The hepatitis C virus (HCV) subgenomic replicon is the primary tool for evaluating the activity of anti-HCV compounds in drug discovery research. Despite the prevalence of HCV genotype 1a (ϳ70% of U.S. HCV patients), few genotype 1a reporter replicon cell lines have been described; this is presumably due to the low replication capacity of such constructs in available Huh-7 cells. In this report, we describe the selection of highly permissive Huh-7 cell lines that support robust replication of genotype 1a subgenomic replicons harboring luciferase reporter genes. These novel cell lines support the replication of multiple genotype 1a replicons (including the H77 and SF9 strains), are significantly more permissive to genotype 1a HCV replication than parental Huh7-Lunet cells, and maintain stable genotype 1a replication levels suitable for antiviral screening. We found that the sensitivity of genotype 1a luciferase replicons to known antivirals was highly consistent between individual genotype 1a clonal cell lines but could vary significantly between genotypes 1a and 1b. Sequencing of the nonstructural region of 12 stable replicon cell clones suggested that the enhanced permissivity is likely due to cellular component(s) in these new cell lines rather than the evolution of novel adaptive mutations in the replicons. These new reagents will enhance drug discovery efforts targeting genotype 1a and facilitate the profiling of compound activity among different HCV genotypes and subtypes.

In order to assess the natural variation in susceptibility to hepatitis C virus (HCV) NS3 protease inhibitors (PIs) among untreated HCV patient samples, the susceptibilities of 39 baseline clinical isolates were determined using a transient-replication assay on a panel of HCV PIs, including two ␣-ketoamides (VX-950 and SCH-503034) and three macrocyclic inhibitors (MK-7009, ITMN-191, and TMC-435350). Some natural variation in susceptibility to all HCV PIs tested was observed among the baseline clinical isolates. The susceptibility to VX-950 correlated strongly with the susceptibility to SCH-503034. A moderate correlation was observed between the susceptibilities to ITMN-191 and MK-7009. In contrast, the phenotypic correlations between the ␣-ketoamides and macrocyclic inhibitors were significantly lower. This difference is partly attributable to reduced susceptibility of the HCV variants containing the NS3 polymorphism Q80K (existing in 47% of genotype 1a isolates) to the macrocyclic compounds but no change in the sensitivity of the same variants to the ␣-ketoamides tested. Our results suggest that the natural variation in baseline susceptibility may contribute to different degrees of antiviral response among patients in vivo, particularly at lower doses.Hepatitis C virus (HCV) is characterized by a high degree of genetic diversity because of its rapid replication rate and turnover, combined with the poor fidelity of the HCV RNA-dependent RNA polymerase (RdRp) (3, 5, 32). The nucleotide sequences among the six different genotypes (GTs) differ at 30 to 35% of nucleotide sites (25,26). Each of the six major GTs of HCV contains a series of closely related subtypes whose nucleotide sequences typically differ from each other by 20 to 25%. Furthermore, 5 to 8% sequence divergence is present between individual strains (variants) of HCV within a given subtype. A comprehensive analysis of HCV NS3 sequences from a larger number of GT-1 isolates found that amino acid polymorphisms were detected all along the protease sequence, including residues associated either with resistance to HCV protease inhibitors (PIs) (V36, I170, and D168) or with compensatory mutations (I72, T72, Q86, and I153) (1, 2, 30). However, many questions remain, including whether natural variation in the NS3 protease sequence impacts the susceptibility of HCV to PIs currently in development and whether there are any relationships among the chemotypes of the PIs and their baseline susceptibilities.Hepatitis C virus NS3/4A serine PIs have demonstrated potent antiviral activity in subjects infected with HCV GT-1 by specifically blocking NS3/4A protease-dependent HCV polyproprotein processing. Among these PIs, VX-950 (telaprevir) and SCH-503034 (boceprevir), the two most clinically advanced NS3/4A serine PIs, are both ␣-ketoamide compounds that covalently bind to the active-site serine of the protease (6,9,10,14,16,22). These drugs also have similar resistance profiles. Mutations V36A/M, T54A, R155K, and A156S in the NS3 protease gene, conferring a low level ...

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The relationship of inhibitory quotient (IQ) with the virologic response to specific inhibitors of human hepatitis C virus (HCV) and the best method to correct for serum protein binding in calculating IQ have not been addressed. A common method is to determine a fold shift by comparing the EC(50) values determined in cell culture in the absence and presence of human serum (fold shift in EC(50) ), but this method has a number of disadvantages. In the present study, the fold shifts in drug concentrations between 100% human plasma (HP) and cell culture medium (CCM) were directly measured using a modified comparative equilibrium dialysis (CED) assay for three HCV protease inhibitors (PIs) and for a novel HCV inhibitor GS-9132. The fold shift values in drug concentration between the HP and CCM (CED ratio) were ∼1 for SCH-503034, VX-950 and GS-9132 and 13 for BILN-2061. These values were ∼3-10-fold lower than the fold shift values calculated from the EC(50) assay for all inhibitors except BILN-2061. Using the CED values, a consistent pharmacokinetic and pharmacodynamic relationship was observed for the four HCV inhibitors analysed. Specifically, an approximate 1 log(10) reduction in HCV RNA was achieved with an IQ close to 1, while 2-3 and greater log(10) reductions in HCV RNA were achieved with IQ values of 3-5 and greater, respectively. Thus, use of CED to define IQ provides a predictive and quantitative approach for the assessment of the in vivo potency of HCV PIs and GS-9132. This method provides a framework for the evaluation of other classes of drugs that are bound by serum proteins but require the presence of serum for in vitro evaluation.