Department of Pharmacology, Institute of Medical Sciences, Varanasi, India.
School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India.
J Biomol Struct Dyn. 2021 Aug;39(12):4427-4432. doi: 10.1080/07391102.2020.1777903. Epub 2020 Jun 17.
Leucoefdin an important constituent of various fruits such as banana, raspberry, etc. was explored to target M protease of SARS Co-V 2. Ligand was found to bind at active site of M with large negative binding energies in molecular docking and simulation study. The docking results showed that Leucoefdin interacted with the M by forming hydrogen bonds, at Leu 141, His163, His 164, and Glu 166. Other non-bonded interactions were seen at Met49, Pro52, Tyr54, Phe140, Leu141, Cys145 and Met165. Results of Leucoefdin was in coherence with the recently reported M protease-inhibitor complex. It even displayed better binding energies (kcal/mol) in HTVS (-6.28), SP (-7.28), XP (-9.29) and MMGBSA (-44.71) as compared to the reference ligand [HTVS (-4.87), SP (-6.79), XP (-5.75) and MMGBSA (-47.76)]. Leucoefdin-M complex on molecular dynamic simulation showed initial fluctuations in RMSD plot for a certain period and attained equilibrium which remained stable during entire simulation for 150 ns. RMSF of protein showed less secondary structure fluctuations and a greater number of H-bond formation with Leucoefdin during 150 ns simulation. Post simulation MMGBSA analysis showed binding energy of -45.98 Kcal/mol. These findings indicated the potential of Leucoefdin as lead compound in R&D for drug discovery and development against SARS CoV-2.Communicated by Ramaswamy H. Sarma.
白果酚是香蕉、覆盆子等各种水果的重要成分,被探索用于针对 SARS Co-V 2 的 M 蛋白酶。在分子对接和模拟研究中,配体被发现与 M 的活性位点结合,具有较大的负结合能。对接结果表明,白果酚通过与 Leu141、His163、His164 和 Glu166 形成氢键与 M 相互作用。还观察到其他非键相互作用位于 Met49、Pro52、Tyr54、Phe140、Leu141、Cys145 和 Met165。白果酚的结果与最近报道的 M 蛋白酶抑制剂复合物一致。它甚至在 HTVS(-6.28)、SP(-7.28)、XP(-9.29)和 MMGBSA(-44.71)中的结合能(kcal/mol)表现更好,而参考配体为 HTVS(-4.87)、SP(-6.79)、XP(-5.75)和 MMGBSA(-47.76)。在分子动力学模拟中,白果酚-M 复合物的 RMSD 图在一定时间内显示出初始波动,并在整个 150ns 模拟过程中达到平衡并保持稳定。蛋白质的 RMSF 显示出较少的二级结构波动和在 150ns 模拟过程中与白果酚形成更多的氢键。模拟后 MMGBSA 分析表明结合能为-45.98Kcal/mol。这些发现表明白果酚作为针对 SARS CoV-2 的药物研发的先导化合物具有潜力。由 Ramaswamy H. Sarma 传达。