title: Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus.
abstract: BACKGROUND
  The inhibitor telaprevir (VX-950) of the hepatitis C virus (HCV) protease NS3-4A has been tested in a recent phase 1b clinical trial in patients infected with HCV genotype 1. This trial revealed residue mutations that confer varying degrees of drug resistance. In particular, two protease positions with the mutations V36A/G/L/M and T54A/S were associated with low to medium levels of drug resistance during viral breakthrough, together with only an intermediate reduction of viral replication fitness. These mutations are located in the protein interior and far away from the ligand binding pocket.
  
  
  RESULTS
  Based on the available experimental structures of NS3-4A, we analyze the binding mode of different ligands. We also investigate the binding mode of VX-950 by protein-ligand docking. A network of non-covalent interactions between amino acids of the protease structure and the interacting ligands is analyzed to discover possible mechanisms of drug resistance. We describe the potential impact of V36 and T54 mutants on the side chain and backbone conformations and on the non-covalent residue interactions. We propose possible explanations for their effects on the antiviral efficacy of drugs and viral fitness. Molecular dynamics simulations of T54A/S mutants and rotamer analysis of V36A/G/L/M side chains support our interpretations. Experimental data using an HCV V36G replicon assay corroborate our findings.
  
  
  CONCLUSIONS
  T54 mutants are expected to interfere with the catalytic triad and with the ligand binding site of the protease. Thus, the T54 mutants are assumed to affect the viral replication efficacy to a larger degree than V36 mutants. Mutations at V36 and/or T54 result in impaired interaction of the protease residues with the VX-950 cyclopropyl group, which explains the development of viral breakthrough variants.
authors.affiliation: Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany. christophwelsch@gmx.net
authors.forename: Christoph
authors.initials: C
authors.lastname: Welsch
authors.forename: Francisco S
authors.initials: FS
authors.lastname: Domingues
authors.forename: Simone
authors.initials: S
authors.lastname: Susser
authors.forename: Iris
authors.initials: I
authors.lastname: Antes
authors.forename: Christoph
authors.initials: C
authors.lastname: Hartmann
authors.forename: Gabriele
authors.initials: G
authors.lastname: Mayr
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlicker
authors.forename: Christoph
authors.initials: C
authors.lastname: Sarrazin
authors.forename: Mario
authors.initials: M
authors.lastname: Albrecht
authors.forename: Stefan
authors.initials: S
authors.lastname: Zeuzem
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
mesh_terms: D000998:Antiviral Agents / Q000494:pharmacology; D001665:Binding Sites; D024882:Drug Resistance, Viral / Q000235:genetics*; D016174:Hepacivirus / Q000187:drug effects / Q000201:enzymology / Q000235:genetics*; D006801:Humans; D008024:Ligands; D056004:Molecular Dynamics Simulation; D020125:Mutation, Missense; D009842:Oligopeptides / Q000494:pharmacology*; D011485:Protein Binding / Q000235:genetics; D012697:Serine Endopeptidases / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000998:Antiviral Agents; D008024:Ligands; D009842:Oligopeptides; D012697:Serine Endopeptidases; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C486464:telaprevir