Theoretical studies of the hydrolysis of antibiotics catalyzed by a metallo-β-lactamase (original) (raw)
Related papers
Structure-based computational study of the hydrolysis of New Delhi metallo-β-lactmase-1
Biochemical and Biophysical Research Communications, 2013
New Delhi metallo-b-lactmase-1 (NDM-1) is an enzyme that confers antibiotic resistance to bacteria and is thus a serious threat to human health. Almost all clinically available b-lactam antibiotics can be hydrolyzed by NDM-1. To determine the mechanism behind the wide substrate diversity and strong catalytic ability of NDM-1, we explored the molecular interactions between NDM-1 and different b-lactam antibiotics using computational methods. Molecular dynamics simulations and binding free energy calculations were performed on enzyme-substrate (ES) complex models of NDM-1-Meropenem, NDM-1-Nitrocefin, and NDM-1-Ampicillin constructed by molecular docking. Our computational results suggest that mutant residues Ile35 and Lys216, and active site loop L1 residues 65-73 in NDM-1 play crucial roles in substrate recognition and binding. The results of our study provide new insights into the mechanism behind the enhanced substrate binding and wider substrate spectrum of NDM-1 compared with its homologous enzymes CcrA and IMP-1. These insights may be useful in the discovery and design of specific and potent inhibitors against NDM-1.
International Journal of Quantum Chemistry, 2020
The combined quantum mechanics/molecular mechanics (QM/MM) simulations of equilibrium geometry configurations followed by electron density analysis provide reliable quantitative structure-property relationship equations to estimate the reactivity of compounds in the active sites of enzymes. The main drawback is high computational cost of such calculations. Here, we report on a benchmark study aiming to optimize computational protocol for the accuracy of predictions. We considered an important example of cephalosporin hydrolysis in the active site of L1 metalloβ-lactamase and found that it is important to consider contributions to the one-electron part of the QM Hamiltonian from all MM system rather than using the cutoff of electrostatic interactions. Switching from the reference PBE0-D3/6-31G (d,p) QM protocol to the reduced PBE0-D3/6-31G scheme decreases the number of basis set functions by almost twice, increasing the error of the rate constant estimates up to 18 seconds −1 compared with the reference 10 seconds −1. Therefore, the QM(PBE0-D3/6-31G)/MM(AMBER) level of theory can be recommended for estimates of cephalosporin reactivity in the search of new antibiotics.
Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), 1999
In this article, we analyze the results of a molecular dynamics simulation in aqueous solution of the N-methylazetidinone molecule, often used to model b-lactam antibiotics. The radial distribution functions (RDFs) corresponding to the most interesting atoms, in terms of reactivity, are presented. We focus our study on the eect of a polar environment on the molecule. The solvent structure around the system is compared to the structure of b-lactam-water complexes, as obtained in a previous study of reaction mechanisms for the neutral and alkaline hydrolyses of N-methylazetidinone. Two types of complexes have been considered which are related to dierent hydrolysis mechanisms having similar energy barriers at the rate-limiting step of the reaction path. In the ®rst type, the b-lactamwater interaction takes place through the oxygen carbonyl atom and there is agreement between the maxima of the RDFs obtained here and the ab initio structure of the complexes previously reported. In the second type, the interaction takes place through the nitrogen atom and we do not predict a coordination layer around the b-lactam nitrogen atom. The results suggest that in aqueous solution hydrolysis of the carbonyl group is the most probable starting point for the overall hydrolysis reaction. Some discussion on the use of cluster models to represent the solvent eect is included.
Helvetica Chimica Acta, 1996
We used semi-empirical and ab initio calculations to investigate the nucleophilic attack of the OHion on the 8-lactam carbonyl group. Both allowed us to detect reaction intermediates pertaining to proton-transfer reactions rather than the studied reaction. We also used the PM3 semi-empirical method to investigate the influence of the solvent on the process. The AMSOL method predicts the occurrence of a potential barrier of 20.7 kcal/mol due to the desolvation of the OHion in approaching theb-lactam carbonyl group. Using the supermolecular approach and a H,O solvation sphere of 20 molecules around the solute, the potential barrier is lowered to 17.5 kcal/mol, which is very close to the experimental value (16.7 kcal/mol).
Modelling nucleophilic attack on β-lactam antibiotics. A PM3 study
Journal of Molecular Structure-theochem, 1993
In the present paper, the nucleophilic attack on the /I-lactamic bond in antibiotics is studied using the MNDO-PM3 semiempirical quantum mechanical approach and full optimization of the molecular geometry. For this purpose Boyd's models of penicillins and cephalosporins are adopted, taking into account the presence of the amidic group in position 3. The penicillin model, and especially the cephalosporin one, are found to be more reactive towards breaking the p-lactamic bond than the reference model for two main reasons: the lower formation energy of the tetrahedric intermediates, and the lower energy barriers on reaching the final products.
Journal of Computational Chemistry, 1992
We used semi-empirical and ab initio calculations to investigate the nucleophilic attack of the OHion on the 8-lactam carbonyl group. Both allowed us to detect reaction intermediates pertaining to proton-transfer reactions rather than the studied reaction. We also used the PM3 semi-empirical method to investigate the influence of the solvent on the process. The AMSOL method predicts the occurrence of a potential barrier of 20.7 kcal/mol due to the desolvation of the OHion in approaching theb-lactam carbonyl group. Using the supermolecular approach and a H,O solvation sphere of 20 molecules around the solute, the potential barrier is lowered to 17.5 kcal/mol, which is very close to the experimental value (16.7 kcal/mol).
Mechanism of Meropenem Hydrolysis by New Delhi Metallo β-Lactamase
ACS Catalysis, 2015
New Delhi metallo β-lactamase (NDM-1) is a recent addition to the metallo-β-lactamases family that is capable of hydrolyzing most of the available antibiotics, including the new generation carbapenems. Here, we report the mechanism of Meropenem hydrolysis catalyzed by NDM-1 based on hybrid quantum-mechanical/molecular-mechanical metadynamics simulations. Our work elicits the molecular details of the catalytic mechanism and free energy profiles along the reaction pathway. We identified the ring opening step involving the nucleophilic addition of the bridging hydroxyl group on the β-lactam ring of the drug as the rate-determining step. Subsequent protonation of β-lactam nitrogen occurs from a bulk water molecule that diffuses into the active site and is preferred over proton transfer from the bridging hydroxyl group or from the protonated Asp 124. The roles of important active site residues of NDM-1 and change in the coordination environment of Zn ions during the hydrolysis are also scrutinized.
Molecular Dynamics Simulations of the TEM-1 β-Lactamase Complexed with Cephalothin
Journal of Medicinal Chemistry, 2005
Herein, we present theoretical results aimed at elucidating the origin of the kinetic preference for penicillins over cephalosporins characteristic of the TEM/SHV subgroup of class A -lactamases. First, we study the conformational properties of cephalothin showing that the C2-down conformer of the dihydrothiazine ring is preferred over the C2-up one by ∼2 kcal/mol in solution (0.4-1.4 kcal/mol in the gas phase). Second, the TEM-1 -lactamase complexed with cephalothin is investigated by carrying out a molecular dynamics simulation. The ∆G binding energy is then estimated using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and quantum chemical PBSA (QM-PBSA) computational schemes. The preferential binding of benzylpenicillin over cephalothin is reproduced by the different energetic calculations, which predict relative ∆∆G binding energies ranging from 1.8 to 5.7 kcal/mol. The benzylpenicillin/ cephalothin ∆∆G binding energy is most likely due to the lower efficacy of cephalosporins than that of penicillins in order to simultaneously bind the "carboxylate pocket" and the "oxyanion hole" in the TEM-1 active site.
Journal of the American Chemical Society, 2013
Bacteria that cause most of the hospital-acquired infections make use of class C β-lactamase (CBL) among other enzymes to resist a wide spectrum of modern antibiotics and pose a major public health concern. Other than the general features, details of the defensive mechanism by CBL, leading to the hydrolysis of drug molecules, remain a matter of debate, in particular, the identification of the general base, and role of active site residues and substrate. In an attempt to unravel the detailed molecular mechanism, we carried out extensive hybrid quantum mechanical/molecular mechanical (QM/MM) Car-Parrinello molecular dynamics (MD) simulation of the reaction with the aid of the metadynamics technique. Based on that we report here the mechanism of the formation of the acyl-enzyme complex from the Henry-Michaelis complex formed by β-lactam antibiotics and CBL. We considered two β-lactam antibiotics, namely cephalothin and aztreonam, belonging to two different subfamilies. A general mechanism for the formation of β-lactam antibiotic-CBL acyl-enzyme complex is elicited and the individual roles of the active site residues and substrate are probed. General base in the acylation step has been identified as Lys 67 while Tyr 150 aids the protonation of β-lactam nitrogen through, either the substrate carboxylate group, or a water molecule.