Title:Molecular Binding and Simulation Studies of Staphylococcus aureus Superantigens with Flavonoid Compounds
Volume: 20
Issue: 4
Author(s): Ramadevi Mohan and Subhashree Venugopal*
Affiliation:
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil nadu, 632 014,India
Keywords:
Staphylococcus aureus, superantigens, flavonoids, Lipinski’s Rule, molecular docking, dynamic simulation,
hydrogen bonds.
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.
