In silico analysis of Phyllanthus amarus phytochemicals as potent drugs against SARS-CoV-2 main protease

Abstract

Phyllanthus amarus, also known as Bhui Korma in India, is well known for its medicinal properties and is used to treat several diseases worldwide. This study aims to identify phytochemicals from P. amarus and assess their anti-viral activity through in silico methods against the main protease (3CLPro/MPro) enzyme of the novel coronavirus. 190 compounds were obtained from literature and docked against 3CLPro and 16 compounds showed higher binding affinity with 3CLPro with their values lying between -8.9 ​kcal/mol to -9.6 ​kcal/mol. The top two compounds, Myricitrin (CID: 5352000) and Quercetin-3-O-glucuronide (CID: 12004528) gave high binding affinity values of -9.6 ​kcal/mol and -9.4 ​kcal/mol respectively and also display favourable binding interactions with the 3CLPro. Both the compounds were further subjected to molecular dynamics simulation and MM-PBSA based binding free energy calculations. ADMET and drug-likeness properties were studied to assess the pharmacokinetic properties of the compounds. Favourable pharmacokinetic results reinforced the applicability of the compounds assessed. Along with continuous studies being carried out with chemical compounds, research needs to expand into all areas, including the use of natural compounds as drug compounds. The identified hits from this study can be taken further for in vitro and in vivo studies to examine their efficacy against COVID-19.

Keywords

• COVID-19
• 3CLPro
• Phyllanthus amarus
• Antiviral activity
• Molecular docking
• ADMET studies