In this work, QM/MM calculations were employed to examine the catalytic mechanism of the retaining glucosyltransferase GTF-SI enzyme, which participates in the process of caries formation. Our goal was to characterize, with atomistic details, the mechanism of sucrose hydrolysis and the catalytic factors that modulate this reaction. Our results suggest a concerted mechanism for sucrose hydrolysis in which the first event corresponds to the glycosidic bond breakage assisted by Glu515, followed by the nucleophilic attack of Asp477, leading to the formation of the Covalent Glycosyl Enzyme (CGE) intermediate. A novel conformational itinerary of the glucosyl moiety along the reaction mechanism was identified: 2H3 → 2H3-E3 → 4C1, and the calculated energy barrier is 16.4 kcal mol-1, which is in good agreement with experimental evidence showing a major contribution coming from the glycosidic bond breakage. Our calculations also revealed that Arg475 and Asp588 play a critical role as TS-stabilizers by electrostatic and charge transfer mechanisms, respectively. This is the first report dealing with the specific features of the mechanism and catalytic residues involved in GTF-SI hydrolysis of sucrose, which is a matter of relevance in enzyme catalysis and could be valuable to aid the design of novel and specific inhibitors targeting GTF-SI.

Quantum-connectivity indices are topographic descriptors combining quantum-chemical and topological information. They are used to describe the water solubility of a noncongeneric data set of organic compounds. A QSPR model is obtained with two quantum-connectivity indices that accounts for more than 90% of the variance in the water solubility of these chemicals. This model is compared to other five QSPR models using constitutional, electrostatic, geometric, quantum-chemical, and topological descriptors calculated by CODESSA. None of these models accounts for more than 85% of the variance in water solubility of the compounds in this data set. The QSPR model obtained with quantum-connectivity indices is also better than that generated from the general pool of 508 CODESSA indices. Models with up to five variables were explored and compared with the model obtained here. It is shown that quantum-connectivity indices contain more structural information than other classes of descriptors at least for describing the water solubility of these 53 chemicals. Structural interpretation of the QSPR model developed as well as the role of the quantum-connectivity indices included in it are also analyzed.

The hydrolysis of carbapenem antibiotics by metallo-β-lactamase enzymes (MBLs) is a biologically crucial reaction that promotes the antibiotic resistance, and consequently, MBLs cause human infections. Therefore, the enzymes that catalyze this reaction are among the most important pharmacological targets, especially those of the VIM type. Despite its relevance in the increase of antimicrobial resistance, the fundamental mechanism of meropenem (carbapenem antibiotic) hydrolysis catalyzed by this enzyme is not fully understood. Here, we report the catalytic mechanism of the meropenem hydrolysis by a VIM-1 metallo-β-lactamase enzyme. We explored the chemical reaction with hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, using three layers, two of them described by high-level ab initio methods at DLPNO-CCSD(T)/CBS plus M06-2X/6-311+G(2d,2p):AMBER. Our results demonstrate that the reaction occurs in three stages: nucleophilic addition, water orientation, and proton transfer. The rate-limiting step in the hydrolysis reaction was the initial stage with a Gibbs energy barrier of 15.7 kcal•mol −1 . This energy value is in excellent agreement with the experimental data of 15.9 kcal•mol −1 (derived from the k cat value of 13 s −1 ). The Gibbs activation energy for the overall reaction was −14.5 kcal•mol −1 . Our biochemical understanding of the enzymatic regulation of meropenem hydrolysis by VIM-1 not only resolves the mechanism but also allows us to identify noncatalytic residues with an effect on the rate-limiting step of the reaction. That is, revisiting the electrostatic role of the residues in the second coordination sphere yields rationally identified mutants that can be used to inhibit the activity of the metallo-β-lactamase enzyme or as a starting point for the design of β-lactam antibiotics.