Identification of Anti-SARS-CoV-2 of Phyllantus Niruri, Curcuma Xanthorrhiza, and Orthosiphon Aristatus Secondary Metabolites through In Silico Studies

Ruth Ellen, Sri Fatmawati, Arli Aditya Parikesit

Abstract

SARS-CoV-2 caused a global pandemic in 2019 with mild flu-like clinical symptoms to severe symptoms that can cause death. Research to find the SARS-CoV-2 drug has been carried out through literature and in silico studies against SARS-CoV-2. Previous studies have reported the antiviral properties of some Indonesian herbs including Phyllantus niruri, Curcuma xanthorrhiza and Orthosiphon aristatus. However, secondary metabolites from these plants have not been tested for anti-SARS-CoV-2. Therefore, the aim of this study is to reveal the anti-SARS-CoV-2 activity of secondary metabolites of these plants through in silico study. Molecular docking and molecular dynamic simulation of compounds were tested using Autodock Vina and GROMACSS 2021.2 against spike (S) glycoprotein and 3-chymotrypsin-like protease (3CLpro) as drug target. Further, the potential SARS-CoV-2 drugs were analyzed for drug similarity and Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties. The results exhibited that rutin (-7.3 kcal/mol), ellagic acid (-7.2 kcal/mol) and ursolic acid (-6.8 kcal/mol) has better docking score for S-glycoprotein than nelfinavir (-6.7 kcal/mol) and remdesivir (-6.6 kcal/mol). In addition, rutin (-8.8 kcal/mol) had a better docking score for 3CLpro than nelfinavir (-8.2 kcal/mol) and remdesivir (-7.8 kcal/mol). It could bind to S-glycoprotein and 3CLpro binding receptor domain. Molecular dynamics simulations showed stable 3CLpro-rutin complex. The ADMET properties of rutin showed it is non-toxic. Therefore, rutin is a good 3CLpro inhibitor and has the potential to be a SARS-CoV-2 drug.

 

Keywords: SARS-CoV-2, in silico, Phyllantus niruri, Curcuma xanthorrhiza, Orthosiphon aristatus.

 

https://doi.org/10.55463/issn.1674-2974.50.7.6


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