 50% have the original sequence. Replicates of the plaques are hybridized to labeled synthetic probe at temperatures and conditions which permit hybridization with the correct strand, but not with the unmodified sequence. The sequences which have been identified by hybridization are recovered and cloned.

[0039] DNA libraries may be probed using the procedure of Grunstein and Hogness Proc. Nat. Acad. Sci. USA (1 975) 73:3961. Briefly, in this procedure the DNA to be probed is immobilized on nitrocellulose filters, denatured, and pre-hybridized with a buffer containing 0-50% formamide, 0.75M NaCl, 75 mM Na citrate, 0.02% (wt/v) each of bovine serum albumin, polyvinylpyrrolidone, and Ficoll®, 50 mM NaH2PO4 (pH 6.5), 0.1% SDS, and 100 m g/mL carrier denatured DNA. The percentage of formamide in the buffer, as well as the time and temperature conditions of the pre-hybridization and subsequent hybridization steps depend on the stringency required. Oligomeric probes which require lower stringency conditions are generally used with low percentages of formamide, lower temperatures, and longer hybridization times. Probes containing more than 30 or 40 nucleotides, such as those derived from cDNA or genomic sequences generally employ higher temperatures, e.g., about 40°-42° C., and a high percentage formamide, e.g., 50%. Following pre-hybridization, 5′-32P-labeled oligonucleotide probe is added to the buffer, and the filters are incubated in this mixture under hybridization conditions. After washing, the treated filters are subjected to autoradiography to show the location of the hybridized probe; DNA in corresponding locations on the original agar plates is used as the source of the desired DNA.

[0040] For routine vector constructions, ligation mixtures are transformed into E. coli strain HB101 or other suitable hosts, and successful transformants selected by antibiotic resistance or other markers. Plasmids from the transformants are then prepared according to the method of Clewell et al, Proc. Nat. Acad. Sci. USA (1969) 62:1159, usually following chloramphenicol amplification (Clewell, J. Bacteriol. (1972) 110:667). The DNA is isolated and analyzed, usually by restriction enzyme analysis and/or sequencing. Sequencing may be performed by the dideoxy method of Sanger et at, Proc. Nat. Acad. Sci. USA (1977) 74:5463, as further described by Messing et at, Nuc. Acids Res. (1981) 9:309, or by the method of Maxam et at, Meth. Enzymol. (1980) 65:499. Problems with band compression, which are sometimes observed in GC-rich regions, were overcome by use of T-deazoguanosine according to Barr et al, Biotechniques (1986) 4:428.

[0041] Target plasmid sequences are replicated by a polymerizing means which utilizes a primer oligonucleotide to initiate the synthesis of the replicate chain. The primers are selected so that they are complementary to sequences of the plasmid. Oligomeric primers which are complementary to regions of the sense and antisense strands of the plasmids can be designed from the plasmid sequences already known in the literature.

[0042] The primers are selected so that their relative positions along a duplex sequence are such that an extension product synthesized from one primer, when it is separated from its template (complement), serves as a template for the extension of the other primer to yield a replicate chain of defined length.

[0043] The primer is preferably single stranded for maximum efficiency in amplification, but may alternatively be double stranded. If double stranded, the primer is first treated to separate its strands before being used to prepare extension products. Preferably, the primer is an oligodeoxyribonucleotide. The primer must be sufficiently long to prime the synthesis of extension products in the presence of the agent for polymerization. The exact lengths of the primers will depend on many factors, including temperature and source of the primer and use of the method. For example, depending on the complexity of the target sequence, the oligonucleotide primer typically contains about 15-45 nucleotides, although it may contain more or fewer nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with the template.

[0044] The primers used herein are selected to be “substantially” complementary to the different strands of each specific sequence to be amplified. Therefore, the primers need not reflect the exact sequence of the template, but must be sufficiently complementary to selectively hybridize with their respective strands. For example, a non-complementary nucleotide fragment may be attached to the 5′-end of the primer, with the remainder of the primer sequence being complementary to the strand. Alternatively, non-complementary bases or longer sequences can be interspersed into the primer, provided that the primer has sufficient complementarity with the sequence of one of the strands to be amplified to hybridize therewith, and to thereby form a duplex structure which can be extended by the polymerizing means. The non-complementary nucleotide sequences of the primers may include restriction enzyme sites. Appending a restriction enzyme site to the end(s) of the target sequence would be particularly helpful for cloning of the target sequence.

[0045] It will be understood that “primer”, as used herein, may refer to more than one primer, particularly in the case where there is some ambiguity in the information regarding the terminal sequence(s) of the target region to be amplified. Hence, a “primer” includes a collection of primer oligonucleotides containing sequences representing the possible variations in the sequence or includes nucleotides which allow a typical basepairing.

[0046] The oligonucleotide primers may be prepared by any suitable method. Methods for preparing oligonucleotides of specific sequence are known in the art, and include, for example, cloning and restriction of appropriate sequences, and direct chemical synthesis. Chemical synthesis methods may include, for example, the phosphotriester method described by Narang et al. (1979), the phosphodiester method disclosed by Brown et al. (1979), the diethylphosphoramidate method disclosed in Beaucage et al. (1981), and the solid support method in U.S. Pat. No. 4,458,066. The primers may be labeled, if desired, by incorporating means detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means.

[0047] Template-dependent extension of the oligonucleotide primer(s) is catalyzed by a polymerizing agent in the presence of adequate amounts of the four deoxyribonucleotide triphosphates (dATP, dGTP, dCTP and dTTP) or analogs, in a reaction medium which is comprised of the appropriate salts, metal cations, and pH buffering system. Suitable polymerizing agents are enzymes known to catalyze primer- and template-dependent DNA synthesis. Known DNA polymerases include, for example, E. coli DNA polymerase I or its Klenow fragment, T4 DNA polymerase, and Taq DNA polymerase. The reaction conditions for catalyzing DNA synthesis with these DNA polymerases are known in the art.

[0048] The products of the synthesis are duplex molecules consisting of the template strands and the primer extension strands, which include the target sequence. These products, in turn, serve as template for another round of replication. In the second round of replication, the primer extension strand of the first cycle is annealed with its complementary primer; synthesis yields a “short” product which is bounded on both the 5′- and the 3′-ends by primer sequences or their complements. Repeated cycles of denaturation, primer annealing, and extension result in the exponential accumulation of the target region defined by the primers. Sufficient cycles are run to achieve the desired amount of polynucleotide containing the target region of nucleic acid. The desired amount may vary, and is determined by the function which the product polynucleotide is to serve.

[0049] The PCR method can be performed in a number of temporal sequences. For example, it can be performed step-wise, where after each step new reagents are added, or in a fashion where all of the reagents are added simultaneously, or in a partial step-wise fashion, where fresh reagents are added after a given number of steps.

[0050] In a preferred method, the PCR reaction is carried out as an automated process which utilizes a thermostable enzyme. In this process the reaction mixture is cycled through a denaturing region, a primer annealing region, and a reaction region. A machine may be employed which is specifically adapted for use with a thermostable enzyme, which utilizes temperature cycling without a liquid handling system, since the enzyme need not be added at every cycle. This type of machine is commercially available from Perkin Elmer Cetus Corp.

[0051] After amplification by PCR, the target polynucleotides are detected by hybridization with a probe polynucleotide which forms a stable hybrid with that of the target sequence under stringent to moderately stringent hybridization and wash conditions. If it is expected that the probes will be completely complementary (i.e., about 99% or greater) to the target sequence, stringent conditions will be used. If some mismatching is expected, for example if variant strains are expected with the result that the probe will not be completely complementary, the stringency of hybridization may be lessened. However, conditions are chosen which rule out nonspecific/adventitious binding. Conditions which affect hybridization, and which select against nonspecific binding are known in the art, and are described in, for example, Maniatis et al. (1982). Generally, lower salt concentration and higher temperature increase the stringency of binding. For example, it is usually considered that stringent conditions are incubation in solutions which contain approximately 0.1×SSC, 0.1% SDS, at about 65° C. incubation/wash temperature, and moderately stringent conditions are incubation in solutions which contain approximately 1-2×SSC, 0.1% SDS and about 50°-65° C. incubation/wash temperature. Low stringency conditions are 2×SSC and about 30°-50° C.

[0052] Probes for plasmid target sequences may be derived from well known restriction sites. The plasmid probes may be of any suitable length which span the target region, but which exclude the primers, and which allow specific hybridization to the target region. If there is to be complete complementarity, i.e., if the strain contains a sequence identical to that of the probe, since the duplex will be relatively stable under even stringent conditions, the probes may be short, i.e., in the range of about 10-30 base pairs. If some degree of mismatch is expected with the probe, i.e., if it is suspected that the probe will hybridize to a variant region, the probe may be of greater length, since length seems to counterbalance some of the effect of the mismatch(es).

[0053] The probe nucleic acid having a sequence complementary to the target sequence may be synthesized using similar techniques described supra. for the synthesis of primer sequences. If desired, the probe may be labeled. Appropriate labels are described supra.

[0054] In some cases, it may be desirable to determine the length of the PCR product detected by the probe. This may be particularly true if it is suspected that variant plasmid products may contain deletions within the target region, or if one wishes to confirm the length of the PCR product. In such cases it is preferable to subject the products to size analysis as well as hybridization with the probe. Methods for determining the size of nucleic acids are known in the art, and include, for example, gel electrophoresis, sedimentation in gradients, and gel exclusion chromatography.

[0055] The presence of the target sequence in a biological sample is detected by determining whether a hybrid has been formed between the polynucleotide probe and the nucleic acid subjected to the PCR amplification technique. Methods to detect hybrids formed between a probe and a nucleic acid sequence are known in the art. For example, for convenience, an unlabeled sample may be transferred to a solid matrix to which it binds, and the bound sample subjected to conditions which allow specific hybridization with a labeled probe; the solid matrix is than examined for the presence of the labeled probe. Alternatively, if the sample is labeled, the unlabeled probe is bound to the matrix, and after the exposure to the appropriate hybridization conditions, the matrix is examined for the presence of label. Other suitable hybridization assays are described supra. Analysis of the nucleotide sequence of the target region(s) may be by direct analysis of the PCR amplified products. A process for direct sequence analysis of PCR amplified products is described in Saiki et al. (1988).

[0056] Alternatively, the amplified target sequence(s) may be cloned prior to sequence analysis. A method for the direct cloning and sequence analysis of enzymatically amplified genomic segments has been described by Scharf (1986). In the method, the primers used in the PCR technique are modified near their 5′-ends to produce convenient restriction sites for cloning directly into, for example, an M13 sequencing vector. After amplification, the PCR products are cleaved with the appropriate restriction enzymes. The restriction fragments are ligated into the M13 vector, and transformed into, for example, a JM 103 host, plated out, and the resulting plaques are screened by hybridization with a labeled oligonucleotide probe. Other methods for cloning and sequence analysis are known in the art.

[0057] Construction of the HCV/SEAP Reporter Gene Plasmid

[0058] General Method

[0059] In the first embodiment, the Tropix® pCMV/SEAP expression vector is used as a starting point for construction of the HCV NS3 protease plasmid construct pHCAP1 (Seq. ID. NOS. 1-7). pHCAP1 is constructed from the pTM3 vector (Moss et al., Nature, 348:91-92 (1990)) in which the nucleotide sequence encoding the portion of the HCV-BK polyprotein domains NS2-NS3-NS4A-NS4B was cloned from the pBKCMV/NS2-NS3-NS4A-NS4B-SEAP (the pBK/HCAP) construct. pBK/HCAP is the eukaryotic expression plasmid in which all the original subcloning and ligation of all the HCV NS gene fragments and SEAP gene was created in. pCMV/SEAP is a mammalian expression vector designed for studies of promoter/enhancer elements with SEAP as a reporter (Berger et al., (1988)). The vector contains a polylinker for promoter/enhancer insertion, as well as an intron and polyadenylation signals from SV40. The vector can be propagated in E.coli due to the pUC19 derived origin of replication and ampicillin resistance gene. Modification of the commercially available plasmids is accomplished by use of PCR techniques including mutational PCR. Although this particular plasmid is described in the examples that follow, it is not the only plasmid or vector which may be used. The T7 RNA polymerase promoter is part of the pTM3 plasmid which was preferred in construction of the pHCAP vector.

[0060] In an alternate embodiment, the pTKgptF2s plasmid (Falkner and Moss, J. Virol. 62:1849-1854 (1988)) can be used instead of the pTM3 plasmid, which places the HCV/SEAP gene construct under transcriptional control of the native vaccinia virus promoter. The only requirement is that the promoter operate when placed in a plasmid having vaccinia virus regions flanking the subcloning region. This requirement allows the plasmid homologous recombination with the wild type vaccinia virus. Other vaccinia virus intermediate plasmids would be operable here as well.

EXAMPLE 1

[0061] The Tropix® pCMV/SEAP expression vector is first modified so that both Sac1 restriction sites are inactivated. This is done by cleaving the plasmid with BamH1 which results in a 5′ cleavage product that contains the plasmid 5′ ATG site and about 250 bp ending at the Bam H1 site, and a 3′ cleavage product having BamH1 sites at its 5′ end and at its 3′ end. The 5′ cleavage fragment was then amplified from the pCMV/SEAP plasmid using primers that were designed to delete the 5′ ATG codon and to create a Sac 1 site on the 5′ end. The downstream 3′ primer spanned the Bam H1 site that is present within the SEAP coding sequence. Thus after PCR, the amplified 5′ fragment has a 5′ Sac 1 site and a Bam H1 site. The 5′ primer introduced an extra codon (a glutamic acid residue) in front of the first leucine residue of the SEAP secretion signal. Furthermore, the first leucine codon was changed from a CTG to a CTC codon (a silent change). The codon change was made to create the second half of the Sac 1 site:

5′-GAGCTC-X-GGATCC-3′ (Seq. ID NO:22)
Sac 1 site 5′ end of SEAP Bam H1

[0062] The modified sequence is then cloned into pGEM3Zf(+) (Promega). The Bam H1-Bam H1 SEAP fragment was subcloned into pAlter-1 (Promega) which is a plasmid that has an f1 origin of replication so it produces a single strand DNA for use in oligo mediated site directed mutagenesis. The Sac 1 sites within the SEAP fragment were mutated by oligo mediated site directed mutagenesis (GAGCTC to GAGCTG—a silent change) and the same change at the second Sac 1 site (GAGCTC to GAGCTG—an amino acid change from Serine to Cysteine) The complete SEAP pGEM3Zf(+) plasmid is then made by subcloning the PCR modified 5′ SEAP fragment into the Sac I-Bam H1 sites of pGEM3Zf(+). The resulting plasmid was then linearized with Bam H1 to allow the subcloning of the 3′ SEAP Bam H1-Bam H1 from the pAlter-1 plasmid which was used for the oligo mediated site directed mutagenesis to disrupt the two internal Sac I sites. A clone with the correct orientation of the Bam H1-Bam H1 fragment distal to the 5′ SEAP fragment was selected after of purified plasmid DNA by restriction enzyme digest. This clone was used in the subsequent subcloning steps for the construction of the HCV/SEAP construct.

[0063] The coding sequences for the HCV proteins and NS3 cleavage sites that comprise the final HCV/SEAP polyprotein were generated in two separate PCRs from cDNA of the HCV-BK strain (Accession No. M58335). Takamizawa, A., et al., J. Virol. 65:1105-1113 1991. The first amplified fragment starts with the amino acid coding sequence of the HCV polyprotein corresponding to the C-terminal 81 amino acids of the putative E2 region, which are upstream of the beginning of the putative NS2 region or amino acid 729

(Seq. ID NO:23)
(ARVCACLWMMLLIAQAEAALENLVVLNSASVAGAHGILSFLVFFCAAWY
IKGRLVPGATYALYGVWPLLLLLLALPPRAYAMDREMAA)

[0064] or nucleotide 2187.

(Seq. ID NO:24)
(GCACGTGTCTGTGCCTGCTTGTGGATGATGCTGCTGATAGCCCAGGCCG
AGGCCGCCTTGGAGAACCTGGTGGTCCTCAATGCGGCGTCTGTGGCCGGC
GCACATGGCATCCTCTCCTTCCTTGTGTTCTTCTGTGCCGCCTGGTACAT
CAAAGGCAGGCTGGTCCCTGGGGCGGCATATGCTCTTTATGGCGTGTGGC
CGCTGCTCCTGCTCTTGCTGGCATTACCACCGCGAGCTTACGCCATGGAC
CGGGAGATGGC)

[0065] and contains the DNA encoding the HCV polyprotein domains NS2-NS3-NS4A through the first 176 amino acids of the NS4B gene.

(Seq. ID NO:25)
(CASHLPYIEQ GMQLAEQFKQ KALGLLQTAT KQAEAAAPVV
ESKWRALETF WAKHMWNFIS GIQYLAGLST LPGNPAIASL
MAFTASITSPLTTQSTLLFN ILGGWVAAQL APPSAASAFV
GAGIAGAAVG SIGLGKVLVD ILAGYGAGVAGALVAFKVMS
GEMPSTEDLV NLLPAIL)

[0066] or amino acid 1886 or nucleotide 5658.

(Seq. ID NO:26)
(TGCGCCTCGCACCTCCCTTACATCGAGCAGGGAATGCAGCTCGCCGAGC
AATTCAAGCAGAAAGCGCTCGGGTTACTGCAAACAGCCACCAAACAAGCG
GAGGCTGCTGCTCCCGTGGTGGAGTCCAAGTGGCGAGCCCTTGAGACATT
CTGGGCGAAGCACATGTGGAATTTCATCAGCGGGATACAGTACTTAGCAG
GCTTATCCACTCTGCCTGGGAACCCCGCAATAGCATCATTGATGGCATTC
ACAGCCTCTATCACCAGCCCGCTCACCACCCAAAGTACCCTCCTGTTTAA
CATCTTGGGGGGGTGGGTGGCTGCCCAACTCGCCCCCCCCAGCGCCGCTT
CGGCTTTCGTGGGCGCCGGCATCGCCGGTGCGGCTGTTGGCAGCATAGGC
CTTGGGAAGGTGCTTGTGGACATTCTGGCGGGTTATGGAGCAGGAGTGGC
CGGCGCGCTCGTGGCCTTTAAGGTCATGAGCGGCGAGATGCCCTCCACCG
AGGACCTGGTCAATCTACTTCCTGCCATC)

[0067] The primers used to amplify the fragment were designed to contain an Eco RI site and an ATG codon in the 5′ primer (Seq. ID NO: 27) and an Xho I site in the 3′ primer (Seq. ID NO: 28). The amplified fragment was accordingly subcloned as an Eco RI-Xho I fragment into pET24a(+) plasmid (Novagen). The second fragment amplified from the HCV strain BK cDNA encompasses the putative NS5A/5B cleavage site (EEASEDVVCCSMSYTWTGAL)(Seq. ID NO: 29). The 5′ primer that was used to amplify the cleavage site was designed to have an Xho I site (Seq. ID NO: 30) whereas the 3′ primer was designed to have a Sac I site (Seq. ID NO: 31). The resulting PCR product was subcloned as an Xho I-Sac I fragment into pET24a(+), which had been digested with Xho I-Hind III, as part of a three way ligation (Seq. ID NO: 32). The third fragment in the three way ligation was the Sac I-Hind III fragment from the SEAP pGEM3Zf(+) plasmid. The Sac I-Hind III fragment encompassed the modified SEAP gene and also 30 base pairs of the pGEM3Zf(+) polylinker which included the multiple cloning sites (MCS) between the Bam H1 and HindIII sites. The final HCV/SEAP construct was assembled using pBKCMV as the vector. pBKCMV was digested with Eco RI and Hind III and then used in a three way ligation with the NS5A/5B-SEAP Xho I-Hind III fragment and the Eco RI-Xho I NS2-NS4B fragment.

[0068] The control plasmids for the assay (pHCAP3, pHCAP4) were constructed in a similar manner to the HCV/SEAP construct. The control plasmids have either an inactive form of NS3 protease or inactive forms of both NS2 protease and NS3 protease. Inactivation of NS2 and NS3 proteases was accomplished by oligo mediated site directed mutagenesis performed on the PCR amplified NS2-NS4B fragment that had been subcloned into pALTER-1 as an Eco R1-Xho 1 fragment together with the NS5A/5B Xho 1-Sac 1 fragment. In order to inactivate the NS3 protease, the catalytic serine residue was substituted with an alanine by replacing thymidine (TOG) with guanine (GCG)(base 2754). The NS2 protease was inactivated by substitution of the catalytic cysteine residue with an alanine residue (TGT→GCT)(bases 2238-2239). The resulting inactivated NS3 protease and inactivated NS2-NS3 proteases variants of the NS2-NS4B fragment were each subcloned into pBKCMV as separate Eco R1-Xho 1 fragments together with the NS5A/5B-SEAP Xho 1-Hind III fragment.

[0069] The pHCAP1 (NS2WTNS3WT)(Seq. ID NOS: 1-7), pHCAP3 (NS2WTNS3MUT) (Seq. ID NOS: 8-14), and pHCAP4 (NS2MUTNS3MUT) (Seq. ID NOS: 15-21) plasmids were constructed using pTM3 as the vector and the appropriate HCV/SEAP fragment from the corresponding pBKHCV/SEAP constructs. The pBKHCV/SEAP constructs were first digested with Eco R1 and the Eco R1 site was filled in using Klenow fragment in a standard fill in reaction. The pBKHCV/SEAP constructs were then digested with Xba I and the gel purified HCV/SEAP fragment was subcloned into pTM3 that had been digested with Sma 1 and Spe 1. Subcloning the HCV/SEAP fragment into the Sma I site will result in an additional 6 amino acids (MGIPQF) (Seq. ID NO: 33) at the N-terminus (codons 1426-1444) if the preferred translational start codon, which is part of the Nco 1 site in pTM3, is used.

[0070] The pHCAP1 (NS2WTNS3WT), pHCAP3 (NS2WTNS3MUT), and pHCAP4 (NS2MUTNS3MUT) plasmids have been used to generate recombinant vaccinia viruses as described in the next section.

[0071] Construction of the HCV/SEAP Reporter Gene Viral Vectors

[0072] Applicants have generated recombinant vaccinia virus using pHCAP1 and the control plasmids, pHCAP3 and pHCAP4. Recombinant vaccinia viruses were generated using standard procedures in which BSC-1 cells were infected with wild type vaccinia virus (strain WR from ATCC) and then transfected with either pHCAP1, pHCAP3, or pHCAP4. Selection of recombinant virus was performed by growth of infected transfected cells in the presence of mycophenolic acid. The recombinant vaccinia viruses are termed vHCAP1, vHCAP3, and vHCAP4 and correspond directly with the pHCAP1, pHCAP3, and pHCAP4 plasmids. Large scale stocks of the vHCAP1, vHCAP3, and vHCAP4 were grown and titered in CV1 cells.

[0073] Transfection of Cell Lines Containing the HCV/SEAP Reporter

[0074] In the first embodiment HeLa cells are transfected with the Hep C/SEAP reporter gene plasmid, pHCAP1, and co-infection with a vTF7.3, a recombinant vaccinia virus (Fuerst et al., Proc. Nat. Acad. Sci. USA, 86:8122-8126 (1986)). vTF7.3 expresses T7 RNA polymerase which is required for transcription of the reporter gene since it is under the control of T7 promoter in the pTM3 plasmid. The pTM3 plasmid is a vaccinia intermediate plasmid which can function as an expression vector in cells when T7 RNA polymerase is provided in trans (FIG. 2).

[0075] As described previously, the Hep C/SEAP reporter gene encodes for a polyprotein with the following gene order: HCV (strain BK) NS2-NS3-NS4A-NS4B′-NS5A/5 B cleavage site—SEAP. Thus the HCV sequences for the amino acid coding sequence of the HCV polyprotein corresponding to the C-terminal 81 amino acids of the putative E2 region, which are upstream of the start of the putative NS2 region (as defined by Grakoui et al. ) or amino acid 729 and continues through the first 176 amino acids of the NS4B gene or amino acid 1886 (Seq. ID NOS: 23-26), and is proximal to the SEAP protein (see FIG. 1). The NS5A/5B cleavage site has been engineered between the end of NS4B′ and the second codon of SEAP.

[0076] The working theory behind the unique design of the reporter gene construct is that the SEAP polyprotein is tethered, as part of the NS2-NS3-NS4A-NS4B′-NS5A/5B cleavage site—SEAP polyprotein, inside the cell. It has been shown that NS2 is a hydrophobic protein and is associated with the outside of the endoplasmic reticulum (ER). Grakoui, et al. (1993). Thus, in the present invention, SEAP is tethered to the ER via the action of NS2. Release of SEAP from the polyprotein tether will occur upon NS3-mediated cleavage at the NS5A/5B cleavage site. SEAP is then secreted from the cell and can be monitored by assaying media for alkaline phosphatase activity (FIG. 1B). It is assumed that it is NS3-mediated cleavage at the NS5A/5B site which is the necessary cleavage to release SEAP from the upstream polyprotein sequences. However NS3-mediated cleavage at other sites within the polyprotein may be responsible for SEAP release and hence its subsequent secretion. Both NS3 and NS3/NS4A, where NS4A is a cofactor for NS3, can mediate cleavage at the NS3/4A and NS4A/4B cleavage sites which are present in polyprotein in addition to the engineered NS5A/5B cleavage site. Thus there may be more than one NS3-mediated cleavage event occurring over the length of the polyprotein before SEAP is available to the cell secretion apparatus and secreted from the cell. Further, in an alternative embodiments the tether may be changed depending upon the chosen cleavage site. In addition, NS2 is an autocatalytic protease; it mediates the cleavage event between it's carboxy-terminal end and the NS3 N-terminus. In the Hep C/SEAP polyprotein, NS2-mediated cleavage at the NS2/NS3 site would release the NS3-NS4A-NS4B′-SEAP polyprotein from the ER.

[0077] The above described system can be used to evaluate potent NS3 inhibitors by monitoring the effect of increasing drug concentration on SEAP activity. NS3 inhibition would be detected as a decrease in SEAP activity. Recognizing that a decrease in SEAP activity could also be due to cell cytotoxicity of a given compound or a non-specific effect on vaccinia virus which would adversely effect SEAP transcription, appropriate controls are used as discussed below.

[0078] In an alternate embodiment, a “cis-only” cleavage assay is contemplated. In this assay the NS2MUTNS3WT variant of the HCV/SEAP (HCAP2) is used so the polyprotein remains tethered to the outside of the endoplasmic reticulum because the NS2 protease cannot catalyze the cleavage between the C-terminus and the NS3 N-terminus. Thus the only way for SEAP to be released from the tether is if the NS3 protease clips in cis at the NS5A/5B cleavage site. There should not be any trans NS3 mediated cleavage events occurring since NS2 is not available to release the NS3 N-terminus from its tether. The control plasmid or virus for this assay is the NS2MUTNS3MUT variant HCAP4.

[0079] DI/DR Assay

[0080] A preferred embodiment involves the co-infection of BHK (ATCC No. CCL-10) or CV1 cells (a COS1 derived line ATCC No. CCL-70) cells with both vHCAP1 and vTF7.3 (ATCC No, VR-2153), with CV1 being more preferred. The latter virus is necessary since the Hep C/SEAP gene remains under control of the T7 RNA polymerase promoter in the vHCAP recombinant viruses. Currently both embodiments which are termed the Hep C/SEAP transfection/infection assay, and the dual recombinant vaccinia virus assay (DI/DR assay) respectively, are useful for HCV protease candidate compound evaluation (FIG. 3).

EXAMPLE 1

[0081] Protocol for vTF7.3 Infection/HCV/SEAP Plasmid Transfection Experiment

[0082] Day 1

[0083] Flat-bottom 96 well plates were seeded with BHK cells at a density of 1×104 cells/well (equivalent to about 85% confluence) after 24 hours. In general, one 96 well plate was used for investigation of each compound of interest (protease inhibitor), plus an additional plate at the same cell density is used where two rows are designated for each compound of interest at increasing concentrations for investigating the cytotoxicity of the compounds themselves in cells alone. Cytotoxicity was determined by XTT assay (Sigma 4626).

[0084] Day 2

[0085] The established monolayer was transfected with either pHCAP1, pHCAP3, pHCAP4, or pTM3 plasmids at a concentration of 0.4 μg/well as part of a DNA Lipofectamine (Gibco BRL) transfection mixture. Infections of the established monolayer with vTF7.3 preceded the transfection step. A working stock of vTF7.3 was diluted to a multiplicity of infection (MOI) of 10 with Optimem. The media was aspirated from the wells (2B-10G) 2 rows at a time. A 50 μL aliquot of vTF7.3 inoculum was added per well and gently shaken every 10 minutes. 30 minutes after inoculum addition, the transfection mixes were made by adding 1 mL of Optimem in 3 mL polystyrene tubes. To the media, 48 μg of plasmid DNA was then added to the tubes and mixed, followed by 144 μL of Lipofectamine™, and then the mixture was incubated (R.T.) for 30 minutes. After incubation, 11 mL of Optimem were added to each of the tubes and gently mixed. The vTF7.3 inoculum was aspirated from the wells and 0.1 mL of transfection mix was added to each well and incubated at 34° C. for 4 hours. Compounds/drugs of interest for testing protease inhibition were prepared as stock solutions of 40 mM in 100% DMSO. For assay use, the compounds were diluted to 640 μM (2×) in Optimem with 4% FBS. The compound dilutions were set up in an unused 96 well plate by adding 100 μL Optimem with 4% FBS to wells 4-10 and 150 μL of compound dilutions to all wells in column 3. A serial dilution of the compounds was then performed by transferring 46 μL from well to well across the plate. The transfection mixture was then aspirated from the cells. Then 75 μL of Optimem with 4% FBS was added to the transfected monolayers. Add 75 μL of the 2× compound dilutions to the transfected monolayers and incubated at 34° C. for 48 hours. The cells were checked microscopically at 24 hours and media is collected at 48 hours for measurement of SEAP activity.

[0086] SEAP Activity Measurement

[0087] After 48 hours, SEAP activity was measured by first transferring 100 μl of media from each well of the 96 well assay plate to a new sterile 96 well plate. Plate(s) were sealed and heated in a heating block at 65 C. for 30 minutes. After 30 minutes, plate(s) were removed and cooled to room temperature. For each heat treated plate, we transferred 50 μl of heat treated media to a Dynex (Dynex 7416) 96 well plate. To each well was added 50 μl of Tropix assay buffer and incubated at room temperature for 5 minutes, followed by an addition to each well of 50 μl of Tropix reaction buffer/CSPD substrate (Tropix), each was mixed, and incubated for an additional 90 minutes at room temperature. Chemiluminescence was read in the Victor multilabel counter from Wallac, Inc. (model number 1420) as one second counts and data is reported as luminescent units/second.

[0088] For Examples 1 and 2:

[0089] XTT Cytotoxicity Assay

[0090] XTT (Sigma 4626) was dissolved in phosphate buffered saline (PBS) to a final concentration of 1 mg/mL. 5 mL was prepared per plate. To this solution was added 5 mM PMS (n-methyldibenzopyrazine methyl sulfate salt) (Sigma P9625) to a final concentration of 20 μM. 50 μL of the XTT solution was added per well to the plate set up for cytotoxicity. The plates were incubated at 37 C. in a 5% CO2 incubator for about 3.5 hours and then the color change was quantitated by reading absorbance in a Vmax plate reader (Molecular Devices) at 450 nm/650 nm. Values were corrected by subtracting media-only background and presented as %viable with the untreated cell control representing 100%.

EXAMPLE 2

[0091] Representative Experiment and Resulting Data using Protocol of Example 1.

[0092] Compounds X, Y, and Z were evaluated in the Vaccinia Virus Infection/Plasmid Transfection assay as outlined in Example 1. BHK cells were seeded into 96 well plates at a density of 1×104 cells/well and grown overnight to approximately 85% confluency. The SEAP activity was monitored 48 hours post drug addition in cells transfected with either pHCAP1, pHCAP4, pTM3, or no DNA. Concurrently, Compounds X, Y, and Z were evaluated for cell cytotoxicity in a separate dose response assay using XTT to measure cell viability.

[0093] For each compound, cells were infected with vTF7.3 followed by the plasmid transfection step. The arrangement of the cells transfected with one of the three plasmids are illustrated in FIG. 10.

[0094] Results for Compounds X, Y, and Z are shown in FIGS. 4A and 4B and Table 1 below. In the three graphs, the amount of SEAP activity detected in cells transfected with the pHCAP1 plasmid ranges from 2 to 7-fold above the amount of SEAP detected in cells transfected with the control plasmids, pHCAP4 and pTM3, or cells only. The EC50 (μM) value represents the concentration of drug at which a 50% reduction in SEAP activity is observed relative to the amount of SEAP activity detected in the absence of drug. The CC50 (μM) value represents the concentration of drug at which a 50% reduction in cell viability is observed relative to cells in the absence of drug. The ratio of EC50/CC50 yields the therapeutic index (TI) which, by convention, should be greater or equal to 10 in order for a compound to be considered as demonstrating antiviral activity.

TABLE 1
Compound	EC50 (μM)	CC50 (μM)	Solubility (μM)	TI
X	45	178	=100	4
Y	>320	112	=100	—
Z	>320	112	=100	—

[0095] Within the compound dose range that was examined, only an EC50 value for Compound X was obtained. However, since the TI value for Compound X was below 10, it was concluded that Compound X does not represent a candidate inhibitor of NS3 protease activity. Compounds Y and Z did not demonstrate any efficacy in this system and, therefore, are not considered potential candidates (FIGS. 4A and 4B).

[0096] For Examples 3 and 4:

[0097] XTT Cytotoxicity Assay

[0098] XTT (Sigma 4626) was dissolved in phosphate buffered saline (PBS) to a final concentration of 1 mg/mL. 5 mL were prepared per plate. To this solution was added 5 mM PMS (n-methyldibenzopyrazine methyl sulfate salt) (Sigma P9625) to a final concentration of 20 μM. This XTT substrate solution was diluted with an equal volume of MEM media containing 4% FBS(V/V). A 100 μL/well of this final solution was added to the original plate which still contains the cell monolayer and about 50 μL incubation media. The plates were Incubated at 37 C. in a 5% CO2 incubator for about 3.5 hours and then the color change was quantitated by reading absorbance in a Vmax plate reader (Molecular Devices) at 450 nm/650 nm. Values were corrected by subtracting media-only background and presented as %viable with the untreated cell control representing 100%.

EXAMPLE 3

[0099] Protocol for Dual Infection/Dose Response (DI/DR) Assay

[0100] Day 1

[0101] Flat-bottom 96-well plates were seeded with CV1 cells at a density of 1×105 cells per well in MEM media containing 10% FBS with no Phenol Red. The plate was set up as shown in FIG. 5. Media only was placed in all the wells on the edge of the plate and only one compound is evaluated per plate (FIG. 5).

[0102] Day 2

[0103] Cells were infected with recombinant vaccinia viruses as follows. There should be about 1.5×105 cells per well after incubation for 24 hours. For every plate needed (a plate for each drug in the experiment) 4 mL of vTF7.3 in MEM with 4% FBS (−) phenol red at a concentration of 2×106 pfu/mL was prepared, and divided into 2 mL aliquots. Either vHCAP1 or vHCAP3 was added to the vTF7.3 aliquots for a final concentration of vHCAP of 1×107 pfu/mL. At 75 μL per well, this concentration of virus stock delivers vTF7.3 at an MOI of 1 and vHCAP1 or vHCAP3 at an MOI of 5. The arrangement of the experimental plate is shown in FIG. 5.

[0104] Drug stock solutions for use in the assay, were made at a concentration of 40 mM in DMSO as in the previous protocol. The 40 mM drug stock solution was diluted to 640 μM in MEM with 4% FBS (−) phenol red to yield a 2× drug working stock solution. Using an empty 96 well plate, the drug dilution series was set up as follows:

[0105] 100 μL of MEM with 4% FBS (−) phenol red was added to all wells in columns 4-10. 150 μL of 2× drug working stock solution was added to all wells in column 3.46 μL of media was transferred from column 3 to wells of column 4 and mixed. Transferring of 46 μL from column 4 to column 5 and out to row 10 was repeated. The remaining 46 μL was discarded. The arrangement of the experimental multiwell plate is shown in FIG. 6.

[0106] Media was aspirated from the CV1 monolayers. After aspiration, 75 μL per well of appropriate virus inoculum or MEM with 4% FBS (−) phenol red was added to the CV1 monolayers, then 75 μL was transferred from each well in the drug dilution series plate to the corresponding wells on the cell monolayer plate. The assay plate was incubated at 37 C. in a 5% CO2 incubator for 48 hours.

[0107] At Day 3, the cells was microscopically checked for phenotypic changes around the 24 hour time point. At Day 4, 100 μL of media was collected from each well of which 50 μL was used in the measurement of SEAP activity. The 100 μL aliquots were transferred to an unused 96 well plate and after the plate was sealed, it was heated to 65 C. for 30 minutes. 50 μL of each heat treated sample was then transferred to its corresponding well in a new 96 well opaque plate (Dynex 7416). Using the Tropix® SEAP Phosphalight™ kit, 50 mL of Tropix assay buffer was added to each well and the plate was incubated at room temperature for 5 minutes. Next, 50 μL of Tropix reaction buffer/CPSD substrate was added and mixed. The plate was incubated for 90 minutes at room temperature. The chemiluminescence was then read using a Victor multi-label counter. The XTT assay for measuring cytotoxicity was also performed on Day 4 as described.

EXAMPLE 4

[0108] Representative Experiment and Resulting Data Using Protocol of Example 3

[0109] Compounds A-I were evaluated in the DI/DR assay using the standard protocol given in Example 3. The data shown in FIG. 7 and FIG. 8 represent assay results obtained at a 48 hour time point post drug addition.

[0110] The EC50 (μM) value represents the concentration of drug at which a 50% reduction in SEAP activity is observed relative to the amount of SEAP activity detected in the absence of drug. However, this latter value, the amount of SEAP activity that is observed in the absence of drug, is first corrected for assay background prior to the calculation of an EC50 value. The correction is made since in the inactive NS3 protease construct, vHCAP3, a background level of SEAP activity is detected (see SEAP Activity graph). This background SEAP activity represents non-NS3 protease mediated SEAP activity and therefore should not be affected by the addition of an NS3 protease inhibitor. It is assumed that a fraction of the SEAP activity that is observed in the active NS3 protease construct, vHCAP1, represents non-NS3 protease mediated SEAP activity. Therefore the amount of SEAP activity detected vHCAP1 is corrected for the fraction that corresponds to non-NS3 protease mediated SEAP activity. The correction is as follows: luminescent units of SEAP activity of vHCAP1-luminescent units of SEAP activity of vHCAP3=Value N (level of NS3 protease dependent SEAP activity). Accordingly, (vHCAP1/SEAP)-N/2=EC50 value.

[0111] The CC50 (μM) value represents the concentration of drug at which a 50% reduction in cell viability is observed relative to cells in the absence of drug. The ratio of EC50/CC50 yields the therapeutic index (TI) which, by convention, should be greater or equal to 10 in order for a compound to be considered as demonstrating antiviral activity.

[0112] In FIG. 7, increasing concentrations of Compound A were observed to have no affect on SEAP activity. In the cell cytotoxicity component of the assay, it was observed that increasing concentrations of Compound A did not result in a reduction of cell viability of cells alone or cells infected with either vHCAP1/vTF7.3 or vHCAP3/vTF7.3. The results obtained with Compounds B-I (FIG. 8) demonstrate a range of observed cytotoxicities from 15 μM to >320 μM which is the upper limit of drug concentrations tested in the DI/DR assay although it is theoretically possible to test drug concentrations above 320 μM. The EC50 values that were observed for Compounds B-I ranged from 18 μM to >320 μM, however, the TI values were under 10. Thus Compounds A-I do not represent potential inhibitors of NS3 protease activity.

Claims

1. A reporter gene system useful in the assessment of compounds which augment or inhibit the activity of Hepatitis C virus NS3 protease comprising: a) a recombinant viral vector comprising a DNA molecule encoding an RNA polymerase promoter compatible with said viral vector and which is expressed upon infection of a target mammalian cell; b) a recombinant plasmid comprising a DNA molecule encoding the HCV/SEAP reporter gene polyprotein which is expressed when transfected into a target mammalian cell; c) said target mammalian cell line being infected first with said recombinant viral vector then transfected with said recombinant plasmid such that the DNA molecule encoding the HCV/SEAP reporter gene is under transcriptional control of said promoter; and d) the target mammalian cell expressing said HCV/SEAP reporter gene polyprotein such that SEAP is secreted from said target mammalian cell.

2. A reporter gene system useful in the assessment of compounds which augment or inhibit the activity of Hepatitis C virus NS3 protease comprising: a) a first recombinant viral vector comprising a DNA molecule encoding an RNA polymerase promoter compatible with said viral vector and which is expressed upon infection of a target mammalian cell; b) a second recombinant viral vector comprising a DNA molecule encoding the HCV/SEAP reporter gene polyprotein which is expressed upon infection of a target mammalian cell; c) said target mammalian cell line being infected first with said first recombinant viral vector then co-infected with said second recombinant plasmid such that the DNA molecule encoding the HCV/SEAP reporter gene is under control of said promoter; and d) the target mammalian cell expresses said HCV/SEAP reporter gene polyprotein such that SEAP is secreted from said target mammalian cell.

3. The reporter gene system of claim 1 wherein said recombinant plasmid is the pTM3 plasmid containing said HepC/SEAP construct.

4. The recombinant plasmid of claim 3 wherein said recombinant plasmid comprises the pHCAP1 plasmid having a DNA molecule encoding the NS2 and NS3 protease polyproteins in a fusion protein fused with the SEAP gene according to the sequence in Seq. ID NO: 1.

5. The recombinant plasmid of claim 3 wherein said recombinant plasmid further comprises the pHCAP3 plasmid containing the active NS2 protease and a mutant NS3 protease in a fusion protein fused with the SEAP gene according to the sequence in Seq. ID NO: 8.

6. The recombinant plasmid of claim 3 wherein said recombinant plasmid further comprises the pHCAP4 plasmid containing the mutant inactive NS2 and mutant inactive NS3 protease in a fusion protein fused with the SEAP gene according to the sequence in Seq. ID NO: 15.

7. The reporter gene system of claim 2 wherein said second recombinant viral vector further comprises the vHCAP1 vector having a DNA molecule encoding the NS2 and NS3 protease polyproteins in a fusion protein fused with the SEAP gene according to the sequence in Seq. ID NO: 1.

8. The reporter gene system of claim 2 wherein said second recombinant viral vector further comprises the vHCAP3 vector containing the active NS2 protease and a mutant NS3 protease in a fusion protein fused with the SEAP gene according to the sequence in Seq. ID NO: 9.

9. The reporter gene system of claim 2 wherein said second recombinant viral vector further comprises the vHCAP4 vector containing the active NS2 protease and a mutant NS3 protease in a fusion protein fused with the SEAP gene according to the sequence in Seq. ID NO: 16.

10. The reporter gene system of claim 1 wherein said recombinant viral vector comprises a virus containing the DNA sequence encoding T7 RNA polymerase promoter.

11. The recombinant viral vector of claim 7 wherein said vector is the vTF7.3 vector.

12. The reporter gene system of claim 2 wherein said first recombinant viral vector comprises a virus containing the DNA sequence encoding the T7 RNA polymerase promoter.

13. The recombinant viral vector of claim 9 wherein said vector is the vTF7.3 vector.

14. The reporter gene system of claim 1 wherein said first recombinant viral vector comprises a virus containing the DNA sequence encoding a vaccinia virus compatible promoter.

15. The first recombinant viral vector of claim 11 wherein said vector is a vaccinia virus derived vector.

16. The reporter gene system of claim 2 wherein said first recombinant viral vector comprises a virus containing the DNA sequence encoding a vaccinia virus compatible promoter.

17. The first recombinant viral vector of claim 13 wherein said vector is a vaccinia virus derived vector.

18. A first recombinant viral vector according to claim 2 wherein the vector is pTM3 plasmid, a Listeria vector, an orthopox virus, avipox virus, canarypox virus, suipox virus, vaccinia virus, baculovirus, human adenovirus, SV40, Herpes Virus or bovine papilloma virus.

19. A second recombinant viral vector according to claim 2 wherein the vector is pTM3 plasmid, a Listeria vector, an orthopox virus, avipox virus, canarypox virus, suipox virus, vaccinia virus, baculovirus, human adenovirus, SV40, Herpes Virus or bovine papilloma virus.

20. The reporter gene system of claim 1 wherein said recombinant viral vector comprises a virus containing a the DNA sequence encoding a promoter selected from the group of mammalian viral vectors consisting of: Simian Virus 40 (SV40), Rous Sarcoma Virus (RSV), Adenovirus (ADV) and Bovine Papilloma Virus (BPV).

21. The reporter gene system of claim 2 wherein said recombinant viral vector comprises a virus containing a the DNA sequence encoding a promoter selected from the group of mammalian viral vectors consisting of: Simian Virus 40 (SV40), Rous Sarcoma Virus (RSV), Adenovirus (ADV) and Bovine Papilloma Virus (BPV).

22. The reporter gene system of claim 1 wherein said target cell line is selected from the group consisting of: HeLa cells, Chinese Hamster Ovary cells, CV1 African Green Monkey cells, BSC 1 cells and Baby Hamster Kidney cells.

23. The reporter gene system of claim 2 wherein said target cell line is selected from the group consisting of: HeLa cells, Chinese Hamster Ovary cells, CV1 African Green Monkey cells, BSC 1 cells and Baby Hamster Kidney cells.

24. An isolated DNA sequence comprising a DNA sequence or variants thereof encoding the HepC/SEAP reporter gene construct according to claim 1.

25. The isolated DNA sequence of claim 24 comprising a DNA sequence or variants thereof in SEQ. ID NO. 1.

26. An isolated DNA sequence comprising a DNA sequence or variants thereof encoding the sequence defined as pHCAP1.

27. An isolated DNA sequence comprising a DNA sequence or variants thereof encoding the sequence defined as pHCAP3.

28. An isolated DNA sequence comprising a DNA sequence or variants thereof encoding the sequence defined as pHCAP4.

29. An isolated DNA sequence comprising a DNA sequence or variants thereof encoding the sequence defined as vHCAP1.

30. An isolated DNA sequence comprising a DNA sequence or variants thereof encoding the sequence defined as vHCAP3.

31. An isolated DNA sequence comprising a DNA sequence or variants thereof encoding the sequence defined as vHCAP4.

32. A method of assessing compounds which augment or inhibit the activity of Hepatitis C virus NS3 protease comprising: a) a control target mammalian cell; b) a first target mammalian cell expressing the pHCAP1 polyprotein; c) a second target mammalian cell expressing the pHCAP4 polyprotein; d) a third target mammalian cell expressing the viral promoter only; e) incubating said control, first, second, and third target mammalian cells for about 24 hours in a suitable growth medium in the presence and/or absence of pharmacologically effective concentrations of candidate compounds; f) measuring the amount of SEAP activity; and g) determining whether said candidate compounds augmented or inhibited hepatitis C NS3 protease by comparing the SEAP activity of said control, first, second, and third target mammalian cells.

33. A method of assessing compounds which augment or inhibit the activity of Hepatitis C virus NS3 protease comprising: a) a control target mammalian cell; b) a first target mammalian cell expressing the vHCAP1 polyprotein; c) a second target mammalian cell expressing the vHCAP4 polyprotein; d) a third target mammalian cell expressing the viral promoter only; e) incubating said control, first, second, and third target mammalian cells for about 24 hours in a suitable growth medium in the presence and/or absence of pharmacologically effective concentrations of candidate compounds; f) measuring the amount of SEAP activity; and g) determining whether said candidate compounds augmented or inhibited hepatitis C NS3 protease by comparing the SEAP activity of said control, first, second, and third target mammalian cells.

34. A method of assessing compounds which augment or inhibit the activity of Hepatitis C virus NS3 protease cis-only cleavage comprising: a) a control target mammalian cell; b) a first target mammalian cell expressing the pHCAP3 polyprotein; c) a second target mammalian cell expressing the pHCAP4 polyprotein; d) a third target mammalian cell expressing the viral promoter only; e) incubating said control, first, second, and third target mammalian cells for about 24 hours in a suitable growth medium in the presence and/or absence of pharmacologically effective concentrations of candidate compounds; f) measuring the amount of SEAP activity; and g) determining whether said candidate compounds augmented or inhibited hepatitis C NS3 protease by comparing the SEAP activity of said control, first, second, and third target mammalian cells.

35. A process for constructing a reporter gene system useful in the assessment of compounds which augment or inhibit the activity of Hepatitis C virus NS3 protease comprising: a) providing a recombinant viral vector comprising a DNA molecule encoding an RNA polymerase promoter compatible with said viral vector and which is expressed upon infection of a target mammalian cell; b) providing a recombinant plasmid comprising a DNA molecule encoding the HCV/SEAP reporter gene polyprotein which is expressed when transfected into a target mammalian cell further comprising the steps of cloning into a suitable vector the NS2-NS3-NS4A-NS4B′-NS5A/5B cleavage site—SEAP polyprotein; c) said target mammalian cell line being infected first with said recombinant viral vector then transfected with said recombinant plasmid such that the DNA molecule encoding the HCV/SEAP reporter gene is under transcriptional control of said promoter; and d) the target mammalian cell expressing said HCV/SEAP reporter gene polyprotein such that SEAP is secreted from said target mammalian cell.

36. A process for constructing a reporter gene system useful in the assessment of compounds which augment or inhibit the activity of Hepatitis C virus NS3 protease comprising: a) providing a first recombinant viral vector comprising a DNA molecule encoding an RNA polymerase promoter compatible with said viral vector and which is expressed upon infection of a target mammalian cell; b) providing a second recombinant viral vector comprising a DNA molecule encoding the HCV/SEAP reporter gene polyprotein which is expressed when transfected into a target mammalian cell further comprising the steps of cloning into a suitable vector the NS2-NS3-NS4A-NS4B′-NS5A/5B cleavage site—SEAP polyprotein; c) said target mammalian cell line being infected first with said first recombinant viral vector then co-infected with said second recombinant plasmid such that the DNA molecule encoding the HCV/SEAP reporter gene is under control of said promoter; and d) the target mammalian cell expresses said HCV/SEAP reporter gene polyprotein such that SEAP is secreted from said target mammalian cell.

37. The isolated DNA sequence of claim 27 comprising a DNA sequence or variants thereof in SEQ. ID NO. 8.

38. The isolated DNA sequence of claim 28 comprising a DNA sequence or variants thereof in SEQ. ID NO. 15.

39. A composition comprising the pHCAP1 polyprotein as described in SEQ. ID NO. 2.

40. A composition comprising the pHCAP3 polyprotein as described in SEQ. ID NO. 9.

41. A composition comprising the pHCAP4 polyprotein as described in SEQ. ID NO. 16.