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Identifying the natural compound Catechin from tropical mangrove plants as a potential lead candidate against 3CLpro from SARS-CoV-2: An integrated in silico approach

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journal contribution
posted on 13.10.2021, 18:40 by Rajat Kumar Jha, Rameez Jabeer Khan, A. Parthiban, Ekampreet Singh, Monika Jain, Gizachew Muluneh Amera, Rashmi Prabha Singh, Purvaja Ramachandran, Ramesh Ramachandran, V. Sachithanandam, Jayaraman Muthukumaran, Amit Kumar Singh

SARS-CoV-2, a member of beta coronaviruses, is a single-stranded, positive-sense RNA virus responsible for the COVID-19 pandemic. With global fatalities of the pandemic exceeding 4.57 million, it becomes crucial to identify effective therapeutics against the virus. A protease, 3CLpro, is responsible for the proteolysis of viral polypeptides into functional proteins, which is essential for viral pathogenesis. This indispensable activity of 3CLpro makes it an attractive target for inhibition studies. The current study aimed to identify potential lead molecules against 3CLpro of SARS-CoV-2 using a manually curated in-house library of antiviral compounds from mangrove plants. This study employed the structure-based virtual screening technique to evaluate an in-house library of antiviral compounds against 3CLpro of SARS-CoV-2. The library was comprised of thirty-three experimentally proven antiviral molecules extracted from different species of tropical mangrove plants. The molecules in the library were virtually screened using AutoDock Vina, and subsequently, the top five promising 3CLpro-ligand complexes along with 3CLpro-N3 (control molecule) complex were subjected to MD simulations to comprehend their dynamic behaviour and structural stabilities. Finally, the MM/PBSA approach was used to calculate the binding free energies of 3CLpro complexes. Among all the studied compounds, Catechin achieved the most significant binding free energy (−40.3 ± 3.1 kcal/mol), and was closest to the control molecule (−42.8 ± 5.1 kcal/mol), and its complex with 3CLpro exhibited the highest structural stability. Through extensive computational investigations, we propose Catechin as a potential therapeutic agent against SARS-CoV-2.

Communicated by Ramaswamy H. Sarma

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