Targeting Key Breast Cancer Regulators with -Derived Compounds: Insights from Network Pharmacology and Molecular Dynamics

Citrus reticulata is a widely consumed citrus fruit known for its strong antioxidant and anticancer potential. However, the specific molecular mechanisms underlying the bioactivity of its metabolites in breast cancer remain poorly understood. Many of these secondary metabolites, including flavonoids and terpenoids, have been reported to modulate key signaling pathways related to cell proliferation, apoptosis, and metastasis. Despite these findings, the precise molecular interactions and stability of Citrus reticulata compounds within cancer-related targets have not been comprehensively elucidated. Therefore, this study aimed to explore the molecular interaction profiles and dynamic behaviors of major Citrus reticulata metabolites through an integrative in silico approach to better understand their potential roles in breast cancer therapy. Citrus reticulata metabolites were curated from KNAPSACK and PubChem, their Homo sapiens targets were predicted with SwissTargetPrediction and PharmMapper, de-duplicated, and standardized/annotated via UniProtKB. Breast cancer genes from GeneCards, OMIM, and DisGeNET were intersected with predicted targets, visualized in FunRich, and analyzed as a STRING PPI network in Cytoscape, followed by DAVID GO and KEGG enrichment. The resulting priorities guided docking in AutoDock Vina, molecular dynamics in GROMACS 2016.3, and MM-PBSA with g_mmpbsa. Venn analysis yielded 45 overlapping targets between Citrus reticulata metabolites (859 predicted targets) and breast cancer genes (218), with 641 and 173 targets unique to each set, respectively. PPI analysis prioritized ten hubs (TP53, JUN, AKT1, ESR1, STAT3, HIF1A, BCL2, CCND1, HDAC1, MAPK3) with top MCC scores for TP53 (1150), JUN (878), and AKT1 (838), supporting TP53 selection. Docking identified 3-O-β-D-glucopyranosyl sitosterol and β-carotene as top binders to TP53 (−8.18 and −7.81 kcal/mol), and MD showed stable RMSD with minimal binding-site RMSF. MM-PBSA ranked 3-O-β-D-glucopyranosyl sitosterol most favorable (−90.220 ± 14.788 kJ/mol), dominated by van der Waals contributions, aligning with prior anticancer evidence for sitosterols and carotenoids. The findings suggest that metabolites from Citrus reticulata have the capacity to interact stably and favorably with TP53, supporting their potential role as anticancer agents. Among them, 3-O-beta-D-glucopyranosyl sitosterol emerged as a promising lead compound for further in vitro and in vivo investigations. This study offers mechanistic insight into the therapeutic relevance of Citrus reticulata and provides a rational basis for advancing natural products in targeted cancer therapy.