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Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2.
Mahmud, Shafi; Uddin, Mohammad Abu Raihan; Zaman, Meemtaheena; Sujon, Khaled Mahmud; Rahman, Md Ekhtiar; Shehab, Mobasshir Noor; Islam, Ariful; Alom, Md Wasim; Amin, Al; Akash, Al Shahriar; Saleh, Md Abu.
  • Mahmud S; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Uddin MAR; Department of Biochemistry and Biotechnology, University of Science and Technology (USTC), Chittagong, Bangladesh.
  • Zaman M; Department of Biochemistry and Biotechnology, University of Science and Technology (USTC), Chittagong, Bangladesh.
  • Sujon KM; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Rahman ME; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Shehab MN; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Islam A; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Alom MW; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
  • Amin A; Institute of Biological Science, University of Rajshahi, Rajshahi, Bangladesh.
  • Akash AS; Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh.
  • Saleh MA; Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh.
J Biomol Struct Dyn ; 39(16): 6281-6289, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-670995
ABSTRACT
Newly emerged SARS-CoV-2 made recent pandemic situations across the globe is accountable for countless unwanted death and insufferable panic associated with co-morbidities among mass people. The scarcity of appropriate medical treatment and no effective vaccine or medicine against SARS-CoV-2 has turned the situation worst. Therefore, in this study, we made a deep literature review to enlist plant-derived natural compounds and considered their binding mechanism with the main protease of SARS-CoV-2 through combinatorial bioinformatics approaches. Among all, a total of 14 compounds were filtered where Carinol, Albanin, Myricetin were had better binding profile than the rest of the compounds with having binding energy of -8.476, -8.036, -8.439 kcal/mol, respectively. Furthermore, MM-GBSA calculations were also considered in this selection process to support docking studies. Besides, 100 ns molecular dynamics simulation endorsed the rigid nature, less conformational variation and binding stiffness. As this study, represents a perfect model for SARS-CoV-2 main protease inhibition through bioinformatics study, these potential drug candidates may assist the researchers to find a superior and effective solution against COVID-19 after future experiments.Communicated by Ramaswamy Sarma.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Reviews Topics: Vaccines Limits: Humans Language: English Journal: J Biomol Struct Dyn Year: 2021 Document Type: Article Affiliation country: 07391102.2020.1796808

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Reviews Topics: Vaccines Limits: Humans Language: English Journal: J Biomol Struct Dyn Year: 2021 Document Type: Article Affiliation country: 07391102.2020.1796808