Fig. 4

Molecular docking studies of gallic acid derivatives against RNA-dependent RNA polymerase (RdRp) of SARS-Cov-2. a Protocol validation of molecular docking experiment using AutoDock Vina, PyMOL, and LigPlot⁺. (a) Comparison of binding modes for re-docked ligand (blue) vs. co-crystalized ligand (red) shown as stick representation. Amino acid residues interaction with (b) co-crystalized and (c) re-docked ligand accomplished in LigPlot⁺. b Binding mode and molecular interaction of hit ligands with RdRp. (a) surface representation of RdRp (PDB: 6 M71) show the binding mode of docked 4-O-(6-galloylglucoside) (green), and dexamethasone (red). 2D interaction of (b) 4-O-(6-galloylglucoside) and (c) dexamethasone