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2021 ; 39
(10
): 3627-3637
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Marine natural compounds as potents inhibitors against the main protease of
SARS-CoV-2-a molecular dynamic study
#MMPMID32410504
Khan MT
; Ali A
; Wang Q
; Irfan M
; Khan A
; Zeb MT
; Zhang YJ
; Chinnasamy S
; Wei DQ
J Biomol Struct Dyn
2021[Jul]; 39
(10
): 3627-3637
PMID32410504
show ga
Sever acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded
RNA (ssRNA) virus, responsible for severe acute respiratory disease (COVID-19). A
large number of natural compounds are under trial for screening compounds,
possessing potential inhibitory effect against the viral infection. Keeping in
view the importance of marine compounds in antiviral activity, we investigated
the potency of some marine natural products to target SARS-CoV-2 main protease
(M(pro)) (PDB ID 6MO3). The crystallographic structure of M(pro) in an apo form
was retrieved from Protein Data Bank and marine compounds from PubChem. These
structures were prepared for docking and the complex with good docking score was
subjected to molecular dynamic (MD) simulations for a period of 100?ns. To
measure the stability, flexibility, and average distance between the target and
compounds, root mean square deviations (RMSD), root mean square fluctuation
(RMSF), and the distance matrix were calculated. Among five marine compounds, C-1
(PubChem CID 11170714) exhibited good activity, interacting with the active site
and surrounding residues, forming many hydrogen and hydrophobic interactions. The
C-1 also attained a stable dynamic behavior, and the average distance between
compound and target remains constant. In conclusion, marine natural compounds may
be used as a potential inhibitor against SARS-CoV-2 for better management of
COVID-19.