Inhibition of SARS-Cov-2 proteases by medicinal plant bioactive constituents: Molecular docking simulation

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that has caused the corona pandemic since 2019 or known as Covid-19. The cleavage of its polyprotein started this viral replication into functional viral proteins by two proteases: 3-chymotrypsin-like protease (3CL protease), also known as main protease (Mpro), and Papain-like protease (PLpro). Medicinal plant bioactive constituents could potentially become protease inhibitor agents of this virus and prevent viral replication. Thus, further might be developed into drug candidates for diseases with no specific drug currently available. The first step of discovering the medicine is virtual screening with a molecular docking simulation approach. The stable conformation structure of the bioactive compounds was docked into the enzymes SARS-CoV-2 Main Protease (PDB ID: 6XMK) and SARS-CoV-2 Papain-Like Protease (PDB ID: 7CMD). Molecular docking simulations were operated using Molegro Virtual Docker (MVD) program after the validation process. In this study, analysis of the docking simulation was carried out of compounds in Andrographis paniculata, Phyllanthus niruri L., Aloe vera, and Sonchus arvensis. They are medicinal plants that have been used as a medicine for generations and may have potential as antivirals. A docking score with a more negative presentation binding energy value has a more significant potential to be a lead compound. Several potential compounds were evaluated for their absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. This method can reduce the trial and error factor in the drug discovery stage, although it needs further proof by experimentation in a wet laboratory.

Activity and potential of Phyllantus niruri L. and Phyllantus urinaria L. as Hepatitis B virus inhibitors: A narrative review of the SANRA protocol

“…Pregnant women were positively infected with HBV in the highest provinces, namely, East Java, Central Java, West Java, East Nusa Tenggara, and South Sulawesi, with 8,071, 5,942, 5,819, 3,148, and 2,685 cases, respectively [3]. Given the high incidence of hepatitis B infection, strategic efforts are needed, especially to carry out prevention and control, as well as to identify and develop drug candidates that are safe and effective in suppressing the development of the virus using medicinal plants [4][5][6].…”