Virtual screening

PubChem

Virus

Protease

Protein Data Bank (RCSB PDB)

Biology

Potency

Protein structure

Medicine

Biochemistry

Protein Data Bank

Drug discovery

Enzyme

In vitro

Docking (animal)

Virology

Chemistry

Veterinary medicine

Stereochemistry

Journal of Biomolecular Structure and Dynamics

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 (Mpro) (PDB ID 6MO3). The crystallographic structure of Mpro 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 (...

Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2—a molecular dynamic study