Abstract
BackgroundCOVID-19 has mutation capability, and there are no specific drug therapies that are available to fight or inhibit the proteins of this virus. The present study aims to investigate the binding affinity of the bioactive and synthetic compounds with the main protease (Mpro) enzymes and angiotensin-converting enzyme 2 (ACE 2) by computational approach. PASS prediction, pharmacokinetics, and toxicological properties prediction studies were performed through the Google PASS prediction and Swiss ADME/T website. Besides, molecular docking studies were accomplished by BIOVIA Discovery Studio 2020, UCSF Chimera, and PyRx autodock vina.ResultsThe docking scores were inferred and the selected compounds showed results varying from −3.2 to −9.8 (kcal/mol). Theaflavin scored the highest docking score to the 5REB, 6VW1, and 1R42 enzymes and showed the binding affinity as −6.3 kcal/mol, −9.8 kcal/mol, and −8.6 kcal/mol, respectively. Again, kaempferol showed the best binding affinity to the 7BQY (−7.1 kcal/mol) and 6Y2FB (−6.6 kcal/mol) enzymes. All the chemical constituents showed better probability in action in pass prediction analysis. Besides, no ligands (except theaflavin) have any conflict with Lipinski’s rules of five, which authorized the drug probability of these ligands.ConclusionTherefore, the selected compounds could be considered a potential herbal treatment source against SARS-CoV-2.
Highlights
COVID-19 has mutation capability, and there are no specific drug therapies that are available to fight or inhibit the proteins of this virus
The causative agent was identified from throat swab samples conducted by the Chinese Center for Disease Control and Prevention (CCDC) on 7 January 2020, and was subsequently named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)
Molecular docking study for SARS-CoV-2 inhibition In the case of the antiviral docking study, the selected compounds were docked against the SARS-CoV-2’s main protease (PDB: 5REB, 7BQY, 6Y2F), and angiotensinconverting enzyme 2 (PDB: 6VW1, 1R42) enzymes and displayed docking scores ranging from −3.2 to −9.8
Summary
COVID-19 has mutation capability, and there are no specific drug therapies that are available to fight or inhibit the proteins of this virus. PASS prediction, pharmacokinetics, and toxicological properties prediction studies were performed through the Google PASS prediction and Swiss ADME/T website. Molecular docking studies were accomplished by BIOVIA Discovery Studio 2020, UCSF Chimera, and PyRx autodock vina. According to the WHO (World Health Organization), SARS-CoV-2 is a pandemic crisis. It first appeared in the Wuhan province of China on 31 December 2019, and spread rapidly in the different parts of the world. The causative agent was identified from throat swab samples conducted by the Chinese Center for Disease Control and Prevention (CCDC) on 7 January 2020, and was subsequently named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Most SARS-CoV-2 infected patients are seen with symptoms such as dry cough, sore throat, and fever. The emergency committee has stated that the spread of COVID-19 may be interrupted by early detection, isolation, prompt treatment, and the implementation of a robust system to trace contacts [3]
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