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Natural Compounds as Inhibitors of SARS-CoV-2 Main Protease (3CLpro): A Molecular Docking and Simulation Approach to Combat COVID-19

Author(s):

Md Tabish Rehman, Mohamed F. AlAjmi and Afzal Hussain*   Pages 1 - 13 ( 13 )

Abstract:


The emergence and dissemination of SARS-CoV-2 has caused high mortality and enormous economic loss. Rapid development of new drug molecules is the need of hour to fight COVID-19. However, the conventional approaches of drug development are time consuming and expensive. Here, we have adopted a computational approach to identify lead molecules from nature. Ligands from natural compounds library available at Selleck Inc (L1400) have been screened for their ability to bind and inhibit the main protease (3CLpro) of SARS-CoV-2. We found that Kaempferol, Quercetin, and Rutin were bound at the substrate binding pocket of 3CLpro with high affinity (105-106 M-1) and interact with the active site residues such as His41 and Cys145 through hydrogen bonding and hydrophobic interactions. In fact, the binding affinity of Rutin (~106 M-1) was much higher than Chloroquine (~103 M-1) and Hydroxychloroquine (~104 M-1), and the reference drug Remdesivir (~105 M-1). The results suggest that natural compounds such as flavonoids have the potential to be developed as novel inhibitors of SARS-CoV-2 with a comparable/higher potency as that of Remdesivir. However, their clinical usage on COVID-19 patients is a subject of further investigations and clinical trials.

Keywords:

SARS-CoV-2, COVID-19, Autodock, Schrodinger, Glide Docking, Natural compounds, Flavonoids.

Affiliation:

Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh-11451,, Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh-11451,, Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh-11451



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