In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation

Rajib Hossain; Chandan Sarkar; Shardar Mohammad Hafiz Hassan; Rasel Ahmed Khan; Mohammad Arman; Pranta Ray; Muhammad Torequl Islam; Sevgi Durna Daştan; Javad Sharifi-Rad; Zainab M Almarhoon; Miquel Martorell; William N Setzer; Daniela Calina

doi:10.1007/s11655-021-3504-5

In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation

Chin J Integr Med. 2022 Mar;28(3):249-256. doi: 10.1007/s11655-021-3504-5. Epub 2021 Dec 15.

Authors

Affiliations

¹ Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh.
² Harmacy Discipline, Life Science School, Khulna University, Khulna, 9280, Bangladesh.
³ Department of Pharmacy, International Islamic University, Chittagong, Bangladesh.
⁴ Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
⁵ Department of Biology, Faculty of Science, Sivas Cumhuriyet University, Sivas, 58140, Turkey.
⁶ Beekeeping Development Application and Research Center, Sivas Cumhuriyet University, Sivas, 58140, Turkey.
⁷ School of Medicine, University of Azuay, Cuenca, Ecuador. javad.sharifirad@gmail.com.
⁸ Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
⁹ Department of Nutrition and Dietetics, Faculty of Pharmacy, and Centre for Healthy Living, University of Concepción, Concepción, 4070386, Chile.
¹⁰ Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
¹¹ Aromatic Plant Research Center, 230 N 1200 E, Suite 100, Lehi, UT, 84043, USA.
¹² Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova, 200349, Romania.

Abstract

Objective: To explore potential natural products against severe acute respiratory syndrome coronavirus (SARS-CoV-2) via the study of structural and non-structural proteins of human coronaviruses.

Methods: In this study, we performed an in-silico survey of 25 potential natural compounds acting against SARS-CoV-2. Molecular docking studies were carried out using compounds against 3-chymotrypsin-like protease (3CL^PRO), papain-like protease (PL^PRO), RNA-dependent RNA polymerase (RdRp), non-structural protein (nsp), human angiotensin converting enzyme 2 receptor (hACE2R), spike glycoprotein (S protein), abelson murine leukemia viral oncogene homolog 1 (ABL1), calcineurin-nuclear factor of activated T-cells (NFAT) and transmembrane protease serine 2.

Results: Among the screened compounds, amentoflavone showed the best binding affinity with the 3CL^PRO, RdRp, nsp13, nsp15, hACE2R. ABL1 and calcineurin-NFAT; berbamine with hACE2R and ABL1; cepharanthine with nsp10, nsp14, nsp16, S protein and ABL1; glucogallin with nsp15; and papyriflavonol A with PL^PRO protein. Other good interacting compounds were juglanin, betulinic acid, betulonic acid, broussooflavan A, tomentin A, B and E, 7-methoxycryptopleurine, aloe emodin, quercetin, tanshinone I, tylophorine and furruginol, which also showed excellent binding affinity towards a number of target proteins. Most of these compounds showed better binding affinities towards the target proteins than the standard drugs used in this study.

Conclusion: Natural products or their derivatives may be one of the potential targets to fight against SARS-CoV-2.

Keywords: SARS-CoV-2; molecular docking; natural products-derived anti-SARS-CoV-2 candidates; nonstructural proteins; structural proteins.

MeSH terms

Animals
Antiviral Agents / pharmacology
Antiviral Agents / therapeutic use
Biological Products* / pharmacology
COVID-19 Drug Treatment*
Humans
Mice
Molecular Docking Simulation
SARS-CoV-2

Substances

Antiviral Agents
Biological Products