In silico docking studies of Ag nanoparticles and its derivatives against NS5B protein (HCV): Integrating nanobiotechnology and nanoinformatics

Abstract

The present study focused on the prediction of interactions of three ligands, i.e., silver nanoparticles, tyrosine-capped silver nanoparticles, and silver oxide nanoparticles, with the nonstructural protein 5B (NS5B) protein of the hepatitis-C virus (HCV). ΑutoDock 4, Discovery Studio, ChemDraw Ultra, OpenBabel, and Chimera software were used. Computational docking helps to evaluate the conformations of small ligands attached to macromolecular proteins. NS5B plays a crucial role in HCV replication. It is an RNA-dependent RNA membrane-associated polymerase, weighing approximately 66-kDa . The results were obtained from AutoDock 4 and visualized in Discovery Studio and Chimera. Silver nanoparticles showed interactions with All these three ligands showed promising results to inhibit the NS5B enzyme preventing HCV replication. The most effective ligand was tyrosine-capped silver nanoparticles. Its relative highest binding energy i.e. -5.29 kcal/mol showed its intense binding with the protein molecule causing more damage to the integral residues forming the active site.