NDLI: Plant-derived compounds effectively inhibit the main protease of SARS-CoV-2: An in silico approach.

Content Provider	Directory of Open Access Journals (DOAJ)
Author	Shafi Mahmud Shamima Afrose Suvro Biswas Abir Nagata Gobindo Kumar Paul Mohasana Akter Mita Md Robiul Hasan Mst Sharmin Sultana Shimu Shahriar Zaman Md Salah Uddin Md Sayeedul Islam Md Abu Saleh
Abstract	The current coronavirus disease 2019 (COVID-19) pandemic, caused by the coronavirus 2 (SARS-CoV-2), involves severe acute respiratory syndrome and poses unprecedented challenges to global health. Structure-based drug design techniques have been developed targeting the main protease of the SARS-CoV-2, responsible for viral replication and transcription, to rapidly identify effective inhibitors and therapeutic targets. Herein, we constructed a phytochemical dataset of 1154 compounds using deep literature mining and explored their potential to bind with and inhibit the main protease of SARS-CoV-2. The three most effective phytochemicals Cosmosiine, Pelargonidin-3-O-glucoside, and Cleomiscosin A had binding energies of -8.4, -8.4, and -8.2 kcal/mol, respectively, in the docking analysis. These molecules could bind to Gln189, Glu166, Cys145, His41, and Met165 residues on the active site of the targeted protein, leading to specific inhibition. The pharmacological characteristics and toxicity of these compounds, examined using absorption, distribution, metabolism, excretion, and toxicity (ADMET) analyses, revealed no carcinogenicity or toxicity. Furthermore, the complexes were simulated with molecular dynamics for 100 ns to calculate the root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen profiles from the simulation trajectories. Our analysis validated the rigidity of the docked protein-ligand. Taken together, our computational study findings might help develop potential drugs to combat the main protease of the SARS-CoV-2 and help alleviate the severity of the pandemic.
e-ISSN	19326203
DOI	10.1371/journal.pone.0273341
Journal	PLoS ONE
Issue Number	8
Volume Number	17
Language	English
Publisher	Public Library of Science (PLoS)
Publisher Date	2022-01-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Medicine Science
Content Type	Text
Resource Type	Article

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