Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus

Welsch Christoph, Domingues, Susser Simone, Antes Iris, Hartmann Christoph, Mayr Gabriele, Schlicker Andreas, Sarrazin Christoph, Albrecht Mario, Zeuzem Stefan, Lengauer Thomas

Description

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. Conclusion 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.

Informations

• Publié par: biomed
• Publié le: 01 janvier 2008
• Nombre de lectures: 6
• Langue: English
• Poids de l'ouvrage: 5 Mo

Extrait

2eVW R t0 oeal e 0 l us.8 s cm e he a 9 r , c Is h sue 1, Article R16 Open Access Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protea se of the hepatitis C virus Christoph Welsch ¤ * , Francisco S Domingues ¤ * , Simone Susser  , Iris Antes * , Christoph Hartmann * , Gabriele Mayr * , Andreas Schlicker * , Christoph Sarrazin  , Mario Albrecht * , Stefan Zeuzem  and Thomas Lengauer * Addresses: * Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.  Department of Internal Medicine I, Johann Wolfgang Goethe University Hospital, 60590 Frankfurt/Main, Germany.  Department of Internal Medicine II, Saarland University Hospital, 66421 Homburg/Saar, Germany. ¤ These authors contributed equally to this work. Correspondence: Christoph Welsch. Email: [e-mail]

Published: 23 January 2008 Received: 17 July 2007 Genome Biology 2008, 9: R16(doi:10.1186/gb-2008-9-1-r16) R A e c v c i e s p e t d e :  d 1 :  7 2   3 N  J o a v n e ua m r b y  e 2 r  0 2 0 0 8 07 The electronic version of this arti cle is the complete one and can be found online at http://genomebiology.com/2008/9/1/R16 © 2008 Welsch et al .; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons. org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the origin al work is properly cited. a<Mnpod>l/eScot r u ulTacr5t 4ub a r aesli ssau nlotaf  ilTyn seiilsam o p rfa etivrhi e rd   ri iennshitisebtri a tnoctcri eoTne lawpitrhe vVirX (-V95X0-,9 e5x0p) loafi ntihneg  htehpea dtietivse lCo pvimruesn t( HofC vVir) apl rbort e a kste hNroSu3g-h4 Av asrhiaonwt s  .t<h/atp >mutations at V36 

Abstract Background: The inhibitor telaprevir (VX-950) of th e hepatitis C virus (HCV) protease NS3-4A has been tested in a recent phase 1b clinical tria l 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 mu tations V36A/G/L/M and T54A/S were associated with low to medium levels of drug resistance during viral breakthrough, together wi th only an intermediate reduction of viral replication fitness. These muta tions are located in the protein interior and far away from the ligand binding pocket. Results: Based on the available experimental structu res 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 intera ctions between amino acids of th e 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 interacti ons. We propose possible explan ations for their effects on the antiviral efficacy of drugs and vira l fitness. Molecular dynamics si mulations of T54A/S mutants and rotamer analysis of V36A/G/L/M side chains suppo rt our interpretations. Experimental data using an HCV V36G replicon assa y corroborate our findings. Conclusion: T54 mutants are expected to interfere with the catalytic triad and with the ligand binding site of the protease. Thus, the T54 muta nts 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 re sidues with the VX-950 cyclopro pyl group, which explains the development of viral breakthrough variants.

Genome Biology 2008, 9: R16