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

被引：17

作者：

Patel, Chirag N. ^{[1
,3
]}

Jani, Siddhi P. ^{[2
]}

Modi, Krunal M. ^{[4
,5
]}

Kumar, Yogesh ^{[6
]}

机构：

[1] NCI, Ctr Canc Res, Chem Biol Lab, Comp Aided Drug Design Grp,NIH, Frederick, MD 21702 USA

[2] Nirma Univ, Inst Sci, Ahmadabad 382481, Gujarat, India

[3] Gujarat Univ, Sch Sci, Dept Bot Bioinformat & Climate Change Impacts Man, Ahmadabad 380009, Gujarat, India

[4] Acad Sci Czech Republ, J Heyrovsky Inst Phys Chem, Dept Mol Electrochem & Catalysis, Dolejskova 2155-3, Prague 8, Czech Republic

[5] Indrashil Univ, Sch Engn, Dept Humanities & Sci, Mehsana 382740, Gujarat, India

[6] Univ Med Ctr Hamburg Eppendorf, Dept Gen Visceral & Thorac Surg, Martinistr 52, D-20246 Hamburg, Germany

来源：

COMPUTERS IN BIOLOGY AND MEDICINE | 2022年 / 151卷

基金：

美国国家卫生研究院;

关键词：

Main proteases (M pro ); DFT calculation; Dynamics simulation; Binding free energy; Omicron; MOLECULAR-DYNAMICS; MECHANICS; COMPLEX; YASARA; DRUG;

D O I：

10.1016/j.compbiomed.2022.106318

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

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