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Jacobs LMC, Consol P, Chen Y. Drug Discovery in the Field of β-Lactams: An Academic Perspective. Antibiotics (Basel) 2024; 13:59. [PMID: 38247618 PMCID: PMC10812508 DOI: 10.3390/antibiotics13010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.
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Affiliation(s)
| | | | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (L.M.C.J.); (P.C.)
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2
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Lizana I, Uribe EA, Delgado EJ. A theoretical approach for the acylation/deacylation mechanisms of avibactam in the reversible inhibition of KPC-2. J Comput Aided Mol Des 2021; 35:943-952. [PMID: 34236545 PMCID: PMC8264174 DOI: 10.1007/s10822-021-00408-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022]
Abstract
Klebsiella pneumoniae carbapenemase (KPC-2) is the most commonly encountered class A β-lactamase variant worldwide, which confer high-level resistance to most available antibiotics. In this article we address the issue by a combined approach involving molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations. The study contributes to improve the understanding, at molecular level, of the acylation and deacylation stages of avibactam involved in the inhibition of KPC-2. The results show that both mechanisms, acylation and deacylation, the reaction occur via the formation of a tetrahedral intermediate. The formation of this intermediate corresponds to the rate limiting stage. The activation barriers are 19.5 kcal/mol and 23.0 kcal/mol for the acylation and deacylation stages, respectively. The associated rate constants calculated, using the Eyring equation, are 1.2 × 10−1 and 3.9 × 10−4 (s−1). These values allow estimating a value of 3.3 × 10−3 for the inhibition constant, in good agreement with the experimental value.
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Affiliation(s)
- Ignacio Lizana
- Grupo QTC, Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.,Millennium Nucleus on Catalytic Processes Towards Sustainable Chemistry, 4070386, Santiago, Chile
| | - Elena A Uribe
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Eduardo J Delgado
- Grupo QTC, Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile. .,Millennium Nucleus on Catalytic Processes Towards Sustainable Chemistry, 4070386, Santiago, Chile.
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3
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Nukaga M, Yoon MJ, Taracilia MA, Hoshino T, Becka SA, Zeiser ET, Johnson JR, Papp-Wallace KM. Assessing the Potency of β-Lactamase Inhibitors with Diverse Inactivation Mechanisms against the PenA1 Carbapenemase from Burkholderia multivorans. ACS Infect Dis 2021; 7:826-837. [PMID: 33723985 DOI: 10.1021/acsinfecdis.0c00682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Burkholderia cepacia complex (Bcc) poses a serious health threat to people with cystic fibrosis or compromised immune systems. Infections often arise from Bcc strains, which are highly resistant to many classes of antibiotics, including β-lactams. β-Lactam resistance in Bcc is conferred largely via PenA-like β-lactamases. Avibactam was previously shown to be a potent inactivator of PenA1. Here, we examined the inactivation mechanism of PenA1, a class A serine carbapenemase from Burkholderia multivorans using β-lactamase inhibitors (β-lactam-, diazabicyclooctane-, and boronate-based) with diverse mechanisms of action. In whole cell based assays, avibactam, relebactam, enmetazobactam, and vaborbactam restored susceptibility to piperacillin against PenA1 expressed in Escherichia coli. The rank order of potency of inactivation in vitro based on kinact/KI or k2/K values (range: 3.4 × 102 to 2 × 106 M-1 s-1) against PenA1 was avibactam > enmetazobactam > tazobactam > relebactam > clavulanic acid > vaborbactam. The contribution of selected amino acids (S70, K73, S130, E166, N170, R220, K234, T237, and D276) in PenA1 toward inactivation was evaluated using site-directed mutagenesis. The S130A, R220A, and K234A variants of PenA1 were less susceptible to inactivation by avibactam. The R220A variant was purified and assessed via steady-state inhibition kinetics and found to possess increased Ki-app values and decreased kinact/KI or k2/K values against all tested inhibitors compared to PenA1. Avibactam was the most affected by the alanine replacement at 220 with a nearly 400-fold decreased acylation rate. The X-ray crystal structure of the R220A variant was solved and revealed loss of the hydrogen bonding network between residues 237 and 276 leaving a void in the active site that was occupied instead by water molecules. Michaelis-Menten complexes were generated to elucidate the molecular contributions of the poorer in vitro inhibition profile of vaborbactam against PenA1 (k2/K, 3.4 × 102 M-1 s-1) and was compared to KPC-2, a class A carbapenemase that is robustly inhibited by vaborbactam. The active site of PenA1 is larger than that of KPC-2, which impacted the ability of vaborbactam to form favorable interactions, and as a result the carboxylate of vaborbactam was drawn toward K234/T235 in PenA1 displacing the boronic acid from approaching the nucleophilic S70. Moreover, in PenA1, the tyrosine at position 105 compared to tryptophan in KPC-2, was more flexible rotating more than 90°, and as a result PenA1's Y105 competed for binding with the cyclic boronate vs the thiophene moiety of vaborbactam, further precluding inhibition of PenA1 by vaborbactam. Given the 400-fold decreased k2/K for the R220A variant compared to PenA1, acyl-enzyme complexes were generated via molecular modeling and compared to the PenA1-avibactam crystal structure. The water molecules occupying the active site of the R220A variant are unable to stabilize the T237 and D276 region of the active site altering the ability of avibactam to form favorable interactions compared to PenA1. The former likely impacts the ability of all inhibitors to effectively acylate this variant enzyme. Based on the summation of all evidence herein, the utility of these newer β-lactamase inhibitors (i.e., relebactam, enmetazobactam, avibactam, and vaborbactam) in combination with a β-lactam against B. multivorans producing PenA1 and the R220A variant is promising.
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Affiliation(s)
- Michiyoshi Nukaga
- Department of Pharmaceutical Sciences, Josai International University, Togane City, Chiba 283-8555, Japan
| | - Michael J. Yoon
- Research Service, Louis Stokes Cleveland VAMC Cleveland, Ohio 44106, United States
| | | | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 263-8522, Japan
| | - Scott A. Becka
- Research Service, Louis Stokes Cleveland VAMC Cleveland, Ohio 44106, United States
| | - Elise T. Zeiser
- Research Service, Louis Stokes Cleveland VAMC Cleveland, Ohio 44106, United States
| | - Joseph R. Johnson
- Research Service, Louis Stokes Cleveland VAMC Cleveland, Ohio 44106, United States
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4
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Structural Investigations of the Inhibition of Escherichia coli AmpC β-Lactamase by Diazabicyclooctanes. Antimicrob Agents Chemother 2021; 65:AAC.02073-20. [PMID: 33199391 PMCID: PMC7849013 DOI: 10.1128/aac.02073-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/12/2020] [Indexed: 12/24/2022] Open
Abstract
β-Lactam antibiotics are presently the most important treatments for infections by pathogenic Escherichia coli, but their use is increasingly compromised by β-lactamases, including the chromosomally encoded class C AmpC serine-β-lactamases (SBLs). The diazabicyclooctane (DBO) avibactam is a potent AmpC inhibitor; the clinical success of avibactam combined with ceftazidime has stimulated efforts to optimize the DBO core. We report kinetic and structural studies, including four high-resolution crystal structures, concerning inhibition of the AmpC serine-β-lactamase from E. coli (AmpC EC ) by clinically relevant DBO-based inhibitors: avibactam, relebactam, nacubactam, and zidebactam. Kinetic analyses and mass spectrometry-based assays were used to study their mechanisms of AmpC EC inhibition. The results reveal that, under our assay conditions, zidebactam manifests increased potency (apparent inhibition constant [K iapp], 0.69 μM) against AmpC EC compared to that of the other DBOs (K iapp = 5.0 to 7.4 μM) due to an ∼10-fold accelerated carbamoylation rate. However, zidebactam also has an accelerated off-rate, and with sufficient preincubation time, all the DBOs manifest similar potencies. Crystallographic analyses indicate a greater conformational freedom of the AmpC EC -zidebactam carbamoyl complex compared to those for the other DBOs. The results suggest the carbamoyl complex lifetime should be a consideration in development of DBO-based SBL inhibitors for the clinically important class C SBLs.
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5
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Das CK, Nair NN. Elucidating the Molecular Basis of Avibactam‐Mediated Inhibition of Class A β‐Lactamases. Chemistry 2020; 26:9639-9651. [DOI: 10.1002/chem.202001261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/10/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Chandan Kumar Das
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
- Current Address: Lehrstuhl für Theoretische ChemieRuhr Universität Bochum 44780 Bochum Germany
| | - Nisanth N. Nair
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
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6
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Russ D, Glaser F, Shaer Tamar E, Yelin I, Baym M, Kelsic ED, Zampaloni C, Haldimann A, Kishony R. Escape mutations circumvent a tradeoff between resistance to a beta-lactam and resistance to a beta-lactamase inhibitor. Nat Commun 2020; 11:2029. [PMID: 32332717 PMCID: PMC7181632 DOI: 10.1038/s41467-020-15666-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
Beta-lactamase inhibitors are increasingly used to counteract antibiotic resistance mediated by beta-lactamase enzymes. These inhibitors compete with the beta-lactam antibiotic for the same binding site on the beta-lactamase, thus generating an evolutionary tradeoff: mutations that increase the enzyme's beta-lactamase activity tend to increase also its susceptibility to the inhibitor. Here, we investigate how common and accessible are mutants that escape this adaptive tradeoff. Screening a deep mutant library of the blaampC beta-lactamase gene of Escherichia coli, we identified mutations that allow growth at beta-lactam concentrations far exceeding those inhibiting growth of the wildtype strain, even in the presence of the enzyme inhibitor (avibactam). These escape mutations are rare and drug-specific, and some combinations of avibactam with beta-lactam drugs appear to prevent such escape phenotypes. Our results, showing differential adaptive potential of blaampC to combinations of avibactam and different beta-lactam antibiotics, suggest that it may be possible to identify treatments that are more resilient to evolution of resistance.
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Affiliation(s)
- Dor Russ
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Fabian Glaser
- Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Einat Shaer Tamar
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Idan Yelin
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Eric D Kelsic
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Claudia Zampaloni
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases, and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Andreas Haldimann
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases, and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Roy Kishony
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel. .,Faculty of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel.
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7
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Bouchet F, Atze H, Fonvielle M, Edoo Z, Arthur M, Ethève-Quelquejeu M, Iannazzo L. Diazabicyclooctane Functionalization for Inhibition of β-Lactamases from Enterobacteria. J Med Chem 2020; 63:5257-5273. [DOI: 10.1021/acs.jmedchem.9b02125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Flavie Bouchet
- Université de Paris, UMR CNRS 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, 45 rue des Saints-Péres, F-75006 Paris, France
| | - Heiner Atze
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), F-75006 Paris, France
| | - Matthieu Fonvielle
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), F-75006 Paris, France
| | - Zainab Edoo
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), F-75006 Paris, France
| | - Michel Arthur
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), F-75006 Paris, France
| | - Mélanie Ethève-Quelquejeu
- Université de Paris, UMR CNRS 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, 45 rue des Saints-Péres, F-75006 Paris, France
| | - Laura Iannazzo
- Université de Paris, UMR CNRS 8601, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, 45 rue des Saints-Péres, F-75006 Paris, France
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8
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Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam. Proc Natl Acad Sci U S A 2020; 117:5818-5825. [PMID: 32123084 DOI: 10.1073/pnas.1922203117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Gram-negative bacteria expressing class A β-lactamases pose a serious health threat due to their ability to inactivate all β-lactam antibiotics. The acyl-enzyme intermediate is a central milestone in the hydrolysis reaction catalyzed by these enzymes. However, the protonation states of the catalytic residues in this complex have never been fully analyzed experimentally due to inherent difficulties. To help unravel the ambiguity surrounding class A β-lactamase catalysis, we have used ultrahigh-resolution X-ray crystallography and the recently approved β-lactamase inhibitor avibactam to trap the acyl-enzyme complex of class A β-lactamase CTX-M-14 at varying pHs. A 0.83-Å-resolution CTX-M-14 complex structure at pH 7.9 revealed a neutral state for both Lys73 and Glu166. Furthermore, the avibactam hydroxylamine-O-sulfonate group conformation varied according to pH, and this conformational switch appeared to correspond to a change in the Lys73 protonation state at low pH. In conjunction with computational analyses, our structures suggest that Lys73 has a perturbed acid dissociation constant (pKa) compared with acyl-enzyme complexes with β-lactams, hindering its function to deprotonate Glu166 and the initiation of the deacylation reaction. Further NMR analysis demonstrated Lys73 pKa to be ∼5.2 to 5.6. Together with previous ultrahigh-resolution crystal structures, these findings enable us to follow the proton transfer process of the entire acylation reaction and reveal the critical role of Lys73. They also shed light on the stability and reversibility of the avibactam carbamoyl acyl-enzyme complex, highlighting the effect of substrate functional groups in influencing the protonation states of catalytic residues and subsequently the progression of the reaction.
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9
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Tooke CL, Hinchliffe P, Lang PA, Mulholland AJ, Brem J, Schofield CJ, Spencer J. Molecular Basis of Class A β-Lactamase Inhibition by Relebactam. Antimicrob Agents Chemother 2019; 63:AAC.00564-19. [PMID: 31383664 PMCID: PMC6761529 DOI: 10.1128/aac.00564-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/04/2019] [Indexed: 12/23/2022] Open
Abstract
β-Lactamase production is the major β-lactam resistance mechanism in Gram-negative bacteria. β-Lactamase inhibitors (BLIs) efficacious against serine β-lactamase (SBL) producers, especially strains carrying the widely disseminated class A enzymes, are required. Relebactam, a diazabicyclooctane (DBO) BLI, is in phase 3 clinical trials in combination with imipenem for the treatment of infections by multidrug-resistant Enterobacteriaceae We show that relebactam inhibits five clinically important class A SBLs (despite their differing spectra of activity), representing both chromosomal and plasmid-borne enzymes, i.e., the extended-spectrum β-lactamases L2 (inhibition constant 3 μM) and CTX-M-15 (21 μM) and the carbapenemases KPC-2, -3, and -4 (1 to 5 μM). Against purified class A SBLs, relebactam is an inferior inhibitor compared with the clinically approved DBO avibactam (9- to 120-fold differences in half maximal inhibitory concentration [IC50]). MIC assays indicate relebactam potentiates β-lactam (imipenem) activity against KPC-producing Klebsiella pneumoniae, with similar potency to avibactam (with ceftazidime). Relebactam is less effective than avibactam in combination with aztreonam against Stenotrophomonas maltophilia K279a. X-ray crystal structures of relebactam bound to CTX-M-15, L2, KPC-2, KPC-3, and KPC-4 reveal its C2-linked piperidine ring can sterically clash with Asn104 (CTX-M-15) or His/Trp105 (L2 and KPCs), rationalizing its poorer inhibition activity than that of avibactam, which has a smaller C2 carboxyamide group. Mass spectrometry and crystallographic data show slow, pH-dependent relebactam desulfation by KPC-2, -3, and -4. This comprehensive comparison of relebactam binding across five clinically important class A SBLs will inform the design of future DBOs, with the aim of improving clinical efficacy of BLI-β-lactam combinations.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Pauline A Lang
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom
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10
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Lizana I, Delgado EJ. Molecular Insights on the Release of Avibactam from the Acyl-Enzyme Complex. Biophys J 2019; 116:1650-1657. [PMID: 31010666 DOI: 10.1016/j.bpj.2019.03.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/13/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Avibactam is a non-β-lactam β-lactamase inhibitor for treating complicated urinary tract and respiratory infections caused by multidrug-resistant bacterial pathogens, a serious public health threat. Despite its importance, the release mechanism of avibactam from the enzyme-inhibitor complex has been scarcely studied from first principles, considering the total protein environment. This information at the molecular level is essential for the rational design of new antibiotics and inhibitors. In this article, we addressed the release of avibactam from the complex CTX-M-15 by means of molecular dynamics simulations and quantum mechanics/molecular mechanics calculations. This study provides molecular information not available earlier, including exploration of the potential energy surfaces, characterization of the observed intermediate, and their critical points, as well. Our results show that unlike that observed in the acylation reaction, the residues Glu166 and Lys73 would be in their neutral forms. Release of avibactam follows a stepwise mechanism in which the first stage corresponds to the formation of a tetrahedral intermediate, whereas the second stage corresponds to the cleavage of the Ser70-C7 bond, mediated by Lys73, either directly or through Ser130.
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Affiliation(s)
- Ignacio Lizana
- Departament of Physical Chemistry, Universidad de Concepción, Concepción, Chile
| | - Eduardo J Delgado
- Departament of Physical Chemistry, Universidad de Concepción, Concepción, Chile; Millenium Nucleus on Catalytic Processes toward Sustainable Chemistry, Santiago, Chile.
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11
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Lizana I, Delgado EJ. Theoretical insights on the inhibition mechanism of a class A Serine Hydrolase by avibactam. J Comput Chem 2018; 39:1943-1948. [PMID: 29707791 DOI: 10.1002/jcc.25340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/08/2018] [Accepted: 04/08/2018] [Indexed: 11/10/2022]
Abstract
The inhibition mechanism of CTX-M-15 class A serine hydrolase by the inhibitor avibactam is addressed by a combined molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach postulating that the residue Ser70 is the sole reacting residue, that is, itself may play the role of the acid-base species required for the enzyme inhibition. Other residues located in the active site have key participation in the positioning of the inhibitor in the right conformation to favor the attack of Ser70, in addition to the stabilization of the transition state by electrostatic interactions with avibactam. The results validate the hypothesis and show that the reaction follows an asynchronous concerted mechanism, in which the nucleophilic attack of the hydroxyl oxygen of Ser70 precedes the protonation of the amidic nitrogen and ring opening. The calculated activation barrier is 16 kcal/mol in agreement with the experimental evidence. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Ignacio Lizana
- Computational Chemistry Group, Department of Physical Chemistry, Faculty of Chemical Sciences, Universidad de Concepcion, Concepcion, Chile
| | - Eduardo J Delgado
- Computational Chemistry Group, Department of Physical Chemistry, Faculty of Chemical Sciences, Universidad de Concepcion, Concepcion, Chile
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12
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Lohans CT, Wang DY, Jorgensen C, Cahill ST, Clifton IJ, McDonough MA, Oswin HP, Spencer J, Domene C, Claridge TDW, Brem J, Schofield CJ. 13C-Carbamylation as a mechanistic probe for the inhibition of class D β-lactamases by avibactam and halide ions. Org Biomol Chem 2018; 15:6024-6032. [PMID: 28678295 DOI: 10.1039/c7ob01514c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The class D (OXA) serine β-lactamases are a major cause of resistance to β-lactam antibiotics. The class D enzymes are unique amongst β-lactamases because they have a carbamylated lysine that acts as a general acid/base in catalysis. Previous crystallographic studies led to the proposal that β-lactamase inhibitor avibactam targets OXA enzymes in part by promoting decarbamylation. Similarly, halide ions are proposed to inhibit OXA enzymes via decarbamylation. NMR analyses, in which the carbamylated lysines of OXA-10, -23 and -48 were 13C-labelled, indicate that reaction with avibactam does not ablate lysine carbamylation in solution. While halide ions did not decarbamylate the 13C-labelled OXA enzymes in the absence of substrate or inhibitor, avibactam-treated OXA enzymes were susceptible to decarbamylation mediated by halide ions, suggesting halide ions may inhibit OXA enzymes by promoting decarbamylation of acyl-enzyme complex. Crystal structures of the OXA-10 avibactam complex were obtained with bromide, iodide, and sodium ions bound between Trp-154 and Lys-70. Structures were also obtained wherein bromide and iodide ions occupy the position expected for the 'hydrolytic water' molecule. In contrast with some solution studies, Lys-70 was decarbamylated in these structures. These results reveal clear differences between crystallographic and solution studies on the interaction of class D β-lactamases with avibactam and halides, and demonstrate the utility of 13C-NMR for studying lysine carbamylation in solution.
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Affiliation(s)
| | - David Y Wang
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.
| | | | - Samuel T Cahill
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.
| | - Ian J Clifton
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.
| | | | - Henry P Oswin
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Carmen Domene
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK. and Department of Chemistry, King's College London, London, SE1 1DB, UK
| | | | - Jürgen Brem
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.
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13
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Kozlov RS, Stetsiouk OU, Andreeva IV. Ceftazidime-avibactam: new rules for the game against multidrug-resistant gram-negative bacteria. CLINICAL MICROBIOLOGY AND ANTIMICROBIAL CHEMOTHERAPY 2018. [DOI: 10.36488/cmac.2018.1.24-34] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The rapid spread of multidrug-resistant Gram-negative bacteria in hospital settings all over the world makes a demand for the new options to overcome antimicrobial resistance. Ceftazidime-avibactam is the first approved antibiotic that contains a new beta-lactamase inhibitor with unique properties. This review provides insight into the spectrum of activity, pharmacological characteristics, data on efficacy and safety of ceftazidime-avibactam obtained from the clinical trials and real clinical practice, as well as prospects for further studies and clinical application of this new antimicrobial agent.
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Affiliation(s)
- Roman S. Kozlov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University (Smolensk, Russia)
| | - Olga U. Stetsiouk
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University (Smolensk, Russia)
| | - Irina V. Andreeva
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University (Smolensk, Russia)
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14
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Das CK, Nair NN. Molecular insights into avibactam mediated class C β-lactamase inhibition: competition between reverse acylation and hydrolysis through desulfation. Phys Chem Chem Phys 2018; 20:14482-14490. [DOI: 10.1039/c8cp01670d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spatial water probability density plots show that the axial –NHOSO3 group of avibactam impedes the deacylating water molecule(s) to enter the active site, while the –NHSO3 group in aztreonam is unable to prevent the water molecule(s) to diffuse into the active site.
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Affiliation(s)
- Chandan Kumar Das
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur
- India
| | - Nisanth N. Nair
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur
- India
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15
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Tuon FF, Rocha JL, Formigoni-Pinto MR. Pharmacological aspects and spectrum of action of ceftazidime-avibactam: a systematic review. Infection 2017; 46:165-181. [PMID: 29110143 DOI: 10.1007/s15010-017-1096-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/27/2017] [Indexed: 12/11/2022]
Abstract
PURPOSE Ceftazidime-avibactam is an antimicrobial association active against several Enterobacteriaceae species, including those resistant to carbapenem. Considering the importance of this drug in the current panorama of multidrug-resistant bacteria, we performed a systematic review about ceftazidime-avibactam with emphasis on clinical and pharmacological published data. METHODS A systematic search of the medical literature was performed. The databases searched included MEDLINE, EMBASE and Web of Science (until September 2017). The search terms used were 'avibactam', 'NXL104' and 'AVE1330A'. Bibliographies from those studies were also reviewed. Ceftazidime was not included as a search term, once relevant studies about avibactam in association with other drugs could be excluded. Only articles in English were selected. No statistical analysis or quality validation was included in this review. RESULTS A total of 151 manuscripts were included. Ceftazidime-avibactam has limited action against anaerobic bacteria. Avibactam is a potent inhibitor of class A, class C, and some class D enzymes, which includes KPC-2. The best pharmacodynamic profile of ceftazidime-avibactam is ƒT > MIC, validated in an animal model of soft tissue infection. Three clinical trials showed the efficacy of ceftazidime-avibactam in patients with intra-abdominal and urinary infections. Ceftazidime-avibactam has been evaluated versus meropenem/doripenem in hospitalized adults with nosocomial pneumonia, neutropenic patients and pediatric patients. CONCLUSION Ceftazidime-avibactam has a favorable pharmacokinetic profile for severe infections and highly active against carbapenemases of KPC-2 type.
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Affiliation(s)
- Felipe Francisco Tuon
- Department of Medicine, School of Health and Biosciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil. .,Hospital de Clínicas-Serviço de Infectologia, 3º. andar, Rua General Carneiro, 180-Alto da Glória, Curitiba, PR, 80060-900, Brazil.
| | - Jaime L Rocha
- Department of Medicine, School of Health and Biosciences, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
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16
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Calvopiña K, Hinchliffe P, Brem J, Heesom KJ, Johnson S, Cain R, Lohans CT, Fishwick CWG, Schofield CJ, Spencer J, Avison MB. Structural/mechanistic insights into the efficacy of nonclassical β-lactamase inhibitors against extensively drug resistantStenotrophomonas maltophiliaclinical isolates. Mol Microbiol 2017; 106:492-504. [DOI: 10.1111/mmi.13831] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Karina Calvopiña
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Philip Hinchliffe
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Jürgen Brem
- Department of Chemistry; University of Oxford; Oxford UK
| | | | - Samar Johnson
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Ricky Cain
- School of Chemistry; University of Leeds; Leeds UK
| | | | | | | | - James Spencer
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
| | - Matthew B. Avison
- School of Cellular & Molecular Medicine; University of Bristol; Bristol UK
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17
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Reversible inactivation of a peptidoglycan transpeptidase by a β-lactam antibiotic mediated by β-lactam-ring recyclization in the enzyme active site. Sci Rep 2017; 7:9136. [PMID: 28831100 PMCID: PMC5567249 DOI: 10.1038/s41598-017-09341-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/17/2017] [Indexed: 11/08/2022] Open
Abstract
β-lactam antibiotics act as suicide substrates of transpeptidases responsible for the last cross-linking step of peptidoglycan synthesis in the bacterial cell wall. Nucleophilic attack of the β-lactam carbonyl by the catalytic residue (Ser or Cys) of transpeptidases results in the opening of the β-lactam ring and in the formation of a stable acyl-enzyme. The acylation reaction is considered as irreversible due to the strain of the β-lactam ring. In contradiction with this widely accepted but poorly demonstrated premise, we show here that the acylation of the L,D-transpeptidase Ldtfm from Enterococcus faecium by the β-lactam nitrocefin is reversible, leading to limited antibacterial activity. Experimentally, two independent methods based on spectrophotometry and mass spectrometry provided evidence that recyclization of the β-lactam ring within the active site of Ldtfm regenerates native nitrocefin. Ring strain is therefore not sufficient to account for irreversible acylation of peptidoglycan transpeptidases observed for most β-lactam antibiotics.
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18
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Interaction of Avibactam with Class B Metallo-β-Lactamases. Antimicrob Agents Chemother 2016; 60:5655-62. [PMID: 27401561 PMCID: PMC5038302 DOI: 10.1128/aac.00897-16] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/05/2016] [Indexed: 11/20/2022] Open
Abstract
β-Lactamases are the most important mechanisms of resistance to the β-lactam antibacterials. There are two mechanistic classes of β-lactamases: the serine β-lactamases (SBLs) and the zinc-dependent metallo-β-lactamases (MBLs). Avibactam, the first clinically useful non-β-lactam β-lactamase inhibitor, is a broad-spectrum SBL inhibitor, which is used in combination with a cephalosporin antibiotic (ceftazidime). There are multiple reports on the interaction of avibactam with SBLs but few such studies with MBLs. We report biochemical and biophysical studies on the binding and reactivity of avibactam with representatives from all 3 MBL subfamilies (B1, B2, and B3). Avibactam has only limited or no activity versus MBL-mediated resistance in pathogens. Avibactam does not inhibit MBLs and binds only weakly to most of the MBLs tested; in some cases, avibactam undergoes slow hydrolysis of one of its urea N-CO bonds followed by loss of CO2, in a process different from that observed with the SBLs studied. The results suggest that while the evolution of MBLs that more efficiently catalyze avibactam hydrolysis should be anticipated, pursuing the development of dual-action SBL and MBL inhibitors based on the diazabicyclooctane core of avibactam may be productive.
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Wang DY, Abboud MI, Markoulides MS, Brem J, Schofield CJ. The road to avibactam: the first clinically useful non-β-lactam working somewhat like a β-lactam. Future Med Chem 2016; 8:1063-84. [PMID: 27327972 DOI: 10.4155/fmc-2016-0078] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Avibactam, which is the first non-β-lactam β-lactamase inhibitor to be introduced for clinical use, is a broad-spectrum serine β-lactamase inhibitor with activity against class A, class C, and, some, class D β-lactamases. We provide an overview of efforts, which extend to the period soon after the discovery of the penicillins, to develop clinically useful non-β-lactam compounds as antibacterials, and, subsequently, penicillin-binding protein and β-lactamase inhibitors. Like the β-lactam inhibitors, avibactam works via a mechanism involving covalent modification of a catalytically important nucleophilic serine residue. However, unlike the β-lactam inhibitors, avibactam reacts reversibly with its β-lactamase targets. We discuss chemical factors that may account for the apparently special nature of β-lactams and related compounds as antibacterials and β-lactamase inhibitors, including with respect to resistance. Avenues for future research including non-β-lactam antibacterials acting similarly to β-lactams are discussed.
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Affiliation(s)
| | | | | | - Jürgen Brem
- Department of Chemistry, University of Oxford, UK
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