Molecular docking predicts one molecule's best orientation to a second when bound to each other to form a stable complex that depends on the key and lock theory [20]. The preferred orientation knowledge predicts the strength of the association or binding affinity between two molecules using scoring functions [21, 22]. Sofosbuvir, a potent anti-HCV RdRp inhibitor (approved by FDA in 2013 against HCV), is tested against SARS-CoV-2 RdRp [2327]. AutoDock Vina 2.4 [21], installed on HP Pavilion g series—precision with Core i3 processor, was employed in this study to assess the binding affinity and mode of interaction between sofosbuvir and remdesivir against SARS-CoV-2 RdRp. A flexible ligand / flexible active site docking scheme is applied with a grid of dimensions of 30 × 30 × 30 Å3. The grid center is maintained at the active site residues, D760 and D761 for SARS-CoV-2 RdRp and D318 and D319 for HCV RdRp, using AutoDock Tools [13]. The centers are at (8.0, 14.7, − 6.4) Å for SARS-CoV-2 RdRp (7BTF) and ( − 17.1, 1.5, 20.6) Å for HCV RdRp (2XI3) with minimal differences in the centers between the different RdRp conformations at spacing 0.375. Moreover, the binding score or affinity of the resulting complexes is detected by the Vina scoring function [21]. Different dynamical states during the Molecular Dynamics Simulation (MDS) run corresponding to the protein's different conformations are used in docking experiments. Additionally, after docking, another MDS run for 20 ns is performed to study the sofosbuvir's binding mode to SARS-CoV-2 and HCV RdRp. Analysis of the docking complexes is done utilizing PyMOL and the Protein–Ligand Interaction Profiler (PLIP) web server (Technical University of Dresden) [28].

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