Density functional theory (DFT), quantum mechanical/molecular mechanical (QM/MM), and molecular dynamics (MD) calculations were applied in studying the reaction of seven different β-lactam ruthenocenyl-ADBA (ADBA = aminodesacetoxybetalactamic acid) antibiotics with the CTX-M enzyme. The mechanism was studied in the gas phase and water solvent, and is summarized as follows: the antibiotic (β-lactam) forms an adduct with the enzyme (protein binding protein, PBP), PBP-OH, then the hydroxyl group of the serine forms a covalent acyl linkage with the β-lactam carbonyl group; serine β-lactamases made by PBPOH hydrolyze the covalent acyl-enzyme linkage, regenerating the enzyme, thus degrading the antibiotics. The catalytic process was characterized by two distinct free energy barriers: the formation of the covalent acyl linkage with β-lactam carbonyl group and its breaking to serine β-lactamases and inactivated drug. Based on kinetic and thermodynamic parameters, the rate-determining step of the process is associated with the second transition state and carbapanem was found as best inhibitory candidate. In order to better establish the interactions between the enzyme and the drug, the catalytical and binding residue of the enzyme was evaluated via QM/MM calculations. The serine 70 residue was found as the preferred catalytic site for the inhibitor by having quite strong nucleophilic oxygen. Also the site is adjacent to more residues, which result in more hydrogen bonds with the inhibitors. The level of inhibition and antibacterial properties of optimized transition state structures were evaluated. Molecular dynamics calculations gave insight about structure-activity relationships (SARs) that connect the computed energy diagrams of β-lactam hydrolysis with reported IC<sub>50</sub> (μM) measurements. Our findings demonstrate how metallocenyl groups can be utilized to enhance the interactions between β-lactam compounds and the target bacterial enzymes.

Theoretical study on hydrolysis of β-lactam antibiotics and their structures with β-lactamases

2019 Spring National Meeting

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