NDLI: Pharmacophore based virtual screening, molecular docking, molecular dynamics and MM-GBSA approach for identification of prospective SARS-CoV-2 inhibitor from natural product databases

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Pharmacophore based virtual screening, molecular docking, molecular dynamics and MM-GBSA approach for identification of prospective SARS-CoV-2 inhibitor from natural product databases

Content Provider	Scilit
Author	Faheem Kumar, Banoth Karan Sekhar, Kondapalli Venkata Gowri Chandra Ojha, Rupal Prajapati, Vijay Kumar Pai, Aravinda Murugesan, Sankaranarayanan
Copyright Year	2020
Description	COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily appeared in Wuhan, China, in December 2019. At present, no proper therapy and vaccinations are available for the disease, and it is increasing day by day with a high mortality rate. Pharmacophore based virtual screening of the selected natural product databases followed by Glide molecular docking and dynamics studies against SARS-CoV-2 main protease was investigated to identify potential ligands that may act as inhibitors. The molecules SN00293542 and SN00382835 revealed the highest docking score of −14.57 and −12.42 kcal/mol, respectively, when compared with the co-crystal ligands of PDB-6Y2F (O6K) and 6W63 (X77) of the SARS-CoV-2 $M^{pro}$. To further validate the interactions of top scored molecules SN00293542 and SN00382835, molecular dynamics study of 100 ns was carried out. This indicated that the protein-ligand complex was stable throughout the simulation period, and minimal backbone fluctuations have ensued in the system. Post-MM-GBSA analysis of molecular dynamics data showed free binding energy-71.7004 +/− 7.98, −56.81+/− 7.54 kcal/mol, respectively. The computational study identified several ligands that may act as potential inhibitors of SARS-CoV-2 $M^{pro}$. The top-ranked molecules SN00293542, and SN00382835 occupied the active site of the target, the main protease like that of the co-crystal ligand. These molecules may emerge as a promising ligands against SARS-CoV-2 and thus needs further detailed investigations. Communicated by Ramaswamy H. Sarma Graphical Abstract
Related Links	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544939/pdf
Ending Page	1386
Page Count	24
Starting Page	1363
ISSN	07391102
e-ISSN	15380254
DOI	10.1080/07391102.2020.1824814
Journal	Journal of Biomolecular Structure and Dynamics
Issue Number	3
Volume Number	40
Language	English
Publisher	Informa UK Limited
Publisher Date	2020-09-28
Access Restriction	Open
Subject Keyword	Journal: Journal of Biomolecular Structure and Dynamics Mathematical and Computational Biology Covid-19 Main Protease Pharmacophore Virtual Screening Molecular Docking Molecular Dynamics Mm-gbsa
Content Type	Text
Resource Type	Article
Subject	Structural Biology Medicine Molecular Biology

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