Paper Citing NAMD - Abstract
Asthana, Shailendra; Shukla, Saumya; Vargiu, Attilio V.; Ceccarelli, Matteo; Ruggerone, Paolo; Paglietti, Giuseppe; Marongiu, Maria E.; Blois, Sylvain; Giliberti, Gabriele; La Colla, Paolo
Different Molecular Mechanisms of Inhibition of Bovine Viral Diarrhea Virus and Hepatitis C Virus RNA-Dependent RNA Polymerases by a Novel Benzimidazole
BIOCHEMISTRY, 52:3752-3764, MAY 28 2013
The virus-encoded RNA-dependent RNA polymerase (RdRp) has emerged as a primary target in the search for selective inhibitors of Flaviviridae. Recently, we reported on the selective inhibition, in cell-based assays, of both BVDV (EC50 = 0.80 +/- 0.06 mu M) and HCV (EC50 = 1.11 +/- 0.15 mu M) by 2-{1-[2-(2,4-dimethoxyphenyl)-1H-benzimidazol-5-yl]ethylidene}hydrazinec arbothioamide (227G). Here we show that, in enzyme assays with recombinant enzymes, 227G inhibits, in a dose-dependent manner, the RdRp of both BVDV (IC50 = 0.0020 +/- 0.0004 mu M) and HCV (IC50 = 0.40 +/- 0.04 mu M). Furthermore, we report on the selection and molecular analysis of a BVDV-resistant mutant, characterized by the presence of the 1261M mutation. By applying a multilevel computational approach, we identified different 227G binding sites on the two RdRps. They were further validated by the good agreement between the calculated affinities and those extrapolated from IC50 values. Our findings suggest different molecular mechanisms of inhibition of the HCV and BVDV RdRps by 227G and indicate the importance of understanding ligand-enzyme interactions at the molecular level for the rational design of new and more potent leads.
