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Plant-derived compounds effectively inhibit the main protease of SARS-CoV-2: An in silico approach.
Mahmud, Shafi; Afrose, Shamima; Biswas, Suvro; Nagata, Abir; Paul, Gobindo Kumar; Mita, Mohasana Akter; Hasan, Md Robiul; Shimu, Mst Sharmin Sultana; Zaman, Shahriar; Uddin, Md Salah; Islam, Md Sayeedul; Saleh, Md Abu.
  • Mahmud S; Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, Australian Capital Territory, Australia.
  • Afrose S; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Biswas S; Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Nagata A; Department of Regenerative Dermatology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
  • Paul GK; Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Mita MA; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Hasan MR; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Shimu MSS; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Zaman S; Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Uddin MS; Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Islam MS; Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
  • Saleh MA; Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
PLoS One ; 17(8): e0273341, 2022.
Article in English | MEDLINE | ID: covidwho-2002327
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Drug Treatment Type of study: Experimental Studies / Prognostic study Limits: Humans Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2022 Document Type: Article Affiliation country: Journal.pone.0273341

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Drug Treatment Type of study: Experimental Studies / Prognostic study Limits: Humans Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2022 Document Type: Article Affiliation country: Journal.pone.0273341