Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4′-O-Nucleotidyltransferase

This work is focused on mechanistic studies of the transfer of an adenylyl group (Adenoside-5′-monophosfate) from adenosine 5′-triphosphate (ATP) to a OH-4′ hydroxyl group of an antibiotic. Using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques, we study the substrate and base-assisted mechanisms of the inactivation process of kanamycin A (KAN) catalyzed by 4′-O-Nucleotidyltransferase [ANT(4′)], an active enzyme against almost all aminoglycoside antibiotics. Free energy surfaces, obtained with Free Energy Perturbation methods at the M06-2X/MM level of theory, show that the most favorable reaction path presents a barrier of 12.2 kcal·mol(−1) that corresponds to the concerted activation of O4′ from KAN by Glu145. In addition, the primary and secondary (18)O kinetic isotope effects (KIEs) have been computed for bridge O3α, and non-bridge O1α, O2α, and O5′ atoms of ATP. The observed normal 1°-KIE of 1.2% and 2°-KIE of 0.07% for the Glu145-assisted mechanism are in very good agreement with experimentally measured data. Additionally, based on the obtained results, the role of electrostatic and compression effects in enzymatic catalysis is discussed.