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This study aims to identify and isolate the secondary metabolites of Zingiber officinale using GC-MS, preparative TLC, and LC-MS/MS methods, to evaluate the inhibitory potency on SARS-CoV-2 3 chymotrypsin-like protease enzyme, as well as to study the molecular interaction and stability by using docking and molecular dynamics simulations. GC-MS analysis suggested for the isolation of terpenoids compounds as major compounds on methanol extract of pseudostems and rhizomes. Isolation and LC-MS/MS analysis identified 5-hydro-7, 8, 2'-trimethoxyflavanone ( 9 ), ( E )-hexadecyl-ferulate ( 1 ), isocyperol ( 2 ), N- isobutyl-(2 E ,4 E )-octadecadienamide ( 3 ), and nootkatone ( 4 ) from the rhizome extract, as well as from the leaves extract with the absence of 9 . Three known steroid compounds, i.e., spinasterone ( 7 ), spinasterol ( 8 ), and 24-methylcholesta-7-en-3 β -on ( 6 ), were further identified from the pseudostem extract. Molecular docking showed that steroids compounds 7 , 8 , and 6 have lower predictive binding energies (MMGBSA) than other metabolites with binding energy of -87.91, -78.11, and -68.80 kcal/mole, respectively. Further characterization on the single isolated compound by NMR showed that 6 was identified and possessed 75% inhibitory activity on SARS-CoV-2 3CL protease enzyme that was slightly different with the positive control GC376 (77%). MD simulations showed the complex stability with compound 6 during 100 ns simulation time.

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GC-MS, LC-MS/MS, Docking and Molecular Dynamics Approaches to Identify Potential SARS-CoV-2 3-Chymotrypsin-Like Protease Inhibitors from Zingiber officinale Roscoe