Impact of Naturally Occurring Variants of HCV Protease on the Binding of Different Classes of Protease Inhibitors

HCV drug discovery efforts have largely focused on genotype 1 virus due to its prevalence and relatively poor response to current therapy. However, patients infected with genotype 2 and 3 viruses account for a significant number of cases and would also benefit from new therapies. In vitro studies using two chemically distinct protease inhibitors with clinical potential showed that one, VX-950, was equally active on proteases from all three genotypes, whereas the other, BILN 2061, was significantly less active on genotype 2 and 3 proteases. Naturally occurring variation near the inhibitor binding site was identified based on sequence alignment of the protease region from genotype 1−3 sequences. Substitution of amino acids in genotype 1 based on genotype 2 and 3 has revealed residues which impact binding of BILN 2061. Substitution of residues 78−80, together with 122 and 132, accounted for most of the reduced sensitivity of genotype 2. The most critical position affecting inhibitor binding to genotype 3 pro...