Docking analysis of propolis's natural compound was successfully performed against SARS-CoV-2 main protease (Mpro) and spike protein subunit 2 (S2). Initially, the propolis's protein was screened using chromatography analysis and successfully identified 22 compounds in the propolis. Four compounds were further investigated, i.e., neoblavaisoflavone, methylophiopogonone A, 3′-Methoxydaidzin, and genistin. The binding affinity of 3′-Methoxydaidzin was −7.7 kcal/mol, which is similar to nelfinavir (control), while the others were −7.6 kcal/mol. However, we found the key residue of Glu A:166 in the methylophiopogonone A and genistin, even though the predicted binding energy slightly higher than nelfinavir. In contrast, the predicted binding affinity of neoblavaisoflavone, methylophiopogonone A, 3′-Methoxydaidzin, and genistin against S2 were −8.1, −8.2, −8.3, and −8.3 kcal/mol, respectively, which is far below of the control (pravastatin, −7.3 kcal/mol). Instead of conventional hydrogen bonding, the π bonding influenced the binding affinity against S2. The results reveal that this is the first report about methylophiopogonone A, 3′-Methoxydaidzin, and genistin as candidates for anti-viral agents. Those compounds can then be further explored and used as a parent backbone molecule to develop a new supplementation for preventing SARS-CoV-2 infections during COVID-19 outbreaks.

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In this research, simulations of molecular docking of

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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.