Integrated Computational Profiling Links Position-specific O-Methylation to Spontaneous Complexation and Improved Binding in Flavonoid-HER2 Systems.

Human epidermal growth factor receptor 2-positive (HER2+) breast cancer is characterized by amplification and overexpression of HER2. This study used a computational workflow to identify O-methylated flavonoids with favorable binding to the HER2 kinase domain and to clarify their binding modes. Among the screened compounds, Eupatolitin, Rhamnetin, Annulatin, Laricitrin, and Sterubin showed the best predicted affinities, with docking scores ranging from -10.092 to -9.260 kcal/mol. Molecular dynamics simulations were then used to assess complex stability, and density functional theory was applied to examine the reactivity of the lead compounds. These analyses were intended for computational prioritization, and experimental validation is required to confirm HER2 inhibition and biological activity. Eupatolitin, which bears methoxy groups at C-6 and C-7, showed the strongest predicted binding, suggesting that 6,7-O-methylation may favor HER2 recognition. This observation prompted a comparison of four parent flavonoids with their 6,7-O-methylated analogues. Across quercetin, myricetin, luteolin, and eriodictyol, 6,7-O-methylation consistently strengthened predicted HER2 binding: docking scores improved by 0.27-0.57 kcal/mol and MM/GBSA ΔGbind improved by 6-10 kcal/mol relative to the parent compounds. In contrast, natural O-methylation at other positions did not enhance binding. Overall, these findings identify Eupatolitin, Rhamnetin, Annulatin, Laricitrin, and Sterubin as promising computational HER2 hits and support position-specific O-methylation at C-6 and C-7 as a useful strategy for optimizing flavonoid scaffolds for HER2 targeting, but experimental validation is required.