Computational modeling study on formation of acyclic clavulanate intermediates in inhibition of class A beta-lactamase: water-assisted proton transfer

Reaction Pathway and Free Energy Barrier for Urea Elimination in Aqueous Solution

To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data.

COMPUTATIONAL MODELING STUDY ON METABOLISM MECHANISM OF OSELTAMIVIR

Oseltamivir (OTV) is widely used in the treatment of both influenza virus A and B infections. Additionally, OTV is an effective antiviral drug in treating the 2009 A ( H1N1 ) influenza virus. Clinical studies concluded that OTV is readily extensively converted to the active carboxylate metabolite after oral administration. In order to investigate the metabolism mechanism of OTV, we carried out density functional theory (DFT) quantum mechanical calculations. The molecule orbital (MO) theory and natural population analysis (NPA) were also employed to help understanding the reaction mechanism. All possible reaction pathways for OTV metabolism are considered, involving hydrolysis of ester and amide. Two mechanisms were considered in this work, viz. concerted mechanism and stepwise mechanism. Our results indicate the stepwise mechanism is more favorable in both hydrolysis reactions and the rate-determining stage is the formation of the tetrahedral intermediate. In addition, the hydrolysis reactions can be assisted by substrate NH2 group and solvent water molecules. The substrate-assisted mechanism for the formation of the carboxylate metabolite is the most favorable one.