EfficientIn SilicoAssay of Inhibitors of Hepatitis C Virus RNA-Dependent RNA Polymerase by Structure-Based Virtual Screening andIn VitroEvaluation

Abstract

To identify a new protective or therapeutic intervention for hepatitis C virus (HCV) infection, we performed efficient structure-based virtual screening to identify novel inhibitory agents for HCV. To this end, we selected NS5B, an RNA-dependent RNA polymerase (RdRp), as the target for the treatment of HCV infection. To decipher the dockable nature of various RdRp X-ray crystals, we docked the crystal ligand (inhibitor) to the crystal receptor (enzyme). The accuracy of regeneration of the crystal pose indicates the amenability of the RdRp binding pocket for structure-based virtual screening. We also utilized a consensus scoring scheme to reduce false positives, thereby ensuring efficient virtual screening. In this study, each molecule that ranked in the top 1% among all screening molecules gained 1 consensus point in a scoring function. Thus, after virtual screening of 57,177 chemicals from the Maybridge Screening collection, 14 molecules gained 8 points across 11 scoring functions. One of them, an isoxazole, showed significant dose-dependent inhibition of HCV RdRp activity and replication. In this study, we have developed a structure-based virtual screening method using HCV RdRp for efficient identification of novel inhibitors.

Identifying New Liver X Receptor Alpha Modulators and Distinguishing Between Agonists and Antagonists By Crystal Ligand Pocket Screening

“…Such a departure from reality, if it happens in the binding site, can severely decrease the accuracy of molecular docking, and thus, the efficiency of virtual screening. Therefore, a further inspection of the 'dockable nature' [8,9] of the ligand pockets of each crystal complex is essential for molecular docking. To raise our confidence for the crystal-binding pockets of LXRα for molecular docking, we used an additional strategy, self-docking, in which a geometry-randomized crystal ligand docks back into the natural crystal-binding cavity.…”

“…To identify new LXRα modulators, we chose a suitable binding site model to conduct efficient structurebased molecular-docking screening. The molecular dockability [8,9] of the x-ray crystal ligand-binding pocket was examined by the self-docking of crystal complex ligands. If the ligand after self-docking can correctly find its crystal pose, it can indicate the dual facts that the native binding pocket and the methodology of molecular docking used are both reliable.…”

Inhibiting Two Cellular Mutant Epidermal Growth Factor Receptor Tyrosine Kinases By Addressing Computationally Assessed Crystal Ligand Pockets

“…The 2ITQ and 3W2R ligands had the lowest RMSD values. We then judged the quality of 2ITQ and 3W2R ligand pockets as most 'molecular dockable' [61]. We chose these two ligand binding sites for the receptor-based virtual screening of mutant EGFR-TK ligand binding.…”

Structural Flexibility in HCV NS5B Polymerase and Molecular Modelling of Anti-HCV Drugs

“…Tyr448 and some other residues like Gln446, Tyr415, Gln449, Arg386 were found to be forming hydrogen bonds with the promising inhibitors. To improve the success rate of virtual screening for HCV NS5B, Lin et al have examined the 26 3D complex crystal structures from Protein Data Bank [154]. A potent HCV NS5B inhibitor has been identified by structure-based virtual screening of the Maybridge Screening Collection along with in vitro cell-based assay.…”