Irreversible Inhibition of Human Ornithine Aminotransferase: A Quantum Mechanics/Molecular Mechanics Study

Abstract

Human ornithine aminotransferase (hOAT) is overexpressed in hepatocellular carcinoma (HCC) and participates in glutamine anabolic metabolism, making it a promising therapeutic target. Although (1S,3S)-3-amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic acid (named here as BCF3 after the (bis)trifluoromethyl feature) has been proposed as a potent inhibitor of hOAT, previous experimental studies have characterized an external aldimine intermediate and the static end-state adduct, but the elementary fluorine-elimination steps and their modulation by the active-site environment remain incompletely understood. Herein, molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations were employed to systematically explore the irreversible inhibitory mechanism mediated by external aldimine II—the key reaction intermediate of BCF3—against hOAT. Conserved active-site water molecules act as proton-shuttling bridges, and residue-dependent electrostatic effects control fluorine elimination. External aldimine II forms a stable covalent adduct with Lys292 and sequentially releases fluorine atoms from the –CF2 moiety via water-mediated Fα− and Fβ− elimination, with feasible barriers of 10.8 and 16.0 kcal/mol, respectively. Negative overall reaction energies indicate that the elimination products are energetically favored in the system. Electrostatic and noncovalent interaction analyses suggest that Arg180 and Gly42 promote fluorine elimination whereas Phe177 suppresses it, providing an atomistic explanation for the superior inhibitory potency of the bis-trifluoromethyl scaffold. The atomistic inhibitory mechanism uncovered in this study provides a theoretical foundation for the future rational design of hOAT-targeted drugs for hepatocellular carcinoma therapy.

The authors' abstract, as published at the source. International Journal of Molecular Sciences, 2026 · DOI ↗