Plant-Derived Secondary Metabolites as Potential Mediators Against COVID-19 by MetA-Analysis, Docking, and Molecular Dynamics Methods

Coronaviruses are viruses that often cause acute complications in the respiratory system with, symptoms similar to those of a cold. Traditions Medicine uses medicinal plants to treat various diseases, including infectious diseases. This research aims to determine the effective antiviral compounds of medicinal plants (Glycyrrhiza glabra, Echinacea purpurea, Panax ginseng, and Cichorium intybus) and the genes involved in their synthesis against coronavirus. In this study, the secondary metabolites were investigated in terms of the inhibition of COVID-19 through meta-analysis. In the database, the interaction of proteins concerning each other and hub genes was obtained from Cytoscape software. To study the ontology of genes from the Enrichr database and then Barsam HeatMap, the expression of the genes was measured relative to each other. As a result of the meta-analysis, 14 genes related to blood coagulation factors and the complement system (immune system) were determined. The compounds of medicinal plants with antiviral and antimicrobial effects were extracted from the PubChem database for docking and then checked by the HeatMap database. As a result of the meta-analysis, 14 genes related to blood clotting factors and the complement system (immune system) were found. The results obtained from the Kegg Pathway server were evaluated, and the two factors coagulation factor X (F10) and coagulation factor II thrombin (F2) as the reactivity of human cells when exposed to the virus and spike protein and main protease as the coronavirus receptor were extracted from the PDB database. Receptor (1A2C, 6lu7, 4Y79, 6VXX)-ligand docking (secondary combinations) was confirmed by the coach-d protein-ligand server. In the end, their validation was done by performing molecular dynamics using Gromax software. According to these results, by reducing the expression of thrombin factor and factor x, it prevents blood clotting, and by inhibiting the spike protein and the main protease of the Coronavirus, it prevents the multiplication of the virus using the antiviral extract of these plants.