title: Different molecular mechanisms of inhibition of bovine viral diarrhea virus and hepatitis C virus RNA-dependent RNA polymerases by a novel benzimidazole.
abstract: 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 μM) and HCV (EC50 = 1.11 ± 0.15 μM) by 2-{1-[2-(2,4-dimethoxyphenyl)-1H-benzimidazol-5-yl]ethylidene}hydrazinecarbothioamide (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 μM) and HCV (IC50 = 0.40 ± 0.04 μM). Furthermore, we report on the selection and molecular analysis of a BVDV-resistant mutant, characterized by the presence of the I261M 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.
authors.affiliation: Dipartimento di Scienze Biomediche, Università degli Studi di Cagliari, Cittadella Universitaria , 09042 Monserrato (CA), Italy.
authors.forename: Shailendra
authors.initials: S
authors.lastname: Asthana
authors.forename: Saumya
authors.initials: S
authors.lastname: Shukla
authors.forename: Attilio V
authors.initials: AV
authors.lastname: Vargiu
authors.forename: Matteo
authors.initials: M
authors.lastname: Ceccarelli
authors.forename: Paolo
authors.initials: P
authors.lastname: Ruggerone
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Paglietti
authors.forename: Maria E
authors.initials: ME
authors.lastname: Marongiu
authors.forename: Sylvain
authors.initials: S
authors.lastname: Blois
authors.forename: Gabriele
authors.initials: G
authors.lastname: Giliberti
authors.forename: Paolo
authors.initials: P
authors.lastname: La Colla
mesh_terms: D000818:Animals; D001562:Benzimidazoles / Q000494:pharmacology*; D002417:Cattle; D002460:Cell Line; D001908:Diarrhea Viruses, Bovine Viral / Q000201:enzymology*; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D016174:Hepacivirus / Q000201:enzymology*; D062105:Molecular Docking Simulation; D012324:RNA-Dependent RNA Polymerase / Q000037:antagonists & inhibitors*
chemical_list: D001562:Benzimidazoles; D004791:Enzyme Inhibitors; D012324:RNA-Dependent RNA Polymerase