Leucoefdin a potential inhibitor against SARS CoV-2 M^pro.

ABSTRACT: Leucoefdin an important constituent of various fruits such as banana, raspberry, etc. was explored to target M^Pro protease of SARS Co-V 2. Ligand was found to bind at active site of M^Pro with large negative binding energies in molecular docking and simulation study. The docking results showed that Leucoefdin interacted with the M^Pro 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^Pro 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^Pro 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.

SUBMITTER: Singh A 

PROVIDER: S-EPMC7309301 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature