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Canabal R, González-Bello C. Chemical sensors for the early diagnosis of bacterial resistance to β-lactam antibiotics. Bioorg Chem 2024; 150:107528. [PMID: 38852309 DOI: 10.1016/j.bioorg.2024.107528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
β-Lactamases are bacterial enzymes that inactivate β-lactam antibiotics and, as such, are the most prevalent cause of antibiotic resistance in Gram-negative bacteria. The ever-increasing production and worldwide dissemination of bacterial strains producing carbapenemases is currently a global health concern. These enzymes catalyze the hydrolysis of carbapenems - the β-lactam antibiotics with the broadest spectrum of activity that are often considered as drugs of last resort. The incidence of carbapenem-resistant pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and carbapenemase or extended spectrum beta-lactamase (ESBL)-producing Enterobacterales, which are frequent in clinical settings, is worrisome since, in some cases, no therapies are available. These include all metallo-β-lactamases (VIM, IMP, NDM, SMP, and L1), and serine-carbapenemases of classes A (KPC, SME, IMI, and GES), and of classes D (OXA-23, OXA-24/40, OXA-48 and OXA-58). Consequently, the early diagnosis of bacterial strains harboring carbapenemases is a pivotal task in clinical microbiology in order to track antibiotic bacterial resistance and to improve the worldwide management of infectious diseases. Recent research efforts on the development of chromogenic and fluorescent chemical sensors for the specific and sensitive detection and quantification of β-lactamase production in multidrug-resistant pathogens are summarized herein. Studies to circumvent the main limitations of the phenotypic and molecular methods are discussed. Recently reported chromogenic and fluorogenic cephalosporin- and carbapenem-based β-lactamase substrates will be reviewed as alternative options to the currently available nitrocefin and related compounds, a chromogenic cephalosporin-based reagent widely used in clinical microbiology laboratories. The scope of these new chemical sensors, along with the synthetic approaches to synthesize them, is also summarized.
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Affiliation(s)
- Rafael Canabal
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
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2
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Gonzalez C, Oueslati S, Rima M, Nermont R, Dortet L, Hopkins KL, Iorga BI, Bonnin RA, Naas T. Molecular, Genetic, and Biochemical Characterization of OXA-484 Carbapenemase, a Difficult-to-Detect R214G Variant of OXA-181. Microorganisms 2024; 12:1391. [PMID: 39065158 PMCID: PMC11278660 DOI: 10.3390/microorganisms12071391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
OXA-244, an R214G variant of OXA-48, is silently spreading worldwide likely because of difficulties in detection using classical screening media. Here, we characterized two clinical isolates of Escherichia coli and Citrobacter youngae that displayed reduced susceptibility to carbapenems but were lacking significant carbapenemase activity as revealed by negative Carba NP test results. However, positive test results were seen for OXA-48-like enzymes by lateral flow immunoassays. WGS revealed the presence of a blaOXA-181-like gene that codes for OXA-484, an R214G variant of OXA-181. BlaOXA-484 gene was located on a 58.4-kb IncP1-like plasmid (pN-OXA-484), that upon transfer into E. coli HB4 with impaired permeability, conferred carbapenem and temocillin resistance (MICs > 32 mg/L). E. coli TOP10 (pTOPO-OXA-484) revealed reduced MICs in most substrates as compared to E. coli TOP10 (pTOPO-OXA-181), especially for imipenem (0.25 mg/L versus 0.75 mg/L) and temocillin (16 mg/L versus 1028 mg/L). Catalytic efficiencies of OXA-484 were reduced as compared to OXA-181 for most ß-lactams including imipenem and temocillin with 27.5- and 21.7-fold reduction, respectively. Molecular modeling confirmed that the salt bridges between R214, D159, and the R1 substituent's carboxylate group of temocillin were not possible with G214 in OXA-484, explaining the reduced affinity for temocillin. In addition, changes in active site's water network may explain the decrease in hydrolysis rate of carbapenems. OXA-484 has weak imipenem and temocillin hydrolytic activities, which may lead to silent spread due to underdetection using selective screening media or biochemical imipenem hydrolysis confirmatory tests.
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Affiliation(s)
- Camille Gonzalez
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, Faculty of Medicine, University Paris-Saclay, INSERM, CEA, 94270 Le Kremlin-Bicêtre, France; (C.G.); (S.O.); (M.R.); (R.N.); (L.D.); (R.A.B.)
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
| | - Saoussen Oueslati
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, Faculty of Medicine, University Paris-Saclay, INSERM, CEA, 94270 Le Kremlin-Bicêtre, France; (C.G.); (S.O.); (M.R.); (R.N.); (L.D.); (R.A.B.)
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
| | - Mariam Rima
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, Faculty of Medicine, University Paris-Saclay, INSERM, CEA, 94270 Le Kremlin-Bicêtre, France; (C.G.); (S.O.); (M.R.); (R.N.); (L.D.); (R.A.B.)
| | - Réva Nermont
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, Faculty of Medicine, University Paris-Saclay, INSERM, CEA, 94270 Le Kremlin-Bicêtre, France; (C.G.); (S.O.); (M.R.); (R.N.); (L.D.); (R.A.B.)
| | - Laurent Dortet
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, Faculty of Medicine, University Paris-Saclay, INSERM, CEA, 94270 Le Kremlin-Bicêtre, France; (C.G.); (S.O.); (M.R.); (R.N.); (L.D.); (R.A.B.)
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
| | - Katie L. Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London NW9 5EQ, UK;
| | - Bogdan I. Iorga
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, 91190 Gif-sur-Yvette, France;
| | - Rémy A. Bonnin
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, Faculty of Medicine, University Paris-Saclay, INSERM, CEA, 94270 Le Kremlin-Bicêtre, France; (C.G.); (S.O.); (M.R.); (R.N.); (L.D.); (R.A.B.)
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)”, Faculty of Medicine, University Paris-Saclay, INSERM, CEA, 94270 Le Kremlin-Bicêtre, France; (C.G.); (S.O.); (M.R.); (R.N.); (L.D.); (R.A.B.)
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
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3
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Rodríguez D, Lence E, Vázquez-Ucha JC, Beceiro A, González-Bello C. Novel Penicillin-Based Sulfone-Siderophore Conjugates for Restoring β-Lactam Antibiotic Efficacy. ACS OMEGA 2024; 9:26484-26494. [PMID: 38911797 PMCID: PMC11191083 DOI: 10.1021/acsomega.4c02984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/25/2024]
Abstract
Membrane permeability is a natural defense barrier that contributes to increased bacterial drug resistance, particularly for Gram-negative pathogens. As such, accurate delivery of the antibacterial agent to the target has become a growing research area in the infectious diseases field as a means of improving drug efficacy. Although the efficient transport of siderophore-antibiotic conjugates into the cytosol still remains challenging, great success has been achieved in the delivery of β-lactam antibiotics into the periplasmic space via bacterial iron uptake pathways. Cefiderocol, the first siderophore-cephalosporin conjugate approved by the US Food and Drug Administration, is a good example. These conjugation strategies have also been applied to the precise delivery of β-lactamase inhibitors, such as penicillin-based sulfone 1, to restore β-lactam antibiotic efficacy in multidrug-resistant bacteria. Herein, we have explored the impact on the bacterial activity of 1 by modifying its iron chelator moiety. A set of derivatives functionalized with diverse iron chelator groups and linkages to the scaffold (compounds 2-8) were synthesized and assayed in vitro. The results on the ability of derivatives 2-8 to recover β-lactam antibiotic efficacy in difficult-to-treat pathogens that produce various β-lactamase enzymes, along with kinetic studies with the isolated enzymes, allowed us to identify compound 2, a novel β-lactamase inhibitor with an expanded spectrum of activity. Molecular dynamics simulation studies provided us with further information regarding the molecular basis of the relative inhibitory properties of the most relevant compound described herein.
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Affiliation(s)
- Diana Rodríguez
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Emilio Lence
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Juan C. Vázquez-Ucha
- Servicio
de Microbiología, Complexo Hospitalario Universitario da Coruña
(CHUAC), Instituto de Investigación
Biomédica da Coruña (INIBIC), Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio
de Microbiología, Complexo Hospitalario Universitario da Coruña
(CHUAC), Instituto de Investigación
Biomédica da Coruña (INIBIC), Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Concepción González-Bello
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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4
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Klamer ZL, June CM, Wawrzak Z, Taracila MA, Grey JA, Benn AMI, Russell CP, Bonomo RA, Powers RA, Leonard DA, Szarecka A. Structural and Dynamic Features of Acinetobacter baumannii OXA-66 β-Lactamase Explain Its Stability and Evolution of Novel Variants. J Mol Biol 2024; 436:168603. [PMID: 38729259 PMCID: PMC11198252 DOI: 10.1016/j.jmb.2024.168603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
OXA-66 is a member of the OXA-51 subfamily of class D β-lactamases native to the Acinetobacter genus that includes Acinetobacter baumannii, one of the ESKAPE pathogens and a major cause of drug-resistant nosocomial infections. Although both wild type OXA-66 and OXA-51 have low catalytic activity, they are ubiquitous in the Acinetobacter genomes. OXA-51 is also remarkably thermostable. In addition, newly emerging, single and double amino acid variants show increased activity against carbapenems, indicating that the OXA-51 subfamily is growing and gaining clinical significance. In this study, we used molecular dynamics simulations, X-ray crystallography, and thermal denaturation data to examine and compare the dynamics of OXA-66 wt and its gain-of-function variants: I129L (OXA-83), L167V (OXA-82), P130Q (OXA-109), P130A, and W222L (OXA-234). Our data indicate that OXA-66 wt also has a high melting temperature, and its remarkable stability is due to an extensive and rigid hydrophobic bridge formed by a number of residues around the active site and harbored by the three loops, P, Ω, and β5-β6. Compared to the WT enzyme, the mutants exhibit higher flexibility only in the loop regions, and are more stable than other robust carbapenemases, such as OXA-23 and OXA-24/40. All the mutants show increased rotational flexibility of residues I129 and W222, which allows carbapenems to bind. Overall, our data support the hypothesis that structural features in OXA-51 and OXA-66 promote evolution of multiple highly stable variants with increased clinical relevance in A. baumannii.
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Affiliation(s)
- Zachary L Klamer
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA
| | - Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA
| | - Zdzislaw Wawrzak
- Life Sciences Collaborative Access Team, Synchrotron Research Center, Northwestern University, Argonne, IL, USA
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Joshua A Grey
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA
| | - Alyssa M I Benn
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA
| | | | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Departments of Pharmacology, Biochemistry, and Molecular Biology and Microbiology, and Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA.
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA.
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI, USA.
| | - Agnieszka Szarecka
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, USA.
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Rima M, Oueslati S, Cotelon G, Creton E, Bonnin RA, Dortet L, Iorga BI, Naas T. Role of amino acid 159 in carbapenem and temocillin hydrolysis of OXA-933, a novel OXA-48 variant. Antimicrob Agents Chemother 2024; 68:e0018024. [PMID: 38526049 PMCID: PMC11064584 DOI: 10.1128/aac.00180-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
OXA-48 has rapidly disseminated worldwide and become one of the most common carbapenemases in many countries with more than 45 variants reported with, in some cases, significant differences in their hydrolysis profiles. The R214 residue, located in the ß5-ß6 loop, is crucial for the carbapenemase activity, as it stabilizes carbapenems in the active site and maintains the shape of the active site through interactions with D159. In this study, we have characterized a novel variant of OXA-48, OXA-933 with a single D159N change. To evaluate the importance of this residue, point mutations were generated (D159A, D159G, D159K, and D159W), kinetic parameters of OXA-933, OXA-48 D159G, and OXA-48 D159K were determined and compared to those of OXA-48 and OXA-244. The blaOXA-933 gene was borne on Tn2208, a 2,696-bp composite transposon made of two IS1 elements surrounded by 9 bp target site duplications and inserted into a non-self-transmissible plasmid pOXA-933 of 7,872 bp in size. Minimal inhibitory concentration values of E. coli expressing the blaOXA-933 gene or of its point mutant derivatives were lower for carbapenems (except for D159G) as compared to those expressing the blaOXA-48 gene. Steady-state kinetic parameters revealed lower catalytic efficiencies for expanded spectrum cephalosporins and carbapenems. A detailed structural analysis confirmed the crucial role of D159 in shaping the active site of OXA-48 enzymes by interacting with R214. Our work further illustrates the remarkable propensity of OXA-48-like carbapenemases to evolve through mutations at positions outside the β5-β6 loop, but interacting with key residues of it.
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Affiliation(s)
- Mariam Rima
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
| | - Saoussen Oueslati
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Garance Cotelon
- French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Le Kremlin-Bicêtre, France
| | - Elodie Creton
- French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Le Kremlin-Bicêtre, France
| | - Rémy A. Bonnin
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Le Kremlin-Bicêtre, France
| | - Bogdan I. Iorga
- Université Paris-Saclay, CNRS UPR 2301, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Thierry Naas
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Le Kremlin-Bicêtre, France
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Fröhlich C, Bunzel HA, Buda K, Mulholland AJ, van der Kamp MW, Johnsen PJ, Leiros HKS, Tokuriki N. Epistasis arises from shifting the rate-limiting step during enzyme evolution of a β-lactamase. Nat Catal 2024; 7:499-509. [PMID: 38828429 PMCID: PMC11136654 DOI: 10.1038/s41929-024-01117-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/25/2024] [Indexed: 06/05/2024]
Abstract
Epistasis, the non-additive effect of mutations, can provide combinatorial improvements to enzyme activity that substantially exceed the gains from individual mutations. Yet the molecular mechanisms of epistasis remain elusive, undermining our ability to predict pathogen evolution and engineer biocatalysts. Here we reveal how directed evolution of a β-lactamase yielded highly epistatic activity enhancements. Evolution selected four mutations that increase antibiotic resistance 40-fold, despite their marginal individual effects (≤2-fold). Synergistic improvements coincided with the introduction of super-stochiometric burst kinetics, indicating that epistasis is rooted in the enzyme's conformational dynamics. Our analysis reveals that epistasis stemmed from distinct effects of each mutation on the catalytic cycle. The initial mutation increased protein flexibility and accelerated substrate binding, which is rate-limiting in the wild-type enzyme. Subsequent mutations predominantly boosted the chemical steps by fine-tuning substrate interactions. Our work identifies an overlooked cause for epistasis: changing the rate-limiting step can result in substantial synergy that boosts enzyme activity.
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Affiliation(s)
| | - H. Adrian Bunzel
- Department of Biosystem Science and Engineering, ETH Zurich, Basel, Switzerland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Karol Buda
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia Canada
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Marc W. van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Pål J. Johnsen
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia Canada
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7
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Wu XR, Chen WY, Liu L, Yang KW. Discovery of hydroxamate as a promising scaffold dually inhibiting metallo- and serine-β-lactamases. Eur J Med Chem 2024; 265:116055. [PMID: 38134748 DOI: 10.1016/j.ejmech.2023.116055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
The bacterial infection mediated by β-lactamases MβLs and SβLs has grown into an emergent health threat, however, development of a molecule that dual inhibits both MβLs and SβLs is challenging. In this work, a series of hydroxamates 1a-g, 2a-e, 3a-c, 4a-c were synthesized, characterized by 1H and 13C NMR and confirmed by HRMS. Biochemical assays revealed that these molecules dually inhibited MβLs (NDM-1, IMP-1) and SβLs (KPC-2, OXA-48), with an IC50 value in the range of 0.64-41.08 and 1.01-41.91 μM (except 1a and 1d on SβLs, IC50 > 50 μM), and 1f was found to be the best inhibitor with an IC50 value in the range of 0.64-1.32 and 0.57-1.01 μM, respectively. Mechanism evaluation indicated that 1f noncompetitively and irreversibly inhibited NDM-1 and KPC-2, with Ki value of 2.5 and 0.55 μM, is a time- and dose-dependent inhibitor of both MβLs and SβLs. MIC tests shown that all hydroxamates increased the antimicrobial effect of MER on E. coli-NDM-1 and E. coli-IMP-1 (expect 1b, 1d, 1g and 2d), resulting in a 2-8-fold reduction in MICs of MER, 1e-g, 2b-d, 3a-c and 4b-c decreased 2-4-fold MICs of MER on E. coli-KPC-2, and 1c, 1f-g, 2a-c, 3b, 4a and 4c decreased 2-16-fold MICs of MER on E. coli-OXA-48. Most importantly, 1f-g, 2b-c, 3b and 4c exhibited the dual synergizing inhibition against both E. coli-MβLs and E. coli-SβLs tested, resulting in a 2-8-fold reduction in MICs of MER, and 1f was found to have the best effect on the drug-resistant bacteria tested. Also, 1f shown synergizing antimicrobial effect on five clinical isolates EC04, EC06, EC08, EC10 and EC24 that produce NDM-1, resulting in a 2-8-fold reduction in MIC of MER, but its effect on E. coli and K. pneumonia-KPC-NDM was not to be observed using the same dose of inhibitor. Mice tests shown that the monotherapy of 1f or 4a in combination with MER significantly reduced the bacterial load of E. coli-NDM-1 and E. coli-OXA-48 cells in liver and spleen, respectively. The discovery in this work offered a promising bifunctional scaffold for creating the specific molecules that dually inhibit MβLs and MβLs, in combating antibiotic-resistant bacteria.
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Affiliation(s)
- Xiao-Rong Wu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Wei-Ya Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Lu Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, PR China.
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8
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Arrigoni R, Ballini A, Santacroce L, Palese LL. The Dynamics of OXA-23 β-Lactamase from Acinetobacter baumannii. Int J Mol Sci 2023; 24:17527. [PMID: 38139363 PMCID: PMC10743560 DOI: 10.3390/ijms242417527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Antibiotic resistance is a pressing topic, which also affects β-lactam antibiotic molecules. Until a few years ago, it was considered no more than an interesting species from an academic point of view, Acinetobacter baumanii is today one of the most serious threats to public health, so much so that it has been declared one of the species for which the search for new antibiotics, or new ways to avoid its resistance, is an absolute priority according to WHO. Although there are several molecular mechanisms that are responsible for the extreme resistance of A. baumanii to antibiotics, a class D β-lactamase is the main cause for the clinical concern of this bacterial species. In this work, we analyzed the A. baumanii OXA-23 protein via molecular dynamics. The results obtained show that this protein is able to assume different conformations, especially in some regions around the active site. Part of the OXA-23 protein has considerable conformational motility, while the rest is less mobile. The importance of these observations for understanding the functioning mechanism of the enzyme as well as for designing new effective molecules for the treatment of A. baumanii is discussed.
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Affiliation(s)
- Roberto Arrigoni
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy;
| | - Andrea Ballini
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Luigi Santacroce
- Interdisciplinary Department of Medicine (DIM), University of Bari ‘Aldo Moro’, 70124 Bari, Italy;
| | - Luigi Leonardo Palese
- Department of Translational Biomedicine and Neurosciences—(DiBraiN), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
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9
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Wu Y, Jiang T, He X, Shao J, Wu C, Mao W, Jia H, He F, Kong Y, Wu J, Sun Q, Sun L, Draz MS, Xie X, Zhang J, Ruan Z. Global Phylogeography and Genomic Epidemiology of Carbapenem-Resistant bla OXA-232-Carrying Klebsiella pneumoniae Sequence Type 15 Lineage. Emerg Infect Dis 2023; 29:2246-2256. [PMID: 37877525 PMCID: PMC10617323 DOI: 10.3201/eid2911.230463] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
Prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) has compromised antimicrobial efficacy against severe infections worldwide. To monitor global spread, we conducted a comprehensive genomic epidemiologic study comparing sequences from 21 blaOXA-232-carrying CRKP isolates from China with K. pneumoniae sequence type (ST) 15 strains from 68 countries available in GenBank. Phylogenetic and phylogeographic analyses revealed all blaOXA-232-carrying CRKP isolates belonged to ST15 lineage and exhibited multidrug resistance. Analysis grouped 330 global blaOXA-232-carrying ST15 CRKP strains into 5 clades, indicating clonal transmission with small genetic distances among multiple strains. The lineage originated in the United States, then spread to Europe, Asia, Oceania, and Africa. Most recent common ancestor was traced back to 2000; mutations averaged ≈1.7 per year per genome. Our research helps identify key forces driving global spread of blaOXA-232-carrying CRKP ST15 lineage and emphasizes the importance of ongoing surveillance of epidemic CRKP.
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10
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Khodaparast L, Khodaparast L, Wu G, Michiels E, Gallardo R, Houben B, Garcia T, De Vleeschouwer M, Ramakers M, Wilkinson H, Duran-Romaña R, Van Eldere J, Rousseau F, Schymkowitz J. Exploiting the aggregation propensity of beta-lactamases to design inhibitors that induce enzyme misfolding. Nat Commun 2023; 14:5571. [PMID: 37689716 PMCID: PMC10492782 DOI: 10.1038/s41467-023-41191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/25/2023] [Indexed: 09/11/2023] Open
Abstract
There is an arms race between beta-lactam antibiotics development and co-evolving beta-lactamases, which provide resistance by breaking down beta-lactam rings. We have observed that certain beta-lactamases tend to aggregate, which persists throughout their evolution under the selective pressure of antibiotics on their active sites. Interestingly, we find that existing beta-lactamase active site inhibitors can act as molecular chaperones, promoting the proper folding of these resistance factors. Therefore, we have created Pept-Ins, synthetic peptides designed to exploit the structural weaknesses of beta-lactamases by causing them to misfold into intracellular inclusion bodies. This approach restores sensitivity to a wide range of beta-lactam antibiotics in resistant clinical isolates, including those with Extended Spectrum variants that pose significant challenges in medical practice. Our findings suggest that targeted aggregation of resistance factors could offer a strategy for identifying molecules that aid in addressing the global antibiotic resistance crisis.
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Affiliation(s)
- Ladan Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Laleh Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Emiel Michiels
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Rodrigo Gallardo
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Bert Houben
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Teresa Garcia
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Matthias De Vleeschouwer
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Hannah Wilkinson
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Ramon Duran-Romaña
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Johan Van Eldere
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology & Immunology, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000, Leuven, Belgium.
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
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11
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Cuicapuza D, Alvarado L, Tocasca N, Aguilar D, Gómez-de-la-Torre JC, Salvatierra G, Tsukayama P, Tamariz J. First Report of OXA-181-Producing Enterobacterales Isolates in Latin America. Microbiol Spectr 2023; 11:e0458422. [PMID: 37022279 PMCID: PMC10269823 DOI: 10.1128/spectrum.04584-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
We characterized five carbapenemase-producing Enterobacterales (CPE) isolates from two health care institutions in Lima, Peru. The isolates were identified as Klebsiella pneumoniae (n = 3), Citrobacter portucalensis (n = 1), and Escherichia coli (n = 1). All were identified as blaOXA-48-like gene carriers using conventional PCR. Whole-genome sequencing found the presence of the blaOXA-181 gene as the only carbapenemase gene in all isolates. Genes associated with resistance to aminoglycosides, quinolones, amphenicols, fosfomycins, macrolides, tetracyclines, sulfonamides, and trimethoprim were also found. The plasmid incompatibility group IncX3 was identified in all genomes in a truncated Tn6361 transposon flanked by ΔIS26 insertion sequences. The qnrS1 gene was also found downstream of blaOXA-181, conferring fluoroquinolone resistance to all isolates. CPE isolates harboring blaOXA-like genes are an increasing public health problem in health care settings worldwide. The IncX3 plasmid is involved in the worldwide dissemination of blaOXA-181, and its presence in these CPE isolates suggests the wide dissemination of blaOXA-181 in Peru. IMPORTANCE Reports of carbapenemase-producing Enterobacterales (CPE) isolates are increasing worldwide. Accurate detection of the β-lactamase OXA-181 (a variant of OXA-48) is important to initiate therapy and preventive measures in the clinic. OXA-181 has been described in CPE isolates in many countries, often associated with nosocomial outbreaks. However, the circulation of this carbapenemase has yet to be reported in Peru. Here, we report the detection of five multidrug-resistant CPE clinical isolates harboring blaOXA-181 in the IncX3-type plasmid, a potential driver of dissemination in Peru.
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Affiliation(s)
- Diego Cuicapuza
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Resistencia Antibiótica e Inmunopatología, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Genómica Microbiana, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Emerge (Emerging Diseases and Climate Change Research Unit), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Norah Tocasca
- Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Daniel Aguilar
- Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | | | - Guillermo Salvatierra
- Laboratorio de Genómica Microbiana, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Emerge (Emerging Diseases and Climate Change Research Unit), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Emerge (Emerging Diseases and Climate Change Research Unit), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Parasites and Microbes Program, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Jesús Tamariz
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Resistencia Antibiótica e Inmunopatología, Universidad Peruana Cayetano Heredia, Lima, Peru
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12
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Dai T, Xie J, Buonomo JA, Moreno A, Banaei N, Bertozzi CR, Rao J. Bioluminogenic Probe for Rapid, Ultrasensitive Detection of β-Lactam-Resistant Bacteria. Anal Chem 2023; 95:7329-7335. [PMID: 37083185 PMCID: PMC10175212 DOI: 10.1021/acs.analchem.3c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Increasingly difficult-to-treat infections by antibiotic-resistant bacteria have become a major public health challenge. Rapid detection of common resistance mechanisms before empiric antibiotic usage is essential for optimizing therapeutic outcomes and containing further spread of resistance to antibiotics among other bacteria. Herein, we present a bioluminogenic probe, D-Bluco, for rapid detection of β-lactamase activity in viable pathogenic bacteria. D-Bluco is a pro-luciferin caged by a β-lactamase-responsive cephalosporin structure and further conjugated with a dabcyl quencher. The caging and quenching significantly decreased the initial background emission and increased the signal-to-background ratio by more than 1200-fold. D-Bluco was shown to detect a broad range of β-lactamases at the femtomolar level. An ultrasensitive RAPID bioluminescence assay using D-Bluco can detect 102 to 103 colony forming unit per milliliter (cfu/mL) of β-lactamase-producing Enterobacterales in urine samples within 30 min. The high sensitivity and rapid detection make the assay attractive for the use of point-of-care diagnostics for lactam-resistant pathogens.
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Affiliation(s)
- Tingting Dai
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jinghang Xie
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Joseph A Buonomo
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Angel Moreno
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, California 94304, United States
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Jianghong Rao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
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13
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Structural and Biochemical Features of OXA-517: a Carbapenem and Expanded-Spectrum Cephalosporin Hydrolyzing OXA-48 Variant. Antimicrob Agents Chemother 2023; 67:e0109522. [PMID: 36648230 PMCID: PMC9933634 DOI: 10.1128/aac.01095-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
OXA-48-producing Enterobacterales have now widely disseminated throughout the world. Several variants have now been reported, differing by just a few amino-acid substitutions or deletions, mostly in the region of the loop β5-β6. As OXA-48 hydrolyzes carbapenems but lacks significant expanded-spectrum cephalosporin (ESC) hydrolytic activity, ESCs were suggested as a therapeutic option. Here, we have characterized OXA-517, a natural variant of OXA-48- with an Arg214Lys substitution and a deletion of Ile215 and Glu216 in the β5-β6 loop, capable of hydrolyzing at the same time ESC and carbapenems. MICs values of E. coli expressing blaOXA-517 gene revealed reduced susceptibility to carbapenems (similarly to OXA-48) and resistance to ESCs. Steady-state kinetic parameters revealed high catalytic efficiencies for ESCs and carbapenems. The blaOXA-517 gene was located on a ca. 31-kb plasmid identical to the prototypical IncL blaOXA-48-carrying plasmid except for an IS1R-mediated deletion of 30.7-kb in the tra operon. The crystal structure of OXA-517, determined to 1.86 Å resolution, revealed an expanded active site compared to that of OXA-48, which allows for accommodation of the bulky ceftazidime substrate. Our work illustrates the remarkable propensity of OXA-48-like carbapenemases to evolve through mutation/deletion in the β5-β6 loop to extend its hydrolysis profile to encompass most β-lactam substrates.
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14
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Studentova V, Sudova V, Bitar I, Paskova V, Moravec J, Pompach P, Volny M, Novak P, Hrabak J. Preferred β-lactone synthesis can explain high rate of false-negative results in the detection of OXA-48-like carbapenemases. Sci Rep 2022; 12:22235. [PMID: 36564543 PMCID: PMC9789108 DOI: 10.1038/s41598-022-26735-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The resistance to carbapenems is usually mediated by enzymes hydrolyzing β-lactam ring. Recently, an alternative way of the modification of the antibiotic, a β-lactone formation by OXA-48-like enzymes, in some carbapenems was identified. We focused our study on a deep analysis of OXA-48-like-producing Enterobacterales, especially strains showing poor hydrolytic activity. In this study, well characterized 74 isolates of Enterobacterales resistant to carbapenems were used. Carbapenemase activity was determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), liquid chromatography/mass spectrometry (LC-MS), Carba-NP test and modified Carbapenem Inactivation Method (mCIM). As meropenem-derived β-lactone possesses the same molecular weight as native meropenem (MW 383.46 g/mol), β-lactonization cannot be directly detected by MALDI-TOF MS. In the spectra, however, the peaks of m/z = 340.5 and 362.5 representing decarboxylated β-lactone and its sodium adduct were detected in 25 out of 35 OXA-48-like producers. In the rest 10 isolates, decarboxylated hydrolytic product (m/z = 358.5) and its sodium adduct (m/z = 380.5) have been detected. The peak of m/z = 362.5 was detected in 3 strains co-producing OXA-48-like and NDM-1 carbapenemases. The respective signal was identified in no strain producing class A or class B carbapenemase alone showing its specificity for OXA-48-like carbapenemases. Using LC-MS, we were able to identify meropenem-derived β-lactone directly according to the different retention time. All strains with a predominant β-lactone production showed negative results of Carba NP test. In this study, we have demonstrated that the strains producing OXA-48-like carbapenemases showing false-negative results using Carba NP test and MALDI-TOF MS preferentially produced meropenem-derived β-lactone. We also identified β-lactone-specific peak in MALDI-TOF MS spectra and demonstrated the ability of LC-MS to detect meropenem-derived β-lactone.
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Affiliation(s)
- Vendula Studentova
- grid.4491.80000 0004 1937 116XBiomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic ,grid.4491.80000 0004 1937 116XDepartment of Microbiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, 323 00 Pilsen, Czech Republic
| | - Vendula Sudova
- grid.4491.80000 0004 1937 116XBiomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic ,grid.4491.80000 0004 1937 116XDepartment of Clinical Biochemistry and Haematology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, 323 00 Pilsen, Czech Republic
| | - Ibrahim Bitar
- grid.4491.80000 0004 1937 116XBiomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic ,grid.4491.80000 0004 1937 116XDepartment of Microbiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, 323 00 Pilsen, Czech Republic
| | - Veronika Paskova
- grid.4491.80000 0004 1937 116XBiomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic ,grid.4491.80000 0004 1937 116XDepartment of Microbiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, 323 00 Pilsen, Czech Republic
| | - Jiri Moravec
- grid.4491.80000 0004 1937 116XBiomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Petr Pompach
- grid.418800.50000 0004 0555 4846Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Michael Volny
- grid.418800.50000 0004 0555 4846Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Petr Novak
- grid.418800.50000 0004 0555 4846Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jaroslav Hrabak
- grid.4491.80000 0004 1937 116XBiomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic ,grid.4491.80000 0004 1937 116XDepartment of Microbiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, 323 00 Pilsen, Czech Republic
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15
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Isler B, Aslan AT, Akova M, Harris P, Paterson DL. Treatment strategies for OXA-48-like and NDM producing Klebsiella pneumoniae infections. Expert Rev Anti Infect Ther 2022; 20:1389-1400. [PMID: 36150216 DOI: 10.1080/14787210.2022.2128764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION OXA-48 and NDM are amongst the most prevalent carbapenemase types associated with Klebsiella pneumoniae worldwide, with an increase in their prevalence in recent years. Knowledge on the treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP) comes from KPC-producing CRKP with limited data available for OXA-48-like and NDM producers. Our aim is to review the literature on the treatment of OXA-48-like and NDM-producing CRKP with the goal of providing an update on the available antibiotic treatment strategies, particularly in light of changing carbapenemase epidemiology and increasing antimicrobial resistance. AREAS COVERED We reviewed studies looking at the antibiotic treatment and outcome of OXA-48-like and/or NDM-producing CRKP. EXPERT OPINION The best available treatment option for OXA-48 producers is ceftazidime-avibactam, where available and when the price permits its use. Colistin remains as the second-line option if in vitro susceptibility is demonstrated with an appropriate method. There is not enough evidence to support the use of meropenem-containing combination therapies for meropenem-resistant OXA-48 producers. Treatment of NDM producers is an unmet need. Ceftazidime-avibactam and aztreonam combination or cefiderocol can be used for NDM producers, where available. Higher cefiderocol MICs against NDM producers is concerning. Aztreonam-avibactam provides hope for the treatment of NDM producers.
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Affiliation(s)
- Burcu Isler
- University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, Australia.,Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - Abdullah Tarık Aslan
- Department of Internal Medicine, Golhisar State Hospital, 15100 Golhisar, Turkey
| | - Murat Akova
- Infectious Diseases and Clinical Microbiology, Hacettepe University School of Medicine, Ankara
| | - Patrick Harris
- University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, Australia
| | - David L Paterson
- University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, Brisbane, Australia.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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16
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Takebayashi Y, Henderson SR, Chirgadze DY, Warburton PJ, Evans BA. OXA-66 structure and oligomerisation of OXA Ab enzymes. Access Microbiol 2022; 4:acmi000412. [PMID: 36415731 PMCID: PMC9675178 DOI: 10.1099/acmi.0.000412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023] Open
Abstract
The OXA β-lactamases are responsible for hydrolysing β-lactam antibiotics and contribute to the multidrug-resistant phenotype of several major human pathogens. The OXAAb enzymes are intrinsic to Acinetobacter baumannii and can confer resistance to carbapenem antibiotics. Here we determined the structure of the most prevalent OXAAb enzyme, OXA-66. The structure of OXA-66 was solved at a resolution of 2.1 Å and found to be very similar to the structure of OXA-51, the only other OXAAb enzyme that has had its structure solved. Our data contained one molecule per asymmetric unit, and analysis of positions responsible for dimer formation in other OXA enzymes suggest that OXA-66 likely exists as a monomer.
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Affiliation(s)
- Yuiko Takebayashi
- Department of Biomedical and Forensic Science, Anglia Ruskin University, Cambridge, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Sara R. Henderson
- Norwich Medical School, University of East Anglia, Norwich, UK
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | - Philip J. Warburton
- Department of Biomedical and Forensic Science, Anglia Ruskin University, Cambridge, UK
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
| | - Benjamin A. Evans
- Department of Biomedical and Forensic Science, Anglia Ruskin University, Cambridge, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
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17
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OXA-48-Like β-Lactamases: Global Epidemiology, Treatment Options, and Development Pipeline. Antimicrob Agents Chemother 2022; 66:e0021622. [PMID: 35856662 PMCID: PMC9380527 DOI: 10.1128/aac.00216-22] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Modern medicine is threatened by the rising tide of antimicrobial resistance, especially among Gram-negative bacteria, where resistance to β-lactams is most often mediated by β-lactamases. The penicillin and cephalosporin ascendancies were, in their turn, ended by the proliferation of TEM penicillinases and CTX-M extended-spectrum β-lactamases. These class A β-lactamases have long been considered the most important. For carbapenems, however, the threat is increasingly from the insidious rise of a class D carbapenemase, OXA-48, and its close relatives. Over the past 20 years, OXA-48 and "OXA-48-like" enzymes have proliferated to become the most prevalent enterobacterial carbapenemases across much of Europe, Northern Africa, and the Middle East. OXA-48-like enzymes are notoriously difficult to detect because they often cause only low-level in vitro resistance to carbapenems, meaning that the true burden is likely underestimated. Despite this, they are associated with carbapenem treatment failures. A highly conserved incompatibility complex IncL plasmid scaffold often carries blaOXA-48 and may carry other antimicrobial resistance genes, leaving limited treatment options. High conjugation efficiency means that this plasmid is sometimes carried by multiple Enterobacterales in a single patient. Producers evade most β-lactam-β-lactamase inhibitor combinations, though promising agents have recently been licensed, notably ceftazidime-avibactam and cefiderocol. The molecular machinery enabling global spread, current treatment options, and the development pipeline of potential new therapies for Enterobacterales that produce OXA-48-like β-lactamases form the focus of this review.
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18
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Direct Colorimetry of Imipenem Decomposition as a Novel Cost-Effective Method for Detecting Carbapenemase-Producing Enterobacteria. Microbiol Spectr 2022; 10:e0093822. [PMID: 35852323 PMCID: PMC9430894 DOI: 10.1128/spectrum.00938-22] [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] [Indexed: 11/26/2022] Open
Abstract
In the absence of a molecule that would collectively inhibit both metallo-β-lactamases and serine-reactive carbapenemases, containment of their genes is the main weapon currently available for confronting carbapenem resistance in hospitals. Cost-effective methodologies rapidly detecting carbapenemase-producing enterobacteria (CPE) would facilitate such measures. Herein, a low-cost CPE detection method was developed that was based on the direct colorimetry of the yellow shift caused by the accumulation of diketopiperazines—products of the acid-catalyzed imipenem oligomerization—induced by carbapenemase action on dense solutions of imipenem/cilastatin. The reactions were studied by spectrophotometry in the visible spectrum using preparations of β-lactamases from the four molecular classes. The effects of various buffers on reaction mixtures containing the potent carbapenemases NDM-1 and NMC-A were monitored at 405 nm. Optimal conditions were used for the analysis of cell suspensions, and the assay was evaluated using 66 selected enterobacteria, including 50 CPE as well as 16 carbapenemase-negative strains overexpressing other β-lactamases. The development of the yellow color was specific for carbapenemase-containing enzyme preparations, and the maximum intensity was achieved in acidic or unbuffered conditions in the presence of zinc. When applied on bacterial cell suspensions, the assay could detect CPE with 98% sensitivity and 100% specificity, with results being comparable to those obtained with the Carba NP technique. Direct colorimetry of carbapenemase-induced imipenem decomposition required minimum reagents while exhibiting high accuracy in detecting CPE. Therefore, it should be considered for screening purposes after further clinical evaluation. IMPORTANCE Currently, the spread of multidrug-resistant (MDR) carbapenemase-producing enterobacteria (CPE), mostly in the clinical setting, is among the most pressing public health problems worldwide. In order to effectively control CPE, use of reliable and affordable methods detecting carbapenemase genes or the respective β-lactamases is of vital importance. Herein, we developed a novel method, based on a previously undescribed phenomenon, that can detect CPE with few reagents by direct colorimetry of bacterial suspensions and imipenem/cilastatin mixtures.
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Avci FG, Tastekil I, Jaisi A, Ozbek Sarica P, Sariyar Akbulut B. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens. Pathog Glob Health 2022; 117:219-234. [PMID: 35758005 PMCID: PMC10081068 DOI: 10.1080/20477724.2022.2088496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Turkey
| | - Ilgaz Tastekil
- Bioengineering Department, Marmara University, Kadikoy, 34722, Turkey
| | - Amit Jaisi
- Drug and Cosmetics Excellence Center, School of Pharmacy, Walailak University, 80160, Nakhon Si Thammarat, Thailand
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20
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Zhang Y, Chen C, Cheng B, Gao L, Qin C, Zhang L, Zhang X, Wang J, Wan Y. Discovery of Quercetin and Its Analogs as Potent OXA-48 Beta-Lactamase Inhibitors. Front Pharmacol 2022; 13:926104. [PMID: 35814247 PMCID: PMC9258905 DOI: 10.3389/fphar.2022.926104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Carbapenem resistance in Enterobacteriaceae caused by OXA-48 β-lactamase is a growing global health threat and has rapidly spread in many regions of the world. Developing inhibitors is a promising way to overcome antibiotic resistance. However, there are few options for problematic OXA-48. Here we identified quercetin, fisetin, luteolin, 3′,4′,7-trihydroxyflavone, apigenin, kaempferol, and taxifolin as potent inhibitors of OXA-48 with IC50 values ranging from 0.47 to 4.54 μM. Notably, the structure-activity relationship revealed that the substitute hydroxyl groups in the A and B rings of quercetin and its structural analogs improved the inhibitory effect against OXA-48. Mechanism studies including enzymatic kinetic assay, isothermal titration calorimetry (ITC), and surface plasmon resonance (SPR) analysis demonstrated that quercetin reversibly inhibited OXA-48 through a noncompetitive mode. Molecular docking suggested that hydroxyl groups at the 3′, 4′ and 7 positions in flavonoids formed hydrogen-bonding interactions with the side chains of Thr209, Ala194, and Gln193 in OXA-48. Quercetin, fisetin, luteolin, and 3′,4′,7-trihydroxyflavone effectively restored the antibacterial efficacy of piperacillin or imipenem against E. coli producing OXA-48, resulting in 2–8-fold reduction in MIC. Moreover, quercetin combined with piperacillin showed antimicrobial efficacy in mice infection model. These studies provide potential lead compounds for the development of β-lactamase inhibitors and in combination with β-lactams to combat OXA-48 producing pathogen.
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Affiliation(s)
- Yuejuan Zhang
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Cheng Chen
- College of Forestry, Northwest A&F University, Yangling, China
| | - Bin Cheng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lei Gao
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Chuan Qin
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Lixia Zhang
- Clinical Laboratory, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Xu Zhang
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Jun Wang
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Yi Wan
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
- *Correspondence: Yi Wan,
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Mitchell JM, June CM, Baggett VL, Lowe BC, Ruble JF, Bonomo RA, Leonard DA, Powers RA. Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40. J Biol Chem 2022; 298:102127. [PMID: 35709986 PMCID: PMC9293634 DOI: 10.1016/j.jbc.2022.102127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
The evolution of multidrug resistance in Acinetobacter spp. increases the risk of our best antibiotics losing their efficacy. From a clinical perspective, the carbapenem-hydrolyzing class D β-lactamase subfamily present in Acinetobacter spp. is particularly concerning because of its ability to confer resistance to carbapenems. The kinetic profiles of class D β-lactamases exhibit variability in carbapenem hydrolysis, suggesting functional differences. To better understand the structure–function relationship between the carbapenem-hydrolyzing class D β-lactamase OXA-24/40 found in Acinetobacter baumannii and carbapenem substrates, we analyzed steady-state kinetics with the carbapenem antibiotics meropenem and ertapenem and determined the structures of complexes of OXA-24/40 bound to imipenem, meropenem, doripenem, and ertapenem, as well as the expanded-spectrum cephalosporin cefotaxime, using X-ray crystallography. We show that OXA-24/40 exhibits a preference for ertapenem compared with meropenem, imipenem, and doripenem, with an increase in catalytic efficiency of up to fourfold. We suggest that superposition of the nine OXA-24/40 complexes will better inform future inhibitor design efforts by providing insight into the complicated and varying ways in which carbapenems are selected and bound by class D β-lactamases.
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Affiliation(s)
- Joshua M Mitchell
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Vincent L Baggett
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Beth C Lowe
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - James F Ruble
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH; Departments of Medicine, Biochemistry, Molecular Biology and Microbiology, Pharmacology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH.
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI.
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22
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Jain D, Verma J, Ghosh AS. Deciphering the role of residues in the loops nearing the active site of OXA-58 in imparting beta-lactamase activity. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35766983 DOI: 10.1099/mic.0.001203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The existence of OXA-58 carbapenemase alone or in combination with other beta-lactam resistance factors poses significant beta-lactam resistance. The exact mechanism of action of OXA type beta-lactamases is debatable due to the involvement of multiple residues within or outside the active site. In the present work, we have elucidated the relative role of residues present in the putative omega (W169, L170, K171) and β6-β7 (A226 and D228) loops on the activity of OXA-58 by substituting into alanine (and aspartate for A226) through site-directed mutagenesis. E. coli cells harbouring OXA-58, substituted at the putative omega loop, manifest a significant decrease in the beta-lactam resistance profile than that of the cells expressing OXA-58. Further, a reduction in the catalytic efficiency is observed for the purified variants of OXA-58 carrying individual substitutions in the putative omega loop than that of OXA-58. However, the addition of NaHCO3 (for carbamylation of K86) increases catalytic efficiency of the individual protein as revealed by nitrocefin hydrolysis assay and steady state kinetics. Moreover, W169A and K171A substitutions show significant effects on the thermal stability of OXA-58. Therefore, we conclude that the putative omega loop residues W169, L170 and K171, individually, have significant role in the activity and stability of OXA-58, mostly by stabilising carbamylated lysine of active site.
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Affiliation(s)
- Diamond Jain
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Jyoti Verma
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
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23
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Hirvonen VA, Weizmann TM, Mulholland AJ, Spencer J, van der Kamp MW. Multiscale Simulations Identify Origins of Differential Carbapenem Hydrolysis by the OXA-48 β-Lactamase. ACS Catal 2022; 12:4534-4544. [PMID: 35571461 PMCID: PMC9097296 DOI: 10.1021/acscatal.1c05694] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/22/2022] [Indexed: 12/27/2022]
Abstract
OXA-48 β-lactamases are frequently encountered in bacterial infections caused by carbapenem-resistant Gram-negative bacteria. Due to the importance of carbapenems in the treatment of healthcare-associated infections and the increasingly wide dissemination of OXA-48-like enzymes on plasmids, these β-lactamases are of high clinical significance. Notably, OXA-48 hydrolyzes imipenem more efficiently than other commonly used carbapenems, such as meropenem. Here, we use extensive multiscale simulations of imipenem and meropenem hydrolysis by OXA-48 to dissect the dynamics and to explore differences in the reactivity of the possible conformational substates of the respective acylenzymes. Quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reaction for both substrates demonstrate that deacylation is favored when the 6α-hydroxyethyl group is able to hydrogen bond to the water molecule responsible for deacylation but disfavored by the increasing hydration of either oxygen of the carboxylated Lys73 general base. Differences in free energy barriers calculated from the QM/MM simulations correlate well with the experimentally observed differences in hydrolytic efficiency between meropenem and imipenem. We conclude that the impaired breakdown of meropenem, compared to imipenem, which arises from a subtle change in the hydrogen bonding pattern between the deacylating water molecule and the antibiotic, is most likely induced by the meropenem 1β-methyl group. In addition to increased insights into carbapenem breakdown by OXA β-lactamases, which may aid in future efforts to design antibiotics or inhibitors, our approach exemplifies the combined use of atomistic simulations in determining the possible different enzyme-substrate substates and their influence on enzyme reaction kinetics.
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Affiliation(s)
- Viivi
H. A. Hirvonen
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Tal Moshe Weizmann
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - James Spencer
- School
of Cellular and Molecular Medicine, University
of Bristol, University
Walk, Bristol BS8 1TD, U.K.
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
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24
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Moguet C, Gonzalez C, Sallustrau A, Gelhaye S, Naas T, Simon S, Volland H. Detection of expanded-spectrum cephalosporin hydrolysis by lateral flow immunoassay. Microb Biotechnol 2022; 15:603-612. [PMID: 34342151 PMCID: PMC8867991 DOI: 10.1111/1751-7915.13892] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/24/2021] [Accepted: 07/03/2021] [Indexed: 12/01/2022] Open
Abstract
Early detection of expanded-spectrum cephalosporin (ESC) resistance is essential not only for an effective therapy but also for the prompt implementation of infection control measures to prevent dissemination in the hospital. We have developed and validated a lateral flow immunoassay (LFIA), called LFIA-CTX test, for the detection of ESC (cefotaxime) hydrolytic activity based on structural discrimination between the intact antibiotic and its hydrolysed product. A single bacterial colony was suspended in an extraction buffer containing cefotaxime. After a 30-min incubation, the solution is loaded on the LFIA for reading within 10 min. A total of 348 well-characterized Gram-negative isolates were tested. Among them, the 38 isolates that did not express any cefotaxime-hydrolysing β-lactamase gave negative results. Of the 310 isolates expressing at least one cefotaxime-hydrolysing β-lactamase, all were tested positive, except three OXA-48-like producers, which were repeatedly detected negative. Therefore, the sensitivity was 99.1% and the specificity was 100%. The LFIA-CTX test is efficient, fast, low-cost and easy to implement in the workflow of a routine microbiology laboratory.
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Affiliation(s)
- Christian Moguet
- Département Médicaments et Technologies pour la Santé (DMTS)SPIUniversité Paris‐SaclayCEA, INRAEGif‐sur‐Yvette91191France
| | - Camille Gonzalez
- Bacteriology‐Hygiene UnitAPHP, Hôpital BicêtreLe Kremlin‐BicêtreFrance
| | - Antoine Sallustrau
- Département Médicaments et Technologies pour la Santé (DMTS)SCBMUniversité Paris‐SaclayCEA, INRAEGif‐sur‐Yvette91191France
| | - Stéphanie Gelhaye
- Département Médicaments et Technologies pour la Santé (DMTS)SPIUniversité Paris‐SaclayCEA, INRAEGif‐sur‐Yvette91191France
| | - Thierry Naas
- Bacteriology‐Hygiene UnitAPHP, Hôpital BicêtreLe Kremlin‐BicêtreFrance
- Team ResistUMR1184Université Paris‐Saclay – INSERM – CEALabEx LermitLe Kremlin‐BicêtreFrance
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase‐producing EnterobacteralesLe Kremlin‐BicêtreFrance
| | - Stéphanie Simon
- Département Médicaments et Technologies pour la Santé (DMTS)SPIUniversité Paris‐SaclayCEA, INRAEGif‐sur‐Yvette91191France
| | - Hervé Volland
- Département Médicaments et Technologies pour la Santé (DMTS)SPIUniversité Paris‐SaclayCEA, INRAEGif‐sur‐Yvette91191France
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To Be or Not to Be an OXA-48 Carbapenemase. Microorganisms 2022; 10:microorganisms10020258. [PMID: 35208713 PMCID: PMC8875484 DOI: 10.3390/microorganisms10020258] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 12/03/2022] Open
Abstract
Since the first description of OXA-48, more than forty variants have been recovered from Enterobacterales isolates. Whereas some OXA-48-related enzymes have been reported as conferring similar resistance patterns, namely, the hydrolysis of carbapenems and penicillins with very weak or almost no activity against expanded-spectrum cephalosporins, some have reduced carbapenem and temocillin hydrolysis, and others hydrolyze expanded-spectrum cephalosporins and carbapenems only marginally. With such drastic differences in the hydrolytic profile, especially of carbapenems, it becomes urgent to establish hydrolytic cutoffs in order to determine when an OXA-48-like enzyme may be considered as a carbapenemase or not. With this aim, the coefficient of activity for imipenem (kcat/Km) was determined for a total of 30 enzymes, including OXA-48, OXA-48-like natural variants, and OXA-48 synthetic mutants. In addition, six different methods for the detection of carbapenemase-producers were performed. The coefficients of activity for imipenem for all the different enzymes went from 550 mM−1·s−1 to 0.02 mM−1·s−1. In order to match the coefficient of activity results with the biochemical confirmatory tests, we suggest the value of 0.27 mM−1·s−1 as the cutoff above which an OXA-48 variant may be considered a carbapenem-hydrolyzing enzyme.
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26
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Multiplex Lateral Flow Immunoassay for the Detection of Expanded-Spectrum Hydrolysis and CTX-M Enzymes. Diagnostics (Basel) 2022; 12:diagnostics12010190. [PMID: 35054357 PMCID: PMC8775197 DOI: 10.3390/diagnostics12010190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 01/21/2023] Open
Abstract
Background: Early detection of expanded-spectrum cephalosporinase (ESC) hydrolyzing ß-lactamases is essential for antibiotic stewardship. Here we have developed a multiplex lateral flow immunoassay (LFIA) that detects cefotaxime-hydrolyzing activity as well as the most prevalent ESC-hydrolyzing ß-lactamases: the CTX-M-like. Methods: The Rapid LFIA ESC test was evaluated retrospectively on 188 (139 Enterobacterales, 30 Pseudomonas spp. and 14 Acinetobacter spp.) agar-grown bacterial isolates with well-characterized ß-lactamase content. One single colony was resuspended in 150 µL extraction buffer containing cefotaxime, incubated at room temperature for 30 min prior to loading on the LFIA for reading within 10 min. Results: Out of the 188 isolates, all 17 that did not express a β-lactamase hydrolyzing cefotaxime gave negative results, and all 171 isolates expressing a β-lactamase known to hydrolyze cefotaxime, gave a positive test result. In addition, all 86 isolates expressing a CTX-M-variant belonging to one of the five CTX-M-subgroups were correctly identified. The sensitivity and specificity was 100% for both tests. Conclusions: The results showed that the multiplex LFIA was efficient, fast, low cost and easy to implement in routine laboratory work for the confirmation of ESC hydrolyzing activity and the presence of CTX-M enzymes.
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Taylor DM, Anglin J, Hu L, Wang L, Sankaran B, Wang J, Matzuk MM, Prasad BV, Palzkill T. Unique Diacidic Fragments Inhibit the OXA-48 Carbapenemase and Enhance the Killing of Escherichia coli Producing OXA-48. ACS Infect Dis 2021; 7:3345-3354. [PMID: 34817169 PMCID: PMC9677231 DOI: 10.1021/acsinfecdis.1c00501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite the advances in β-lactamase inhibitor development, limited options exist for the class D carbapenemase known as OXA-48. OXA-48 is one of the most prevalent carbapenemases in carbapenem-resistant Enterobacteriaceae infections and is not susceptible to most available β-lactamase inhibitors. Here, we screened various low-molecular-weight compounds (fragments) against OXA-48 to identify functional scaffolds for inhibitor development. Several biphenyl-, naphthalene-, fluorene-, anthraquinone-, and azobenzene-based compounds were found to inhibit OXA-48 with low micromolar potency despite their small size. Co-crystal structures of OXA-48 with several of these compounds revealed key interactions with the carboxylate-binding pocket, Arg214, and various hydrophobic residues of β-lactamase that can be exploited in future inhibitor development. A number of the low-micromolar-potency inhibitors, across different scaffolds, synergize with ampicillin to kill Escherichia coli expressing OXA-48, albeit at high concentrations of the respective inhibitors. Additionally, several compounds demonstrated micromolar potency toward the OXA-24 and OXA-58 class D carbapenemases that are prevalent in Acinetobacter baumannii. This work provides foundational information on a variety of chemical scaffolds that can guide the design of effective OXA-48 inhibitors that maintain efficacy as well as potency toward other major class D carbapenemases.
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Affiliation(s)
- Doris Mia Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin Anglin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lingfei Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, CA, 94720, USA
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martin M. Matzuk
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - B.V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
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28
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Loch JI, Imiolczyk B, Sliwiak J, Wantuch A, Bejger M, Gilski M, Jaskolski M. Crystal structures of the elusive Rhizobium etli L-asparaginase reveal a peculiar active site. Nat Commun 2021; 12:6717. [PMID: 34795296 PMCID: PMC8602277 DOI: 10.1038/s41467-021-27105-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/01/2021] [Indexed: 12/04/2022] Open
Abstract
Rhizobium etli, a nitrogen-fixing bacterial symbiont of legume plants, encodes an essential L-asparaginase (ReAV) with no sequence homology to known enzymes with this activity. High-resolution crystal structures of ReAV show indeed a structurally distinct, dimeric enzyme, with some resemblance to glutaminases and β-lactamases. However, ReAV has no glutaminase or lactamase activity, and at pH 9 its allosteric asparaginase activity is relatively high, with Km for L-Asn at 4.2 mM and kcat of 438 s-1. The active site of ReAV, deduced from structural comparisons and confirmed by mutagenesis experiments, contains a highly specific Zn2+ binding site without a catalytic role. The extensive active site includes residues with unusual chemical properties. There are two Ser-Lys tandems, all connected through a network of H-bonds to the Zn center, and three tightly bound water molecules near Ser48, which clearly indicate the catalytic nucleophile.
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Affiliation(s)
- Joanna I Loch
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Barbara Imiolczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Joanna Sliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Wantuch
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Miroslaw Gilski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Mariusz Jaskolski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
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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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Lund BA, Thomassen AM, Carlsen TJW, Leiros HKS. Biochemical and biophysical characterization of the OXA-48-like carbapenemase OXA-436. Acta Crystallogr F Struct Biol Commun 2021; 77:312-318. [PMID: 34473108 PMCID: PMC8411929 DOI: 10.1107/s2053230x21008645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/18/2021] [Indexed: 11/08/2023] Open
Abstract
The crystal structure of the class D β-lactamase OXA-436 was solved to a resolution of 1.80 Å. Higher catalytic rates were found at higher temperatures for the clinically important antibiotic imipenem, indicating better adaptation of OXA-436 to its mesophilic host than OXA-48, which is believed to originate from an environmental source. Furthermore, based on the most populated conformations during 100 ns molecular-dynamics simulations, it is postulated that the modulation of activity involves conformational shifts of the α3-α4 and β5-β6 loops. While these changes overall do not cause clinically significant shifts in the resistance profile, they show that antibiotic-resistance enzymes exist in a continuum. It is believed that these seemingly neutral differences in the sequence exist on a path leading to significant changes in substrate selectivity.
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Affiliation(s)
- Bjarte Aarmo Lund
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ane Molden Thomassen
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Trine Josefine Warg Carlsen
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Hanna-Kirsti Schrøder Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
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Rima M, Emeraud C, Bonnin RA, Gonzalez C, Dortet L, Iorga BI, Oueslati S, Naas T. Biochemical characterization of OXA-244, an emerging OXA-48 variant with reduced β-lactam hydrolytic activity. J Antimicrob Chemother 2021; 76:2024-2028. [PMID: 33993262 DOI: 10.1093/jac/dkab142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND OXA-48-producing Enterobacterales have widely disseminated globally with an increasing number of variants identified. Among them, OXA-244 is increasingly reported, despite detection difficulties. OBJECTIVES To determine the steady-state kinetic parameters of OXA-244. METHODS The blaOXA-244 gene was amplified, cloned into plasmids p-TOPO and pET41b+, and transformed into Escherichia coli TOP10 for MIC determination and E. coli BL21 DE3 for purification. Steady-state kinetic parameters and IC50s of clavulanic acid, tazobactam and NaCl were determined using purified OXA-244. Molecular modelling was also performed. RESULTS A reduction in MICs of temocillin and carbapenems was observed in E. coli expressing OXA-244 as compared with OXA-48. The kinetic parameters revealed a reduced carbapenemase activity of OXA-244 as compared with OXA-48, especially for imipenem, which was 10-fold lower. Similarly, catalytic efficiency (kcat/Km) was reduced by 4-fold and 20-fold for ampicillin and temocillin, respectively. Kinetic parameters for cephalosporins were, however, similar. Molecular modelling studies evidenced the key role of R214 in OXA-48, establishing salt bridges with D159 and with the carboxylate group of the R1 substituent of temocillin. These interactions are not possible with G214 in OXA-244, explaining the reduced affinity of temocillin for this enzyme. The R214G mutation in OXA-244 is also likely to induce changes in the active site's water network that would explain the decrease in the hydrolysis rate of carbapenems. CONCLUSIONS Our data confirm that the R214G mutation (present in OXA-244) results in reduced carbapenem- and temocillin-hydrolysing activity, confirming the crucial role of residue 214 in the hydrolysis of these substrates by OXA-48-like β-lactamases.
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Affiliation(s)
- Mariam Rima
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France
| | - Cecile Emeraud
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Camille Gonzalez
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Bogdan I Iorga
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Saoussen Oueslati
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, LabEx LERMIT, and Joint Research Unit EERA 'Evolution and Ecology of Resistance to Antibiotics', Institut Pasteur-APHP-University Paris Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
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Abstract
Class D β-lactamases are composed of 14 families and the majority of the member enzymes are included in the OXA family. The genes for class D β-lactamases are frequently identified in the chromosome as an intrinsic resistance determinant in environmental bacteria and a few of these are found in mobile genetic elements carried by clinically significant pathogens. The most dominant OXA family among class D β-lactamases is superheterogeneous and the family needs to have an updated scheme for grouping OXA subfamilies through phylogenetic analysis. The OXA enzymes, even the members within a subfamily, have a diverse spectrum of resistance. Such varied activity could be derived from their active sites, which are distinct from those of the other serine β-lactamases. Their substrate profile is determined according to the size and position of the P-, Ω- and β5-β6 loops, assembling the active-site channel, which is very hydrophobic. Also, amino acid substitutions occurring in critical structures may alter the range of hydrolysed substrates and one subfamily could include members belonging to several functional groups. This review aims to describe the current class D β-lactamases including the functional groups, occurrence types (intrinsic or acquired) and substrate spectra and, focusing on the major OXA family, a new model for subfamily grouping will be presented.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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Discovery of Novel Chemical Series of OXA-48 β-Lactamase Inhibitors by High-Throughput Screening. Pharmaceuticals (Basel) 2021; 14:ph14070612. [PMID: 34202402 PMCID: PMC8308845 DOI: 10.3390/ph14070612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
The major cause of bacterial resistance to β-lactams is the production of hydrolytic β-lactamase enzymes. Nowadays, the combination of β-lactam antibiotics with β-lactamase inhibitors (BLIs) is the main strategy for overcoming such issues. Nevertheless, particularly challenging β-lactamases, such as OXA-48, pose the need for novel and effective treatments. Herein, we describe the screening of a proprietary compound collection against Klebsiella pneumoniae OXA-48, leading to the identification of several chemotypes, like the 4-ideneamino-4H-1,2,4-triazole (SC_2) and pyrazolo[3,4-b]pyridine (SC_7) cores as potential inhibitors. Importantly, the most potent representative of the latter series (ID2, AC50 = 0.99 μM) inhibited OXA-48 via a reversible and competitive mechanism of action, as demonstrated by biochemical and X-ray studies; furthermore, it slightly improved imipenem’s activity in Escherichia coli ATCC BAA-2523 β-lactam resistant strain. Also, ID2 showed good solubility and no sign of toxicity up to the highest tested concentration, resulting in a promising starting point for further optimization programs toward novel and effective non-β-lactam BLIs.
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Detection of carbapenemase producing enterobacteria using an ion sensitive field effect transistor sensor. Sci Rep 2021; 11:12061. [PMID: 34103596 PMCID: PMC8187427 DOI: 10.1038/s41598-021-91202-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/24/2021] [Indexed: 02/05/2023] Open
Abstract
The timely and accurate detection of carbapenemase-producing Enterobacterales (CPE) is imperative to manage this worldwide problem in an effective fashion. Herein we addressed the question of whether the protons produced during imipenem hydrolysis could be detected using an ion sensitive field effect transistor (ISFET). Application of the methodology on enzyme preparations showed that the sensor is able to detect carbapenemases of the NDM, IMP, KPC and NMC-A types at low nanomolar concentrations while VIM and OXA-48 responded at levels above 100 nM. Similar results were obtained when CPE cell suspensions were tested; NDM, IMP, NMC-A and KPC producers caused fast reductions of the output potential. Reduction rates with VIM-type and especially OXA-48 producing strains were significantly lower. Based on results with selected CPEs and carbapenemase-negative enterobacteria, a threshold of 10 mV drop at 30 min was set. Applying this threshold, the method exhibited 100% sensitivity for NDM, IMP and KPC and 77.3% for VIM producers. The OXA-48-positive strains failed to pass the detection threshold. A wide variety of carbapenemase-negative control strains were all classified as negative (100% specificity). In conclusion, an ISFET-based approach may have the potential to be routinely used for non OXA-48-like CPE detection in the clinical laboratory.
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Antimicrobial Resistance Conferred by OXA-48 β-Lactamases: Towards a Detailed Mechanistic Understanding. Antimicrob Agents Chemother 2021; 65:AAC.00184-21. [PMID: 33753332 DOI: 10.1128/aac.00184-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OXA-48-type β-lactamases are now routinely encountered in bacterial infections caused by carbapenem-resistant Enterobacterales These enzymes are of high and growing clinical significance due to the importance of carbapenems in treatment of health care-associated infections by Gram-negative bacteria, the wide and increasing dissemination of OXA-48 enzymes on plasmids, and the challenges posed by their detection. OXA-48 confers resistance to penicillin (which is efficiently hydrolyzed) and carbapenem antibiotics (which is more slowly broken down). In addition to the parent enzyme, a growing array of variants of OXA-48 is now emerging. The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins. The growth in importance and diversity of the OXA-48 group has motivated increasing numbers of studies that aim to elucidate the relationship between structure and specificity and establish the mechanistic basis for β-lactam turnover in this enzyme family. In this review, we collate recently published structural, kinetic, and mechanistic information on the interactions between clinically relevant β-lactam antibiotics and inhibitors and OXA-48 β-lactamases. Collectively, these studies are starting to form a detailed picture of the underlying bases for the differences in β-lactam specificity between OXA-48 variants and the consequent differences in resistance phenotype. We focus specifically on aspects of carbapenemase and cephalosporinase activities of OXA-48 β-lactamases and discuss β-lactamase inhibitor development in this context. Throughout the review, we also outline key open research questions for future investigation.
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Abstract
Very low antibiotic concentrations have been shown to drive the evolution of antimicrobial resistance. While substantial progress has been made to understand the driving role of low concentrations during resistance development for different antimicrobial classes, the importance of β-lactams, the most commonly used antibiotics, is still poorly studied. Our current understanding of how low antibiotic concentrations shape the evolution of contemporary β-lactamases is limited. Using the widespread carbapenemase OXA-48, we tested the long-standing hypothesis that selective compartments with low antibiotic concentrations cause standing genetic diversity that could act as a gateway to developing clinical resistance. Here, we subjected Escherichia coli expressing blaOXA-48, on a clinical plasmid, to experimental evolution at sub-MICs of ceftazidime. We identified and characterized seven single variants of OXA-48. Susceptibility profiles and dose-response curves showed that they increased resistance only marginally. However, in competition experiments at sub-MICs of ceftazidime, they demonstrated strong selectable fitness benefits. Increased resistance was also reflected in elevated catalytic efficiencies toward ceftazidime. These changes are likely caused by enhanced flexibility of the Ω- and β5-β6 loops and fine-tuning of preexisting active site residues. In conclusion, low-level concentrations of β-lactams can drive the evolution of β-lactamases through cryptic phenotypes which may act as stepping-stones toward clinical resistance. IMPORTANCE Very low antibiotic concentrations have been shown to drive the evolution of antimicrobial resistance. While substantial progress has been made to understand the driving role of low concentrations during resistance development for different antimicrobial classes, the importance of β-lactams, the most commonly used antibiotics, is still poorly studied. Here, we shed light on the evolutionary impact of low β-lactam concentrations on the widespread β-lactamase OXA-48. Our data indicate that the exposure to β-lactams at very low concentrations enhances β-lactamase diversity and drives the evolution of β-lactamases by significantly influencing their substrate specificity. Thus, in contrast to high concentrations, low levels of these drugs may substantially contribute to the diversification and divergent evolution of these enzymes, providing a standing genetic diversity that can be selected and mobilized when antibiotic pressure increases.
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Ma CW, Ng KKH, Yam BHC, Ho PL, Kao RYT, Yang D. Rapid Broad Spectrum Detection of Carbapenemases with a Dual Fluorogenic-Colorimetric Probe. J Am Chem Soc 2021; 143:6886-6894. [PMID: 33909441 DOI: 10.1021/jacs.1c00462] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Carbapenems stand as one of the last-resort antibiotics; however, their efficacy is threatened by the rising number and rapid spread of carbapenemases. Effective antimicrobial stewardship thus calls for rapid tests for these enzymes to aid appropriate prescription and infection control. Herein, we report the first effective pan-carbapenemase reporter CARBA-H with a broad scope covering all three Ambler classes. Using a chemical biology approach, we demonstrated that the absence of the 1β-substituent in the carbapenem core is key to pan-carbapenemase recognition, which led to our rational design and probe development. CARBA-H provides a dual colorimetric-fluorogenic response upon carbapenemase-mediated hydrolysis. A clear visual readout can be obtained within 15 min when tested against a panel of carbapenemase-producing Enterobacteriaceae (CPE) clinical isolates that notably includes OXA-48 and OXA-181-producing strains. Furthermore, CARBA-H can be applied to the detection of carbapemenase activity in CPE-spiked urine samples.
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Affiliation(s)
- Chi-Wang Ma
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Kenneth King-Hei Ng
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Bill Hin-Cheung Yam
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Pak-Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Richard Yi-Tsun Kao
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dan Yang
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Investigation of the presence of carbapenemases in carbapenem-resistant Klebsiella pneumoniae strains by MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) and comparison with real-time PCR method. Indian J Med Microbiol 2021; 39:300-305. [PMID: 33824061 DOI: 10.1016/j.ijmmb.2021.03.013] [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: 10/22/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 11/20/2022]
Abstract
PURPOSE We aimed to develop a new procedure for rapid detection of the carbapenemase activity using MALDI-TOF MS, and to determine the sensitivity and specificity of the method. Also, we aimed to determine the distribution of carbapenemase genes among the K.pneumoniae strains isolated in our hospital using real-time PCR. METHOD Between January 2017-February 2019; K. pneumoniae strains(n = 74) isolated from blood culture samples were included. Klebsiella pneumoniae NCTC 13438 was used as a positive control and Escherichia coli ATCC 25922 as a negative control. First, Imipenem, meropenem, and ertapenem MIC values of strains were determined. Then blaKPC, blaOXA-48, and/or blaNDM genes were investigated with PCR. Carbapenemase activity was investigated in strains with the newly developed method using MALDI-TOF MS. The performance of the new method was evaluated for both the second and fourth hours of the incubation period. RESULTS While 65 strains were found resistant to tested carbapenems, nine of them were susceptible. Of the 65 resistant strains, 57 had blaOXA-48, 15 had blaNDM, and four had blaKPC genes. BlaOXA-48 and blaNDM genes were detected together in 11 strains. BlaOXA-48, blaNDM, and blaKPC genes were not detected in any of the susceptible strains. The sensitivity and specificity of MALDI-TOF MS at the second hour were 83.1% and 100%, respectively. At the fourth hour, the sensitivity and specificity of MALDI-TOF MS were 100%. No false-positive results were observed. CONCLUSION The sensitivity of the method at the fourth hour was better than the second hour. The false-negative results observed in the second hour disappeared when the incubation period was extended to 4 h. MALDI-TOF MS which is still under development is a fast, cost-effective, promising method for the detection of carbapenemase activity.
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Hansen GT. Continuous Evolution: Perspective on the Epidemiology of Carbapenemase Resistance Among Enterobacterales and Other Gram-Negative Bacteria. Infect Dis Ther 2021; 10:75-92. [PMID: 33492641 PMCID: PMC7954928 DOI: 10.1007/s40121-020-00395-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022] Open
Abstract
The global emergence of carbapenemase-producing bacteria capable of hydrolyzing the once effective carbapenem antibiotics is considered a contemporary public health concern. Carbapenemase enzymes, once constrained to isolates of Klebsiella pneumoniae, are now routinely reported in different bacteria within the Enterobacterales order of bacteria, creating the acronym CRE which now defines Carbapenem-Resistant Enterobacterales. CRE harboring different types of enzymes, including the most prevalent types KPC, VIM, IMP, NDM, and OXA-48, are now routinely reported and more importantly, are now frequently present in many infections world-wide. Defining and updating the contemporary epidemiology of both the US and global burden of carbapenem-resistant infections is now more important than ever. This review describes the global distribution and continued evolution of carbapenemases which continue to spread at alarming rates. Informed understanding of the current epidemiology of CRE, coupled with advances in antibiotic options, and the use rapid diagnostics offers the potential for rapid identification and management of carbapenem-resistant infections.
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Affiliation(s)
- Glen T Hansen
- Department of Pathology and Laboratory Medicine, Hennepin County Medical Center, Minneapolis, MN, USA.
- Department of Pathology and Laboratory Medicine, University of Minnesota, School of Medicine, Minneapolis, MN, USA.
- Department of Medicine, Infectious Disease, University of Minnesota, School of Medicine, Minneapolis, MN, USA.
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Stojanoski V, Hu L, Sankaran B, Wang F, Tao P, Prasad BVV, Palzkill T. Mechanistic Basis of OXA-48-like β-Lactamases' Hydrolysis of Carbapenems. ACS Infect Dis 2021; 7:445-460. [PMID: 33492952 DOI: 10.1021/acsinfecdis.0c00798] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are an important source of resistance to these last resort β-lactam antibiotics. OXA-48 is a member of a group of CHDLs named OXA-48-like enzymes. On the basis of sequence similarity, OXA-163 can be classified as an OXA-48-like enzyme, but it has altered substrate specificity. Compared to OXA-48, it shows impaired activity for carbapenems but displays an enhanced hydrolysis of oxyimino-cephalosporins. Here, we address the mechanistic and structural basis for carbapenem hydrolysis by OXA-48-like enzymes. Pre-steady-state kinetic analysis indicates that the rate-limiting step for OXA-48 and OXA-163 hydrolysis of carbapenems is deacylation and that the greatly reduced carbapenemase activity of OXA-163 compared to that of OXA-48 is due entirely to a slower deacylation reaction. Furthermore, our structural data indicate that the positioning of the β5-β6 loop is necessary for carbapenem hydrolysis by OXA-48. A major difference between the OXA-48 and OXA-163 complexes with carbapenems is that the 214-RIEP-217 deletion in OXA-163 creates a large opening in the active site that is absent in the OXA-48/carbapenem structures. We propose that the larger active site results in less constraint on the conformation of the 6α-hydroxyethyl group in the acyl-enzyme. The acyl-enzyme intermediate assumes multiple conformations, most of which are incompatible with rapid deacylation. Consistent with this hypothesis, molecular dynamics simulations indicate that the most stable complex is formed between OXA-48 and imipenem, which correlates with the OXA-48 hydrolysis of imipenem being the fastest observed. Furthermore, the OXA-163 complexes with imipenem and meropenem are the least stable and show significant conformational fluctuations, which correlates with the slow hydrolysis of these substrates.
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Affiliation(s)
| | | | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States,
| | - Feng Wang
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States
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Davies DT, Leiris S, Zalacain M, Sprynski N, Castandet J, Bousquet J, Lozano C, Llanos A, Alibaud L, Vasa S, Pattipati R, Valige R, Kummari B, Pothukanuri S, De Piano C, Morrissey I, Holden K, Warn P, Marcoccia F, Benvenuti M, Pozzi C, Tassone G, Mangani S, Docquier JD, Pallin D, Elliot R, Lemonnier M, Everett M. Discovery of ANT3310, a Novel Broad-Spectrum Serine β-Lactamase Inhibitor of the Diazabicyclooctane Class, Which Strongly Potentiates Meropenem Activity against Carbapenem-Resistant Enterobacterales and Acinetobacter baumannii. J Med Chem 2020; 63:15802-15820. [DOI: 10.1021/acs.jmedchem.0c01535] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David T. Davies
- Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France
| | - Simon Leiris
- Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France
| | | | - Nicolas Sprynski
- Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France
| | - Jérôme Castandet
- Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France
| | - Justine Bousquet
- Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France
| | - Clarisse Lozano
- Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France
| | - Agustina Llanos
- Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France
| | | | - Srinivas Vasa
- GVK Biosciences Pvt. Ltd., Survey No. 125
and 126, IDA, Mallapur, Hyderabad, Telangana 500 076, India
| | - Ramesh Pattipati
- GVK Biosciences Pvt. Ltd., Survey No. 125
and 126, IDA, Mallapur, Hyderabad, Telangana 500 076, India
| | - Ravindar Valige
- GVK Biosciences Pvt. Ltd., Survey No. 125
and 126, IDA, Mallapur, Hyderabad, Telangana 500 076, India
| | - Bhaskar Kummari
- GVK Biosciences Pvt. Ltd., Survey No. 125
and 126, IDA, Mallapur, Hyderabad, Telangana 500 076, India
| | - Srinivasu Pothukanuri
- GVK Biosciences Pvt. Ltd., Survey No. 125
and 126, IDA, Mallapur, Hyderabad, Telangana 500 076, India
| | - Cyntia De Piano
- International Health Management Associates (IHMA), Rte. De I’Ile-au-Bois 1A, 1870 Monthey, Switzerland
| | - Ian Morrissey
- International Health Management Associates (IHMA), Rte. De I’Ile-au-Bois 1A, 1870 Monthey, Switzerland
| | - Kirsty Holden
- Evotec (UK) Ltd., Block 23, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Peter Warn
- Evotec (UK) Ltd., Block 23, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Francesca Marcoccia
- Dipartimento di Biotecnologie Mediche, University of Siena, Viale Bracci 16, Siena 53100, Italy
| | - Manuela Benvenuti
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, Via Aldo Moro 2, Siena 53100, Italy
| | - Cecilia Pozzi
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, Via Aldo Moro 2, Siena 53100, Italy
| | - Giusy Tassone
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, Via Aldo Moro 2, Siena 53100, Italy
| | - Stefano Mangani
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, Via Aldo Moro 2, Siena 53100, Italy
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, University of Siena, Viale Bracci 16, Siena 53100, Italy
| | - David Pallin
- Charles River Laboratories, 8-9 The Spire Green Centre, Harlow, Essex CM19 5TR, U.K
| | - Richard Elliot
- Charles River Laboratories, 8-9 The Spire Green Centre, Harlow, Essex CM19 5TR, U.K
| | - Marc Lemonnier
- Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France
| | - Martin Everett
- Antabio SAS, 436 rue Pierre et Marie Curie, 31670 Labège, France
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42
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Aertker KMJ, Chan HTH, Lohans CT, Schofield CJ. Analysis of β-lactone formation by clinically observed carbapenemases informs on a novel antibiotic resistance mechanism. J Biol Chem 2020; 295:16604-16613. [PMID: 32963107 PMCID: PMC7864059 DOI: 10.1074/jbc.ra120.014607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/07/2020] [Indexed: 01/18/2023] Open
Abstract
An important mechanism of resistance to β-lactam antibiotics is via their β-lactamase-catalyzed hydrolysis. Recent work has shown that, in addition to the established hydrolysis products, the reaction of the class D nucleophilic serine β-lactamases (SBLs) with carbapenems also produces β-lactones. We report studies on the factors determining β-lactone formation by class D SBLs. We show that variations in hydrophobic residues at the active site of class D SBLs (i.e. Trp105, Val120, and Leu158, using OXA-48 numbering) impact on the relative levels of β-lactones and hydrolysis products formed. Some variants, i.e. the OXA-48 V120L and OXA-23 V128L variants, catalyze increased β-lactone formation compared with the WT enzymes. The results of kinetic and product studies reveal that variations of residues other than those directly involved in catalysis, including those arising from clinically observed mutations, can alter the reaction outcome of class D SBL catalysis. NMR studies show that some class D SBL variants catalyze formation of β-lactones from all clinically relevant carbapenems regardless of the presence or absence of a 1β-methyl substituent. Analysis of reported crystal structures for carbapenem-derived acyl-enzyme complexes reveals preferred conformations for hydrolysis and β-lactone formation. The observation of increased β-lactone formation by class D SBL variants, including the clinically observed carbapenemase OXA-48 V120L, supports the proposal that class D SBL-catalyzed rearrangement of β-lactams to β-lactones is important as a resistance mechanism.
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Affiliation(s)
| | - H T Henry Chan
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Christopher T Lohans
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom; Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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43
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De Belder D, Ghiglione B, Pasteran F, de Mendieta JM, Corso A, Curto L, Di Bella A, Gutkind G, Gomez SA, Power P. Comparative Kinetic Analysis of OXA-438 with Related OXA-48-Type Carbapenem-Hydrolyzing Class D β-Lactamases. ACS Infect Dis 2020; 6:3026-3033. [PMID: 32970406 DOI: 10.1021/acsinfecdis.0c00537] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel variants of OXA-48-type enzymes with the ability to hydrolyze oxyimino-cephalosporins and carbapenems are increasingly reported. Since its first report in 2011, OXA-163 is now extensively spread throughout Argentina, and several variants like OXA-247 have emerged. Here, we characterized a new blaOXA-48-like variant, OXA-438, and we performed a comparative kinetic analysis with the local variants OXA-247 and OXA-163 and the internationally disseminated OXA-48. blaOXA-163, blaOXA-247, and blaOXA-438 were located in a 70 kb IncN2 conjugative plasmid. OXA-438 presented mutations in the vicinity of conserved KTG (214-216), with a 2-aa deletion (R220-I221) and a D224E shift (as in OXA-163) compared to OXA-48. Despite Kpn163 (OXA-163), Kpn247 (OXA-247) and Eco438 (OXA-438) were resistant to meropenem and ertapenem, and the transconjugants (TC) remained susceptible (however, the carbapenems minimum inhibitory concentrations were ≥3 times 2-fold dilutions higher than the acceptor strain). TC163 and Eco48 were resistant to oxyimino-cephalosporins, unlike TC247 and TC438. kcat/Km values for cefotaxime in OXA-163 were slightly higher than the rest of the variants that were accompanied by a lower Km for carbapenems. For OXA-163, OXA-247, and OXA-438, the addition of NaHCO3 improved kcat values for both cefotaxime and ceftazidime; carbapenems kcat/Km values were higher than for oxyimino-cephalosporins. Mutations occurring near the conserved KTG in OXA-247 and OXA-438 are probably responsible for the improved carbapenems hydrolysis and decreased inactivation of oxyimino-cephalosporins compared to OXA-163. Dichroism results suggest that deletions at the β5-β6 loop seem to impact the structural stability of OXA-48 variants. Finally, additional mechanisms are probably involved in the resistance pattern observed in the clinical isolates.
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Affiliation(s)
- Denise De Belder
- Servicio Antimicrobianos - National Reference Laboratory in Antimicrobial Resistance (NRLAR), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires 1282, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1452, Argentina
| | - Barbara Ghiglione
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1452, Argentina
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Departamento de Microbiología, Inmunología, Biotecnología y Genética, Laboratorio de Resistencia Bacteriana, Universidad de Buenos Aires, Buenos Aires 1113, Argentina
| | - Fernando Pasteran
- Servicio Antimicrobianos - National Reference Laboratory in Antimicrobial Resistance (NRLAR), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires 1282, Argentina
| | - Juan Manuel de Mendieta
- Servicio Antimicrobianos - National Reference Laboratory in Antimicrobial Resistance (NRLAR), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires 1282, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos - National Reference Laboratory in Antimicrobial Resistance (NRLAR), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires 1282, Argentina
| | - Lucrecia Curto
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1452, Argentina
- IQUIFIB, Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Buenos Aires 1113, Argentina
| | - Adriana Di Bella
- Hospital Nacional “Profesor Alejandro Posadas”, El Palomar, Buenos Aires 1684, Argentina
| | - Gabriel Gutkind
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1452, Argentina
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Departamento de Microbiología, Inmunología, Biotecnología y Genética, Laboratorio de Resistencia Bacteriana, Universidad de Buenos Aires, Buenos Aires 1113, Argentina
| | - Sonia A. Gomez
- Servicio Antimicrobianos - National Reference Laboratory in Antimicrobial Resistance (NRLAR), Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires 1282, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1452, Argentina
| | - Pablo Power
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1452, Argentina
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Departamento de Microbiología, Inmunología, Biotecnología y Genética, Laboratorio de Resistencia Bacteriana, Universidad de Buenos Aires, Buenos Aires 1113, Argentina
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44
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De Angelis G, Del Giacomo P, Posteraro B, Sanguinetti M, Tumbarello M. Molecular Mechanisms, Epidemiology, and Clinical Importance of β-Lactam Resistance in Enterobacteriaceae. Int J Mol Sci 2020; 21:ijms21145090. [PMID: 32708513 PMCID: PMC7404273 DOI: 10.3390/ijms21145090] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 12/16/2022] Open
Abstract
Despite being members of gut microbiota, Enterobacteriaceae are associated with many severe infections such as bloodstream infections. The β-lactam drugs have been the cornerstone of antibiotic therapy for such infections. However, the overuse of these antibiotics has contributed to select β-lactam-resistant Enterobacteriaceae isolates, so that β-lactam resistance is nowadays a major concern worldwide. The production of enzymes that inactivate β-lactams, mainly extended-spectrum β-lactamases and carbapenemases, can confer multidrug resistance patterns that seriously compromise therapeutic options. Further, β-lactam resistance may result in increases in the drug toxicity, mortality, and healthcare costs associated with Enterobacteriaceae infections. Here, we summarize the updated evidence about the molecular mechanisms and epidemiology of β-lactamase-mediated β-lactam resistance in Enterobacteriaceae, and their potential impact on clinical outcomes of β-lactam-resistant Enterobacteriaceae infections.
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Affiliation(s)
- Giulia De Angelis
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.D.A.); (B.P.); (M.S.)
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
| | - Paola Del Giacomo
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.D.A.); (B.P.); (M.S.)
- Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.D.A.); (B.P.); (M.S.)
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
| | - Mario Tumbarello
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Correspondence:
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45
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Stewart NK, Bhattacharya M, Toth M, Smith CA, Vakulenko SB. A surface loop modulates activity of the Bacillus class D β-lactamases. J Struct Biol 2020; 211:107544. [PMID: 32512156 DOI: 10.1016/j.jsb.2020.107544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/25/2020] [Accepted: 06/02/2020] [Indexed: 12/23/2022]
Abstract
The expression of β-lactamases is a major mechanism of bacterial resistance to the β-lactam antibiotics. Four molecular classes of β-lactamases have been described (A, B, C and D), however until recently the class D enzymes were thought to exist only in Gram-negative bacteria. In the last few years, class D enzymes have been discovered in several species of Gram-positive microorganisms, such as Bacillus and Clostridia, and an investigation of their kinetic and structural properties has begun in earnest. Interestingly, it was observed that some species of Bacillus produce two distinct class D β-lactamases, one highly active and the other with only basal catalytic activity. Analysis of amino acid sequences of active (BPU-1 from Bacillus pumilus) and inactive (BSU-2 from Bacillus subtilis and BAT-2 from Bacillus atrophaeus) enzymes suggests that presence of three additional amino acid residues in one of the surface loops of inefficient β-lactamases may be responsible for their severely diminished activity. Our structural and docking studies show that the elongated loop of these enzymes severely restricts binding of substrates. Deletion of the three residues from the loops of BSU-2 and BAT-2 β-lactamases relieves the steric hindrance and results in a significant increase in the catalytic activity of the enzymes. These data show that this surface loop plays an important role in modulation of the catalytic activity of Bacillus class D β-lactamases.
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Affiliation(s)
- Nichole K Stewart
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | | | - Marta Toth
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Clyde A Smith
- Department of Chemistry, Stanford University, Stanford, CA, USA; Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA, USA.
| | - Sergei B Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.
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46
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Tsivkovski R, Totrov M, Lomovskaya O. Biochemical Characterization of QPX7728, a New Ultrabroad-Spectrum Beta-Lactamase Inhibitor of Serine and Metallo-Beta-Lactamases. Antimicrob Agents Chemother 2020; 64:e00130-20. [PMID: 32152086 PMCID: PMC7269513 DOI: 10.1128/aac.00130-20] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/04/2020] [Indexed: 12/19/2022] Open
Abstract
QPX7728 is a new ultrabroad-spectrum inhibitor of serine and metallo-beta-lactamases (MBLs) from a class of cyclic boronates that gave rise to vaborbactam. The spectrum and mechanism of beta-lactamase inhibition by QPX7728 were assessed using purified enzymes from all molecular classes. QPX7728 inhibits class A extended-spectrum beta-lactamases (ESBLs) (50% inhibitory concentration [IC50] range, 1 to 3 nM) and carbapenemases such as KPC (IC50, 2.9 ± 0.4 nM) as well as class C P99 (IC50 of 22 ± 8 nM) with a potency that is comparable to or higher than recently FDA-approved beta-lactamase inhibitors (BLIs) avibactam, relebactam, and vaborbactam. Unlike those other BLIs, QPX7728 is also a potent inhibitor of class D carbapenemases such as OXA-48 from Enterobacteriaceae and OXA enzymes from Acinetobacter baumannii (OXA-23/24/58, IC50 range, 1 to 2 nM) as well as MBLs such as NDM-1 (IC50, 55 ± 25 nM), VIM-1 (IC50, 14 ± 4 nM), and IMP-1 (IC50, 610 ± 70 nM). Inhibition of serine enzymes by QPX7728 is associated with progressive inactivation with a high-efficiency k2/K ranging from 6.3 × 104 (for P99) to 9.9 × 105 M-1 s-1 (for OXA-23). This inhibition is reversible with variable stability of the QPX7728-beta-lactamase complexes with target residence time ranging from minutes to several hours: 5 to 20 min for OXA carbapenemases from A. baumannii, ∼50 min for OXA-48, and 2 to 3 h for KPC and CTX-M-15. QPX7728 inhibited all tested serine enzymes at a 1:1 molar ratio. Metallo-beta-lactamases NDM, VIM, and IMP were inhibited by a competitive mechanism with fast-on-fast-off kinetics, with Ki s of 7.5 ± 2.1 nM, 32 ± 14 nM, and 240 ± 30 nM for VIM-1, NDM-1, and IMP-1, respectively. QPX7728's ultrabroad spectrum of BLI inhibition combined with its high potency enables combinations with multiple different beta-lactam antibiotics.
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47
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Dabos L, Zavala A, Bonnin RA, Beckstein O, Retailleau P, Iorga BI, Naas T. Substrate Specificity of OXA-48 after β5-β6 Loop Replacement. ACS Infect Dis 2020; 6:1032-1043. [PMID: 32156115 DOI: 10.1021/acsinfecdis.9b00452] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
OXA-48 carbapenemase has rapidly spread in many countries worldwide with several OXA-48-variants being described, differing by a few amino acid (AA) substitutions or deletions, mostly in the β5-β6 loop. While single AA substitutions have only a minor impact on OXA-48 hydrolytic profiles, others with 4 AA deletions result in loss of carbapenem hydrolysis and gain of expanded-spectrum cephalosporin (ESC) hydrolysis. We have replaced the β5-β6 loop of OXA-48 with that of OXA-18, a clavulanic-acid inhibited oxacillinase capable of hydrolyzing ESCs but not carbapenems. The hybrid enzyme OXA-48Loop18 was able to hydrolyze ESCs and carbapenems (although with a lower kcat), even though the β5-β6 loop was longer and its sequence quite different from that of OXA-48. The kinetic parameters of OXA-48Loop18 were in agreement with the MIC values. X-ray crystallography and molecular modeling suggest that the conformation of the grafted loop allows the binding of bulkier substrates, unlike that of the native loop, expanding the hydrolytic profile. This seems to be due not only to differences in AA sequence, but also to the backbone conformation the loop can adopt. Finally, our results provide further experimental evidence for the role of the β5-β6 loop in substrate selectivity of OXA-48-like enzymes and additional details on the structure-function relationship of β-lactamases, demonstrating how localized changes in these proteins can alter or expand their function, highlighting their plasticity.
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Affiliation(s)
- Laura Dabos
- EA7361 “Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases”, Université Paris Sud, Université Paris Saclay, LabEx Lermit, Faculty of Medicine, 94270 Le Kremlin-Bicêtre, France
- Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur−APHP−Université Paris Sud, 75015 Paris, France
| | - Agustin Zavala
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, 91190 Gif-sur-Yvette, France
| | - Rémy A. Bonnin
- EA7361 “Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases”, Université Paris Sud, Université Paris Saclay, LabEx Lermit, Faculty of Medicine, 94270 Le Kremlin-Bicêtre, France
- Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur−APHP−Université Paris Sud, 75015 Paris, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
| | - Oliver Beckstein
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, 85281 Arizona, United States
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, 91190 Gif-sur-Yvette, France
| | - Bogdan I. Iorga
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, 91190 Gif-sur-Yvette, France
| | - Thierry Naas
- EA7361 “Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases”, Université Paris Sud, Université Paris Saclay, LabEx Lermit, Faculty of Medicine, 94270 Le Kremlin-Bicêtre, France
- Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur−APHP−Université Paris Sud, 75015 Paris, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicêtre, France
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48
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Taylor DM, Anglin J, Park S, Ucisik MN, Faver JC, Simmons N, Jin Z, Palaniappan M, Nyshadham P, Li F, Campbell J, Hu L, Sankaran B, Prasad BV, Huang H, Matzuk MM, Palzkill T. Identifying Oxacillinase-48 Carbapenemase Inhibitors Using DNA-Encoded Chemical Libraries. ACS Infect Dis 2020; 6:1214-1227. [PMID: 32182432 PMCID: PMC7673237 DOI: 10.1021/acsinfecdis.0c00015] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacterial resistance to β-lactam antibiotics is largely mediated by β-lactamases, which catalyze the hydrolysis of these drugs and continue to emerge in response to antibiotic use. β-Lactamases that hydrolyze the last resort carbapenem class of β-lactam antibiotics (carbapenemases) are a growing global health threat. Inhibitors have been developed to prevent β-lactamase-mediated hydrolysis and restore the efficacy of these antibiotics. However, there are few inhibitors available for problematic carbapenemases such as oxacillinase-48 (OXA-48). A DNA-encoded chemical library approach was used to rapidly screen for compounds that bind and potentially inhibit OXA-48. Using this approach, a hit compound, CDD-97, was identified with submicromolar potency (Ki = 0.53 ± 0.08 μM) against OXA-48. X-ray crystallography showed that CDD-97 binds noncovalently in the active site of OXA-48. Synthesis and testing of derivatives of CDD-97 revealed structure-activity relationships and informed the design of a compound with a 2-fold increase in potency. CDD-97, however, synergizes poorly with β-lactam antibiotics to inhibit the growth of bacteria expressing OXA-48 due to poor accumulation into E. coli. Despite the low in vivo activity, CDD-97 provides new insights into OXA-48 inhibition and demonstrates the potential of using DNA-encoded chemistry technology to rapidly identify β-lactamase binders and to study β-lactamase inhibition, leading to clinically useful inhibitors.
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Affiliation(s)
- Doris Mia Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin Anglin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suhyeorn Park
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Melek N. Ucisik
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John C. Faver
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas Simmons
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhuang Jin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pranavanand Nyshadham
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Feng Li
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James Campbell
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, CA, 94720, USA
| | - B.V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongbing Huang
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martin M. Matzuk
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
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49
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Hirvonen VHA, Mulholland AJ, Spencer J, van der Kamp MW. Small Changes in Hydration Determine Cephalosporinase Activity of OXA-48 β-Lactamases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00596] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Viivi H. A. Hirvonen
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD United Kingdom
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS United Kingdom
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50
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Gupta D, Singh A, Somvanshi P, Singh A, Khan AU. Structure-Based Screening of Non-β-Lactam Inhibitors against Class D β-Lactamases: An Approach of Docking and Molecular Dynamics. ACS OMEGA 2020; 5:9356-9365. [PMID: 32363287 PMCID: PMC7191842 DOI: 10.1021/acsomega.0c00356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
Abstract
The manifestation of class D β-lactamases in the community raises significant concern as they can hydrolyze carbapenem antibiotics. Hence, it is exceptionally alluring to design novel inhibitors. Structure-based virtual screening using docking programs and molecular dynamics simulations was employed to identify two novel non-β-lactam compounds that possess the ability to block different OXA variants. Furthermore, the presence of a nonpolar aliphatic amino acid, valine, near the active site serine, was identified in all OXA variants that can be accounted to block the catalytic activity of OXA enzymes.
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Affiliation(s)
- Divya Gupta
- Interdisciplinary
Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India
- Department of Life Sciences, Uttarakhand
Technical University, Dehradun 248007 Uttarakhand, India
| | - Aditi Singh
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi 110070, India
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi 110070, India
| | - Ajeet Singh
- Department of Biotechnology, G. B. Pant Engineering College, Pauri 246194, India
| | - Asad U. Khan
- Interdisciplinary
Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Malaysia
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