Binding of metronidazole to Enterococcus faecalis homoserine kinase: Binding studies, docking studies, and molecular dynamics simulation studies

Background: Enterococcus faecalis (Ef) is an opportunistic virulent bacterial pathogen resistant to a diverse class of antibiotics by possession of a wide range of resistance mechanisms. Aim and Objective: Looking at the increasing number of infections caused by Ef, it is essential to develop alternative strategies to fight against Ef. In this regard, homoserine kinase (HSK) is an important enzyme of threonine biosynthesis pathway in Ef. Threonine is an essential amino acid, and HSK catalyzes the formation of O-phospho-L-homoserine production, which is an important step in threonine metabolism. Therefore, Enterococcus faecalis homoserine kinase (EfHSK) becomes an ideal target for antimicrobial drug development. Methodology: We report binding studies, docking studies, and molecular dynamics (MD) simulation studies of EfHSK. Fluorescence spectroscopy studies indicated the binding of metronidazole with EfHSK. Result: Docking studies further showed that amino acid residues such as Asn124 and Gly83 in the phosphate-binding loop of EfHSK play a vital role in the formation of H-bonds with the ligand metronidazole. The site where ligand was bound is a deep groove, which is regarded as the binding cavity of the protein. Docking studies were further confirmed by MD simulation studies. Conclusion: Metronidazole might be considered as a potential inhibitor of EfHSK, as this occupies the binding pocket and eventually can reduce the kinase activity of this enzyme.