Theoretical studies of the hydrolysis of antibiotics catalyzed by a metallo-β-lactamase

Abstract

In this paper, hybrid QM/MM molecular dynamics (MD) simulations have been performed to explore the mechanisms of hydrolysis of two antibiotics, Imipenen (IMI), an antibiotic belonging to the subgroup of carbapenems, and the Cefotaxime (CEF), a third-generation cephalosporin antibiotic, in the active site of a mono-nuclear β-lactamase, CphA from Aeromonas hydrophila. According to our results, significant different transition state structures are obtained for the hydrolysis of both antibiotics:while the TS of the CEF is a ionic species with negative charge on nitrogen, the IMI TS presents a tetrahedral-like character with negative charge on oxygen atom of the carbonyl group of the lactam ring. Thus, dramatic conformational changes can take place in the cavity of CphA to accommodate different substrates, which would be the origin of its substrate promiscuity. This feature of the β-lactamase would be in turn, associated to the different mechanisms that the protein employs to hydrolyze the different antibiotics; i.e. the catalytic promiscuity. Since CphA shows only activity against carbapenem antibiotic, this study will be used to shed some light into the origin of the selectivity of the different MbL and, as a consequence, into the discovery of specific and potent MβL inhibitors against a broad spectrum of bacterial pathogens.

β-Lactamases and β-Lactamase Inhibitors in the 21st Century

“…Computational studies of β-lactam binding and hydrolysis by MBLs are similarly constrained by the absence of experimental structures for the Michaelis complex, as well as by the challenges associated with accounting for the flexibility of coordination geometry that is a feature of Zn(II) metalloenzyme systems [129]. In consequence, the findings of QM/MM studies of carbapenem hydrolysis by binuclear MBLs vary in several aspects; notably, interactions involving the substrate carboxylate and Zn2, which in some cases are proposed to occur only on formation of anionic species [130], [131]; the identity of the nucleophile, in one study [121] considered to be bulk water rather than the bridging hydroxide; and the protonation route(s) for N4 [131].…”

Special issue in computational modeling on biological systems

“…[8] It is stressed how, despite a wealth of biochemical, structural and computational data, the way in which GTP hydrolysis is activated and regulated is still a controversial topic, and well-designed computational study on another problem with medical applications; the mechanisms of hydrolysis of two antibiotics in the active site of a mono-nuclear β-lactamase. [12] The study, based on molecular dynamics simulations with multiscale methods, explores the reaction paths and highlights the dramatic conformational changes that can take place in the cavity of the enzyme to accommodate different substrates, which would be the origin of its substrate promiscuity. This feature would be in turn, associated to the different mechanisms that β-lactamases employ to hydrolyze the different antibiotics;…”

Environmental fate of cefquinome: Adsorption and degradation

“…The β-lactam antibiotics are preeminent in the treatment of bacterial infection due to their excellent clinical efficacy and safety, accounting for more than half of the world's antibiotic market (Testero et al, 2003;Meliá et al, 2015). Cefquinome (CEQ), the fourth generation of cephalosporins only used in animals with a C-3 bicyclic pyridinium group, is stable and effective against chromosomal and plasmid-encoded βlactamases (Chin et al, 1992;Ahmad et al, 2015).…”