Network pharmacology, molecular docking, and molecular dynamics simulations shed light on the mechanism behind Gynostemma pentaphyllum’s efficacy against osteosarcoma

Osteosarcoma (OS) is the most common type of malignant bone tumor, that poses a serious threat to the lives and health of children and adolescents. Traditional Chinese medicines (TCM) have gained attention for treating OS because of their potent anti-cancer effects and fewer side effects. It is commonly understood that Gynostemma pentaphyllum (Thunb.) Makino (GP) exhibits inhibitory effects on most tumors. However, the knowledge of the systematic mechanisms involved is limited. In this study, the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was searched to screen the effective ingredients and corresponding target genes of GP, and disease target databases were searched to identify relevant targets for OS. Venn analysis was used to visualize overlapping genes, which were further extracted using the protein-protein interaction network. R software was used to conduct gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analysis, molecular docking and molecular dynamics simulation further validate the binding efficacy of potential therapeutic targets to compound molecules. In total, 161 and 1981 proteins were identified as target genes of GP and OS, respectively, and 104 overlapping genes were identified. Through analysis of the core subnetwork, 12 hub genes were identified, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses revealed that the PI3K/Akt signaling pathway was the most significant. Molecular docking and molecular dynamics simulations show that a high affinity between quercetin and these targets, especially with the combination of TNF free energy (Δ Gbind) minimum, MM/PBSA and MM/GBSA is 42.85 kcal/mol, respectively, and 45.29 kcal/mol. The active ingredients Rhamnazin and Quercetin in Gypenoylum play a therapeutic role in OS through several key targets and pathways. This study provides ideas and references for further research on drug development.