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.

Perspectives towards antiviral drug discovery against Ebola virus

“…Recent studies have reported notable examples of MD‐driven drug discovery . These studies prove the usefulness of MD simulation in understanding molecular interactions and the mechanism of drug binding, especially against the drug‐resistant viruses …”

Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2

“…appears to be the ideal target with the highest number of surface-accessible and strategically placed drug-binding sites. Furthermore, RdRPs are emerging as antiviral targets for RNA viruses [33][34][35].…”

Quinolinecarboxamides Inhibit the Replication of the Bovine Viral Diarrhea Virus by Targeting a Hot Spot for the Inhibition of Pestivirus Replication in the RNA-Dependent RNA Polymerase

“…In vitro selected TO502-2403 res carried an amino acid transition from phenylalanine (F) in the WT to proline (P), at position 224, the TO505-6180 res virus carried a phenylalanine (F) to tyrosine (Y) mutation at position 224 (F224Y), and an asparagine (N) to aspartic acid (D) mutation at position 264 (N264D) of the viral RNA-dependent RNA polymerase. Interestingly, amino acid position F224 was previously shown to be involved in the antiviral resistance of BVDV to VP32947 [17], BPIP [20], and LZ37 [22], whereas mutation N264D was reported to be key in the phenotypic resistance against DB772 [23], 5,6-dimethoxy-1-indanone [26], and 2-phenylbenzimidazole [28]. Here, for the first time we reported the selection of a drug-resistant virus that combines both the F224P/Y and the N264D mutation.…”

“…They either target a cellular protein/enzyme, i.e., α-glycosidase (which is involved in the maturation of virions [15]), as well as viral encoded enzymes such as the NS3 protease and helicase/NTPase [16], or the NS5B RNA-dependent RNA polymerase (RdRp). Polymerase inhibitors include nucleoside [14] and non-nucleoside inhibitors, such as N-propyl-N-[2-(2H-1,2,4-triazino [5,6-b]indol-3-ylthio)ethyl]-1-propanamine (VP32947) [17], a thiazole urea derivative [18], a cyclic urea derivative [19], imidazo-pyridines (BPIP) [20], ethyl 2-methylimidazo [1,2-a]pyrrolo [2,3-c]pyridin-8-carboxylate (AG110) [21], pyraz olotriazolopyrimidinamine (LZ37) [22], 2-(2-benzimidazolyl)-5-[4-(2-imidazolino)phenyl]furan (DB772) [23], 5,6-dimethoxy-1-indanone [24,25], 2-phenylbenzimidazole [26], substituted 2,6-bis (benzimidazol-2-yl)pyridines [27], benzimidazole derivative [28], and arylazoenamine derivatives [29].…”