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Inhibitory effect of thymoquinone from Nigella sativa against SARS-CoV-2 main protease. An in-silico study

Khan et al., Brazilian Journal of Biology, doi:10.1590/1519-6984.25066
Jan 2022  
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In Silico analysis of thymoquinone from nigella sativa showing good binding affinity with SARS-CoV-2 Mpro.
Khan et al., 24 Jan 2022, peer-reviewed, 7 authors. Contact: tahirmicrobiologist@gmail.com, muhammad.tahir8@imbb.uol.edu.pk, dqwei@sjtu.edu.cn.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperNigella SativaAll
Inhibitory effect of thymoquinone from Nigella sativa against SARS-CoV-2 main protease. An in-silico study
M T Khan, A Ali, X Wei, T Nadeem, S Muhammad, A G Al-Sehemi, Dongqing Wei
Brazilian Journal of Biology, doi:10.1590/1519-6984.25066
Nigella sativa is known for the safety profile, containing a wealth of useful antiviral compounds. The main protease (Mpro, 3CLpro) of severe acute respiratory syndrome 2 (SARS-CoV-2) is being considered as one of the most attractive viral target, processing the polyproteins during viral pathogenesis and replication. In the current investigation we analyzed the potency of active component, thymoquinone (TQ) of Nigella sativa against SARS-CoV-2 Mpro. The structures of TQ and Mpro was retrieved from PubChem (CID10281) and Protein Data Bank (PDB ID 6MO3) respectively. The Mpro and TQ were docked and the complex was subjected to molecular dynamic (MD) simulations for a period 50ns. Protein folding effect was analyzed using radius of gyration (Rg) while stability and flexibility was measured, using root means square deviations (RMSD) and root means square fluctuation (RMSF) respectively. The simulation results shows that TQ is exhibiting good binding activity against SARS-CoV-2 Mpro, interacting many residues, present in the active site (His41, Cys145) and also the Glu166, facilitating the pocket shape. Further, experimental approaches are needed to validate the role of TQ against virus infection. The TQ is interfering with pocket maintaining residues as well as active site of virus Mpro which may be used as a potential inhibitor against SARS-CoV-2 for better management of COVID-19.
References
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Protein ' 'folding effect was analyzed using radius of gyration (Rg) while stability and flexibility was ' 'measured, using root means square deviations (RMSD) and root means square fluctuation (RMSF) ' 'respectively. The simulation results shows that TQ is exhibiting good binding activity ' 'against SARS-CoV-2 Mpro, interacting many residues, present in the active site (His41, ' 'Cys145) and also the Glu166, facilitating the pocket shape. Further, experimental approaches ' 'are needed to validate the role of TQ against virus infection. The TQ is interfering with ' 'pocket maintaining residues as well as active site of virus Mpro which may be used as a ' 'potential inhibitor against SARS-CoV-2 for better management of COVID-19.</jats:p>', 'alternative-id': ['S1519-69842024000100270'], 'author': [ { 'ORCID': 'http://orcid.org/0000-0003-1158-2133', 'affiliation': [{'name': 'The University of Lahore, Pakistan'}], 'authenticated-orcid': False, 'family': 'Khan', 'given': 'M. 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Um estudo in silico'], 'prefix': '10.1590', 'published': {'date-parts': [[2024]]}, 'published-online': {'date-parts': [[2024]]}, 'publisher': 'FapUNIFESP (SciELO)', 'reference': [ { 'DOI': '10.1016/j.phymed.2013.10.023', 'article-title': 'Radiation-modifying abilities of Nigella sativa and thymoquinone on ' 'radiation-induced nitrosative stress in the brain tissue', 'author': 'AHLATCI A.', 'doi-asserted-by': 'crossref', 'first-page': '740', 'issue': '5', 'journal-title': 'Phytomedicine', 'key': 'ref1', 'volume': '21', 'year': '2014'}, { 'article-title': 'Black cumin (Nigella sativa) and its active constituent, thymoquinone: ' 'an overview on the analgesic and anti-inflammatory effects', 'author': 'AMIN B.', 'first-page': '8', 'issue': '1-2', 'journal-title': 'Planta Medica', 'key': 'ref2', 'volume': '82', 'year': '2016'}, { 'DOI': '10.1093/emboj/cdf327', 'article-title': 'Structure of coronavirus main proteinase reveals combination of a ' 'chymotrypsin fold with an extra alpha-helical 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