4.6. In Silico Study

To explore the bioactive sites of ROS and RNS species, including hydrogen peroxide, ozone, and nitrates with amino acids of E. coli and S. aureus, the AutoDock Vina [42] interface was used for molecular docking. The ROS/RNS species (hydrogen peroxide, ozone, and nitrates) were automatically docked into the binding pocket of a target protein using the Lamarckian genetic algorithm, empirically producing a scoring function. The X-ray crystallographic structures of E. coli and S. aureus (PDB: 4PRV) [43] and (PDB: 3VOB) [44] protein receptor were taken from the protein data bank and further modified for docking calculations. The accuracy of AutoDock in the prediction of ligand confirmation was assured using the redocking procedure explained in [44,45]. One hundred docking poses for each inhibitor were calculated. Kollman united atom partial charges, AutoDock atom types, and polar only hydrogen atoms were taken into account while preparing the protein [46,47].