Keywords : Molecular dynamics and Zinc
SCREENING AND IDENTIFICATION OF POTENTIAL INHIBITORS AGAINST UDP-N ACETYL GLUCOSAMINE ENOLPYRUVYL TRANSFERASE(MURA) IN STREPTOCOCCUS PNEUMONIA: AN INSILICO APPROACH
European Journal of Molecular & Clinical Medicine,
2020, Volume 7, Issue 11, Pages 9422-9439
Streptococcus pneumoniae are the most common cause of pneumonia and meningitis in infants and adults. Peptidoglycan layer is an essential component of cell wall composed of alternating units of N-acetylglicosamine (GlcNAc) and N-acetylmuramic acid (MurNAc). UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is a key enzyme involved in peptidoglycan synthesis. The Biosynthesis of peptidoglycan in cytoplasm is catalysed by MurA which transfer enolpyrul group from phosphophenol pyruvate (PEP) to UDP Nacetylglucosamine to form UDP -N-acetylenolpyruvate. Present study was aimed to develop novel antimicrobial agents against MurA enzyme through insilico analysis approach. The three dimensional structure of MurA enzyme was modelled computationally by using Modeller9v10. Later this enzyme model subjected to molecular dynamics simulations using NAMD 2.5 software with CHARMM27 force field tip 3p model of water. Initially energy minimization carried 5000 runs for 10 ps time and subsequent minimized model was simulated with 1,00,000 runs for 2 ns time period. The final resolved model reliability was assessed by prochek using Ramchandran plot calculations, verify 3D and WHATCHECK programs. From Zinc database 5000 similar structure compounds with fosfomycin were virtually screened against MurA by Autodock vina in PyRx virtual screening tool. The docking results reveal that the compounds Zinc50247, Zinc3020559, Zinc1884559, Zinc3154681, Zinc19286884, Zinc58219 and Zinc3978065 have -10.3, -10.1, -9.8, -9.8, - 9.2, -9.1 and -9.0 k.cal/mol binding affinity respectively, with MurA enzyme. We found that, the Amino acids Asp306, Tyr329, Gly115, Arg121, Arg322, Ser125, Leu91 and Phe125 present in the enzyme binding pocket are showing molecular interactions with ligands. MurA being a potential drug target in treating Streptococcus pneumonia infections, in this study we found that Zinc50247 effectively inhibits the MurA enzyme and can act as potential therapeutic agent.