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Binding interaction of benzamide derivatives as inhibitors of DNA gyrase and Sec14p using Molegro Virtual Docker based on binding free energy

Abstract The docking simulation of benzamide derivatives as ligands and protein targets (DNA–gyrase) was performed and Sec14p binding mode interaction was predicted based on binding free energy analysis. Software Molegro Virtual Docking (MVD) was used to visualize the ligand–protein binding interactions. The results indicated the prevalence of steric or hydrophobic interactions among all the benzamide ligands besides hydrogen bonding or electrostatic interactions. The compounds B2, B4 against DNA gyrase, and compounds B3, B5 against Sec14p showed an uncompetitive pattern of inhibition as compared with the reference molecule. While compounds B1, B5 exhibited the best MolDock scores, i.e., −109.736 and −114.391 kcal/mol respectively for DNA gyrase, also compounds B1 and B2 against Sec14p displayed −100.105 and −119.451 kcal/mol sequentially. It was evident from the comparison of MolDock score for both the bacterial and fungal protein receptors that all the ligands were found to be more potent against DNA gyrase than Sec14p. However, only compound B2 with MolDock score −119.451 kcal/mol showed exceptional activity against Sec14p and was predicted to have potency as a lead compound to find a new anti-fungal therapeutic agent. Docking studies further highlighted the unique interactions such as tail-end hydrophobic rings of benzamide inhibitors with catalytically important amino acid residues, allowing flexibility in binding to both the receptors different from other inhibitors. These findings showed us that B1, B2 against Staphylococcus aureus and B5 against Saccharomyces cerevisiae could be leading compounds to discover new multidrug-resistant strains.