Computational study on the drug resistance mechanism of hepatitis C virus NS5B RNA-dependent RNA polymerase mutants to BMS-791325 by molecular dynamics simulation and binding free energy calculations

Hepatitis C Virus (HCV) NS5B RNA-dependent RNA polymerase is an attractive target for anti-HCV development. Several mutations such as A421V, L392I and P495L in thumb I pocket of HCV NS5B polymerase have been proved to be resistant to BMS-791325 (Phase III clinical trial). A deep understanding of the resistance mechanism conferred by these mutations is important to the design and discovery of more new effective drugs against resistant HCV strains. We performed molecular dynamics (MD) simulations, free energy calculation and adaptive biasing force (ABF) simulation to study the possible resistance mechanism conferred by the above mutants. MD simulation results show the hydrophobic interaction is the driving force for BMS-791325 binding. ABF simulation proves that attenuation of the hydrophilic interaction between R503 and BMS-791325 is the first step for drug to escape from the binding site. Loss of the hydrophilic interaction makes drug easily to move out of the hydrophobic pocket. The simulation results further reveal that A421V, L392I and P495L mutants reduce drug binding affinity. P495L mutant makes the binding pocket more flexible and cannot anchor BMS-791325. The altered hydrophilic interactions of mutant residues are the essential reasons leading to drug resistance in A421V and L392I mutants. Our results will provide useful information to develop effective HCV NS5B inhibitors against resistance.