1
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Medrano FJ, Hernando-Amado S, Martínez JL, Romero A. A new type of Class C β-lactamases defined by PIB-1. A metal-dependent carbapenem-hydrolyzing β-lactamase, from Pseudomonas aeruginosa: Structural and functional analysis. Int J Biol Macromol 2024; 277:134298. [PMID: 39097051 DOI: 10.1016/j.ijbiomac.2024.134298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/18/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024]
Abstract
Antibiotic resistance is one of most important health concerns nowadays, and β-lactamases are the most important resistance determinants. These enzymes, based on their structural and functional characteristics, are grouped in four categories (A, B, C and D). We have solved the structure of PIB-1, a Pseudomonas aeruginosa chromosomally-encoded β-lactamase, in its apo form and in complex with meropenem and zinc. These crystal structures show that it belongs to the Class C β-lactamase group, although it shows notable differences, especially in the Ω- and P2-loops, which are important for the enzymatic activity. Functional analysis showed that PIB-1 is able to degrade carbapenems but not cephalosporins, the typical substrate of Class C β-lactamases, and that its catalytic activity increases in the presence of metal ions, especially zinc. They do not bind to the active-site but they induce the formation of trimers that show an increased capacity for the degradation of the antibiotics, suggesting that this oligomer is more active than the other oligomeric species. While PIB-1 is structurally a Class C β-lactamase, the low sequence conservation, substrate profile and its metal-dependence, prompts us to position this enzyme as the founder of a new group inside the Class C β-lactamases. Consequently, its diversity might be wider than expected.
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Affiliation(s)
- Francisco Javier Medrano
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Sara Hernando-Amado
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28043 Madrid, Spain
| | - José Luis Martínez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28043 Madrid, Spain
| | - Antonio Romero
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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2
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Castanheira M, Mendes RE, Gales AC. Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex. Clin Infect Dis 2023; 76:S166-S178. [PMID: 37125466 PMCID: PMC10150277 DOI: 10.1093/cid/ciad109] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.
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Affiliation(s)
| | | | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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3
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The Class A β-Lactamase Produced by Burkholderia Species Compromises the Potency of Tebipenem against a Panel of Isolates from the United States. Antibiotics (Basel) 2022; 11:antibiotics11050674. [PMID: 35625319 PMCID: PMC9137479 DOI: 10.3390/antibiotics11050674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 12/04/2022] Open
Abstract
Tebipenem-pivoxil hydrobromide, an orally bioavailable carbapenem, is currently in clinical development for the treatment of extended-spectrum β-lactamase- and AmpC-producing Enterobacterales. Previously, tebipenem was found to possess antimicrobial activity against the biothreat pathogens, Burkholderia pseudomallei and Burkholderia mallei. Thus, herein, tebipenem was evaluated against a panel of 150 curated strains of Burkholderia cepacia complex (Bcc) and Burkholderia gladioli, pathogens that infect people who are immunocompromised or have cystic fibrosis. Using the provisional susceptibility breakpoint of 0.12 mg/L for tebipenem, 100% of the Bcc and B. gladioli tested as being provisionally resistant to tebipenem. Bcc and B. gladioli possess two inducible chromosomal β-lactamases, PenA and AmpC. Using purified PenA1 and AmpC1, model β-lactamases expressed in Burkholderia multivorans ATCC 17616, PenA1 was found to slowly hydrolyze tebipenem, while AmpC1 was inhibited by tebipenem with a k2/K value of 1.9 ± 0.1 × 103 M−1s−1. In addition, tebipenem was found to be a weak inducer of blaPenA1 expression. The combination of the slow hydrolysis by PenA1 and weak induction of blaPenA1 likely compromises the potency of tebipenem against Bcc and B. gladioli.
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4
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Srikanth D, Vinayak Joshi S, Ghouse Shaik M, Pawar G, Bujji S, Kanchupalli V, Chopra S, Nanduri S. A Comprehensive Review on Potential Therapeutic Inhibitors of Nosocomial Acinetobacter baumannii Superbugs. Bioorg Chem 2022; 124:105849. [DOI: 10.1016/j.bioorg.2022.105849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/20/2022]
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5
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Chiou J, Cheng Q, Shum PTF, Wong MHY, Chan EWC, Chen S. Structural and Functional Characterization of OXA-48: Insight into Mechanism and Structural Basis of Substrate Recognition and Specificity. Int J Mol Sci 2021; 22:ijms222111480. [PMID: 34768916 PMCID: PMC8583920 DOI: 10.3390/ijms222111480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/21/2021] [Indexed: 02/04/2023] Open
Abstract
Class D β-lactamase OXA-48 is widely distributed among Gram-negative bacteria and is an important determinant of resistance to the last-resort carbapenems. Nevertheless, the detailed mechanism by which this β-lactamase hydrolyzes its substrates remains poorly understood. In this study, the complex structures of OXA-48 and various β-lactams were modeled and the potential active site residues that may interact with various β-lactams were identified and characterized to elucidate their roles in OXA-48 substrate recognition. Four residues, namely S70, K73, S118, and K208 were found to be essential for OXA-48 to undergo catalytic hydrolysis of various penicillins and carbapenems both in vivo and in vitro. T209 was found to be important for hydrolysis of imipenem, whereas R250 played a major role in hydrolyzing ampicillin, imipenem, and meropenem most likely by forming a H-bond or salt-bridge between the side chain of these two residues and the carboxylate oxygen ions of the substrates. Analysis of the effect of substitution of alanine in two residues, W105 and L158, revealed their roles in mediating the activity of OXA-48. Our data show that these residues most likely undergo hydrophobic interaction with the R groups and the core structure of the β-lactam ring in penicillins and the carbapenems, respectively. Unlike OXA-58, mass spectrometry suggested a loss of the C6-hydroxyethyl group during hydrolysis of meropenem by OXA-48, which has never been demonstrated in Class D carbapenemases. Findings in this study provide comprehensive knowledge of the mechanism of the substrate recognition and catalysis of OXA-type β-lactamases.
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Affiliation(s)
- Jiachi Chiou
- State Key Laboratory of Chiroscience, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; (J.C.); (Q.C.); (P.T.-f.S.); (M.H.-y.W.); (E.W.-c.C.)
| | - Qipeng Cheng
- State Key Laboratory of Chiroscience, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; (J.C.); (Q.C.); (P.T.-f.S.); (M.H.-y.W.); (E.W.-c.C.)
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Perry Tim-fat Shum
- State Key Laboratory of Chiroscience, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; (J.C.); (Q.C.); (P.T.-f.S.); (M.H.-y.W.); (E.W.-c.C.)
| | - Marcus Ho-yin Wong
- State Key Laboratory of Chiroscience, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; (J.C.); (Q.C.); (P.T.-f.S.); (M.H.-y.W.); (E.W.-c.C.)
| | - Edward Wai-chi Chan
- State Key Laboratory of Chiroscience, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; (J.C.); (Q.C.); (P.T.-f.S.); (M.H.-y.W.); (E.W.-c.C.)
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
- Correspondence:
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6
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Hussain HI, Aqib AI, Seleem MN, Shabbir MA, Hao H, Iqbal Z, Kulyar MFEA, Zaheer T, Li K. Genetic basis of molecular mechanisms in β-lactam resistant gram-negative bacteria. Microb Pathog 2021; 158:105040. [PMID: 34119627 PMCID: PMC8445154 DOI: 10.1016/j.micpath.2021.105040] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022]
Abstract
Antibiotic-resistant bacteria are considered one of the major global threats to human and animal health. The most harmful among the resistant bacteria are β-lactamase producing Gram-negative species (β-lactamases). β-lactamases constitute a paradigm shift in the evolution of antibiotic resistance. Therefore, it is imperative to present a comprehensive review of the mechanisms responsible for developing antimicrobial resistance. Resistance due to β-lactamases develops through a variety of mechanisms, and the number of resistant genes are involved that can be transferred between bacteria, mostly via plasmids. Over time, these new molecular-based resistance mechanisms have been progressively disclosed. The present review article provides information on the recent findings regarding the molecular mechanisms of resistance to β-lactams in Gram-negative bacteria, including CTX-M-type ESBLs with methylase activity, plasmids harbouring phages with β-lactam resistance genes, the co-presence of β-lactam resistant genes of unique combinations and the presence of β-lactam and non-β-lactam antibiotic-resistant genes in the same bacteria. Keeping in view, the molecular level resistance development, multifactorial and coordinated measures may be taken to counter the challenge of rapidly increasing β-lactam resistance.
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Affiliation(s)
- Hafiz Iftikhar Hussain
- Department of Pathology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Amjad Islam Aqib
- Department of Medicine, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan.
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, USA
| | | | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zahid Iqbal
- Department of Pharmacology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China.
| | | | - Tean Zaheer
- Department of Parasitology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, PR China.
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7
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Gholap S, Yao C, Green O, Babjak M, Jakubec P, Malatinský T, Ihssen J, Wick L, Spitz U, Shabat D. Chemiluminescence Detection of Hydrogen Sulfide Release by β-Lactamase-Catalyzed β-Lactam Biodegradation: Unprecedented Pathway for Monitoring β-Lactam Antibiotic Bacterial Resistance. Bioconjug Chem 2021; 32:991-1000. [PMID: 33896185 PMCID: PMC8382227 DOI: 10.1021/acs.bioconjchem.1c00149] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/12/2021] [Indexed: 12/20/2022]
Abstract
β-Lactamase positive bacteria represent a growing threat to human health because of their resistance to commonly used antibiotics. Therefore, development of new diagnostic methods for identification of β-lactamase positive bacteria is of high importance for monitoring the spread of antibiotic-resistant bacteria. Here, we report the discovery of a new biodegradation metabolite (H2S), generated through β-lactamase-catalyzed hydrolysis of β-lactam antibiotics. This discovery directed us to develop a distinct molecular technique for monitoring bacterial antibiotic resistance. The technique is based on a highly efficient chemiluminescence probe, designed for detection of the metabolite, hydrogen sulfide, that is released upon biodegradation of β-lactam by β-lactamases. Such an assay can directly indicate if antibiotic bacterial resistance exists for a certain examined β-lactam. The assay was successfully demonstrated for five different β-lactam antibiotics and eight β-lactam resistant bacterial strains. Importantly, in a functional bacterial assay, our chemiluminescence probe was able to clearly distinguish between a β-lactam resistant bacterial strain and a sensitive one. As far as we know, there is no previous documentation for such a biodegradation pathway of β-lactam antibiotics. Bearing in mind the data obtained in this study, we propose that hydrogen sulfide should be considered as an emerging β-lactam metabolite for detection of bacterial resistance.
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Affiliation(s)
- Sachin
Popat Gholap
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 Israel
| | - Chunyan Yao
- Biosynth
Carbosynth, Rietlistrasse
4 Postfach 125 9422 Staad, Switzerland
| | - Ori Green
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 Israel
| | - Matej Babjak
- Department
of Organic Chemistry, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 81237 Bratislava, Slovakia
| | - Pavol Jakubec
- Auchem
s.r.o., A. Hlinku 1452/3, 022 01 Čadca, Slovakia
| | | | - Julian Ihssen
- Biosynth
Carbosynth, Rietlistrasse
4 Postfach 125 9422 Staad, Switzerland
| | - Lukas Wick
- Biosynth
Carbosynth, Rietlistrasse
4 Postfach 125 9422 Staad, Switzerland
| | - Urs Spitz
- Biosynth
Carbosynth, Rietlistrasse
4 Postfach 125 9422 Staad, Switzerland
| | - Doron Shabat
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 Israel
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8
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Caselli E, Fini F, Introvigne ML, Stucchi M, Taracila MA, Fish ER, Smolen KA, Rather PN, Powers RA, Wallar BJ, Bonomo RA, Prati F. 1,2,3-Triazolylmethaneboronate: A Structure Activity Relationship Study of a Class of β-Lactamase Inhibitors against Acinetobacter baumannii Cephalosporinase. ACS Infect Dis 2020; 6:1965-1975. [PMID: 32502340 PMCID: PMC7458062 DOI: 10.1021/acsinfecdis.0c00254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Boronic acid transition state inhibitors (BATSIs) are known reversible covalent
inhibitors of serine β-lactamases. The selectivity and high potency of specific
BATSIs bearing an amide side chain mimicking the β-lactam’s amide side
chain are an established and recognized synthetic strategy. Herein, we describe a new
class of BATSIs where the amide group is replaced by a bioisostere triazole; these
compounds were designed as molecular probes. To this end, a library of 26
α-triazolylmethaneboronic acids was synthesized and tested against the clinically
concerning Acinetobacter-derived cephalosporinase, ADC-7. In steady
state analyses, these compounds demonstrated
Ki values ranging from 90 nM to 38
μM (±10%). Five compounds were crystallized in complex with ADC-7
β-lactamase, and all the crystal structures reveal the triazole is in the putative
amide binding site, thus confirming the triazole–amide bioisosterism. The easy
synthetic access of these new inhibitors as prototype scaffolds allows the insertion of
a wide range of chemical groups able to explore the enzyme binding site and provides
insights on the importance of specific residues in recognition and catalysis. The best
inhibitor identified, compound 6q
(Ki 90 nM), places a tolyl group near
Arg340, making favorable cation−π interactions. Notably, the structure of
6q does not resemble the natural substrate of the β-lactamase yet
displays a pronounced inhibition activity, in addition to lowering the minimum
inhibitory concentration (MIC) of ceftazidime against three bacterial strains expressing
class C β-lactamases. In summary, these observations validate the
α-triazolylboronic acids as a promising template for further inhibitor design.
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Affiliation(s)
- Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Francesco Fini
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Maria Luisa Introvigne
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Mattia Stucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Magdalena A. Taracila
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Research Service, Cleveland, Ohio 44106, United States
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Erin R. Fish
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Kali A. Smolen
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Philip N. Rather
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, Georgia 30322 United States
| | - Rachel A. Powers
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Bradley J. Wallar
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Robert A. Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Research Service, Cleveland, Ohio 44106, United States
- Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106, United States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio 44106, United States
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
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9
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Krajnc A, Lang PA, Panduwawala TD, Brem J, Schofield CJ. Will morphing boron-based inhibitors beat the β-lactamases? Curr Opin Chem Biol 2019; 50:101-110. [PMID: 31004962 PMCID: PMC6591701 DOI: 10.1016/j.cbpa.2019.03.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/13/2023]
Abstract
The β-lactams remain the most important antibacterials, but their use is increasingly compromised by resistance, importantly by β-lactamases. Although β-lactam and non-β-lactam inhibitors forming stable acyl-enzyme complexes with nucleophilic serine β-lactamases (SBLs) are widely used, these are increasingly susceptible to evolved SBLs and do not inhibit metallo-β-lactamases (MBLs). Boronic acids and boronate esters, especially cyclic ones, can potently inhibit both SBLs and MBLs. Vaborbactam, a monocyclic boronate, is approved for clinical use, but its β-lactamase coverage is limited. Bicyclic boronates rapidly react with SBLs and MBLs forming stable enzyme-inhibitor complexes that mimic the common anionic high-energy tetrahedral intermediates in SBL/MBL catalysis, as revealed by crystallography. The ability of boronic acids to 'morph' between sp2 and sp3 hybridisation states may help enable potent inhibition. There is limited structure-activity relationship information on the (bi)cyclic boronate inhibitors compared to β-lactams, hence scope for creativity towards new boron-based β-lactamase inhibitors/antibacterials.
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Affiliation(s)
- Alen Krajnc
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Pauline A Lang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tharindi D Panduwawala
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
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10
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Libreros-Zúñiga GA, dos Santos Silva C, Salgado Ferreira R, Dias MVB. Structural Basis for the Interaction and Processing of β-Lactam Antibiotics by l,d-Transpeptidase 3 (Ldt Mt3) from Mycobacterium tuberculosis. ACS Infect Dis 2019; 5:260-271. [PMID: 30556998 DOI: 10.1021/acsinfecdis.8b00244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting Mycobacterium tuberculosis peptidoglycans with β-lactam antibiotics represents a strategy to address increasing resistance to antitubercular drugs. β-Lactams inhibit peptidoglycan synthases such as l,d-transpeptidases, a group of carbapenem-sensitive enzymes that stabilize peptidoglycans through 3 → 3 cross-links. M. tuberculosis encodes five l,d-transpeptidases (LdtMt1-5), of which LdtMt3 is one of the less understood. Herein, we structurally characterized the apo and faropenem-acylated forms of LdtMt3 at 1.3 and 1.8 Å resolution, respectively. These structures revealed a fold and catalytic diad similar to those of other LdtsMt enzymes, supporting its involvement in transpeptidation reactions despite divergences in active site size and charges. The LdtMt3-faropenem structure indicated that faropenem is degraded after Cys-246 acylation, and possibly only a β-OH-butyrate or an acetyl group (C2H3O) covalently attached to the enzyme remains, an observation that strongly supports the notion that LdtMt3 is inactivated by β-lactams. Docking simulations with intact β-lactams predicted key LdtMt3 residues that interact with these antibiotics. We also characterized the heat of acylation involved in the binding and reaction of LdtMt3 for ten β-lactams belonging to four different classes, and imipenem had the highest inactivation constant. This work provides key insights into the structure, binding mechanisms, and degradation of β-lactams by LdtMt3, which may be useful for the development of additional β-lactams with potential antitubercular activity.
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Affiliation(s)
- Gerardo Andrés Libreros-Zúñiga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374 São Paulo, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265 São José do Rio Preto, Brazil
- Departamento de Microbiología, Facultad de Salud, Universidad del Valle, Calle 4B No. 36-00 Cali, Colombia
| | - Catharina dos Santos Silva
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374 São Paulo, Brazil
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Belo Horizonte, Brazil
| | - Marcio Vinicius Bertacine Dias
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374 São Paulo, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265 São José do Rio Preto, Brazil
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11
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Caselli E, Romagnoli C, Powers RA, Taracila MA, Bouza AA, Swanson HC, Smolen KA, Fini F, Wallar BJ, Bonomo RA, Prati F. Inhibition of Acinetobacter-Derived Cephalosporinase: Exploring the Carboxylate Recognition Site Using Novel β-Lactamase Inhibitors. ACS Infect Dis 2018; 4:337-348. [PMID: 29144725 DOI: 10.1021/acsinfecdis.7b00153] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Boronic acids are attracting a lot of attention as β-lactamase inhibitors, and in particular, compound S02030 ( Ki = 44 nM) proved to be a good lead compound against ADC-7 ( Acinetobacter-derived cephalosporinase), one of the most significant resistance determinants in A. baumannii. The atomic structure of the ADC-7/S02030 complex highlighted the importance of critical structural determinants for recognition of the boronic acids. Herein, to elucidate the role in recognition of the R2-carboxylate, which mimics the C3/C4 found in β-lactams, we designed, synthesized, and characterized six derivatives of S02030 (3a). Out of the six compounds, the best inhibitors proved to be those with an explicit negative charge (compounds 3a-c, 3h, and 3j, Ki = 44-115 nM), which is in contrast to the derivatives where the negative charge is omitted, such as the amide derivative 3d ( Ki = 224 nM) and the hydroxyamide derivative 3e ( Ki = 155 nM). To develop a structural characterization of inhibitor binding in the active site, the X-ray crystal structures of ADC-7 in a complex with compounds 3c, SM23, and EC04 were determined. All three compounds share the same structural features as in S02030 but only differ in the carboxy-R2 side chain, thereby providing the opportunity of exploring the distinct binding mode of the negatively charged R2 side chain. This cephalosporinase demonstrates a high degree of versatility in recognition, employing different residues to directly interact with the carboxylate, thus suggesting the existence of a "carboxylate binding region" rather than a binding site in ADC enzymes. Furthermore, this class of compounds was tested against resistant clinical strains of A. baumannii and are effective at inhibiting bacterial growth in conjunction with a β-lactam antibiotic.
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Affiliation(s)
- Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 101, 41125, Modena, Italy
| | - Chiara Romagnoli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 101, 41125, Modena, Italy
| | - Rachel A. Powers
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Magdalena A. Taracila
- Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Alexandra A. Bouza
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Hollister C. Swanson
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Kali A. Smolen
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Francesco Fini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 101, 41125, Modena, Italy
| | - Bradley J. Wallar
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs
Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
- Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 101, 41125, Modena, Italy
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12
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Daniels BE, Stivala CE. A solid-phase approach for the synthesis of α-aminoboronic acid peptides. RSC Adv 2018; 8:3343-3347. [PMID: 35541192 PMCID: PMC9077542 DOI: 10.1039/c7ra13479g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 01/10/2018] [Indexed: 01/06/2023] Open
Abstract
A solid-phase synthesis of α-aminoboronic acid peptides using a 1-glycerol polystyrene resin is described.
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13
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Docquier JD, Mangani S. An update on β-lactamase inhibitor discovery and development. Drug Resist Updat 2017; 36:13-29. [PMID: 29499835 DOI: 10.1016/j.drup.2017.11.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 11/27/2022]
Abstract
Antibiotic resistance, and the emergence of pan-resistant clinical isolates, seriously threatens our capability to treat bacterial diseases, including potentially deadly hospital-acquired infections. This growing issue certainly requires multiple adequate responses, including the improvement of both diagnosis methods and use of antibacterial agents, and obviously the development of novel antibacterial drugs, especially active against Gram-negative pathogens, which represent an urgent medical need. Considering the clinical relevance of both β-lactam antibiotics and β-lactamase-mediated resistance, the discovery and development of combinations including a β-lactamase inhibitor seems to be particularly attractive, despite being extremely challenging due to the enormous diversity, both structurally and mechanistically, of the potential β-lactamase targets. This review will cover the evolution of currently available β-lactamase inhibitors along with the most recent research leading to new β-lactamase inhibitors of potential clinical interest or already in the stage of clinical development.
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Affiliation(s)
- Jean-Denis Docquier
- Department of Medical Biotechnology, University of Siena, Viale Bracci 16, 53100 Siena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
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14
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Bianchet MA, Pan YH, Basta LAB, Saavedra H, Lloyd EP, Kumar P, Mattoo R, Townsend CA, Lamichhane G. Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase Ldt Mt2 by biapenem and tebipenem. BMC BIOCHEMISTRY 2017; 18:8. [PMID: 28545389 PMCID: PMC5445500 DOI: 10.1186/s12858-017-0082-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/09/2017] [Indexed: 05/29/2023]
Abstract
Background The carbapenem subclass of β-lactams is among the most potent antibiotics available today. Emerging evidence shows that, unlike other subclasses of β-lactams, carbapenems bind to and inhibit non-classical transpeptidases (L,D-transpeptidases) that generate 3 → 3 linkages in bacterial peptidoglycan. The carbapenems biapenem and tebipenem exhibit therapeutically valuable potencies against Mycobacterium tuberculosis (Mtb). Results Here, we report the X-ray crystal structures of MtbL,D-transpeptidase-2 (LdtMt2) complexed with biapenem or tebipenem. Despite significant variations in carbapenem sulfur side chains, biapenem and tebipenem ultimately form an identical adduct that docks to the outer cavity of LdtMt2. We propose that this common adduct is an enzyme catalyzed decomposition of the carbapenem adduct by a mechanism similar to S-conjugate elimination by β-lyases. Conclusion The results presented here demonstrate biapenem and tebipenem bind to the outer cavity of LdtMt2, covalently inactivate the enzyme, and subsequently degrade via an S-conjugate elimination mechanism. We discuss structure based drug design based on the findings and propose that the S-conjugate elimination can be leveraged to design novel agents to deliver and locally release antimicrobial factors to act synergistically with the carbapenem carrier. Electronic supplementary material The online version of this article (doi:10.1186/s12858-017-0082-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mario A Bianchet
- Department of Neurology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA. .,Department of Biophysics and Biophysical Chemistry, Structural Enzymology and Thermodynamics Group, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA.
| | - Ying H Pan
- Department of Neurology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | | | - Harry Saavedra
- Department of Neurology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Evan P Lloyd
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Pankaj Kumar
- Division of Infectious Diseases, Center for Tuberculosis Research, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Rohini Mattoo
- Division of Infectious Diseases, Center for Tuberculosis Research, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA.,Division of Infectious Diseases, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Baltimore, MD, 21231, USA
| | - Gyanu Lamichhane
- Division of Infectious Diseases, Center for Tuberculosis Research, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA. .,Division of Infectious Diseases, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Baltimore, MD, 21231, USA.
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15
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Non-classical transpeptidases yield insight into new antibacterials. Nat Chem Biol 2016; 13:54-61. [PMID: 27820797 PMCID: PMC5477059 DOI: 10.1038/nchembio.2237] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/31/2016] [Indexed: 01/30/2023]
Abstract
Bacterial survival requires an intact peptidoglycan layer, a three-dimensional exoskeleton that encapsulates the cytoplasmic membrane. Historically, the final steps of peptidoglycan synthesis are known to be carried out by D,D-transpeptidases, enzymes that are inhibited by the β-lactams, which constitute >50% of all antibacterials in clinical use. Here, we show that the carbapenem subclass of β-lactams are distinctly effective not only because they inhibit D,D-transpeptidases and are poor substrates for β-lactamases, but primarily because they also inhibit non-classical transpeptidases, namely the L,D-transpeptidases, which generate the majority of linkages in the peptidoglycan of mycobacteria. We have characterized the molecular mechanisms responsible for inhibition of L,D-transpeptidases of Mycobacterium tuberculosis and a range of bacteria including ESKAPE pathogens, and used this information to design, synthesize and test simplified carbapenems with potent antibacterial activity.
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16
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Kurz SG, Hazra S, Bethel CR, Romagnoli C, Caselli E, Prati F, Blanchard JS, Bonomo RA. Inhibiting the β-Lactamase of Mycobacterium tuberculosis (Mtb) with Novel Boronic Acid Transition-State Inhibitors (BATSIs). ACS Infect Dis 2015; 1:234-42. [PMID: 27622739 DOI: 10.1021/acsinfecdis.5b00003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BlaC, the single chromosomally encoded β-lactamase of Mycobacterium tuberculosis, has been identified as a promising target for novel therapies that rely upon β-lactamase inhibition. Boronic acid transition-state inhibitors (BATSIs) are a class of β-lactamase inhibitors which permit rational inhibitor design by combinations of various R1 and R2 side chains. To explore the structural determinants of effective inhibition, we screened a panel of 25 BATSIs to explore key structure-function relationships. We identified a cefoperazone analogue, EC19, which displayed slow, time-dependent inhibition against BlaC with a potency similar to that of clavulanate (Ki* of 0.65 ± 0.05 μM). To further characterize the molecular basis of inhibition, we solved the crystallographic structure of the EC19-BlaC(N172A) complex and expanded our analysis to variant enzymes. The results of this structure-function analysis encourage the design of a novel class of β-lactamase inhibitors, BATSIs, to be used against Mycobacterium tuberculosis.
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Affiliation(s)
- Sebastian G. Kurz
- Department of Medicine, Tufts Medical Center, 600 Washington Street, No. 257, Boston, Massachusetts 02111, United States
| | - Saugata Hazra
- Department of Biotechnology, Indian Institute of Technology Roorkee (IITR), Roorkee, Uttarakhand 247667, India
| | - Christopher R. Bethel
- Research Service, Louis
Stokes Cleveland Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
| | - Chiara Romagnoli
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - Emilia Caselli
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - Fabio Prati
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - John S. Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Robert A. Bonomo
- Research Service, Louis
Stokes Cleveland Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
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17
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Arai S, Yonezawa Y, Okazaki N, Matsumoto F, Shibazaki C, Shimizu R, Yamada M, Adachi M, Tamada T, Kawamoto M, Tokunaga H, Ishibashi M, Blaber M, Tokunaga M, Kuroki R. Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs(+)-selective binding site. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:541-54. [PMID: 25760604 PMCID: PMC4356365 DOI: 10.1107/s1399004714027734] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/19/2014] [Indexed: 11/17/2022]
Abstract
Environmentally friendly absorbents are needed for Sr(2+) and Cs(+), as the removal of the radioactive Sr(2+) and Cs(+) that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs(+) or Sr(2+). The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P31 using X-ray crystallography. Moreover, the locations of bound Sr(2+) and Cs(+) ions were identified by anomalous X-ray diffraction. The location of one Cs(+)-specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na(+) (90 mM Na(+)/10 mM Cs(+)). From an activity assay using isothermal titration calorimetry, the bound Sr(2+) and Cs(+) ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs(+)-binding site provides important information that is useful for the design of artificial Cs(+)-binding sites that may be useful in the bioremediation of radioactive isotopes.
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Affiliation(s)
- Shigeki Arai
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Yasushi Yonezawa
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Nobuo Okazaki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Fumiko Matsumoto
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Chie Shibazaki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Rumi Shimizu
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Mitsugu Yamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Motoyasu Adachi
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Taro Tamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Masahide Kawamoto
- Saga Prefectural Regional Industry Support Center, Kyushu Synchrotron Light Research Center, 8-7 Yayoigaoka, Tosu, Saga 841-0005, Japan
| | - Hiroko Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Matsujiro Ishibashi
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Michael Blaber
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
- College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300, USA
| | - Masao Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Ryota Kuroki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
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18
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Effect of asparagine substitutions in the YXN loop of a class C β-lactamase of Acinetobacter baumannii on substrate and inhibitor kinetics. Antimicrob Agents Chemother 2014; 59:1472-7. [PMID: 25534745 DOI: 10.1128/aac.03537-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Class C cephalosporinases are a growing threat, and inhibitors of these enzymes are currently unavailable. Studies exploring the YXN loop asparagine in the Escherichia coli AmpC, P99, and CMY-2 enzymes have suggested that interactions between C6' or C7' substituents on penicillins or cephalosporins and this Asn are important in determining substrate specificity and enzymatic stability. We sought to characterize the YXN loop asparagine in the clinically important ADC-7 class C β-lactamase of Acinetobacter baumannii. Mutagenesis at the N148 position in ADC-7 yields functional mutants (N152G, -S, -T, -Q, -A, and -C) that retain cephalosporinase activity. Using standard assays, we show that N148G, -S, and -T variants possess good catalytic activity toward cefoxitin and ceftaroline but that cefepime is a poor substrate. Because N152 variants of CMY-2, another class C β-lactamase, are more readily inhibited by tazobactam due to higher rates of inactivation, we also tested if the N148 substitutions in ADC-7 would affect inactivation by sulfone inhibitors, sulbactam and tazobactam, class A β-lactamase, and A. baumannii penicillin-binding protein (PBP) inhibitors with in vitro activity against ADC-7. The 50% inhibitory concentrations (IC50s) for tazobactam and sulbactam were improved, with 7-fold and 2-fold reductions, respectively, for the N148S variant. A homology model of the N148S ADC-7 enzyme in a Michaelis-Menten complex with tazobactam showed a loss of interaction between N148 and the sulfone moiety of the inhibitor. We postulate that this may result in more-rapid secondary ring opening of the inhibitor, as the unbound sulfone is an excellent leaving group, leading to more-rapid formation of the stable linearized inhibitor.
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19
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Powers RA, Swanson HC, Taracila MA, Florek NW, Romagnoli C, Caselli E, Prati F, Bonomo RA, Wallar BJ. Biochemical and structural analysis of inhibitors targeting the ADC-7 cephalosporinase of Acinetobacter baumannii. Biochemistry 2014; 53:7670-9. [PMID: 25380506 PMCID: PMC4263437 DOI: 10.1021/bi500887n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
β-Lactam
resistance in Acinetobacter baumannii presents one
of the greatest challenges to contemporary antimicrobial chemotherapy.
Much of this resistance to cephalosporins derives from the expression
of the class C β-lactamase enzymes, known as Acinetobacter-derived cephalosporinases (ADCs). Currently, β-lactamase inhibitors
are structurally similar to β-lactam substrates and are not
effective inactivators of this class C cephalosporinase. Herein, two boronic acid transition state inhibitors
(BATSIs S02030 and SM23) that are chemically distinct from β-lactams
were designed and tested for inhibition of ADC enzymes. BATSIs SM23
and S02030 bind with high affinity to ADC-7, a chromosomal cephalosporinase
from Acinetobacter baumannii (Ki = 21.1 ± 1.9 nM and 44.5 ± 2.2 nM, respectively).
The X-ray crystal structures of ADC-7 were determined in both the
apo form (1.73 Å resolution) and in complex with S02030 (2.0
Å resolution). In the complex, S02030 makes several canonical
interactions: the O1 oxygen of S02030 is bound in the oxyanion hole,
and the R1 amide group makes key interactions with conserved residues
Asn152 and Gln120. In addition, the carboxylate group of the inhibitor
is meant to mimic the C3/C4 carboxylate found
in β-lactams. The C3/C4 carboxylate recognition
site in class C enzymes is comprised of Asn346 and Arg349 (AmpC numbering),
and these residues are conserved in ADC-7. Interestingly, in the ADC-7/S02030
complex, the inhibitor carboxylate group is observed to interact with
Arg340, a residue that distinguishes ADC-7 from the related class
C enzyme AmpC. A thermodynamic analysis suggests that ΔH driven compounds may be optimized to generate
new lead agents. The ADC-7/BATSI complex provides insight into recognition
of non-β-lactam inhibitors by ADC enzymes and offers a starting
point for the structure-based optimization of this class of novel
β-lactamase inhibitors against a key resistance target.
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Affiliation(s)
- Rachel A Powers
- Department of Chemistry, Grand Valley State University , 1 Campus Drive, Allendale, Michigan 49401, United States
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20
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Abstract
The production of β-lactamase is one of the primary resistance mechanisms used by Gram-negative bacterial pathogens to counter β-lactam antibiotics, such as penicillins, cephalosporins and carbapenems. There is an urgent need to develop novel β-lactamase inhibitors in response to ever evolving β-lactamases possessing an expanded spectrum of β-lactam hydrolyzing activity. Whereas traditional high-throughput screening has proven ineffective against serine β-lactamases, fragment-based approaches have been successfully employed to identify novel chemical matter, which in turn has revealed much about the specific molecular interactions possible in the active site of serine and metallo β-lactamases. In this review, we summarize recent progress in the field, particularly: the identification of novel inhibitor chemotypes through fragment-based screening; the use of fragment-protein structures to understand key features of binding hot spots and inform the design of improved leads; lessons learned and new prospects for β-lactamase inhibitor development using fragment-based approaches.
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Affiliation(s)
- Derek A Nichols
- University of South Florida College of Medicine, Department of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry & Small Molecule Discovery Center, University of California San Francisco, 1700 4th Street, Byers Hall S504, San Francisco, CA 94158, USA
| | - Yu Chen
- University of South Florida College of Medicine, Department of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612, USA
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21
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Drawz SM, Papp-Wallace KM, Bonomo RA. New β-lactamase inhibitors: a therapeutic renaissance in an MDR world. Antimicrob Agents Chemother 2013; 58:1835-46. [PMID: 24379206 PMCID: PMC4023773 DOI: 10.1128/aac.00826-13] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
As the incidence of Gram-negative bacterial infections for which few effective treatments remain increases, so does the contribution of drug-hydrolyzing β-lactamase enzymes to this serious clinical problem. This review highlights recent advances in β-lactamase inhibitors and focuses on agents with novel mechanisms of action against a wide range of enzymes. To this end, we review the β-lactamase inhibitors currently in clinical trials, select agents still in preclinical development, and older therapeutic approaches that are being revisited. Particular emphasis is placed on the activity of compounds at the forefront of the developmental pipeline, including the diazabicyclooctane inhibitors (avibactam and MK-7655) and the boronate RPX7009. With its novel reversible mechanism, avibactam stands to be the first new β-lactamase inhibitor brought into clinical use in the past 2 decades. Our discussion includes the importance of selecting the appropriate partner β-lactam and dosing regimens for these promising agents. This "renaissance" of β-lactamase inhibitors offers new hope in a world plagued by multidrug-resistant (MDR) Gram-negative bacteria.
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Affiliation(s)
- Sarah M. Drawz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Krisztina M. Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
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22
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Watkins RR, Papp-Wallace KM, Drawz SM, Bonomo RA. Novel β-lactamase inhibitors: a therapeutic hope against the scourge of multidrug resistance. Front Microbiol 2013; 4:392. [PMID: 24399995 PMCID: PMC3871716 DOI: 10.3389/fmicb.2013.00392] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/02/2013] [Indexed: 11/25/2022] Open
Abstract
The increasing incidence and prevalence of multi-drug resistance (MDR) among contemporary Gram-negative bacteria represents a significant threat to human health. Since their discovery, β-lactam antibiotics have been a major component of the armamentarium against these serious pathogens. Unfortunately, a wide range of β-lactamase enzymes have emerged that are capable of inactivating these powerful drugs. In the past 30 years, a major advancement in the battle against microbes has been the development of β-lactamase inhibitors, which restore the efficacy of β-lactam antibiotics (e.g., ampicillin/sulbactam, amoxicillin/clavulanate, ticarcillin/clavulanate, and piperacillin/tazobactam). Unfortunately, many newly discovered β-lactamases are not inactivated by currently available inhibitors. Is there hope? For the first time in many years, we can anticipate the development and introduction into clinical practice of novel inhibitors. Although these inhibitors may still not be effective for all β-lactamases, their introduction is still welcome. This review focuses on the novel β-lactamase inhibitors that are closest to being introduced in the clinic.
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Affiliation(s)
- Richard R Watkins
- Department of Internal Medicine, Northeast Ohio Medical University Rootstown, OH, USA ; Division of Infectious Diseases, Akron General Medical Center Akron, OH, USA
| | - Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center Cleveland, OH, USA ; Department of Medicine, Case Western Reserve University Cleveland, OH, USA
| | - Sarah M Drawz
- Department of Lab Medicine and Pathology, University of Minnesota Minneapolis, MN, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center Cleveland, OH, USA ; Department of Medicine, Case Western Reserve University Cleveland, OH, USA ; Pharmacology, Case Western Reserve University Cleveland, OH, USA ; Molecular Biology and Microbiology, Case Western Reserve University Cleveland, OH, USA
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23
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Papp-Wallace KM, Mallo S, Bethel CR, Taracila MA, Hujer AM, Fernández A, Gatta JA, Smith KM, Xu Y, Page MGP, Desarbre E, Bou G, Bonomo RA. A kinetic analysis of the inhibition of FOX-4 β-lactamase, a plasmid-mediated AmpC cephalosporinase, by monocyclic β-lactams and carbapenems. J Antimicrob Chemother 2013; 69:682-90. [PMID: 24235094 DOI: 10.1093/jac/dkt434] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Class C β-lactamases are prevalent among Enterobacteriaceae; however, these enzymes are resistant to inactivation by commercially available β-lactamase inhibitors. In order to find novel scaffolds to inhibit class C β-lactamases, the comparative efficacy of monocyclic β-lactam antibiotics (aztreonam and the siderophore monosulfactam BAL30072), the bridged monobactam β-lactamase inhibitor BAL29880, and carbapenems (imipenem, meropenem, doripenem and ertapenem) were tested in kinetic assays against FOX-4, a plasmid-mediated class C β-lactamase (pmAmpC). METHODS The FOX-4 β-lactamase was purified. Steady-state kinetics, electrospray ionization mass spectrometry (ESI-MS) and ultraviolet difference (UVD) spectroscopy were conducted using the β-lactam scaffolds described. RESULTS The K(i) values for the monocyclic β-lactams against FOX-4 β-lactamase were 0.04 ± 0.01 μM (aztreonam) and 0.66 ± 0.03 μM (BAL30072), and the Ki value for the bridged monobactam BAL29880 was 8.9 ± 0.5 μM. For carbapenems, the Ki values ranged from 0.27 ± 0.05 μM (ertapenem) to 2.3 ± 0.3 μM (imipenem). ESI-MS demonstrated the formation of stable covalent adducts when the monocyclic β-lactams and carbapenems were reacted with FOX-4 β-lactamase. UVD spectroscopy suggested the appearance of different chromophoric intermediates. CONCLUSIONS Monocyclic β-lactam and carbapenem antibiotics are effective mechanism-based inhibitors of FOX-4 β-lactamase, a clinically important pmAmpC, and provide stimulus for the development of new inhibitors to inactivate plasmidic and chromosomal class C β-lactamases.
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Affiliation(s)
- Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
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Structures of the class D Carbapenemases OXA-23 and OXA-146: mechanistic basis of activity against carbapenems, extended-spectrum cephalosporins, and aztreonam. Antimicrob Agents Chemother 2013; 57:4848-55. [PMID: 23877677 DOI: 10.1128/aac.00762-13] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Class D β-lactamases that hydrolyze carbapenems such as imipenem and doripenem are a recognized danger to the efficacy of these "last-resort" β-lactam antibiotics. Like all known class D carbapenemases, OXA-23 cannot hydrolyze the expanded-spectrum cephalosporin ceftazidime. OXA-146 is an OXA-23 subfamily clinical variant that differs from the parent enzyme by a single alanine (A220) inserted in the loop connecting β-strands β5 and β6. We discovered that this insertion enables OXA-146 to bind and hydrolyze ceftazidime with an efficiency comparable to those of other extended-spectrum class D β-lactamases. OXA-146 also binds and hydrolyzes aztreonam, cefotaxime, ceftriaxone, and ampicillin with higher efficiency than OXA-23 and preserves activity against doripenem. In this study, we report the X-ray crystal structures of both the OXA-23 and OXA-146 enzymes at 1.6-Å and 1.2-Å resolution. A comparison of the two structures shows that the extra alanine moves a methionine (M221) out of its normal position, where it forms a bridge over the top of the active site. This single amino acid insertion also lengthens the β5-β6 loop, moving the entire backbone of this region further away from the active site. A model of ceftazidime bound in the active site reveals that these two structural alterations are both likely to relieve steric clashes between the bulky R1 side chain of ceftazidime and OXA-23. With activity against all four classes of β-lactam antibiotics, OXA-146 represents an alarming new threat to the treatment of infections caused by Acinetobacter spp.
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Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ. The enzymes of β-lactam biosynthesis. Nat Prod Rep 2013; 30:21-107. [DOI: 10.1039/c2np20065a] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Lin L, Tan B, Pantapalangkoor P, Ho T, Hujer AM, Taracila MA, Bonomo RA, Spellberg B. Acinetobacter baumannii rOmpA vaccine dose alters immune polarization and immunodominant epitopes. Vaccine 2012; 31:313-8. [PMID: 23153442 DOI: 10.1016/j.vaccine.2012.11.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/03/2012] [Accepted: 11/04/2012] [Indexed: 01/13/2023]
Abstract
BACKGROUND The rOmpA vaccine has been shown to protect mice from lethal infection caused by extreme-drug-resistant (XDR) Acinetobacter baumannii. The role of dose in immunology of the rOmpA vaccine was explored. METHODS Mice were vaccinated with various doses of rOmpA plus aluminum hydroxide (Al(OH)(3)) adjuvant. The impact of dose on antibody titers, cytokine production, and immunodominant epitopes was defined. RESULTS Anti-rOmpA IgG and IgG subtype titers were higher at larger vaccine doses (30 and 100 μg vs. 3 μg). The 3 μg dose induced a balanced IFN-γ-IL-4 immune response while the 100 μg dose induced a polarized IL-4/Type 2 response. Epitope mapping revealed distinct T cell epitopes that activated IFN-γ-, IL-4-, and IL-17-producing splenocytes. Vaccination with the 100 μg dose caused epitope spreading among IL-4-producing splenocytes, while it induced fewer reactive epitopes among IFN-γ-producing splenocytes. CONCLUSIONS Vaccine dose escalation resulted in an enhanced Type 2 immune response, accompanied by substantial IL-4-inducing T cell epitope spreading and restricted IFN-γ-inducing epitopes. These results inform continued development of the rOmpA vaccine against A. baumannii, and also are of general importance in that they indicate that immune polarization and epitope selectivity can be modulated by altering vaccine dose.
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Affiliation(s)
- Lin Lin
- Division of General Internal Medicine, Los Angeles Biomedical Research Institute at Harbor-University of California at Los Angeles Medical Center, Torrance, CA 90502, United States
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Roca I, Espinal P, Vila-Farrés X, Vila J. The Acinetobacter baumannii Oxymoron: Commensal Hospital Dweller Turned Pan-Drug-Resistant Menace. Front Microbiol 2012; 3:148. [PMID: 22536199 PMCID: PMC3333477 DOI: 10.3389/fmicb.2012.00148] [Citation(s) in RCA: 243] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 03/28/2012] [Indexed: 12/28/2022] Open
Abstract
During the past few decades Acinetobacter baumannii has evolved from being a commensal dweller of health-care facilities to constitute one of the most annoying pathogens responsible for hospitalary outbreaks and it is currently considered one of the most important nosocomial pathogens. In a prevalence study of infections in intensive care units conducted among 75 countries of the five continents, this microorganism was found to be the fifth most common pathogen. Two main features contribute to the success of A. baumannii: (i) A. baumannii exhibits an outstanding ability to accumulate a great variety of resistance mechanisms acquired by different mechanisms, either mutations or acquisition of genetic elements such as plasmids, integrons, transposons, or resistant islands, making this microorganism multi- or pan-drug-resistant and (ii) The ability to survive in the environment during prolonged periods of time which, combined with its innate resistance to desiccation and disinfectants, makes A. baumannii almost impossible to eradicate from the clinical setting. In addition, its ability to produce biofilm greatly contributes to both persistence and resistance. In this review, the pathogenesis of the infections caused by this microorganism as well as the molecular bases of antibacterial resistance and clinical aspects such as treatment and potential future therapeutic strategies are discussed in depth.
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Affiliation(s)
- Ignasi Roca
- Department of Clinical Microbiology, School of Medicine, IDIBAPS and Barcelona Centre for International Health Research, Hospital Clínic-Universitat de Barcelona Barcelona, Spain
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Zervosen A, Bouillez A, Herman A, Amoroso A, Joris B, Sauvage E, Charlier P, Luxen A. Synthesis and evaluation of boronic acids as inhibitors of Penicillin Binding Proteins of classes A, B and C. Bioorg Med Chem 2012; 20:3915-24. [PMID: 22579615 DOI: 10.1016/j.bmc.2012.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 04/05/2012] [Accepted: 04/07/2012] [Indexed: 10/28/2022]
Abstract
In response to the widespread use of β-lactam antibiotics bacteria have evolved drug resistance mechanisms that include the production of resistant Penicillin Binding Proteins (PBPs). Boronic acids are potent β-lactamase inhibitors and have been shown to display some specificity for soluble transpeptidases and PBPs, but their potential as inhibitors of the latter enzymes is yet to be widely explored. Recently, a (2,6-dimethoxybenzamido)methylboronic acid was identified as being a potent inhibitor of Actinomadura sp. R39 transpeptidase (IC(50): 1.3 μM). In this work, we synthesized and studied the potential of a number of acylaminomethylboronic acids as inhibitors of PBPs from different classes. Several derivatives inhibited PBPs of classes A, B and C from penicillin sensitive strains. The (2-nitrobenzamido)methylboronic acid was identified as a good inhibitor of a class A PBP (PBP1b from Streptococcus pneumoniae, IC(50) = 26 μM), a class B PBP (PBP2xR6 from Streptococcus pneumoniae, IC(50) = 138 μM) and a class C PBP (R39 from Actinomadura sp., IC(50) = 0.6 μM). This work opens new avenues towards the development of molecules that inhibit PBPs, and eventually display bactericidal effects, on distinct bacterial species.
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Affiliation(s)
- Astrid Zervosen
- Centre de Recherches du Cyclotron, B30, Université de Liège, Sart-Tilman, B-4000 Liège, Belgium.
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Papp-Wallace KM, Endimiani A, Taracila MA, Bonomo RA. Carbapenems: past, present, and future. Antimicrob Agents Chemother 2011; 55:4943-60. [PMID: 21859938 PMCID: PMC3195018 DOI: 10.1128/aac.00296-11] [Citation(s) in RCA: 860] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In this review, we summarize the current "state of the art" of carbapenem antibiotics and their role in our antimicrobial armamentarium. Among the β-lactams currently available, carbapenems are unique because they are relatively resistant to hydrolysis by most β-lactamases, in some cases act as "slow substrates" or inhibitors of β-lactamases, and still target penicillin binding proteins. This "value-added feature" of inhibiting β-lactamases serves as a major rationale for expansion of this class of β-lactams. We describe the initial discovery and development of the carbapenem family of β-lactams. Of the early carbapenems evaluated, thienamycin demonstrated the greatest antimicrobial activity and became the parent compound for all subsequent carbapenems. To date, more than 80 compounds with mostly improved antimicrobial properties, compared to those of thienamycin, are described in the literature. We also highlight important features of the carbapenems that are presently in clinical use: imipenem-cilastatin, meropenem, ertapenem, doripenem, panipenem-betamipron, and biapenem. In closing, we emphasize some major challenges and urge the medicinal chemist to continue development of these versatile and potent compounds, as they have served us well for more than 3 decades.
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Affiliation(s)
- Krisztina M. Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
- Departments of Medicine
| | - Andrea Endimiani
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
- Institute for Infectious Diseases, University of Bern 3010, Bern, Switzerland
- Departments of Medicine
| | | | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
- Departments of Medicine
- Pharmacology
- Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106
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Espinal P, Roca I, Vila J. Clinical impact and molecular basis of antimicrobial resistance in non-baumannii Acinetobacter. Future Microbiol 2011; 6:495-511. [PMID: 21585259 DOI: 10.2217/fmb.11.30] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Species of Acinetobacter other than Acinetobacter baumannii are involved in nosocomial infections. Acinetobacter lwoffii, Acinetobacter genomospecies 3 and Acinetobacter genomospecies 13TU are found in community- and nosocomial-acquired infections as well as in neonatal intensive care units. The non-baumannii Acinetobacter are normally highly susceptible to ciprofloxacin, ampicillin/sulbactam, gentamicin and tigecycline. Carbepenems show good activity although resistant isolates have been reported. Resistance to β-lactams other than carbapenems is associated with overexpression of chromosomal cephalosporinases and extended-spectrum β-lactamase acquisition, whereas resistance to carbapenems involves acquisition of carbapenemases. Quinolone resistance is related to gyrA and/or parC mutations but overexpresion of efflux proteins also plays an important role. With the development of novel and more accurate typing methodologies, an increase in infections caused by non-baumannii Acinetobacter might be observed in the future.
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Affiliation(s)
- Paula Espinal
- Department of Microbiology, Hospital Clinic, School of Medicine, University of Barcelona, CRESIB, IDIBAPS, Spain
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Contreras-Martel C, Amoroso A, Woon ECY, Zervosen A, Inglis S, Martins A, Verlaine O, Rydzik AM, Job V, Luxen A, Joris B, Schofield CJ, Dessen A. Structure-guided design of cell wall biosynthesis inhibitors that overcome β-lactam resistance in Staphylococcus aureus (MRSA). ACS Chem Biol 2011; 6:943-51. [PMID: 21732689 DOI: 10.1021/cb2001846] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Lactam antibiotics have long been a treatment of choice for bacterial infections since they bind irreversibly to Penicillin-Binding Proteins (PBPs), enzymes that are vital for cell wall biosynthesis. Many pathogens express drug-insensitive PBPs rendering β-lactams ineffective, revealing a need for new types of PBP inhibitors active against resistant strains. We have identified alkyl boronic acids that are active against pathogens including methicillin-resistant S. aureus (MRSA). The crystal structures of PBP1b complexed to 11 different alkyl boronates demonstrate that in vivo efficacy correlates with the mode of inhibitor side chain binding. Staphylococcal membrane analyses reveal that the most potent alkyl boronate targets PBP1, an autolysis system regulator, and PBP2a, a low β-lactam affinity enzyme. This work demonstrates the potential of boronate-based PBP inhibitors for circumventing β-lactam resistance and opens avenues for the development of novel antibiotics that target Gram-positive pathogens.
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Affiliation(s)
| | - Ana Amoroso
- Centre d'Ingénierie des Protéines, Institut de Chimie, B6a, Université de Liège, Sart Tilman, B4000 Liège, Belgium
| | - Esther C. Y. Woon
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Astrid Zervosen
- Centre de Recherches du Cyclotron, B30, Université de Liège, Sart Tilman, B4000 Liège, Belgium
| | - Steven Inglis
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | | | - Olivier Verlaine
- Centre d'Ingénierie des Protéines, Institut de Chimie, B6a, Université de Liège, Sart Tilman, B4000 Liège, Belgium
| | - Anna M. Rydzik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | | | - André Luxen
- Centre de Recherches du Cyclotron, B30, Université de Liège, Sart Tilman, B4000 Liège, Belgium
| | - Bernard Joris
- Centre d'Ingénierie des Protéines, Institut de Chimie, B6a, Université de Liège, Sart Tilman, B4000 Liège, Belgium
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Dubois D, Baron O, Cougnoux A, Delmas J, Pradel N, Boury M, Bouchon B, Bringer MA, Nougayrède JP, Oswald E, Bonnet R. ClbP is a prototype of a peptidase subgroup involved in biosynthesis of nonribosomal peptides. J Biol Chem 2011; 286:35562-35570. [PMID: 21795676 DOI: 10.1074/jbc.m111.221960] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The pks genomic island of Escherichia coli encodes polyketide (PK) and nonribosomal peptide (NRP) synthases that allow assembly of a putative hybrid PK-NRP compound named colibactin that induces DNA double-strand breaks in eukaryotic cells. The pks-encoded machinery harbors an atypical essential protein, ClbP. ClbP crystal structure and mutagenesis experiments revealed a serine-active site and original structural features compatible with peptidase activity, which was detected by biochemical assays. Ten ClbP homologs were identified in silico in NRP genomic islands of closely and distantly related bacterial species. All tested ClbP homologs were able to complement a clbP-deficient E. coli mutant. ClbP is therefore a prototype of a new subfamily of extracytoplasmic peptidases probably involved in the maturation of NRP compounds. Such peptidases will be powerful tools for the manipulation of NRP biosynthetic pathways.
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Affiliation(s)
- Damien Dubois
- Laboratoire de Bactériologie Clinique, Centre Hospitalier de Clermont-Ferrand, Clermont-Ferrand F-63003, France; Institut National de Recherche Agronomique, Clermont Université, JE 2526 Université d'Auvergne, Unité Sous Contrat 2018, Clermont-Ferrand F-63001, France
| | - Olivier Baron
- INSERM U1043, Toulouse F-31076, France; Centre National de Recherche Scientifique, U5282, Toulouse F-31076, France; Institut National de Recherche Agronomique, Unité Sous Contrat, Toulouse F-31076, France; Université Paul Sabatier-Toulouse III, Centre de Physiopathologie de Toulouse Purpan, Toulouse F-31076, France; Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse F-31059, France
| | - Antony Cougnoux
- Institut National de Recherche Agronomique, Clermont Université, JE 2526 Université d'Auvergne, Unité Sous Contrat 2018, Clermont-Ferrand F-63001, France
| | - Julien Delmas
- Laboratoire de Bactériologie Clinique, Centre Hospitalier de Clermont-Ferrand, Clermont-Ferrand F-63003, France; Institut National de Recherche Agronomique, Clermont Université, JE 2526 Université d'Auvergne, Unité Sous Contrat 2018, Clermont-Ferrand F-63001, France
| | - Nathalie Pradel
- Institut National de Recherche Agronomique, Clermont Université, JE 2526 Université d'Auvergne, Unité Sous Contrat 2018, Clermont-Ferrand F-63001, France
| | - Michèle Boury
- INSERM U1043, Toulouse F-31076, France; Centre National de Recherche Scientifique, U5282, Toulouse F-31076, France; Institut National de Recherche Agronomique, Unité Sous Contrat, Toulouse F-31076, France; Université Paul Sabatier-Toulouse III, Centre de Physiopathologie de Toulouse Purpan, Toulouse F-31076, France
| | | | - Marie-Agnès Bringer
- Institut National de Recherche Agronomique, Clermont Université, JE 2526 Université d'Auvergne, Unité Sous Contrat 2018, Clermont-Ferrand F-63001, France
| | - Jean-Philippe Nougayrède
- INSERM U1043, Toulouse F-31076, France; Centre National de Recherche Scientifique, U5282, Toulouse F-31076, France; Institut National de Recherche Agronomique, Unité Sous Contrat, Toulouse F-31076, France; Université Paul Sabatier-Toulouse III, Centre de Physiopathologie de Toulouse Purpan, Toulouse F-31076, France
| | - Eric Oswald
- INSERM U1043, Toulouse F-31076, France; Centre National de Recherche Scientifique, U5282, Toulouse F-31076, France; Institut National de Recherche Agronomique, Unité Sous Contrat, Toulouse F-31076, France; Université Paul Sabatier-Toulouse III, Centre de Physiopathologie de Toulouse Purpan, Toulouse F-31076, France; Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse F-31059, France.
| | - Richard Bonnet
- Laboratoire de Bactériologie Clinique, Centre Hospitalier de Clermont-Ferrand, Clermont-Ferrand F-63003, France; Institut National de Recherche Agronomique, Clermont Université, JE 2526 Université d'Auvergne, Unité Sous Contrat 2018, Clermont-Ferrand F-63001, France.
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Extended-spectrum AmpC cephalosporinase in Acinetobacter baumannii: ADC-56 confers resistance to cefepime. Antimicrob Agents Chemother 2011; 55:4922-5. [PMID: 21788456 DOI: 10.1128/aac.00704-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ADC-56, a novel extended-spectrum AmpC (ESAC) β-lactamase, was identified in an Acinetobacter baumannii clinical isolate. ADC-56 possessed an R148Q change compared with its putative progenitor, ADC-30, which enabled it to hydrolyze cefepime. Molecular modeling suggested that R148 interacted with Q267, E272, and I291 through a hydrogen bond network which constrained the H-10 helix. This permitted cefepime to undergo conformational changes in the active site, with the carboxyl interacting with R340, likely allowing for better binding and turnover.
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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.
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Drawz SM, Taracila M, Caselli E, Prati F, Bonomo RA. Exploring sequence requirements for C₃/C₄ carboxylate recognition in the Pseudomonas aeruginosa cephalosporinase: Insights into plasticity of the AmpC β-lactamase. Protein Sci 2011; 20:941-58. [PMID: 21404358 DOI: 10.1002/pro.612] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 02/11/2011] [Accepted: 02/14/2011] [Indexed: 11/06/2022]
Abstract
In Pseudomonas aeruginosa, the chromosomally encoded class C cephalosporinase (AmpC β-lactamase) is often responsible for high-level resistance to β-lactam antibiotics. Despite years of study of these important β-lactamases, knowledge regarding how amino acid sequence dictates function of the AmpC Pseudomonas-derived cephalosporinase (PDC) remains scarce. Insights into structure-function relationships are crucial to the design of both β-lactams and high-affinity inhibitors. In order to understand how PDC recognizes the C₃/C₄ carboxylate of β-lactams, we first examined a molecular model of a P. aeruginosa AmpC β-lactamase, PDC-3, in complex with a boronate inhibitor that possesses a side chain that mimics the thiazolidine/dihydrothiazine ring and the C₃/C₄ carboxylate characteristic of β-lactam substrates. We next tested the hypothesis generated by our model, i.e. that more than one amino acid residue is involved in recognition of the C₃/C₄ β-lactam carboxylate, and engineered alanine variants at three putative carboxylate binding amino acids. Antimicrobial susceptibility testing showed that the PDC-3 β-lactamase maintains a high level of activity despite the substitution of C₃/C₄ β-lactam carboxylate recognition residues. Enzyme kinetics were determined for a panel of nine penicillin and cephalosporin analog boronates synthesized as active site probes of the PDC-3 enzyme and the Arg349Ala variant. Our examination of the PDC-3 active site revealed that more than one residue could serve to interact with the C₃/C₄ carboxylate of the β-lactam. This functional versatility has implications for novel drug design, protein evolution, and resistance profile of this enzyme.
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Affiliation(s)
- Sarah M Drawz
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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Touchet S, Carreaux F, Carboni B, Bouillon A, Boucher JL. Aminoboronic acids and esters: from synthetic challenges to the discovery of unique classes of enzyme inhibitors. Chem Soc Rev 2011; 40:3895-914. [DOI: 10.1039/c0cs00154f] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Novel insights into the mode of inhibition of class A SHV-1 beta-lactamases revealed by boronic acid transition state inhibitors. Antimicrob Agents Chemother 2010; 55:174-83. [PMID: 21041505 DOI: 10.1128/aac.00930-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Boronic acid transition state inhibitors (BATSIs) are potent class A and C β-lactamase inactivators and are of particular interest due to their reversible nature mimicking the transition state. Here, we present structural and kinetic data describing the inhibition of the SHV-1 β-lactamase, a clinically important enzyme found in Klebsiella pneumoniae, by BATSI compounds possessing the R1 side chains of ceftazidime and cefoperazone and designed variants of the latter, compounds 1 and 2. The ceftazidime and cefoperazone BATSI compounds inhibit the SHV-1 β-lactamase with micromolar affinity that is considerably weaker than their inhibition of other β-lactamases. The solved crystal structures of these two BATSIs in complex with SHV-1 reveal a possible reason for SHV-1's relative resistance to inhibition, as the BATSIs adopt a deacylation transition state conformation compared to the usual acylation transition state conformation when complexed to other β-lactamases. Active-site comparison suggests that these conformational differences might be attributed to a subtle shift of residue A237 in SHV-1. The ceftazidime BATSI structure revealed that the carboxyl-dimethyl moiety is positioned in SHV-1's carboxyl binding pocket. In contrast, the cefoperazone BATSI has its R1 group pointing away from the active site such that its phenol moiety moves residue Y105 from the active site via end-on stacking interactions. To work toward improving the affinity of the cefoperazone BATSI, we synthesized two variants in which either one or two extra carbons were added to the phenol linker. Both variants yielded improved affinity against SHV-1, possibly as a consequence of releasing the strain of its interaction with the unusual Y105 conformation.
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Endimiani A, Doi Y, Bethel CR, Taracila M, Adams-Haduch JM, O'Keefe A, Hujer AM, Paterson DL, Skalweit MJ, Page MGP, Drawz SM, Bonomo RA. Enhancing resistance to cephalosporins in class C beta-lactamases: impact of Gly214Glu in CMY-2. Biochemistry 2010; 49:1014-23. [PMID: 19938877 DOI: 10.1021/bi9015549] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biochemical properties of CMY-32, a class C enzyme possessing a single-amino acid substitution in the Omega loop (Gly214Glu), were compared to those of the parent enzyme, CMY-2, a widespread class C beta-lactamase. In parallel with our microbiological characterization, the Gly214Glu substitution in CMY-32 reduced catalytic efficiency (k(cat)/K(m)) by 50-70% against "good" substrates (i.e., cephalothin) while increasing k(cat)/K(m) against "poor" substrates (i.e., cefotaxime). Additionally, CMY-32 was more susceptible to inactivation by sulfone beta-lactamase inhibitors (i.e., sulbactam and tazobactam) than CMY-2. Timed electrospray ionization mass spectrometry (ESI-MS) analysis of the reaction of CMY-2 and CMY-32 with different substrates and inhibitors suggested that both beta-lactamases formed similar intermediates during catalysis and inactivation. We next showed that the carbapenems (imipenem, meropenem, and doripenem) form long-lived acyl-enzyme intermediates and present evidence that there is beta-lactamase-catalyzed elimination of the C(6) hydroxyethyl substituent. Furthermore, we discovered that the monobactam aztreonam and BAL29880, a new beta-lactamase inhibitor of the monobactam class, inactivate CMY-2 and CMY-32 by forming an acyl-enzyme intermediate that undergoes elimination of SO(3)(2-). Molecular modeling and dynamics simulations suggest that the Omega loop is more constrained in CMY-32 than CMY-2. Our model also proposes that Gln120 adopts a novel conformation in the active site while new interactions form between Glu214 and Tyr221, thus explaining the increased level of cefotaxime hydrolysis. When it is docked in the active site, we observe that BAL29880 exploits contacts with highly conserved residues Lys67 and Asn152 in CMY-2 and CMY-32. These findings highlight (i) the impact of single-amino acid substitutions on protein evolution in clinically important AmpC enzymes and (ii) the novel insights into the mechanisms by which carbapenems and monobactams interact with CMY-2 and CMY-32 beta-lactamases.
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Affiliation(s)
- Andrea Endimiani
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, USA
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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.
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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
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