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Computational investigation of natural compounds as potential main protease (Mpro) inhibitors for SARS-CoV-2 virus

CN. Patel, SP. Jani, S. Prasanth Kumar, KM. Modi, Y. Kumar

. 2022 ; 151 (Pt A) : 106318. [pub] 20221118

Jazyk angličtina Země Spojené státy americké

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/bmc22032316

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is significantly impacting human lives, overburdening the healthcare system and weakening global economies. Plant-derived natural compounds are being largely tested for their efficacy against COVID-19 targets to combat SARS-CoV-2 infection. The SARS-CoV-2 Main protease (Mpro) is considered an appealing target because of its role in replication in host cells. We curated a set of 7809 natural compounds by combining the collections of five databases viz Dr Duke's Phytochemical and Ethnobotanical database, IMPPAT, PhytoHub, AromaDb and Zinc. We applied a rigorous computational approach to identify lead molecules from our curated compound set using docking, dynamic simulations, the free energy of binding and DFT calculations. Theaflavin and ginkgetin have emerged as better molecules with a similar inhibition profile in both SARS-CoV-2 and Omicron variants.

Citace poskytuje Crossref.org

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$a Patel, Chirag N $u Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD, 21702, USA; Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India. Electronic address: chiragpatel269@gmail.com
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$a The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is significantly impacting human lives, overburdening the healthcare system and weakening global economies. Plant-derived natural compounds are being largely tested for their efficacy against COVID-19 targets to combat SARS-CoV-2 infection. The SARS-CoV-2 Main protease (Mpro) is considered an appealing target because of its role in replication in host cells. We curated a set of 7809 natural compounds by combining the collections of five databases viz Dr Duke's Phytochemical and Ethnobotanical database, IMPPAT, PhytoHub, AromaDb and Zinc. We applied a rigorous computational approach to identify lead molecules from our curated compound set using docking, dynamic simulations, the free energy of binding and DFT calculations. Theaflavin and ginkgetin have emerged as better molecules with a similar inhibition profile in both SARS-CoV-2 and Omicron variants.
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$a Jani, Siddhi P $u Institute of Science, Nirma University, Ahmedabad, 382481, Gujarat, India
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$a Prasanth Kumar, Sivakumar $u Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
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$a Modi, Krunal M $u Department of Molecular Electrochemistry and Catalysis, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejskova 2155/3, 182 23 Prague 8, Czech Republic; Department of Humanities and Science, School of Engineering, Indrashil University, Mehsana, 382740, Gujarat, India. Electronic address: kmodi5033@gmail.com
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$a Kumar, Yogesh $u Department of General Visceral and Thoracic Surgery, University Medical Center Hamburg- Eppendorf, Martinistrasse 52, Hamburg, 20246, Germany
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