Integrating computational chemistry, network pharmacology and in vitro experimental assays for deciphering the antitumor effects of naturally occurring sesquiterpene lactone-parthenolide in human oral carcinoma cells

This study evaluates the anticancer efficacy of Parthenolide against SCC-9 oral squamous cell carcinoma cells using an integrated in silico and in vitro strategy. Pharmacokinetic behavior and drug-likeness were predicted using SwissADME, while organ-specific and systemic toxicity were assessed via Protox-3.0. Parthenolide-associated targets and oral cancer–related genes were obtained from the Comparative Toxicogenomics Database and GeneCards, respectively. Common targets were identified using Jvenn and subjected to protein–protein interaction (PPI) analysis through STRING, with network visualization and hub gene identification performed in Cytoscape using the CytoHubba plugin. Functional enrichment analysis was conducted using ShinyGO, and gene expression patterns along with survival relevance were analyzed through GEPIA2. Molecular docking and normal mode analysis (NMA) were carried out using CB-Dock2, Discovery Studio, and iMODS. In vitro validation involved MTT assay, colony formation assay, Annexin V/PI flow cytometry, DAPI nuclear staining, and Western blot analysis in SCC-9 cells. Parthenolide demonstrated favorable drug-like characteristics, including high gastrointestinal absorption, blood–brain barrier permeability, and an absence of major predicted toxicities. A total of 42 shared targets were identified, primarily associated with apoptosis, IL-17 signaling, and TNF signaling pathways. PPI network analysis highlighted IL1B, TNF, and TP53 as key hub genes. Molecular docking revealed strong binding affinities of Parthenolide with TNF (–7.5 kcal/mol), TP53 (–6.2 kcal/mol), and IL1B (–6.0 kcal/mol), involving critical interactions such as hydrogen bonding. NMA results indicated that the Parthenolide–TP53 complex was the most stable, with an eigenvalue of 4.705 × 10−4. Experimentally, Parthenolide significantly decreased SCC-9 cell viability and markedly suppressed colony formation at 120 µM. Annexin V/PI analysis confirmed apoptosis induction, with a substantial increase in apoptotic cell populations at higher concentrations. DAPI staining demonstrated pronounced nuclear fragmentation, while Western blotting revealed downregulation of IL1B and TNF alongside upregulation of TP53. Collectively, these findings indicate that Parthenolide exerts anticancer activity in oral squamous cell carcinoma by modulating inflammatory and apoptotic pathways, underscoring its potential as a promising candidate.