Computational study on the drug resistance mechanism of HCV NS5B RNA-dependent RNA polymerase mutants V494I, V494A, M426A, and M423T to Filibuvir

• Molecular modeling methods was used to study the selectivity mechanisms of Filibuvir toward wild-type and mutant NS5B RdRp.
• We give a good explanation of the differences in curative efficacy of Filibuvir.
• The computational results could give valuable information for developing novel and safer HCV antiviral drugs.

Filibuvir, a potent non-nucleoside inhibitor of the hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp), has shown great promise in phase IIb clinical trial. However, drug resistant mutations towards Filibuvir have been identified. In the present study, the drug resistance mechanism of wild-type (WT) and mutant NS5B polymerases (including V494I, V494A, M426A, and M423T) toward Filibuvir was investigated by molecular modeling methods. The predicted binding free energy of these five complexes is highly consistent with the experimental EC50 values of Filibuvir to the wild-type and mutant NS5B RdRps, V494I < WT < V494A < M426A < M423T. Analysis of the individual energy terms indicates that the loss of binding affinity is mainly attributed to the decrease in the van der Waals interaction contribution. Through detailed analysis of the interaction between FBV and RdRpV494I, RdRpWT, RdRpV494A, RdRpM426A, and RdRpM423T, several conclusions are made. Firstly, the smaller size of residue 494 side chain results in the smaller binding affinity between FBV and RdRp. Secondly, the poor inhibition capacity of Filibuvir toward RdRpM426A is mainly due to the decrease in the van der Walls interaction between Filibuvir and residue Leu-497M426A caused by the spatial structure change of Ala-426M426A. Thirdly, the decrease in the binding affinity in mutation M423T is attributed to the smaller binding cave and the cyclopentyl group of Filibuvir exposing outside the cave. Our computational results will provide valuable information for developing more potent and selective inhibitors toward HCV NS5B polymerase.