Network pharmacology and molecular simulation-based analysis of Citrus aurantium metabolites targeting breast cancer pathways

Abstract

Citrus aurantium is a plant known for its diverse bioactive constituents, yet its therapeutic potential in hormone-dependent breast cancer remains underexplored. This study applied a network pharmacology approach to identify breast cancer-associated targets, followed by molecular docking, molecular dynamics simulation, and MM-PBSA energy analysis to evaluate ligand–receptor interactions. From an initial dataset of 111 metabolites, 24 compounds were predicted to interact with ESR1, a central node identified through protein–protein interaction network analysis. Several flavonoid derivatives demonstrated favorable docking interactions at key ESR1 residues, including GLU353, ALA350, LEU387, ARG394, LYS449, and PRO324. Molecular dynamics simulations up to 300 ns revealed that the native ligand complex maintained the greatest stability, 5,7,3′,4′-tetrahydroxyflavone achieved persistent receptor engagement with moderate flexibility, and hesperetin showed higher deviations yet equilibrated with selective residue interactions. MM-PBSA binding free energy calculations confirmed that 5,7,3′,4′-tetrahydroxyflavone possessed the strongest affinity (−79.695 ​kJ/mol), followed by the native ligand (−72.521 ​kJ/mol), while hesperetin displayed weaker but still favorable binding (−55.737 ​kJ/mol). These energetic contributions were largely driven by van der Waals and electrostatic forces, partially offset by polar solvation. The integrated computational findings highlight 5,7,3′,4′-tetrahydroxyflavone as the most promising ESR1 binder from Citrus aurantium, while hesperetin remains a viable candidate through its selective pharmacophoric interactions. Collectively, these findings establish a solid foundation for subsequent experimental validation and support the development of Citrus aurantium-derived compounds as potential therapies for estrogen receptor-positive breast cancer.