Molecular Binding and Simulation Studies of Staphylococcus aureus Superantigens with Flavonoid Compounds

Abstract

Background: Superantigens of Staphylococcus aureus namely enterotoxin A, exfoliative toxin A, and Toxic shock syndrome toxin-1 cause detrimental effects on the cells of the immune system.

Methods: In this work, the toxins were downloaded from the Protein DataBank database and energies were minimized using KoBaMIN server. Forty flavonoids compounds were identified by pubchem compound database through extensive literature study and their 3D structures were obtained by submitting SMILES to CORINA tool. Based on Lipinski's rule of five, the molecules were filtered that resulted in 27 compounds. Molecular docking was performed for identifying the binding and interaction sites of flavonoids with the toxins using Autodock 4.

Results and conclusion: The docked complexes were then subjected to molecular dynamics simulation using Gromacs. The analysis revealed the stability of the complexes as indicated by three hydrogen bonds formed during the simulation time period of 20 ns.

Keywords: Lipinski’s Rule; Staphylococcus aureus; dynamic simulation; flavonoids; hydrogen bonds; molecular docking; superantigens.