Electronic-Structure Determinants of Flavonoid Inhibition at the Molybdenum Cofactor of Xanthine Oxidase: A QM/MM Study

Abstract

Flavonoid-mediated inhibition of xanthine oxidase (XO) is well established at the empirical level; however, while molecular docking, MD, and MM-PBSA/MM-GBSA methods have been widely applied, the quantum-mechanical origin of the structure–activity relationship at the molybdenum cofactor (MoCo) remains unresolved. Hybrid QM/MM calculations (B3LYP/def2-SVP) on five dietary flavonoids bound to the MoCo active site of bovine XO (50 snapshots total) revealed that all five exhibit net charge redistribution at the MoCo interface, with the magnitude varying nearly 9-fold. The charge-redistribution descriptor |CTlig| correlated with Ki (r = – 0.922, p = 0.026; Spearman ρ = – 1.000), and Hirshfeld charge analysis independently confirmed the Mulliken-derived ranking (r = 0.942, p = 0.017), while representative def2-TZVP calculations preserved the principal compound hierarchy (Spearman ρ = 0.900), supporting robustness to both charge partitioning and basis-set effects. Frontier orbital analysis links the observed structure–activity relationship to the saturated C2–C3 bond of naringenin, which interrupts π-conjugation and limits electronic communication toward the MoCo environment. The electrostatic interaction energy further correlated with Ki (r = – 0.890, p = 0.043), whereas total interfragment contact density showed no correlation, indicating that within this five-compound series, inhibitory potency was more closely associated with charge-redistribution magnitude and electrostatic interaction than with the interfragment contact-density descriptor.