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2021 ; 39
(12
): 4427-4432
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Leucoefdin a potential inhibitor against SARS CoV-2 M(pro)
#MMPMID34281489
Singh A
; Mishra A
J Biomol Struct Dyn
2021[Aug]; 39
(12
): 4427-4432
PMID34281489
show ga
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.