QM/MM Study of a VIM-1 Metallo-β-Lactamase Enzyme: The Catalytic Reaction Mechanism

Medina, Fabiola E.; Jaña, Gonzalo A.

doi:10.1021/acscatal.1c04786

Cited by 17 publications

(17 citation statements)

References 111 publications

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“…Tremendous experimental − and theoretical − efforts are being made to explore reaction mechanisms of various carbapenems’ hydrolysis by metallo-β-lactamases. There is no doubt that the reaction is initiated by the nucleophilic attack of a carbonyl carbon atom of the carbapenem β-lactam ring by an oxygen atom of a hydroxide anion located between zinc cations in the active site.…”

Section: Introductionmentioning

confidence: 99%

Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution

Krivitskaya

Khrenova

2022

J. Chem. Inf. Model.

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Deactivation of the β-lactam antibiotics in the active sites of the β-lactamases is among the main mechanisms of bacterial antibiotic resistance. As drugs of last resort, carbapenems are efficiently hydrolyzed by metallo-β-lactamases, presenting a serious threat to human health. Our study reveals mechanistic aspects of the imipenem hydrolysis by bizinc metallo-β-lactamases, NDM-1 and L1, belonging to the B1 and the B3 subclasses, respectively. The results of QM(PBE0-D3/6-31G**)/MM simulations show that the enamine product with the protonated nitrogen atom is formed as the major product in NDM-1 and as the only product in the L1 active site. In NDM-1, there is also another reaction pathway that leads to the formation of the (S)-enantiomer of the imine form of the hydrolyzed imipenem; this process occurs with the higher energy barriers. The absence of the second pathway in L1 is due to the different amino acid composition of the active site loop. In L1, the hydrophobic Pro226 residue is located above the pyrroline ring of imipenem that blocks protonation of the carbon atom. Electron density analysis is performed at the stationary points to compare reaction pathways in L1 and NDM-1. Tautomerization from the enamine to the imine form likely happens in solution after the dissociation of the hydrolyzed imipenem from the active site of the enzyme. Classical molecular dynamics simulations of the hydrolyzed imipenem in solution, both with the neutral enamine and the negatively charged N–C2–C3 fragment, demonstrate a huge diversity of conformations. The vast majority of conformations blocks the C3-atom from the side required for the (S)-imine formation upon tautomerization. Thus, according to our calculations, formation of the (R)-imine is more likely. QM(PBE0-D3/6-31G**)/MM molecular dynamics simulations of the hydrolyzed imipenem with the negatively charged N–C2–C3 fragment followed by the Laplacian bond order analysis demonstrate that the NC2–C3 – resonance structure is the most pronounced that facilitates formation of the imine form. The proposed mechanism of the enzymatic enamine formation and its subsequent tautomerization to the imine form in solution is in agreement with the recent spectroscopic and NMR studies.

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Section: Introductionmentioning

confidence: 99%

Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution

Krivitskaya

Khrenova

2022

J. Chem. Inf. Model.

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“…Prior to considering a variety of DFT functionals, the impact of the basis set size was investigated using the M06-2X functional based on its ability to accurately describe kinetics involving main-group elements and non-covalent interactions, as well as enzymatic reactions. , As the Pople basis set used for the geometry optimizations is systematically increased from 6-31G(d) to 6-311+G(2d,2p), the calculated Gibbs energy of activation varies from 91.4 to 142.7 kJ/mol, a variation of 51.3 kJ/mol (Δ ⧧ G OPT , Table ). Specifically, the addition of polarization functions on hydrogen atoms to 6-31G(d) increases the reaction barrier by 15.7 kJ/mol, while subsequent inclusion of heavy-atom diffuse functions or expansion to the triple-zeta variant leads to a negligible energy impact (0.6–3.2 kJ/mol).…”

Section: Resultsmentioning

confidence: 99%

The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1

et al. 2022

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Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/ apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.

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“…80 In metallo-βlactamase, the nucleophilic addition stage is the rate-limiting step with an energy barrier of 15.7 kcal/mol. 81 QM/MM calculations showed a favorable proton transfer in esterase EstB from Bukholderia gladioli. 82 The deacylation reaction mechanism of penicillin-binding protein and class C βlactamase have been modeled using the QM/MM method.…”

Section: ■ Discussionmentioning

confidence: 96%

“…3α-hydroxysteroid dehydrogenase (3α-HSD) catalyzes 5α-dihydrotestosterone (5α-DHT) into 3α-androstanediol by proton transfer from Y55 without the formation of an alkoxide ion as an intermediate . In metallo-β-lactamase, the nucleophilic addition stage is the rate-limiting step with an energy barrier of 15.7 kcal/mol . QM/MM calculations showed a favorable proton transfer in esterase EstB from Bukholderia gladioli .…”

Section: Discussionmentioning

confidence: 99%

Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus

Dalal

Golemi-Kotra

Kumar

2022

J. Chem. Inf. Model.

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FmtA is a novel esterase that shares the penicillinbinding protein (PBP) core structural folding but found to hydrolyze the removal of D-Ala from teichoic acids. Molecular docking, dynamics, and MM-GBSA of FmtA and its variants S127A, K130A, Y211A, D213A, and K130AY211A, in the presence or absence of wall teichoic acid (WTA), suggest that active site residues S127, K130, Y211, D213, N343, and G344 play a role in substrate binding. Quantum mechanics (QM)/molecular mechanics (MM) calculations reveal that during WTA catalysis, K130 deprotonates S127, and the nucleophilic S127 attacks the carbonyl carbon of D-Ala bound to WTA. The tetrahedral intermediate (TI) complex is stabilized by hydrogen bonding to the oxyanion holes. The TI complex displays a high energy gap and collapses to an energetically favorable acyl-enzyme complex.

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QM/MM Study of a VIM-1 Metallo-β-Lactamase Enzyme: The Catalytic Reaction Mechanism

Cited by 17 publications

References 111 publications

Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution

Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution

The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1

Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus

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