Integrative transcriptomics and structure-based screening identifies Phyllanthus amarus phytocompounds as potential WNT5A modulators in ovarian cancer

Introduction Ovarian cancer is one of the most lethal gynecological malignancies, largely due to its asymptomatic onset, heterogeneous molecular landscape, and frequent late-stage diagnosis. Identifying key oncogenic drivers and novel therapeutic candidates is important for understanding disease progression and guiding future research efforts. Methods An integrative computational pipeline was employed to identify differentially expressed genes prioritize a candidate target, and screen plant compounds for anticancer potential. Transcriptomic datasets (GSE14407, GSE18520, and GSE26712) were retrieved from Gene Expression Omnibus and analyzed using GEO2R. The three-dimensional structure of WNT5A was obtained from AlphaFold. GC–MS profiling of Phyllanthus amarus Schumach. and Thonn. Identified phytocompounds for virtual screening, followed by molecular docking, ADME, and toxicity prediction. Molecular dynamics simulations, Free Energy Landscape and Dynamic Cross-Correlation Matrix analyses were performed. Further, Free energy perturbation (FEP) calculations were performed to estimate relative binding free energies across alchemical λ states. Results A total of 103 consistently upregulated genes were identified, among which WNT5A emerged as a key regulator associated with tumor progression, metastasis, and chemoresistance. Enrichment analysis indicated involvement in mesenchymal development, extracellular matrix organization, and receptor-mediated signaling. GC–MS identified 48 compounds, and docking revealed several ligands with favorable interactions with WNT5A . MD simulations supported the structural stability of selected complexes, while FEL and DCCM analyses indicated stable conformational states and ligand-influenced residue dynamics. The FEP-derived free energy estimates further supported the stability and favorable binding of selected ligands toward WNT5A. These results enhance confidence in the computational predictions and complement the MD and docking analyses. Discussion This integrative in silico framework highlights WNT5A as a potential therapeutic target and identifies bioactive compounds from P. amarus as candidates for further investigation. These findings provide preliminary computational insights and warrant experimental validation to improve treatment outcomes in healthcare settings.