title: Impact of naturally occurring variants of HCV protease on the binding of different classes of protease inhibitors.
abstract: 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 protease was 168. Substitution of residues at positions 168, 123, and 132 fully accounted for the reduced sensitivity of genotype 3. Comparative studies of BILN 2061 and a closely related nonmacrocycle inhibitor suggested that the rigidity of BILN 2061, while conferring greater potency against genotype 1, rendered it more sensitive to variations near the binding site. Free energy perturbation analysis confirmed the experimental observations. The identification of naturally occurring variations which can affect inhibitor binding is an important step in the design of broad-spectrum, second generation protease inhibitors.
authors.affiliation: Antiviral Therapy, Schering-Plough Research Institute, Kenilworth, New Jersey 07033, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Tong
authors.forename: Zhuyan
authors.initials: Z
authors.lastname: Guo
authors.forename: Jacquelyn
authors.initials: J
authors.lastname: Wright-Minogue
authors.forename: Ellen
authors.initials: E
authors.lastname: Xia
authors.forename: Andrew
authors.initials: A
authors.lastname: Prongay
authors.forename: Vincent
authors.initials: V
authors.lastname: Madison
authors.forename: Ping
authors.initials: P
authors.lastname: Qiu
authors.forename: Srikanth
authors.initials: S
authors.lastname: Venkatraman
authors.forename: Francisco
authors.initials: F
authors.lastname: Velazquez
authors.forename: F George
authors.initials: FG
authors.lastname: Njoroge
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Malcolm
mesh_terms: D001665:Binding Sites / Q000187:drug effects / Q000235:genetics; D001667:Binding, Competitive / Q000187:drug effects / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics; D015195:Drug Design; D014644:Genetic Variation; D016174:Hepacivirus / Q000201:enzymology* / Q000235:genetics; D006801:Humans; D066298:In Vitro Techniques; D047908:Intracellular Signaling Peptides and Proteins; D008958:Models, Molecular; D011994:Recombinant Proteins / Q000737:chemistry / Q000187:drug effects / Q000235:genetics; D012697:Serine Endopeptidases / Q000737:chemistry / Q000187:drug effects* / Q000235:genetics; D015842:Serine Proteinase Inhibitors / Q000145:classification / Q000494:pharmacology*; D013329:Structure-Activity Relationship; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D002352:Carrier Proteins; D047908:Intracellular Signaling Peptides and Proteins; D011994:Recombinant Proteins; D012697:Serine Endopeptidases; D015842:Serine Proteinase Inhibitors; D017361:Viral Nonstructural Proteins; D014764:Viral Proteins; C084422:NS3 protein, hepatitis C virus; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C455041:NS4A cofactor peptide, Hepatitis C virus