Therapeutic potential of date seed (Phoenix dactylifera) powder against human breast cancer: integrated computational and experimental analyses

Palm date ( Phoenix dactylifera L.) seeds are a widely discarded agricultural by-product that contain diverse bioactive phytochemicals. The present study investigated the anti-breast cancer potential of P. dactylifera seed extract through an integrated approach combining network pharmacology, molecular docking, molecular dynamics (MD) simulation, and in vitro experimental validation. HR-LCMS profiling of the ethanolic seed extract identified 57 compounds across both positive and negative ionization modes. Following ADME-based screening (OB greater than 30%, DL greater than or equal to 0.18), eight active compounds were retained for downstream analysis. Network pharmacology identified 214 shared targets between the active compounds and breast cancer-related genes, enriched across 156 KEGG pathways including PI3K-Akt, JAK-STAT, ErbB, and HIF-1 signaling. Protein–protein interaction analysis revealed STAT3, AKT1, and EGFR as the top hub targets. Molecular docking showed that tubulosine, oxolucidine B, and deoxytubulosine exhibited binding affinities ranging from − 7.1 to − 11.2 kcal/mol against the three hub targets. MD simulations over 100 ns confirmed the conformational stability of the oxolucidine B-AKT1, deoxytubulosine-EGFR, and oxolucidine B-STAT3 complexes, as assessed by RMSD, RMSF, Rg, hydrogen bond, and SASA analyses. In vitro MTT assay on MCF-7 cells yielded an IC 50 of 416.21 μg/mL, and the extract inhibited cell migration (approximately 30–40% wound closure vs. 85–90% in control at 44 h) and invasion (approximately 60% reduction in migrated cells) at the IC 50 concentration. These findings point to palm date seeds as a source of multi-target phytochemicals warranting further fractionation and mechanistic validation for breast cancer research.