Molecular insights into the in silico discovery of corilagin from Terminalia chebula as a potential dual inhibitor of SARS-CoV-2 structural proteins

The spike (S) glycoprotein and nucleocapsid (N) proteins are the crucial pathogenic proteins of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) virus during its interaction with the host. Even FDA-approved drugs like dexamethasone and grazoprevir are not able to curb the viral progr...

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Published in:Journal of biomolecular structure & dynamics 2023-12, Vol.ahead-of-print (ahead-of-print), p.1-16
Main Authors: Pradeep, Sushma, Patil, Shashank M, Dharmashekara, Chandan, Jain, Anisha, Ramu, Ramith, Shirahatti, Prithvi S, Mandal, Subhankar P, Reddy, Pruthvish, Srinivasa, Chandrashekar, Patil, Sharanagouda S, Ortega-Castro, Joaqúın, Frau, Juan, Flores-Holgúın, Norma, Shivamallu, Chandan, Kollur, Shiva Prasad, Glossman-Mitnik, Daniel
Format: Article
Language:English
Subjects:
binding free energy calculations
corilagin
PASS pharmacological analysis
SARS CoV-2
Terminalia chebula
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Summary:The spike (S) glycoprotein and nucleocapsid (N) proteins are the crucial pathogenic proteins of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) virus during its interaction with the host. Even FDA-approved drugs like dexamethasone and grazoprevir are not able to curb the viral progression inside the host and are reported with adverse effects on body metabolism. In this context, we aim to report corilagin a novel, potential dual inhibitor of S and N proteins from Terminalia chebula. The bioactive compounds of T. chebula were subjected to a series of computational investigations including molecular docking simulations, molecular dynamics (MD) simulations, binding free energy calculations, and PASS pharmacological analysis. The results obtained from these studies revealed that corilagin was highly interactive with the S (-8.9 kcal/mol) and N (-9.2 kcal/mol) proteins, thereby showing dual inhibition activity. It was also found to be stable enough to induce biological activity inside the inhibitor binding pocket of the target enzymes throughout the dynamics simulation run for 100 ns. This is also confirmed by the changes in the protein conformations, evaluated using free energy landscapes. Outcomes from this investigation identify corilagin as the lead potential dual inhibitor of S and N proteins of SARS-CoV-2, which could be taken for biological studies in near future. Communicated by Ramaswamy H. Sarma
ISSN:0739-1102
1538-0254
DOI:10.1080/07391102.2022.2158943