In Silico Phytochemical Compounds Screening of Allium sativum Targeting the Mpro of SARS-CoV-2

Abstract

The global pandemic of coronavirus disease is still widely spread across the world causing catastrophic effect in both human life and global economy. By the end of year 2021, it has caused a total of 5.437.636 deaths across the world. Indonesia has rich plant biodiversity including medicinal plants that may be used for combating the virus. One of the commonly used medicinal plants comes from Allium species and it has been proved to have antiviral activity. Conducting an in silico study, we screened bioactive compounds that came from Allium sativum to fight against coronavirus through the inhibition of 3CL-Pro, one of the major protease that have an active role for viral replication. Molecular docking of compounds from Allium sativum to 3CL-Pro resulting in the discovery of 5 compounds that have the best binding affinity to 3CL-Pro, which are squalene, 1,4-dihydro-2,3-benzoxathiin 3-oxide, 1,2,3-propanetriyl ester, trans-13-octadecenoic acid and methyl-11-hexadecenoate with binding affinity of -7, -6.5, -5.9, -5.7 and -5.6 kcal/mol, respectively. It is very likely that these compounds can be candidates for therapeutic agents and these candidates need to be studied further.

Bioactive Compounds from Purslane (Portulaca oleracea L.) and Star Anise (Illicium verum Hook) as SARS-CoV-2 Antiviral Agent via Dual Inhibitor Mechanism: In Silico Approach

“…29 The bond affinity value that used in this study is the smallest because it indicates the presence of additional stability and higher inhibition activity performed by the ligand towards the protein target. 30,31 The presence of bond types, amino acids on the active side, and amino acid residues on the ligands affects the affinity of the bond between the ligands and receptors. 12 The more hydrogen bonds, the more stable the ligand-protein interaction.…”

In Silico Screening of Bioactive Compounds from Syzygium cumini L. and Moringa oleifera L. Against SARS-CoV-2 via Tetra Inhibitors

“…The lowest binding affinity indicates the maximum level of stable interaction indicating that the ligand inhibitory activity against the target protein is larger. 31,32 All bioactive compounds have activity against target proteins (Table 2). However, the compounds to be analyzed next are those with the lowest binding affinity and that follow Lipinski rules of five.…”

In Silico Study of Entry Inhibitor from Moringa oleifera Bioactive Compounds against SARS-CoV-2 Infection

“…27 A recent report has shown that remdesivir is able to inhibit replication of SARS-CoV-2 in in vitro and in vivo experiment. 38,39 Remdesivir is an adenosine analogue that inhibits SARS-CoV-2 RdRp. [32][33][34][35][36][37][38][39][40] Therefore, remdesivir can be used as a positive control in this study.…”

“…38,39 Remdesivir is an adenosine analogue that inhibits SARS-CoV-2 RdRp. [32][33][34][35][36][37][38][39][40] Therefore, remdesivir can be used as a positive control in this study. According to the result docking simulations.…”