1
|
Soulié M, Deletraz A, Wehbie M, Mahler F, Chantemargue B, Bouchemal I, Le Roy A, Petit-Härtlein I, Fieschi F, Breyton C, Ebel C, Keller S, Durand G. Rigid Cyclic Fluorinated Detergents: Fine-Tuning the Hydrophilic-Lipophilic Balance Controls Self-Assembling and Biochemical Properties. ACS APPLIED MATERIALS & INTERFACES 2024; 16:32971-32982. [PMID: 38885044 DOI: 10.1021/acsami.4c03359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
We report herein the synthesis of three detergents bearing a perfluorinated cyclohexyl group connected through a short, hydrogenated spacer (i.e., propyl, butyl, or pentyl) to a β-maltoside polar head that are, respectively, called FCymal-3, FCymal-4, and FCymal-5. Increasing the length of the spacer decreased the critical micellar concentration (CMC), as demonstrated by surface tension (SFT) and isothermal titration calorimetry (ITC), from 5 mM for FCymal-3 to 0.7 mM for FCymal-5. The morphology of the micelles was studied by dynamic light scattering (DLS), analytical ultracentrifugation (AUC), and small-angle X-ray scattering (SAXS), indicating heterogeneous rod-like shapes. While micelles of FCymal-3 and -4 have similar hydrodynamic diameters of ∼10 nm, those of FCymal-5 were twice as large. We also investigated the ability of the detergents to solubilize lipid membranes made of 1-palmitoyl-2-oleyl-sn-glycero-3-phosphocholine (POPC). Molecular modeling indicated that the FCymal detergents generate disorder in lipid bilayers, with FCymal-3 being inserted more deeply into bilayers than FCymal-4 and -5. This was experimentally confirmed using POPC vesicles that were completely solubilized within 2 h with FCymal-3, whereas FCymal-5 required >8 h. A similar trend was noticed for the direct extraction of membrane proteins from E. coli membranes, with FCymal-3 being more potent than FCymal-5. An opposite trend was observed in terms of stabilization of the two model membrane proteins bacteriorhodopsin (bR) and SpNOX. In all three FCymal detergents, bR was stable for at least 2 months with no signs of aggregation. However, while the structural integrity of bR was fully preserved in FCymal-4 and -5, minor bleaching was observed in FCymal-3. Similarly, SpNOX exhibited the least activity in FCymal-3 and the highest activity in FCymal-5. By combining solubilizing and stabilizing potency, FCymal detergents push forward our expectations of the usefulness of fluorinated detergents for handling and investigating membrane proteins.
Collapse
Affiliation(s)
- Marine Soulié
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
- Avignon Université, Unité Propre de Recherche et d'Innovation, Equipe Synthèse et Systèmes Colloïdaux Bio-organiques, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Anais Deletraz
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Moheddine Wehbie
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| | - Florian Mahler
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | | | - Ilham Bouchemal
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Aline Le Roy
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Christine Ebel
- Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Sandro Keller
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Grégory Durand
- Institut des Biomolécules Max Mousseron (UMR 5247 UM-CNRS-ENSCM), Equipe Chimie Bioorganique et Systèmes amphiphiles, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
- Avignon Université, Unité Propre de Recherche et d'Innovation, Equipe Synthèse et Systèmes Colloïdaux Bio-organiques, 301 Rue Baruch de Spinoza, 84916 Avignon Cedex 9, France
| |
Collapse
|
2
|
Abstract
Class C β-lactamases or cephalosporinases can be classified into two functional groups (1, 1e) with considerable molecular variability (≤20% sequence identity). These enzymes are mostly encoded by chromosomal and inducible genes and are widespread among bacteria, including Proteobacteria in particular. Molecular identification is based principally on three catalytic motifs (64SXSK, 150YXN, 315KTG), but more than 70 conserved amino-acid residues (≥90%) have been identified, many close to these catalytic motifs. Nevertheless, the identification of a tiny, phylogenetically distant cluster (including enzymes from the genera Legionella, Bradyrhizobium, and Parachlamydia) has raised questions about the possible existence of a C2 subclass of β-lactamases, previously identified as serine hydrolases. In a context of the clinical emergence of extended-spectrum AmpC β-lactamases (ESACs), the genetic modifications observed in vivo and in vitro (point mutations, insertions, or deletions) during the evolution of these enzymes have mostly involved the Ω- and H-10/R2-loops, which vary considerably between genera, and, in some cases, the conserved triplet 150YXN. Furthermore, the conserved deletion of several amino-acid residues in opportunistic pathogenic species of Acinetobacter, such as A. baumannii, A. calcoaceticus, A. pittii and A. nosocomialis (deletion of residues 304-306), and in Hafnia alvei and H. paralvei (deletion of residues 289-290), provides support for the notion of natural ESACs. The emergence of higher levels of resistance to β-lactams, including carbapenems, and to inhibitors such as avibactam is a reality, as the enzymes responsible are subject to complex regulation encompassing several other genes (ampR, ampD, ampG, etc.). Combinations of resistance mechanisms may therefore be at work, including overproduction or change in permeability, with the loss of porins and/or activation of efflux systems.
Collapse
|
3
|
van den Akker F, Bonomo RA. Exploring Additional Dimensions of Complexity in Inhibitor Design for Serine β-Lactamases: Mechanistic and Intra- and Inter-molecular Chemistry Approaches. Front Microbiol 2018; 9:622. [PMID: 29675000 PMCID: PMC5895744 DOI: 10.3389/fmicb.2018.00622] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/19/2018] [Indexed: 01/14/2023] Open
Abstract
As a bacterial resistance strategy, serine β-lactamases have evolved from cell wall synthesizing enzymes known as penicillin-binding proteins (PBP), by not only covalently binding β-lactam antibiotics but, also acquiring mechanisms of deacylating these antibiotics. This critical deacylation step leads to release of hydrolyzed and inactivated β-lactams, thereby providing resistance for the bacteria against these antibiotics targeting the cell wall. To combat β-lactamase-mediated antibiotic resistance, numerous β-lactamase inhibitors were developed that utilize various strategies to inactivate the β-lactamase. Most of these compounds are “mechanism-based” inhibitors that in some manner mimic the β-lactam substrate, having a carbonyl moiety and a negatively charged carboxyl or sulfate group. These compounds form a covalent adduct with the catalytic serine via an initial acylation step. To increase the life-time of the inhibitory covalent adduct intermediates, a remarkable array of different strategies was employed to improve inhibition potency. Such approaches include post-acylation intra- and intermolecular chemical rearrangements as well as affecting the deacylation water. These approaches transform the inhibitor design process from a 3-dimensional problem (i.e., XYZ coordinates) to one with additional dimensions of complexity as the reaction coordinate and time spent at each chemical state need to be taken into consideration. This review highlights the mechanistic intricacies of the design efforts of the β-lactamase inhibitors which so far have resulted in the development of “two generations” and 5 clinically available inhibitors.
Collapse
Affiliation(s)
- Focco van den Akker
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Robert A Bonomo
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States.,Medicine, Pharmacology, Molecular Biology and Microbiology, Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, United States.,Medical Service and Geriatric Research, Education, and Clinical Centers (GRECC), Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States.,Case Western Reserve University-VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, United States
| |
Collapse
|
4
|
Cyclic Boronates Inhibit All Classes of β-Lactamases. Antimicrob Agents Chemother 2017; 61:AAC.02260-16. [PMID: 28115348 PMCID: PMC5365654 DOI: 10.1128/aac.02260-16] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/17/2017] [Indexed: 01/09/2023] Open
Abstract
β-Lactamase-mediated resistance is a growing threat to the continued use of β-lactam antibiotics. The use of the β-lactam-based serine-β-lactamase (SBL) inhibitors clavulanic acid, sulbactam, and tazobactam and, more recently, the non-β-lactam inhibitor avibactam has extended the utility of β-lactams against bacterial infections demonstrating resistance via these enzymes. These molecules are, however, ineffective against the metallo-β-lactamases (MBLs), which catalyze their hydrolysis. To date, there are no clinically available metallo-β-lactamase inhibitors. Coproduction of MBLs and SBLs in resistant infections is thus of major clinical concern. The development of “dual-action” inhibitors, targeting both SBLs and MBLs, is of interest, but this is considered difficult to achieve due to the structural and mechanistic differences between the two enzyme classes. We recently reported evidence that cyclic boronates can inhibit both serine- and metallo-β-lactamases. Here we report that cyclic boronates are able to inhibit all four classes of β-lactamase, including the class A extended spectrum β-lactamase CTX-M-15, the class C enzyme AmpC from Pseudomonas aeruginosa, and class D OXA enzymes with carbapenem-hydrolyzing capabilities. We demonstrate that cyclic boronates can potentiate the use of β-lactams against Gram-negative clinical isolates expressing a variety of β-lactamases. Comparison of a crystal structure of a CTX-M-15:cyclic boronate complex with structures of cyclic boronates complexed with other β-lactamases reveals remarkable conservation of the small-molecule binding mode, supporting our proposal that these molecules work by mimicking the common tetrahedral anionic intermediate present in both serine- and metallo-β-lactamase catalysis.
Collapse
|
5
|
Vessally E, Hosseinian A, Edjlali L, Bekhradnia A, Esrafili MD. New route to 1,4-oxazepane and 1,4-diazepane derivatives: synthesis from N-propargylamines. RSC Adv 2016. [DOI: 10.1039/c6ra20718a] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
N-Propargylamines are one of the most useful and versatile building blocks in organic synthesis that are successfully transformed into many significant N-heterocycles.
Collapse
Affiliation(s)
| | - Akram Hosseinian
- Department of Engineering Science
- College of Engineering
- University of Tehran
- Tehran
- Iran
| | - Ladan Edjlali
- Department of Chemistry
- Tabriz Branch
- Islamic Azad University
- Tabriz
- Iran
| | - Ahmadreza Bekhradnia
- Pharmaceutical Sciences Research Center
- Department of Medicinal Chemistry
- Mazandaran University of Medical Sciences
- Sari
- Iran
| | | |
Collapse
|
6
|
Hazra S, Kurz SG, Wolff K, Nguyen L, Bonomo RA, Blanchard JS. Kinetic and Structural Characterization of the Interaction of 6-Methylidene Penem 2 with the β-Lactamase from Mycobacterium tuberculosis. Biochemistry 2015; 54:5657-64. [PMID: 26237118 DOI: 10.1021/acs.biochem.5b00698] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis is intrinsically resistant to most β-lactam antibiotics because of the constitutive expression of the blaC-encoded β-lactamase. This enzyme has extremely high activity against penicillins and cephalosporins, but weaker activity against carbapenems. The enzyme can be inhibited by clavulanate, avibactam, and boronic acids. In this study, we investigated the ability of 6-methylidene β-lactams to inhibit BlaC. One such compound, penem 2, inhibited BlaC more than 70 times more efficiently than clavulanate. The compound forms a covalent complex with BlaC as shown by mass spectrometry. Crystallization of the complex revealed that the bound inhibitor was covalently attached via the Ser70 active site residue and that the covalently, acylated form of the inhibitor had undergone additional chemistry yielding a 4,7-thiazepine ring in place of the β-lactam and a thiazapyroline ring generated as a result of β-lactam ring opening. The stereochemistry of the product of the 7-endo-trig cyclization was the opposite of that observed previously for class A and D β-lactamases. Addition of penem 2 greatly synergized the antibacterial properties of both ampicillin and meropenem against a growing culture of M. tuberculosis. Strikingly, penem 2 alone showed significant growth inhibition, suggesting that in addition to its capability of efficiently inhibiting BlaC, it also inhibited the peptidoglycan cross-linking transpeptidases.
Collapse
Affiliation(s)
- Saugata Hazra
- Department of Biotechnology, Indian Institute of Technology, Roorkee , Roorkee, Uttarakhand 247667, India
| | - Sebastian G Kurz
- Tufts University School of Medicine , 800 Washington Street, #257, Boston, Massachusetts 02111, United States
| | - Kerstin Wolff
- Early Discovery, Infectious Diseases Antibacterial & Antifungal, Merck Research Laboratories , Kenilworth, New Jersey 07033, United States
| | | | - Robert A Bonomo
- Department of Medicine, Louis Stokes Cleveland Veterans Affairs Medical Center , Cleveland, Ohio 44106, United States
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
| |
Collapse
|
7
|
Tsang MW, Chan PH, Liu SY, Wong KY, Leung YC. A fluorescein-labeled AmpC β-lactamase allows rapid characterization of β-lactamase inhibitors by real-time fluorescence monitoring of the β-lactamase-inhibitor interactions. Biotechnol J 2015; 11:257-65. [PMID: 26250526 DOI: 10.1002/biot.201400861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 06/02/2015] [Accepted: 08/04/2015] [Indexed: 11/10/2022]
Abstract
Rapid emergence of class C β-lactamases has urged an immediate need for developing class C β-lactamase specific inhibitors for effective clinical treatment. To facilitate the development of effective class C β-lactamase inhibitors, we propose a new approach for a rapid analysis of the interaction of AmpC β-lactamase and its inhibitors using our recently developed V211Cf fluorescent β-lactamase biosensor during drug screening. Since the fluorescein of V211Cf can report the local environment change in the active site of AmpC β-lactamase, fluorescence responses of V211Cf toward its substrates/inhibitors can provide real-time traces of the dynamic change of the interaction of the β-lactamase with its substrates/inhibitors. In this study, we found that V211Cf displayed distinct fluorescence signal patterns toward different kinds of inhibitors (including clavulanic acid, sulbactam, tazobactam and 2-thiopheneboronic acid) due to the differences in their interactions with β-lactamase. V211Cf not only enables a high throughput screening for inhibitors but can also provide a rapid preliminary indication on the inhibitor's potency and stability to β-lactamase's hydrolytic action as well as how the inhibitors interact with the target enzyme, thereby speeding up the drug discovery and development cycle of class C β-lactamase inhibitors.
Collapse
Affiliation(s)
- Man-Wah Tsang
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Pak-Ho Chan
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Sze-Yan Liu
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Yun-Chung Leung
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| |
Collapse
|
8
|
Öztürk H, Ozkirimli E, Özgür A. Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models. PLoS One 2015; 10:e0117874. [PMID: 25689853 PMCID: PMC4331424 DOI: 10.1371/journal.pone.0117874] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/03/2015] [Indexed: 01/28/2023] Open
Abstract
β-lactamase mediated antibiotic resistance is an important health issue and the discovery of new β-lactam type antibiotics or β-lactamase inhibitors is an area of intense research. Today, there are about a thousand β-lactamases due to the evolutionary pressure exerted by these ligands. While β-lactamases hydrolyse the β-lactam ring of antibiotics, rendering them ineffective, Penicillin-Binding Proteins (PBPs), which share high structural similarity with β-lactamases, also confer antibiotic resistance to their host organism by acquiring mutations that allow them to continue their participation in cell wall biosynthesis. In this paper, we propose a novel approach to include ligand sharing information for classifying and clustering β-lactamases and PBPs in an effort to elucidate the ligand induced evolution of these β-lactam binding proteins. We first present a detailed summary of the β-lactamase and PBP families in the Protein Data Bank, as well as the compounds they bind to. Then, we build two different types of networks in which the proteins are represented as nodes, and two proteins are connected by an edge with a weight that depends on the number of shared identical or similar ligands. These models are analyzed under three different edge weight settings, namely unweighted, weighted, and normalized weighted. A detailed comparison of these six networks showed that the use of ligand sharing information to cluster proteins resulted in modules comprising proteins with not only sequence similarity but also functional similarity. Consideration of ligand similarity highlighted some interactions that were not detected in the identical ligand network. Analysing the β-lactamases and PBPs using ligand-centric network models enabled the identification of novel relationships, suggesting that these models can be used to examine other protein families to obtain information on their ligand induced evolutionary paths.
Collapse
Affiliation(s)
- Hakime Öztürk
- Department of Computer Engineering, Bogazici University, Istanbul, Bebek, Turkey
| | - Elif Ozkirimli
- Department of Chemical Engineering, Bogazici University, Istanbul, Bebek, Turkey
- * E-mail: (EO), (AÖ)
| | - Arzucan Özgür
- Department of Computer Engineering, Bogazici University, Istanbul, Bebek, Turkey
- * E-mail: (EO), (AÖ)
| |
Collapse
|
9
|
Bhattacharya M, Toth M, Antunes NT, Smith CA, Vakulenko SB. Structure of the extended-spectrum class C β-lactamase ADC-1 from Acinetobacter baumannii. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:760-71. [PMID: 24598745 PMCID: PMC3949520 DOI: 10.1107/s1399004713033014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/05/2013] [Indexed: 11/10/2022]
Abstract
ADC-type class C β-lactamases comprise a large group of enzymes that are encoded by genes located on the chromosome of Acinetobacter baumannii, a causative agent of serious bacterial infections. Overexpression of these enzymes renders A. baumannii resistant to various β-lactam antibiotics and thus severely compromises the ability to treat infections caused by this deadly pathogen. Here, the high-resolution crystal structure of ADC-1, the first member of this clinically important family of antibiotic-resistant enzymes, is reported. Unlike the narrow-spectrum class C β-lactamases, ADC-1 is capable of producing resistance to the expanded-spectrum cephalosporins, rendering them inactive against A. baumannii. The extension of the substrate profile of the enzyme is likely to be the result of structural differences in the R2-loop, primarily the deletion of three residues and subsequent rearrangement of the A10a and A10b helices. These structural rearrangements result in the enlargement of the R2 pocket of ADC-1, allowing it to accommodate the bulky R2 substituents of the third-generation cephalosporins, thus enhancing the catalytic efficiency of the enzyme against these clinically important antibiotics.
Collapse
Affiliation(s)
- Monolekha Bhattacharya
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nuno Tiago Antunes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California USA
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| |
Collapse
|
10
|
Rodkey EA, McLeod DC, Bethel CR, Smith KM, Xu Y, Chai W, Che T, Carey PR, Bonomo RA, van den Akker F, Buynak JD. β-Lactamase inhibition by 7-alkylidenecephalosporin sulfones: allylic transposition and formation of an unprecedented stabilized acyl-enzyme. J Am Chem Soc 2013; 135:18358-69. [PMID: 24219313 PMCID: PMC4042847 DOI: 10.1021/ja403598g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The inhibition of the class A SHV-1 β-lactamase by 7-(tert-butoxycarbonyl)methylidenecephalosporin sulfone was examined kinetically, spectroscopically, and crystallographically. An 1.14 Å X-ray crystal structure shows that the stable acyl-enzyme, which incorporates an eight-membered ring, is a covalent derivative of Ser70 linked to the 7-carboxy group of 2-H-5,8-dihydro-1,1-dioxo-1,5-thiazocine-4,7-dicarboxylic acid. A cephalosporin-derived enzyme complex of this type is unprecedented, and the rearrangement leading to its formation may offer new possibilities for inhibitor design. The observed acyl-enzyme derives its stability from the resonance stabilization conveyed by the β-aminoacrylate (i.e., vinylogous urethane) functionality as there is relatively little interaction of the eight-membered ring with active site residues. Two mechanistic schemes are proposed, differing in whether, subsequent to acylation of the active site serine and opening of the β-lactam, the resultant dihydrothiazine fragments on its own or is assisted by an adjacent nucleophilic atom, in the form of the carbonyl oxygen of the C7 tert-butyloxycarbonyl group. This compound was also found to be a submicromolar inhibitor of the class C ADC-7 and PDC-3 β-lactamases.
Collapse
Affiliation(s)
- Elizabeth A. Rodkey
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, United States
| | - David C. McLeod
- Department of Chemistry, Southern Methodist University, 3215 Daniel Ave., Dallas, Texas 75275, United States
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
| | - Kerri M. Smith
- Department of Chemistry, Cleveland State University, 2121 Euclid Ave., Cleveland, Ohio 44115, United States
| | - Yan Xu
- Department of Chemistry, Cleveland State University, 2121 Euclid Ave., Cleveland, Ohio 44115, United States
| | - Weirui Chai
- Department of Chemistry, Southern Methodist University, 3215 Daniel Ave., Dallas, Texas 75275, United States
| | - Tao Che
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, United States
| | - Paul R. Carey
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, United States
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, United States
| | - John D. Buynak
- Department of Chemistry, Southern Methodist University, 3215 Daniel Ave., Dallas, Texas 75275, United States
- Center for Drug Discovery, Design, and Development, Southern Methodist University, Dallas, Texas 75275, United States
| |
Collapse
|
11
|
Ke W, Pattanaik P, Bethel CR, Sheri A, Buynak JD, Bonomo RA, van den Akker F. Structures of SHV-1 β-lactamase with penem and penam sulfone inhibitors that form cyclic intermediates stabilized by carbonyl conjugation. PLoS One 2012; 7:e49035. [PMID: 23145056 PMCID: PMC3493512 DOI: 10.1371/journal.pone.0049035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/03/2012] [Indexed: 11/22/2022] Open
Abstract
Bacterial β-lactamase enzymes are in large part responsible for the decreased ability of β-lactam antibiotics to combat infections. The inability to overcome β-lactamase mediated resistance spurred the development of inhibitors with penems and penam sulfones being amongst the most potent and broad spectrum mechanism-based inactivators. These inhibitors form covalent, “suicide-type” inhibitory intermediates that are attached to the catalytic S70 residue. To further probe the details of the mechanism of β-lactamase inhibition by these novel compounds, we determined the crystal structures of SHV-1 bound with penem 1, and penam sulfones SA1-204 and SA3-53. Comparison with each other and with previously determined crystal structures of members of these classes of inhibitors suggests that the final conformation of the covalent adduct can vary greatly amongst the complex structures. In contrast, a common theme of carbonyl conjugation as a mechanism to avoid deacylation emerges despite that the penem and penam sulfone inhibitors form different types of intermediates. The detailed insights gained from this study could be used to further improve new mechanism-based inhibitors of these common class A serine β-lactamases.
Collapse
Affiliation(s)
- Wei Ke
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Priyaranjan Pattanaik
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Anjaneyulu Sheri
- Department of Chemistry, Southern Methodist University, Dallas, Texas, United States of America
| | - John D. Buynak
- Department of Chemistry, Southern Methodist University, Dallas, Texas, United States of America
| | - Robert A. Bonomo
- Department of Medicine, Pharmacology, and Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
| |
Collapse
|
12
|
Substitutions at position 105 in SHV family β-lactamases decrease catalytic efficiency and cause inhibitor resistance. Antimicrob Agents Chemother 2012; 56:5678-86. [PMID: 22908166 DOI: 10.1128/aac.00711-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ambler position 105 in class A β-lactamases is implicated in resistance to clavulanic acid, although no clinical isolates with mutations at this site have been reported. We hypothesized that Y105 is important in resistance to clavulanic acid because changes in positioning of the inhibitor for ring oxygen protonation could occur. In addition, resistance to bicyclic 6-methylidene penems, which are interesting structural probes that inhibit all classes of serine β-lactamases with nanomolar affinity, might emerge with substitutions at position 105, especially with nonaromatic substitutions. All 19 variants of SHV-1 with variations at position 105 were prepared. Antimicrobial susceptibility testing showed that Escherichia coli DH10B expressing Y105 variants retained activity against ampicillin, except for the Y105L variant, which was susceptible to all β-lactams, similar to the case for the host control strain. Several variants had elevated MICs to ampicillin-clavulanate. However, all the variants remained susceptible to piperacillin in combination with a penem inhibitor (MIC, ≤2/4 mg/liter). The Y105E, -F, -M, and -R variants demonstrated reduced catalytic efficiency toward ampicillin compared to the wild-type (WT) enzyme, which was caused by increased K(m). Clavulanic acid and penem K(i) values were also increased for some of the variants, especially Y105E. Mutagenesis at position 105 in SHV yields mutants resistant to clavulanate with reduced catalytic efficiency for ampicillin and nitrocefin, similar to the case for the class A carbapenemase KPC-2. Our modeling analyses suggest that resistance is due to oxyanion hole distortion. Susceptibility to a penem inhibitor is retained although affinity is decreased, especially for the Y105E variant. Residue 105 is important to consider when designing new inhibitors.
Collapse
|
13
|
Exploring the inhibition of CTX-M-9 by beta-lactamase inhibitors and carbapenems. Antimicrob Agents Chemother 2011; 55:3465-75. [PMID: 21555770 DOI: 10.1128/aac.00089-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Currently, CTX-M β-lactamases are among the most prevalent and most heterogeneous extended-spectrum β-lactamases (ESBLs). In general, CTX-M enzymes are susceptible to inhibition by β-lactamase inhibitors. However, it is unknown if the pathway to inhibition by β-lactamase inhibitors for CTX-M ESBLs is similar to TEM and SHV β-lactamases and why bacteria possessing only CTX-M ESBLs are so susceptible to carbapenems. Here, we have performed a kinetic analysis and timed electrospray ionization mass spectrometry (ESI-MS) studies to reveal the intermediates of inhibition of CTX-M-9, an ESBL representative of this family of enzymes. CTX-M-9 β-lactamase was inactivated by sulbactam, tazobactam, clavulanate, meropenem, doripenem, ertapenem, and a 6-methylidene penem, penem 1. K(i) values ranged from 1.6 ± 0.3 μM (mean ± standard error) for tazobactam to 0.02 ± 0.01 μM for penem 1. Before and after tryptic digestion of the CTX-M-9 β-lactamase apo-enzyme and CTX-M-9 inactivation by inhibitors (meropenem, clavulanate, sulbactam, tazobactam, and penem 1), ESI-MS and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identified different adducts attached to the peptide containing the active site Ser70 (+52, 70, 88, and 156 ± 3 atomic mass units). This study shows that a multistep inhibition pathway results from modification or fragmentation with clavulanate, sulbactam, and tazobactam, while a single acyl enzyme intermediate is detected when meropenem and penem 1 inactivate CTX-M-9 β-lactamase. More generally, we propose that Arg276 in CTX-M-9 plays an essential role in the recognition of the C(3) carboxylate of inhibitors and that the localization of this positive charge to a "region of the active site" rather than a specific residue represents an important evolutionary strategy used by β-lactamases.
Collapse
|
14
|
Rimoldi I, Cesarotti E, Zerla D, Molinari F, Albanese D, Castellano C, Gandolfi R. 3-(Hydroxy(phenyl)methyl)azetidin-2-ones obtained via catalytic asymmetric hydrogenation or by biotransformation. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.tetasy.2011.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
15
|
Ligand-dependent disorder of the Omega loop observed in extended-spectrum SHV-type beta-lactamase. Antimicrob Agents Chemother 2011; 55:2303-9. [PMID: 21357298 DOI: 10.1128/aac.01360-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among Gram-negative bacteria, resistance to β-lactams is mediated primarily by β-lactamases (EC 3.2.6.5), periplasmic enzymes that inactivate β-lactam antibiotics. Substitutions at critical amino acid positions in the class A β-lactamase families result in enzymes that can hydrolyze extended-spectrum cephalosporins, thus demonstrating an "extended-spectrum" β-lactamase (ESBL) phenotype. Using SHV ESBLs with substitutions in the Ω loop (R164H and R164S) as target enzymes to understand this enhanced biochemical capability and to serve as a basis for novel β-lactamase inhibitor development, we determined the spectra of activity and crystal structures of these variants. We also studied the inactivation of the R164H and R164S mutants with tazobactam and SA2-13, a unique β-lactamase inhibitor that undergoes a distinctive reaction chemistry in the active site. We noted that the reduced Ki values for the R164H and R164S mutants with SA2-13 are comparable to those with tazobactam (submicromolar). The apo enzyme crystal structures of the R164H and R164S SHV variants revealed an ordered Ω loop architecture that became disordered when SA2-13 was bound. Important structural alterations that result from the binding of SA2-13 explain the enhanced susceptibility of these ESBL enzymes to this inhibitor and highlight ligand-dependent Ω loop flexibility as a mechanism for accommodating and hydrolyzing β-lactam substrates.
Collapse
|
16
|
Bebrone C, Lassaux P, Vercheval L, Sohier JS, Jehaes A, Sauvage E, Galleni M. Current challenges in antimicrobial chemotherapy: focus on ß-lactamase inhibition. Drugs 2010; 70:651-79. [PMID: 20394454 DOI: 10.2165/11318430-000000000-00000] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The use of the three classical beta-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam) in combination with beta-lactam antibacterials is currently the most successful strategy to combat beta-lactamase-mediated resistance. However, these inhibitors are efficient in inactivating only class A beta-lactamases and the efficiency of the inhibitor/antibacterial combination can be compromised by several mechanisms, such as the production of naturally resistant class B or class D enzymes, the hyperproduction of AmpC or even the production of evolved inhibitor-resistant class A enzymes. Thus, there is an urgent need for the development of novel inhibitors. For serine active enzymes (classes A, C and D), derivatives of the beta-lactam ring such as 6-beta-halogenopenicillanates, beta-lactam sulfones, penems and oxapenems, monobactams or trinems seem to be potential starting points to design efficient molecules (such as AM-112 and LK-157). Moreover, a promising non-beta-lactam molecule, NXL-104, is now under clinical development. In contrast, an ideal inhibitor of metallo-beta-lactamases (class B) remains to be found, despite the huge number of potential molecules already described (biphenyl tetrazoles, cysteinyl peptides, mercaptocarboxylates, succinic acid derivatives, etc.). The search for such an inhibitor is complicated by the absence of a covalent intermediate in their catalytic mechanisms and the fact that beta-lactam derivatives often behave as substrates rather than as inhibitors. Currently, the most promising broad-spectrum inhibitors of class B enzymes are molecules presenting chelating groups (thiols, carboxylates, etc.) combined with an aromatic group. This review describes all the types of molecules already tested as potential beta-lactamase inhibitors and thus constitutes an update of the current status in beta-lactamase inhibitor discovery.
Collapse
Affiliation(s)
- Carine Bebrone
- Biological Macromolecules, Centre for Protein Engineering, University of Liège, Liège, Belgium.
| | | | | | | | | | | | | |
Collapse
|
17
|
Tremblay LW, Xu H, Blanchard JS. Structures of the Michaelis complex (1.2 Å) and the covalent acyl intermediate (2.0 Å) of cefamandole bound in the active sites of the Mycobacterium tuberculosis β-lactamase K73A and E166A mutants. Biochemistry 2010; 49:9685-7. [PMID: 20961112 DOI: 10.1021/bi1015088] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The genome of Mycobacterium tuberculosis (TB) contains a gene that encodes a highly active β-lactamase, BlaC, that imparts TB with resistance to β-lactam chemotherapy. The structure of covalent BlaC-β-lactam complexes suggests that active site residues K73 and E166 are essential for acylation and deacylation, respectively. We have prepared the K73A and E166A mutant forms of BlaC and have determined the structures of the Michaelis complex of cefamandole and the covalently bound acyl intermediate of cefamandole at resolutions of 1.2 and 2.0 Å, respectively. These structures provide insight into the details of the catalytic mechanism.
Collapse
Affiliation(s)
- Lee W Tremblay
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | | | | |
Collapse
|
18
|
De Pascale G, Wright GD. Antibiotic resistance by enzyme inactivation: from mechanisms to solutions. Chembiochem 2010; 11:1325-34. [PMID: 20564281 DOI: 10.1002/cbic.201000067] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Gianfranco De Pascale
- DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street W, Hamilton, ON L8N 3Z5 Canada
| | | |
Collapse
|
19
|
Mechanistic studies of the inactivation of TEM-1 and P99 by NXL104, a novel non-beta-lactam beta-lactamase inhibitor. Antimicrob Agents Chemother 2010; 54:5132-8. [PMID: 20921316 DOI: 10.1128/aac.00568-10] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NXL104 is a potent inhibitor of class A and C serine β-lactamases, including KPC carbapenemases. Native and NXL104-inhibited TEM-1 and P99 β-lactamases analyzed by liquid chromatography-electrospray ionization-time of flight mass spectrometry revealed that the inactivated enzymes formed a covalent adduct with NXL104. The principal inhibitory characteristics of NXL104 against TEM-1 and P99 β-lactamases were determined, including partition ratios, dissociation constants (K), rate constants for deactivation (k(2)), and reactivation rates. NXL104 is a potent inhibitor of TEM-1 and P99, characterized by high carbamylation efficiencies (k(2)/K of 3.7 × 10(5) M(-1) s(-1) for TEM-1 and 1 × 10(4) M(-1) s(-1) for P99) and slow decarbamylation. Complete loss of β-lactamase activity was obtained at a 1/1 enzyme/NXL104 ratio, with a k(3) value (rate constant for formation of product and free enzyme) close to zero for TEM-1 and P99. Fifty percent inhibitory concentrations (IC(50)s) were evaluated on selected β-lactamases, and NXL104 was shown to be a very potent inhibitor of class A and C β-lactamases. IC(50)s obtained with NXL104 (from 3 nM to 170 nM) were globally comparable on the β-lactamases CTX-M-15 and SHV-4 with those obtained with the comparators (clavulanate, tazobactam, and sulbactam) but were far lower on TEM-1, KPC-2, P99, and AmpC than those of the comparators. In-depth studies on TEM-1 and P99 demonstrated that NXL104 had a comparable or better affinity and inactivation rate than clavulanate and tazobactam and in all cases an improved stability of the covalent enzyme/inhibitor complex.
Collapse
|
20
|
Kluge AF, Petter RC. Acylating drugs: redesigning natural covalent inhibitors. Curr Opin Chem Biol 2010; 14:421-7. [PMID: 20457000 DOI: 10.1016/j.cbpa.2010.03.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 02/18/2010] [Accepted: 03/26/2010] [Indexed: 11/26/2022]
Abstract
Structural modification of naturally occurring beta-lactams and beta-lactones is a highly effective strategy for generating drugs for treating bacterial infections, cancer, obesity, and hyperlipidemia. These drugs acylate catalytic amino acids (serine, threonine, or cysteine) in enzyme targets such as penicillin-binding proteins (PBPs), beta-lactamases, lipases, HMG-CoA reductase, fatty acid synthetase, and the 20S proteasome. Optimally performing drugs combine features of high target affinity, chemoselective reactivity, and high stability of the acylated target protein. This review provides a perspective on these two classes of acylating agents and summarizes recent advances in mechanism and structure-based design of acylating drugs.
Collapse
Affiliation(s)
- Arthur F Kluge
- Avila Therapeutics, 100 Beaver Street, Waltham, MA 02453, USA
| | | |
Collapse
|
21
|
Abstract
Since the introduction of penicillin, beta-lactam antibiotics have been the antimicrobial agents of choice. Unfortunately, the efficacy of these life-saving antibiotics is significantly threatened by bacterial beta-lactamases. beta-Lactamases are now responsible for resistance to penicillins, extended-spectrum cephalosporins, monobactams, and carbapenems. In order to overcome beta-lactamase-mediated resistance, beta-lactamase inhibitors (clavulanate, sulbactam, and tazobactam) were introduced into clinical practice. These inhibitors greatly enhance the efficacy of their partner beta-lactams (amoxicillin, ampicillin, piperacillin, and ticarcillin) in the treatment of serious Enterobacteriaceae and penicillin-resistant staphylococcal infections. However, selective pressure from excess antibiotic use accelerated the emergence of resistance to beta-lactam-beta-lactamase inhibitor combinations. Furthermore, the prevalence of clinically relevant beta-lactamases from other classes that are resistant to inhibition is rapidly increasing. There is an urgent need for effective inhibitors that can restore the activity of beta-lactams. Here, we review the catalytic mechanisms of each beta-lactamase class. We then discuss approaches for circumventing beta-lactamase-mediated resistance, including properties and characteristics of mechanism-based inactivators. We next highlight the mechanisms of action and salient clinical and microbiological features of beta-lactamase inhibitors. We also emphasize their therapeutic applications. We close by focusing on novel compounds and the chemical features of these agents that may contribute to a "second generation" of inhibitors. The goal for the next 3 decades will be to design inhibitors that will be effective for more than a single class of beta-lactamases.
Collapse
Affiliation(s)
- Sarah M. Drawz
- Departments of Pathology, Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Robert A. Bonomo
- Departments of Pathology, Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| |
Collapse
|
22
|
Chen Y, McReynolds A, Shoichet BK. Re-examining the role of Lys67 in class C beta-lactamase catalysis. Protein Sci 2009; 18:662-9. [PMID: 19241376 DOI: 10.1002/pro.60] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Lys67 is essential for the hydrolysis reaction mediated by class C beta-lactamases. Its exact catalytic role lies at the center of several different proposed reaction mechanisms, particularly for the deacylation step, and has been intensely debated. Whereas a conjugate base hypothesis postulates that a neutral Lys67 and Tyr150 act together to deprotonate the deacylating water, previous experiments on the K67R mutants of class C beta-lactamases suggested that the role of Lys67 in deacylation is mainly electrostatic, with only a 2- to 3-fold decrease in the rate of the mutant vs the wild type enzyme. Using the Class C beta-lactamase AmpC, we have reinvestigated the activity of this K67R mutant enzyme, using biochemical and structural studies. Both the rates of acylation and deacylation were affected in the AmpC K67R mutant, with a 61-fold decrease in k(cat), the deacylation rate. We have determined the structure of the K67R mutant by X-ray crystallography both in apo and transition state-analog complexed forms, and observed only minimal conformational changes in the catalytic residues relative to the wild type. These results suggest that the arginine side chain is unable to play the same catalytic role as Lys67 in either the acylation or deacylation reactions catalyzed by AmpC. Therefore, the activity of this mutant can not be used to discredit the conjugate base hypothesis as previously concluded, although the reaction catalyzed by the K67R mutant itself likely proceeds by an alternative mechanism. Indeed, a manifold of mechanisms may contribute to hydrolysis in class C beta-lactamases, depending on the enzyme (wt or mutant) and the substrate, explaining why different mutants and substrates seem to support different pathways. For the WT enzyme itself, the conjugate base mechanism may be well favored.
Collapse
Affiliation(s)
- Yu Chen
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158-2550, USA
| | | | | |
Collapse
|
23
|
Drawz SM, Bethel CR, Hujer KM, Hurless KN, Distler AM, Caselli E, Prati F, Bonomo RA. The role of a second-shell residue in modifying substrate and inhibitor interactions in the SHV beta-lactamase: a study of ambler position Asn276. Biochemistry 2009; 48:4557-66. [PMID: 19351161 DOI: 10.1021/bi9003292] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inhibitor-resistant class A beta-lactamases of the TEM and SHV families that arise by single amino acid substitutions are a significant threat to the efficacy of beta-lactam/beta-lactamase inhibitor combinations. To better understand the basis of the inhibitor-resistant phenotype in SHV, we performed mutagenesis to examine the role of a second-shell residue, Asn276. Of the 19 variants expressed in Escherichia coli, only the Asn276Asp enzyme demonstrated reduced susceptibility to ampicillin/clavulanate (MIC increased from 50/2 --> 50/8 microg/mL) while maintaining high-level resistance to ampicillin (MIC = 8192 microg/mL). Steady-state kinetic analyses of Asn276Asp revealed slightly diminished k(cat)/K(m) for all substrates tested. In contrast, we observed a 5-fold increase in K(i) for clavulanate (7.4 +/- 0.9 microM for Asn276Asp vs 1.4 +/- 0.2 microM for SHV-1) and a 40% reduction in k(inact)/K(I) (0.013 +/- 0.002 microM(-1 )s(-1) for Asn276Asp vs 0.021 +/- 0.004 microM(-1) s(-1) for SHV-1). Timed electrospray ionization mass spectrometry of clavulanate-inhibited SHV-1 and SHV Asn276Asp showed nearly identical mass adducts, arguing for a similar pathway of inactivation. Molecular modeling shows that novel electrostatic interactions are formed between Arg244Neta2 and both 276AspOdelta1 and Odelta2; these new forces restrict the spatial position of Arg244, a residue important in the recognition of the C(3)/C(4) carboxylate of beta-lactam substrates and inhibitors. Testing the functional consequences of this interaction, we noted considerable free energy costs (+DeltaDeltaG) for substrates and inhibitors. A rigid carbapenem (meropenem) was most affected by the Asn276Asp substitution (46-fold increase in K(i) vs SHV-1). We conclude that residue 276 is an important second-shell residue in class A beta-lactamase-mediated resistance to substrates and inhibitors, and only Asn is able to precisely modulate the conformational flexibility of Arg244 required for successful evolution in nature.
Collapse
Affiliation(s)
- Sarah M Drawz
- Department of Pathology, CaseWestern Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Tioni MF, Llarrull LI, Poeylaut-Palena AA, Martí MA, Saggu M, Periyannan GR, Mata EG, Bennett B, Murgida DH, Vila AJ. Trapping and characterization of a reaction intermediate in carbapenem hydrolysis by B. cereus metallo-beta-lactamase. J Am Chem Soc 2009; 130:15852-63. [PMID: 18980308 DOI: 10.1021/ja801169j] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallo-beta-lactamases hydrolyze most beta-lactam antibiotics. The lack of a successful inhibitor for them is related to the previous failure to characterize a reaction intermediate with a clinically useful substrate. Stopped-flow experiments together with rapid freeze-quench EPR and Raman spectroscopies were used to characterize the reaction of Co(II)-BcII with imipenem. These studies show that Co(II)-BcII is able to hydrolyze imipenem in both the mono- and dinuclear forms. In contrast to the situation met for penicillin, the species that accumulates during turnover is an enzyme-intermediate adduct in which the beta-lactam bond has already been cleaved. This intermediate is a metal-bound anionic species with a novel resonant structure that is stabilized by the metal ion at the DCH or Zn2 site. This species has been characterized based on its spectroscopic features. This represents a novel, previously unforeseen intermediate that is related to the chemical nature of carbapenems, as confirmed by the finding of a similar intermediate for meropenem. Since carbapenems are the only substrates cleaved by B1, B2, and B3 lactamases, identification of this intermediate could be exploited as a first step toward the design of transition-state-based inhibitors for all three classes of metallo-beta-lactamases.
Collapse
Affiliation(s)
- Mariana F Tioni
- Instituto de Biologia Molecular y Celular de Rosario and Biophysics Section, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Universidad Nacional de Rosario, Rosario, Argentina
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Venkatesan A, Agarwal A, Abe T, Ushirogochi H, Takasaki T, Mihira A, Mansour T. Targeting Val 216 in Class A β-Lactamases with Tricyclic 6-Methylidene Penems. ChemMedChem 2008; 3:1658-61. [DOI: 10.1002/cmdc.200800167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
26
|
Mansour TS, Agarwal A, Venkatesan A, Abe T, Mihira A, Takasaki T, Sato K, Ushirogochi H, Yamamura I, Isoda T, Li Z, Yang Y, Kumagai T. On the absolute configuration in 1,4-dihydrothiazepine covalent complexes derived from inhibition of class A and C beta-lactamases with 6-methylidene penems. ChemMedChem 2008; 2:1713-6. [PMID: 17868160 DOI: 10.1002/cmdc.200700144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tarek S Mansour
- Chemical and Screening Sciences and Infectious Diseases Wyeth Research, 401 North Middeltown Road, Pearl River, NY 10965, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Abstract
The partnering of a beta-lactam with a beta-lactamase inhibitor is a highly effective strategy that can be used to combat bacterial resistance to beta-lactam antibiotics mediated by serine beta-lactamases (EC 3.2.5.6). To this end, we tested two novel penem inhibitors against OXA-1, a class D beta-lactamase that is resistant to inactivation by tazobactam. The K(i) of each penem inhibitor for OXA-1 was in the nM range (K(i) of penem 1, 45 +/- 8 nM; K(i) of penem 2, 12 +/- 2 nM). The first-order rate constant for enzyme and inhibitor complex inactivation of penems 1 and 2 for OXA-1 beta-lactamase were 0.13 +/- 0.01 s(-1) and 0.11 +/- 0.01 s(-1), respectively. By using an inhibitor-to-enzyme ratio of 1:1, 100% inactivation was achieved in <or=900 s and the recovery of OXA-1 beta-lactamase activity was not detected at 24 h. Covalent adducts of penems 1 and 2 (changes in molecular masses, +306 +/- 3 and +321 +/- 3 Da, respectively) were identified by electrospray ionization mass spectrometry (ESI-MS). After tryptic digestion of OXA-1 inactivated by penems 1 and 2, ESI-MS and matrix-assisted laser desorption ionization-time-of-flight MS identified the adducts of 306 +/- 3 and 321 +/- 3 Da attached to the peptide containing the active-site Ser67. The base hydrolysis of penem 2, monitored by serial (1)H nuclear magnetic resonance analysis, suggested that penem 2 formed a linear imine species that underwent 7-endo-trig cyclization to ultimately form a cyclic enamine, the 1,4-thiazepine derivative. Susceptibility testing demonstrated that the penem inhibitors at 4 mg/liter effectively restored susceptibility to piperacillin. Penem beta-lactamase inhibitors which demonstrate high affinities and which form long-lived acyl intermediates may prove to be extremely useful against the broad range of inhibitor-resistant serine beta-lactamases present in gram-negative bacteria.
Collapse
|
28
|
Theoretical study of the reaction from 7-alkylidenecephalosporin sulfone to bicyclic intermediates in inhibiting β-lactamase. Struct Chem 2008. [DOI: 10.1007/s11224-008-9311-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
29
|
Ding H, Zhang Y, Yao W, Xu D, Ma C. Thiazepine moiety-controlled regioselective rearrangements of 7-oxanorbornadiene derivatives. Chem Commun (Camb) 2008:5797-9. [DOI: 10.1039/b813371a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
30
|
Mansour TS, Bradford PA, Venkatesan AM. Recent Developments in β-Lactamases and Inhibitors. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2008. [DOI: 10.1016/s0065-7743(08)00015-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
|
31
|
Li R, Feng D, He M. Theoretical study of the reaction from 6-methylidene penem to seven-membered ring intermediates. J Phys Chem A 2007; 111:4720-5. [PMID: 17477514 DOI: 10.1021/jp070685q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A sort of beta-lactamase inhibitor, 6-methylidene penem can inhibit both class A and class C serine beta-lactamase. Its inhibition mechanism involves yielding a seven-membered ring intermediate after acylation of the serine. Density functional theory (DFT) method was used on the molecular model to determine the mechanism of producing the seven-membered ring intermediate. Solvent effects were considered via polarizable continuum model (PCM). Moreover, a water-assisted process was considered in the hydrogen transfer process. The results show that the seven-membered ring intermediate can be obtained via two possible mechanisms, namely, concerted mechanism and stepwise mechanism. In stepwise mechanism, a new thiirane intermediate which has never been reported was found. The product of stepwise mechanism, e, has five tautomerics, and they can be tautomerized by hydrogen transfer.
Collapse
Affiliation(s)
- Rui Li
- Institute of Theoretical Chemistry and College of Life Science, Shandong University, Jinan 250100, People's Republic of China
| | | | | |
Collapse
|
32
|
Doi Y, Paterson DL. Detection of plasmid-mediated class C β-lactamases. Int J Infect Dis 2007; 11:191-7. [PMID: 17339123 DOI: 10.1016/j.ijid.2006.07.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2006] [Revised: 07/18/2006] [Accepted: 07/27/2006] [Indexed: 10/23/2022] Open
Abstract
Plasmid-mediated class C beta-lactamases are reported from Enterobacteriaceae with increasing frequency. They likely originate from chromosomal AmpC of certain Gram-negative bacterial species and subsequently are mobilized onto transmissible plasmids. There are reports of unfavorable clinical outcomes in patients infected with these organisms and treated with broad-spectrum cephalosporins. However, unlike class A extended-spectrum beta-lactamases (ESBLs), no screening and confirmatory tests have been uniformly established for strains that produce class C beta-lactamases. Reduced susceptibility to cefoxitin is a sensitive but not specific indicator of class C beta-lactamase production. Simple confirmatory tests including tests using boronic acid compounds as specific class C beta-lactamase inhibitors have recently been developed. Their utilization will enable clinical microbiology laboratories to report those strains producing plasmid-mediated class C beta-lactamases as being resistant to all broad-spectrum cephalosporins, thus allowing physicians to prescribe appropriate antimicrobial therapy.
Collapse
Affiliation(s)
- Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh Medical Center, Falk Medical Building Suite 3A, 3601 Fifth Avenue, Pittsburgh, PA 15213, USA
| | | |
Collapse
|
33
|
Hata M, Fujii Y, Tanaka Y, Ishikawa H, Ishii M, Neya S, Tsuda M, Hoshino T. Substrate deacylation mechanisms of serine-beta-lactamases. Biol Pharm Bull 2007; 29:2151-9. [PMID: 17077507 DOI: 10.1248/bpb.29.2151] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The substrate deacylation mechanisms of serine-beta-lactamases (classes A, C and D) were investigated by theoretical calculations. The deacylation of class A proceeds via four elementary reactions. The rate-determining process is the tetrahedral intermediate (TI) formation and the activation energy is 24.6 kcal/mol at the DFT level. The deacylation does not proceed only by Glu166, which acts as a general base, but Lys73 also participates in the reaction. The C3-carboxyl group of the substrate reduces the barrier height at the TI formation (substrate-assisted catalysis). In the case of class C, the deacylation consists of two elementary processes. The activation energy of the TI formation has been estimated to be 30.5 kcal/mol. Tyr150Oeta is stabilized in the deprotonated state in the acyl-enzyme complex and works as a general base. This situation can exist due to the interaction with two positively charged side chains of lysine (Lys67 and Lys315). The deacylation of class D also consists of two elementary reaction processes. The activation energy of the TI formation is ca. 30 kcal/mol. It is thought that the side chain of Lys70 is deprotonated and acts as a general base. When Lys70 is carbamylated, the activation energy is reduced to less than 20 kcal/mol. This suggests that the high hydrolysis activity of class D with carbamylated Lys70 is due to the reduction of activation energy for deacylation. From these results, it is concluded that the contribution of the lysine residue adjacent to the serine residue is indispensable for the enzymatic reactions by serine-beta-lactamases.
Collapse
Affiliation(s)
- Masayuki Hata
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Terwilliger TC, Adams PD, Moriarty NW, Cohn JD. Ligand identification using electron-density map correlations. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2007; 63:101-7. [PMID: 17164532 PMCID: PMC2483487 DOI: 10.1107/s0907444906046233] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 11/02/2006] [Indexed: 01/13/2023]
Abstract
A procedure for the identification of ligands bound in crystal structures of macromolecules is described. Two characteristics of the density corresponding to a ligand are used in the identification procedure. One is the correlation of the ligand density with each of a set of test ligands after optimization of the fit of that ligand to the density. The other is the correlation of a fingerprint of the density with the fingerprint of model density for each possible ligand. The fingerprints consist of an ordered list of correlations of each the test ligands with the density. The two characteristics are scored using a Z-score approach in which the correlations are normalized to the mean and standard deviation of correlations found for a variety of mismatched ligand-density pairs, so that the Z scores are related to the probability of observing a particular value of the correlation by chance. The procedure was tested with a set of 200 of the most commonly found ligands in the Protein Data Bank, collectively representing 57% of all ligands in the Protein Data Bank. Using a combination of these two characteristics of ligand density, ranked lists of ligand identifications were made for representative (F(o) - F(c))exp(i(phi)c) difference density from entries in the Protein Data Bank. In 48% of the 200 cases, the correct ligand was at the top of the ranked list of ligands. This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule.
Collapse
|
35
|
Venkatesan AM, Agarwal A, Abe T, Ushirogochi H, Yamamura I, Ado M, Tsuyoshi T, Dos Santos O, Gu Y, Sum FW, Li Z, Francisco G, Lin YI, Petersen PJ, Yang Y, Kumagai T, Weiss WJ, Shlaes DM, Knox JR, Mansour TS. Structure-Activity Relationship of 6-Methylidene Penems Bearing 6,5 Bicyclic Heterocycles as Broad-Spectrum β-Lactamase Inhibitors: Evidence for 1,4-Thiazepine Intermediates with C7 R Stereochemistry by Computational Methods. J Med Chem 2006; 49:4623-37. [PMID: 16854068 DOI: 10.1021/jm060021p] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The design and synthesis of a series of 6-methylidene penems containing [6,5]-fused bicycles (thiophene, imidazole, or pyrazle-fused system) as novel class A, B, and C beta-lactamase inhibitors is described. These penems proved to be potent inhibitors of the TEM-1 (class A) and AmpC (class C) beta-lactamases and less so against the class B metallo-beta-lactamase CcrA. Their in vitro and in vivo activities in combination with piperacillin are discussed. On the basis of the crystallographic structures of a serine-bound reaction intermediate of 2 with SHV-1 (class A) and GC1 (class C) enzymes, compounds 14a-l were designed and synthesized. Penems are proposed to form a seven-membered 1,4 thiazepine ring in both class A and C beta-lactamases. The interaction energy calculation for the enzyme-bound intermediates favor the formation of the C7 R enantiomer over the S enantiomer of the 1,4-thiazepine in both beta-lactamases, which is consistent with those obtained from the crystal structure of 2 with SHV-1 and GC1.
Collapse
Affiliation(s)
- Aranapakam M Venkatesan
- Wyeth Research, Chemical and Screening Sciences, Department of Infectious Disease and Biological Technologies, 401 N. Middletown Road, Pearl River, New York 10965, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J Am Chem Soc 2006; 128:2970-6. [PMID: 16506777 PMCID: PMC1544378 DOI: 10.1021/ja056806m] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Beta-lactamases confer bacterial resistance to beta-lactam antibiotics, such as penicillins. The characteristic class C beta-lactamase AmpC catalyzes the reaction with several key residues including Ser64, Tyr150, and Lys67. Here, we describe a 1.07 A X-ray crystallographic structure of AmpC beta-lactamase in complex with a boronic acid deacylation transition-state analogue. The high quality of the electron density map allows the determination of many proton positions. The proton on the Tyr150 hydroxyl group is clearly visible and is donated to the boronic oxygen mimicking the deacylation water. Meanwhile, Lys67 hydrogen bonds with Ser64Ogamma, Asn152Odelta1, and the backbone oxygen of Ala220. This suggests that this residue is positively charged and has relinquished the hydrogen bond with Tyr150 observed in acyl-enzyme complex structures. Together with previous biochemical and NMR studies, these observations indicate that Tyr150 is protonated throughout the reaction coordinate, disfavoring mechanisms that involve a stable tyrosinate as the general base for deacylation. Rather, the hydroxyl of Tyr150 appears to be well positioned to electrostatically stabilize the negative charge buildup in the tetrahedral high-energy intermediate. This structure, in itself, appears consistent with a mechanism involving either Tyr150 acting as a transient catalytic base in conjunction with a neutral Lys67 or the lactam nitrogen as the general base. Whereas mutagenesis studies suggest that Lys67 may be replaced by an arginine, disfavoring the conjugate base mechanism, distinguishing between these two hypotheses may ultimately depend on direct determination of the pK(a) of Lys67 along the reaction coordinate.
Collapse
Affiliation(s)
- Yu Chen
- Department of Pharmaceutical Chemistry, University of California-San Francisco, QB3 Building Room 508D, 1700 4th Street, San Francisco, CA 94143-2550, USA
| | | | | | | | | |
Collapse
|
37
|
Hata M, Tanaka Y, Fujii Y, Neya S, Hoshino T. A Theoretical Study on the Substrate Deacylation Mechanism of Class C β-Lactamase. J Phys Chem B 2005; 109:16153-60. [PMID: 16853052 DOI: 10.1021/jp045403q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The whole reaction of the deacylation of class C beta-lactamase was investigated by performing quantum chemical calculations under physiological conditions. In this study, the X-ray crystallographic structure of the inhibitor moxalactam-bound class C beta-lactamase (Patera et al. J. Am. Chem. Soc. 2000, 122, 10504-10512.) was utilized and moxalactam was changed into the substrate cefaclor. A model for quantum chemical calculations was constructed using an energy-minimized structure of the substrate-bound enzyme obtained by molecular mechanics calculation, in which the enzyme was soaked in thousands of TIP3P water molecules. It was found that the deacylation reaction consisted of two elementary processes. The first process was formation of a tetrahedral intermediate, which was initiated by the activation of catalytic water by Tyr150, and the second process was detachment of the hydroxylated substrate from the enzyme, which associated with proton transfer from the side chain of Lys67 to Ser64O(gamma). The first process is a rate-determining process, and the activation energy was estimated to be 30.47 kcal/mol from density functional theory calculations considering electron correlation (B3LYP/6-31G**). The side chain of Tyr150 was initially in a deprotonated state and was stably present in the active site of the acyl-enzyme complex, being held by Lys67 and Lys315 cooperatively.
Collapse
Affiliation(s)
- Masayuki Hata
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.
| | | | | | | | | |
Collapse
|
38
|
Sulton D, Pagan-Rodriguez D, Zhou X, Liu Y, Hujer AM, Bethel CR, Helfand MS, Thomson JM, Anderson VE, Buynak JD, Ng LM, Bonomo RA. Clavulanic acid inactivation of SHV-1 and the inhibitor-resistant S130G SHV-1 beta-lactamase. Insights into the mechanism of inhibition. J Biol Chem 2005; 280:35528-36. [PMID: 15987690 DOI: 10.1074/jbc.m501251200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clavulanic acid is a potent mechanism-based inhibitor of TEM-1 and SHV-1beta-lactamases, enzymes that confer resistance to beta-lactams in many gram-negative pathogens. This compound has enjoyed widespread clinical use as part of beta-lactam beta-lactamase inhibitor therapy directed against penicillin-resistant pathogens. Unfortunately, the emergence of clavulanic acid-resistant variants of TEM-1 and SHV-1 beta-lactamase significantly compromise the efficacy of this combination. A single amino acid change at Ambler position Ser130 (Ser --> Gly) results in resistance to inactivation by clavulanate in the SHV-1 and TEM-1beta-lactamases. Herein, we investigated the inactivation of SHV-1 and the inhibitor-resistant S130G variant beta-lactamases by clavulanate. Using liquid chromatography electrospray ionization mass spectrometry, we detected multiple modified proteins when SHV-1 beta-lactamase is inactivated by clavulanate. Matrix-assisted laser desorption ionization-time of flight mass spectrometry was used to study tryptic digests of SHV-1 and S130Gbeta-lactamases (+/- inactivation with clavulanate) and identified peptides modified at the active site Ser70. Ultraviolet (UV) difference spectral studies comparing SHV-1 and S130Gbeta-lactamases inactivated by clavulanate showed that the formation of reaction intermediates with absorption maxima at 227 and 280 nm are diminished and delayed when S130Gbeta-lactamase is inactivated. We conclude that the clavulanic acid inhibition of the S130G beta-lactamase must follow a branch of the normal inactivation pathway. These findings highlight the importance of understanding the intermediates formed in the inactivation process of inhibitor-resistant beta-lactamases and suggest how strategic chemical design can lead to novel ways to inhibit beta-lactamases.
Collapse
Affiliation(s)
- Deley Sulton
- Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Michaux C, Charlier P, Frère JM, Wouters J. Crystal structure of BRL 42715, C6-(N1-methyl-1,2,3-triazolylmethylene)penem, in complex with Enterobacter cloacae 908R beta-lactamase: evidence for a stereoselective mechanism from docking studies. J Am Chem Soc 2005; 127:3262-3. [PMID: 15755127 DOI: 10.1021/ja0426241] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BRL 42715, C6-(N1-methyl-1,2,3-triazolylmethylene)penem, is an active-site-directed inactivator of bacterial beta-lactamases. The crystal structure of Enterobacter cloacae 908R class C beta-lactamase in complex with BRL 42715, docking, and energy minimization studies explain stereoselectivity of the binding of C6-(heterocyclic methylene)penems against class C beta-lactamase.
Collapse
Affiliation(s)
- Catherine Michaux
- Laboratoire de Chimie Biologique Structurale, Université of Namur, 5000 Namur, Belgium
| | | | | | | |
Collapse
|
40
|
Fisher JF, Meroueh SO, Mobashery S. Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity. Chem Rev 2005; 105:395-424. [PMID: 15700950 DOI: 10.1021/cr030102i] [Citation(s) in RCA: 684] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | | | |
Collapse
|
41
|
Georgopapadakou NH. β-Lactamase inhibitors: evolving compounds for evolving resistance targets. Expert Opin Investig Drugs 2005; 13:1307-18. [PMID: 15461559 DOI: 10.1517/13543784.13.10.1307] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The many and diverse beta-lactamases produced by bacteria, particularly by Gram-negative pathogens, are increasingly posing a serious threat to the clinical utility of beta-lactams. First-generation inhibitors (clavulanic acid, sulbactam, tazobactam) focus on Ambler class A enzymes. However, recent structural upgrades of class A beta-lactamases (e.g. TEM, SHV) have extended their spectrum (extended-spectrum beta-lactamases and carbapenemases [Sme, NMC-A, IMI-1]) and have brought about the possibility of beta-lactamase-inhibitor resistance. Furthermore, the mobilisation and spread of originally chromosomal class C enzymes (CMY, MIR), the growing clinical importance of class B enzymes (IMP, VIM), the emergence of inhibitor-resistant, broad spectrum class D (OXA) enzymes and the co-existence of different classes of beta-lactamases in the same pathogen have spurred research toward universal inhibitors. A complicating issue is target accessibility in Gram-negative bacteria, particularly in Enterobacter, Acinetobacter, Pseudomonas, Stenotrophomonas and other organisms, which is necessary in order for the inhibitor to synergise with vulnerable beta-lactam antibiotics. Several new, broad-spectrum inhibitors have emerged: cephem sulfones and oxapenems are upgrades of penam sulfones and oxapenams, respectively, with cephem sulfones possibly extending their inhibition to class B metallo-enzymes; and boronates and phosphonates are designed de novo, based on common structural and mechanistic features of serine beta-lactamases.
Collapse
|
42
|
Weiss WJ, Petersen PJ, Murphy TM, Tardio L, Yang Y, Bradford PA, Venkatesan AM, Abe T, Isoda T, Mihira A, Ushirogochi H, Takasake T, Projan S, O'Connell J, Mansour TS. In vitro and in vivo activities of novel 6-methylidene penems as beta-lactamase inhibitors. Antimicrob Agents Chemother 2005; 48:4589-96. [PMID: 15561830 PMCID: PMC529194 DOI: 10.1128/aac.48.12.4589-4596.2004] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Novel penem molecules with heterocycle substitutions at the 6 position via a methylidene linkage were investigated for their activities and efficacy as beta-lactamase inhibitors. The concentrations of these molecules that resulted in 50% inhibition of enzyme activity were 0.4 to 3.1 nM for the TEM-1 enzyme, 7.8 to 72 nM for Imi-1, 1.5 to 4.8 nM for AmpC, and 14 to 260 nM for a CcrA metalloenzyme. All the inhibitors were more stable than imipenem against hydrolysis by hog and human dehydropeptidases. Piperacillin was combined with a constant 4-microg/ml concentration of each inhibitor for MIC determinations. The combinations reduced piperacillin MICs by 2- to 32-fold for extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae strains. The MICs for piperacillin-resistant (MIC of piperacillin, >64 microg/ml) strains of Enterobacter spp., Citrobacter spp., and Serratia spp. were reduced to the level of susceptibility (MIC of piperacillin, < or =16 microg/ml) when the drug was combined with 4, 2, or 1 microg of these penem inhibitors/ml. Protection against acute lethal bacterial infections with class A and C beta-lactamase- and ESBL-producing organisms in mice was also demonstrated with piperacillin plus inhibitor. Median effective doses were reduced by approximately two- to eightfold compared to those of piperacillin alone when the drug was combined with the various inhibitors at a 4:1 ratio. Pharmacokinetic analysis after intravenous administration of the various inhibitors showed mean residence times of 0.1 to 0.5 h, clearance rates of 15 to 81 ml/min/kg, and volumes of distribution between 0.4 and 2.5 liters/kg. The novel methylidene penem molecules inhibit both class A and class C enzymes and warrant further investigation for potential as therapeutic agents when used in combination with a beta-lactam antibiotic.
Collapse
Affiliation(s)
- William J Weiss
- Infectious Disease and Oncology, Wyeth Research, Pearl River, New York 10965, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Venkatesan AM, Gu Y, Dos Santos O, Abe T, Agarwal A, Yang Y, Petersen PJ, Weiss WJ, Mansour TS, Nukaga M, Hujer AM, Bonomo RA, Knox JR. Structure−Activity Relationship of 6-Methylidene Penems Bearing Tricyclic Heterocycles as Broad-Spectrum β-Lactamase Inhibitors: Crystallographic Structures Show Unexpected Binding of 1,4-Thiazepine Intermediates. J Med Chem 2004; 47:6556-68. [PMID: 15588091 DOI: 10.1021/jm049680x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The design and synthesis of a series of seven tricyclic 6-methylidene penems as novel class A and C serine beta-lactamase inhibitors is described. These compounds proved to be very potent inhibitors of the TEM-1 and AmpC beta-lactamases and less so against the class B metallo-beta-lactamase CcrA. In combination with piperacillin, their in vitro activities enhanced susceptibility of all class C resistant strains from various bacteria. Crystallographic structures of a serine-bound reaction intermediate of 17 with the class A SHV-1 and class C GC1 enzymes have been established to resolutions of 2.0 and 1.4 A, respectively, and refined to R-factors equal 0.163 and 0.145. In both beta-lactamases, a seven-membered 1,4-thiazepine ring has formed. The stereogenic C7 atom in the ring has the R configuration in the SHV-1 intermediate and has both R and S configurations in the GC1 intermediate. Hydrophobic stacking interactions between the tricyclic C7 substituent and a tyrosine side chain, rather than electrostatic or hydrogen bonding by the C3 carboxylic acid group, dominate in both complexes. The formation of the 1,4- thiazepine ring structures is proposed based on a 7-endo-trig cyclization.
Collapse
|
44
|
Venkatesan AM, Agarwal A, Abe T, Ushirogochi H, Yamamura I, Kumagai T, Petersen PJ, Weiss WJ, Lenoy E, Yang Y, Shlaes DM, Ryan JL, Mansour TS. Novel imidazole substituted 6-methylidene-penems as broad-spectrum β-lactamase inhibitors. Bioorg Med Chem 2004; 12:5807-17. [PMID: 15498657 DOI: 10.1016/j.bmc.2004.08.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Revised: 08/20/2004] [Accepted: 08/26/2004] [Indexed: 10/26/2022]
Abstract
Beta-lactamases are serine and metallo-dependent enzymes produced by the bacteria in defense against beta-lactam antibiotics. Production of class-A, class-B, and class-C enzymes by the bacteria make the use of beta-lactam antibiotics ineffective in certain cases. To overcome resistance to beta-lactam antibiotics, several beta-lactamase inhibitors such as clavulanic acid, sulbactam, and tazobactam are widely used in the clinic in combination with beta-lactam antibiotics. However, single point mutations within these enzymes have allowed bacteria to overcome the inhibitory effect of the commercially approved beta-lactamase inhibitors. Although the commercially available beta-lactamase inhibitor/beta-lactam antibiotic combinations are effective against class-A producing bacteria and many extended spectrum beta-lactamase (ESBL's) producing bacteria they are less effective against class-C enzymes expressing bacteria. To circumvent this problem, based on modeling studies several novel imidazole substituted 6-methylidene-penem derivatives were synthesized and tested against various beta-lactamase producing isolates. The present paper deals with the synthesis and structure-activity relationships (SAR) of these compounds.
Collapse
|
45
|
Tabei K, Feng X, Venkatesan AM, Abe T, Hideki U, Mansour TS, Siegel MM. Mechanism of inactivation of beta-lactamases by novel 6-methylidene penems elucidated using electrospray ionization mass spectrometry. J Med Chem 2004; 47:3674-88. [PMID: 15214794 DOI: 10.1021/jm049903j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reactions of 6-methylidene penems 4-7 with beta-lactamases (TEM-1, SHV-1, Amp-C) were characterized by electrospray ionization mass spectrometry (ESI-MS). The kinetics of the reactions were monitored, demonstrating that only one penem molecule reacts to form an acyl-enzyme complex. For penem 5, the ESI-MS/MS spectrum of the hydrolysis product produced in the reaction was identical to the spectrum generated from a synthesized dihydro[1,4]thiazepine 10, confirming the rearrangement of the penem ring system to a seven-membered dihydro[1,4]thiazepine structure. Gas-phase ESI-MS/MS fragmentation data were rationalized due to tautomerization between imine and enamine substructures. ESI-MS/MS analysis of the T-6 trypsin-digested fragments of TEM-1 and SHV-1 demonstrated that the penems were only attached to Ser-70 of these class A beta-lactamases and that the penem ring structures were rearranged to seven-membered dihydro[1,4]thiazepines.
Collapse
Affiliation(s)
- Keiko Tabei
- Wyeth Research, Chemical and Screening Sciences, Chemical Technologies and Medicinal Chemistry, Pearl River, NY 10965, USA
| | | | | | | | | | | | | |
Collapse
|
46
|
Nukaga M, Kumar S, Nukaga K, Pratt RF, Knox JR. Hydrolysis of third-generation cephalosporins by class C beta-lactamases. Structures of a transition state analog of cefotoxamine in wild-type and extended spectrum enzymes. J Biol Chem 2003; 279:9344-52. [PMID: 14660590 DOI: 10.1074/jbc.m312356200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial resistance to the third-generation cephalosporins is an issue of great concern in current antibiotic therapeutics. An important source of this resistance is from production of extended-spectrum (ES) beta-lactamases by bacteria. The Enterobacter cloacae GC1 enzyme is an example of a class C ES beta-lactamase. Unlike wild-type (WT) forms, such as the E. cloacae P99 and Citrobacter freundii enzymes, the ES GC1 beta-lactamase is able to rapidly hydrolyze third-generation cephalosporins such as cefotaxime and ceftazidime. To understand the basis for this ES activity, m-nitrophenyl 2-(2-aminothiazol-4-yl)-2-[(Z)-methoxyimino]acetylaminomethyl phosphonate has been synthesized and characterized. This phosphonate was designed to generate a transition state analog for turnover of cefotaxime. The crystal structures of complexes of the phosphonate with both ES GC1 and WT C. freundii GN346 beta-lactamases have been determined to high resolution (1.4-1.5 Angstroms). The serine-bound analog of the tetrahedral transition state for deacylation exhibits a very different binding geometry in each enzyme. In the WT beta-lactamase the cefotaxime-like side chain is crowded against the Omega loop and must protrude from the binding site with its methyloxime branch exposed. In the ES enzyme, a mutated Omega loop adopts an alternate conformation allowing the side chain to be much more buried. During the binding and turnover of the cefotaxime substrate by this ES enzyme, it is proposed that ligand-protein contacts and intra-ligand contacts are considerably relieved relative to WT, facilitating positioning and activation of the hydrolytic water molecule. The ES beta-lactamase is thus able to efficiently inactivate third-generation cephalosporins.
Collapse
Affiliation(s)
- Michiyoshi Nukaga
- Department of Molecular and Cell Biology, The University of Connecticut, Storrs, Connecticut 06269-3125, USA
| | | | | | | | | |
Collapse
|