Mechanism of Inhibition By, and of Drug Resistance to, a Benzimidazole Inhibitor of the RNA-Dependent RNA Polymerase of Bovine Viral Diarrhoea Virus

Bovine viral diarrhoea virus (BVDV), a major pathogen in cattle and other ruminants, has been used as a surrogate in vitro model for the development of HCV inhibitors. Recently, we have identified a very potent and selective benzimidazole derivative (227G) that: i) targets the RNA-dependent RNA polymerase (RdRp) of both BVDV and HCV, ii) allows the selection of BVDV resistant mutants characterized by the point mutation I261M located in the finger domain of the enzyme. This work deals with the effects of 227G and I261M on the function of the wt and mutated BVDV RdRp, respectively, investigated by using non-conventional approaches that include molecular dynamics, cluster analysis, flexible docking and metadynamics. Briefly, binding of 227G to the wt RdRp induces conformational changes that prevent entrance of the RNA primer into the enzyme's polymerization cavity. Viceversa, the I261M mutation results in structural changes that allow access of the primer to the polymerization cavity and binding of 227G into a site different from that occupied by the inhibitor in the wt enzyme.