1
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Villanueva M, Vostal LE, Cohen DN, Biesbrock D, Kuwaye EP, Driver SG, Hart KM. Differential effects of disulfide bond formation in TEM-1 versus CTX-M-9 β-lactamase. Protein Sci 2024; 33:e4816. [PMID: 37897253 PMCID: PMC10731493 DOI: 10.1002/pro.4816] [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: 06/30/2023] [Revised: 08/18/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
To investigate how disulfide bonds can impact protein energy landscapes, we surveyed the effects of adding or removing a disulfide in two β-lactamase enzymes, TEM-1 and CTX-M-9. The homologs share a structure and 38% sequence identity, but only TEM-1 contains a native disulfide bond. They also differ in thermodynamic stability and in the number of states populated at equilibrium: CTX-M-9 is two-state whereas TEM-1 has an additional intermediate state. We hypothesized that the disulfide bond is the major underlying determinant for these observed differences in their energy landscapes. To test this, we removed the disulfide bridge from TEM-1 and introduced a disulfide bridge at the same location in CTX-M-9. This modest change to sequence modulates the stabilities-and therefore populations-of TEM-1's equilibrium states and, more surprisingly, creates a novel third state in CTX-M-9. Unlike TEM-1's partially folded intermediate, this third state is a higher-order oligomer with reduced cysteines that retains the native fold and is fully active. Sub-denaturing concentrations of urea shifts the equilibrium to the monomeric form, allowing the disulfide bond to form. Interestingly, comparing the stability of the oxidized monomer with a variant lacking cysteines reveals the disulfide is neither stabilizing nor destabilizing in CTX-M-9, in contrast with the observed stabilization in TEM-1. Thus, we can conclude that engineering disulfide bonds is not always an effective stabilization strategy even when analogous disulfides exist in more stable structural homologs. This study also illustrates how homo-oligomerization can result from a small number of mutations, suggesting complex formation might be easily accessed during a protein family's evolution.
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Affiliation(s)
- Miranda Villanueva
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Biological Chemistry DepartmentDavid Geffen School of Medicine, UCLALos AngelesCaliforniaUSA
| | - Lauren E. Vostal
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Laboratory of Chemistry and Cell BiologyThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Drew N. Cohen
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Devin Biesbrock
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Laboratory of Cellular and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Elise P. Kuwaye
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Department of Biological SciencesColumbia UniversityNew YorkNew YorkUSA
| | - Sasha G. Driver
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
| | - Kathryn M. Hart
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
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2
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Zhao Q, Sha L, Wu Z, Meng L, Yang F, Wu L, Yu C, Zhang H, Yu J, Jin Z. Evolution of carbapenem resistance in klebsiella pneumoniae and escherichia coli carrying bla NDM-1 gene: imipenem exposure results in sustained resistance memory of strains in vitro. Ann Clin Microbiol Antimicrob 2023; 22:46. [PMID: 37308958 DOI: 10.1186/s12941-023-00598-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/29/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Antibiotics exert an outstanding selective pressure on bacteria, forcing their chromosomal gene mutations and drug resistance genes to spread. The objective of this study is to evaluate the expression of the New Delhi Metallo-β-Lactamase-1 gene (blaNDM-1) in the clinical isolate (Klebsiella pneumoniae TH-P12158), transformant strains Escherichia coli BL21 (DE3)-blaNDM-1, and Escherichia coli DH5α- blaNDM-1 when exposed to imipenem. METHODS β-Lactamase genes (blaSHV, blaTEM-1, blaCTX-M-9, blaIMP, blaNDM-1, blaKPC, blaOXA, blaGES, and blaDHA) from randomly selected carbapenems-sensitive K.pneumoniae (n = 20) and E.coli (n = 20) strains were amplified by PCR. The recombinant plasmid of pET-28a harboring blaNDM-1 was transformed into E.coli BL21 (DE3) and E.coli DH5α by electroporation. The resistance phenotype and higher blaNDM-1 expression in K.pneumoniae TH-P12158, transformant E.coli BL21 (DE3)-blaNDM-1, and E.coli DH5α-blaNDM-1 were observed when exposed to imipenem with grade increasing, decreasing, and canceling doses, respectively. RESULTS After being exposed to different doses of imipenem, the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) of antimicrobial drugs and blaNDM-1 expression of strains increased, which was positively correlated with doses of imipenem. On the contrary, with the decrease or cancellation of imipenem doses, the blaNDM-1 expression was deteriorated, while the MIC and MBC values remained relatively stable. These results demonstrated that low doses of imipenem (˂MIC) could press blaNDM-1 positive strains producing stable drug resistance memory and altered blaNDM-1 expression. CONCLUSIONS Low doses of imipenem could press blaNDM-1 positive strains producing sustained resistance memory and altered blaNDM-1 expression. In particular, the positive correlation between the resistance genes expression and antibiotics exposure shows promising guiding significance for clinical medication.
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Affiliation(s)
- Qiong Zhao
- Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Hubei, 442000, Shiyan, China
| | - Longhua Sha
- Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Hubei, 442000, Shiyan, China
| | - Zhaomeng Wu
- Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Hubei, 442000, Shiyan, China
| | - Lixue Meng
- Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Hubei, 442000, Shiyan, China
| | - Feixiang Yang
- Department of Clinical Laboratory, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Hubei, Shiyan, 442008, China
| | - Lingling Wu
- Department of Clinical Laboratory, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Hubei, Shiyan, 442008, China
| | - Chunfang Yu
- Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Hubei, 442000, Shiyan, China
| | - Hua Zhang
- Department of Clinical Laboratory, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Hubei, Shiyan, 442008, China.
| | - Jingdan Yu
- Laboratory Medicine, Wuhan Asia General Hospital, Hubei, Wuhan, 430050, China.
| | - Zhixiong Jin
- Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Hubei, 442000, Shiyan, China.
- Department of Clinical Laboratory, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Hubei, Shiyan, 442008, China.
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Hubei, 442000, Shiyan, China.
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3
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Yin C, Song Z, Tian H, Palzkill T, Tao P. Unveiling the structural features that regulate carbapenem deacylation in KPC-2 through QM/MM and interpretable machine learning. Phys Chem Chem Phys 2023; 25:1349-1362. [PMID: 36537692 PMCID: PMC11162551 DOI: 10.1039/d2cp03724f] [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: 12/12/2022]
Abstract
Resistance to carbapenem β-lactams presents major clinical and economical challenges for the treatment of pathogen infections. The fast hydrolysis of carbapenems by carbapenemase-producing bacterial strains enables the effective deactivation of carbapenem antibiotics. In this study, we aim to unravel the structural features that distinguish the notable deacylation activity of carbapenemases. The deacylation reactions between imipenem (IPM) and the KPC-2 class A serine-based β-lactamases (ASβLs) are modeled with combined quantum mechanical/molecular mechanical (QM/MM) minimum energy pathway (MEP) calculations and interpretable machine-learning (ML) methods. We first applied a dual-level computational protocol to achieve fast sampling of QM/MM MEPs. A tree-based ensemble ML model was employed to learn the MEP activation barriers from the conformational features of the KPC-2/IPM active site. The barrier-predicting model was then unboxed using the Shapley additive explanation (SHAP) importance attribution methods to derive mechanistic insights, which were also verified by additional QM/MM wavefunction analysis. Essentially, we show that potential hydrogen bonding interactions of the general base and the tautomerization states of the carbapenem pyrroline ring could concertedly regulate the activation barrier of KPC-2/IPM deacylation. Nonetheless, we demonstrate the efficacy of interpretable ML to assist the analysis of QM/MM simulation data for robust extraction of human-interpretable mechanistic insights.
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Affiliation(s)
- Chao Yin
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75205, USA.
| | - Zilin Song
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75205, USA.
| | - Hao Tian
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75205, USA.
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75205, USA.
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4
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Chudyk EI, Beer M, Limb MAL, Jones CA, Spencer J, van der Kamp MW, Mulholland AJ. QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-Lactamases. ACS Infect Dis 2022; 8:1521-1532. [PMID: 35877936 PMCID: PMC9379904 DOI: 10.1021/acsinfecdis.2c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Indexed: 11/28/2022]
Abstract
β-lactam antibiotic resistance in Gram-negative bacteria, primarily caused by β-lactamase enzymes that hydrolyze the β-lactam ring, has become a serious clinical problem. Carbapenems were formerly considered "last resort" antibiotics because they escaped breakdown by most β-lactamases, due to slow deacylation of the acyl-enzyme intermediate. However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting the treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, and CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, and SME-1). QM/MM molecular dynamics simulations confirm the two enzyme groups to differ in the preferred acyl-enzyme orientation: carbapenem-inhibited enzymes favor hydrogen bonding of the carbapenem hydroxyethyl group to deacylating water (DW). QM/MM simulations of deacylation give activation free energies in good agreement with experimental hydrolysis rates, correctly distinguishing carbapenemases. For the carbapenem-inhibited enzymes, free energies for deacylation are significantly higher than for the carbapenemases, even when the hydroxyethyl group was restrained to prevent interaction with the DW. Analysis of these simulations, and additional simulations of mutant enzymes, shows how factors including the hydroxyethyl orientation, the active site volume, and architecture (conformations of Asn170 and Asn132; organization of the oxyanion hole; and the Cys69-Cys238 disulfide bond) collectively determine catalytic efficiency toward carbapenems.
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Affiliation(s)
- Ewa I. Chudyk
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Michael Beer
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Cellular and Molecular Medicine, University
of Bristol Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Michael A. L. Limb
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Charlotte A. Jones
- 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 Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Marc W. van der Kamp
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Biochemistry, University of Bristol Medical
Sciences Building, University Walk, Bristol BS8 1TD, United
Kingdom
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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5
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Agarwal V, Tiwari A, Varadwaj P. Mutations responsible for the carbapenemase activity of SME-1. RSC Adv 2022; 12:22826-22842. [PMID: 36105999 PMCID: PMC9377157 DOI: 10.1039/d2ra02849b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/12/2022] [Indexed: 11/21/2022] Open
Abstract
SME-1 is a carbapenemase, produced by Serratia marcescens organism and causes nosocomial infections such as in bloodstream, wounds, urinary tract, or respiratory tract infections. Treatment of such infections becomes very complex due its resistance towards penicillins, cephalosporins, monobactams, and carbapenems. Resistance to such antibiotics is of great medical concern. The misuse and overuse of these antibiotics result in the clinical mutation and production of novel β-lactamase enzymes such as SME-1, which show resistance to carbapenems. Class A contains most of the clinically significant extended spectrum of β-lactamase enzymes and carbapenemases. In this study, class A β-lactamase SME-1 sequence, structure, and binding were compared with naturally mutated class A β-lactamase enzymes and a wild-type TEM-1. This study was performed for revealing mutations, which could be responsible for the carbapenemase activity of SME-1. The dynamic characteristics of SME-1 enzymes manifest a different degree of conservation and variability, which confers them to possess carbapenemase activities. Met69Cys, Glu104Tyr, Tyr105His, Ala237Ser, and Gly238Cys mutations occur in SME-1 as compared to wild-type TEM-1. These mutated residues are present close to active site residues such as Ser70, Lys73, Ser130, Asn132, Glu166, and Asn170, which participate in the hydrolytic reaction of β-lactam antibiotics. Furthermore, these mutated residues demonstrate altered interactions with the β-lactam antibiotics (results in altered binding) and within themselves (results in active site structure alterations), which results in expanding the spectrum of activity of these enzymes. This study provides important insights into the structure and activity relationship of SME-1 enzymes. This is evident from the Ω-loop structure modification, which forms the wall of the active site and repositioning of residues involved in hydrolytic reactions, when present in the complex with meropenem in a stable state of MD simulation at 50 ns. Hence, Met69Cys, Glu104Tyr, Tyr105His, Ala237Ser, and Gly238Cys mutations could result in an altered active site structure, binding, and activity of SME-1 with meropenem and thus become resistantant against meropenem, which is a carbapenem.
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Affiliation(s)
- Vidhu Agarwal
- Indian Institute of Information Technology Devghat, Jhalwa, Prayagraj-211015 Allahabad U P India +919236666060
| | - Akhilesh Tiwari
- Indian Institute of Information Technology Devghat, Jhalwa, Prayagraj-211015 Allahabad U P India +919236666060
| | - Pritish Varadwaj
- Indian Institute of Information Technology Devghat, Jhalwa, Prayagraj-211015 Allahabad U P India +919236666060
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6
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Kaderabkova N, Bharathwaj M, Furniss RCD, Gonzalez D, Palmer T, Mavridou DAI. The biogenesis of β-lactamase enzymes. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35943884 DOI: 10.1099/mic.0.001217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The discovery of penicillin by Alexander Fleming marked a new era for modern medicine, allowing not only the treatment of infectious diseases, but also the safe performance of life-saving interventions, like surgery and chemotherapy. Unfortunately, resistance against penicillin, as well as more complex β-lactam antibiotics, has rapidly emerged since the introduction of these drugs in the clinic, and is largely driven by a single type of extra-cytoplasmic proteins, hydrolytic enzymes called β-lactamases. While the structures, biochemistry and epidemiology of these resistance determinants have been extensively characterized, their biogenesis, a complex process including multiple steps and involving several fundamental biochemical pathways, is rarely discussed. In this review, we provide a comprehensive overview of the journey of β-lactamases, from the moment they exit the ribosomal channel until they reach their final cellular destination as folded and active enzymes.
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Affiliation(s)
- Nikol Kaderabkova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Manasa Bharathwaj
- Centre to Impact AMR, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - R Christopher D Furniss
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Diego Gonzalez
- Laboratoire de Microbiologie, Institut de Biologie, Université de Neuchâtel, Neuchâtel, 2000, Switzerland
| | - Tracy Palmer
- Microbes in Health and Disease, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA.,John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
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7
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Penicillanic Acid Sulfones Inactivate the Extended-Spectrum β-Lactamase CTX-M-15 through Formation of a Serine-Lysine Cross-Link: an Alternative Mechanism of β-Lactamase Inhibition. mBio 2022; 13:e0179321. [PMID: 35612361 PMCID: PMC9239225 DOI: 10.1128/mbio.01793-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
β-Lactamases hydrolyze β-lactam antibiotics and are major determinants of antibiotic resistance in Gram-negative pathogens. Enmetazobactam (formerly AAI101) and tazobactam are penicillanic acid sulfone (PAS) β-lactamase inhibitors that differ by an additional methyl group on the triazole ring of enmetazobactam, rendering it zwitterionic. In this study, ultrahigh-resolution X-ray crystal structures and mass spectrometry revealed the mechanism of PAS inhibition of CTX-M-15, an extended-spectrum β-lactamase (ESBL) globally disseminated among Enterobacterales. CTX-M-15 crystals grown in the presence of enmetazobactam or tazobactam revealed loss of the Ser70 hydroxyl group and formation of a lysinoalanine cross-link between Lys73 and Ser70, two residues critical for catalysis. Moreover, the residue at position 70 undergoes epimerization, resulting in formation of a d-amino acid. Cocrystallization of enmetazobactam or tazobactam with CTX-M-15 with a Glu166Gln mutant revealed the same cross-link, indicating that this modification is not dependent on Glu166-catalyzed deacylation of the PAS-acylenzyme. A cocrystal structure of enmetazobactam with CTX-M-15 with a Lys73Ala mutation indicates that epimerization can occur without cross-link formation and positions the Ser70 Cβ closer to Lys73, likely facilitating formation of the Ser70-Lys73 cross-link. A crystal structure of a tazobactam-derived imine intermediate covalently linked to Ser70, obtained after 30 min of exposure of CTX-M-15 crystals to tazobactam, supports formation of an initial acylenzyme by PAS inhibitors on reaction with CTX-M-15. These data rationalize earlier results showing CTX-M-15 deactivation by PAS inhibitors to involve loss of protein mass, and they identify a distinct mechanism of β-lactamase inhibition by these agents.
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8
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Schauer J, Gatermann SG, Hoffmann D, Hupfeld L, Pfennigwerth N. GPC-1, a novel class A carbapenemase detected in a clinical Pseudomonas aeruginosa isolate. J Antimicrob Chemother 2021; 75:911-916. [PMID: 31960033 DOI: 10.1093/jac/dkz536] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/05/2019] [Accepted: 12/02/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To investigate the carbapenem resistance mechanism of a carbapenem-resistant clinical Pseudomonas aeruginosa isolate. METHODS A carbapenem-resistant P. aeruginosa isolate was recovered from a tracheal swab from a patient of a general ward in central Germany. Various phenotypic tests confirmed production of a carbapenemase that could not be identified further by PCR. A novel bla gene was identified by WGS and its carbapenemase activity was verified by heterologous expression in an Escherichia coli cloning strain. Kinetic parameters of the novel β-lactamase were determined by spectrophotometric measurements using purified enzyme. RESULTS WGS confirmed the presence of a novel class A carbapenemase. The novel bla gene was named GPC-1 (GPC standing for German Pseudomonas Carbapenemase) and exhibited 77% amino acid identity to BKC-1. WGS also showed that blaGPC-1 was located on the chromosome surrounded by multiple ISs as part of a 26 kb genetic island. Heterologous expression of GPC-1 in E. coli TOP10 led to increased MICs of penicillins, oxyimino-cephalosporins, aztreonam and imipenem, but not of meropenem or ertapenem. Spectrophotometric measurements supported the MIC studies, but detected a slight hydrolysis of ertapenem and meropenem when using high concentrations of purified enzyme. CONCLUSIONS The biochemical characterization of GPC-1 emphasizes the ongoing emergence of novel carbapenemases. Strains expressing a weak carbapenemase like GPC-1 might go unrecognized by routine diagnostics due to low MICs for the bacterial strains producing such enzymes.
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Affiliation(s)
- Jennifer Schauer
- German National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Sören G Gatermann
- German National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Daniel Hoffmann
- SYNLAB MVZ Kassel GmbH, Kurt-Wolters-Straße 2-4, 34125 Kassel, Germany
| | - Lars Hupfeld
- SYNLAB MVZ Kassel GmbH, Kurt-Wolters-Straße 2-4, 34125 Kassel, Germany
| | - Niels Pfennigwerth
- German National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
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9
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The Carbapenemase BKC-1 from Klebsiella pneumoniae Is Adapted for Translocation by Both the Tat and Sec Translocons. mBio 2021; 12:e0130221. [PMID: 34154411 PMCID: PMC8262980 DOI: 10.1128/mbio.01302-21] [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] [Indexed: 12/11/2022] Open
Abstract
The cell envelope of Gram-negative bacteria consists of two membranes surrounding the periplasm and peptidoglycan layer. β-Lactam antibiotics target the periplasmic penicillin-binding proteins that synthesize peptidoglycan, resulting in cell death. The primary means by which bacterial species resist the effects of β-lactam drugs is to populate the periplasmic space with β-lactamases. Resistance to β-lactam drugs is spread by lateral transfer of genes encoding β-lactamases from one species of bacteria to another. However, the resistance phenotype depends in turn on these “alien” protein sequences being recognized and exported across the cytoplasmic membrane by either the Sec or Tat protein translocation machinery of the new bacterial host. Here, we examine BKC-1, a carbapenemase from an unknown bacterial source that has been identified in a single clinical isolate of Klebsiella pneumoniae. BKC-1 was shown to be located in the periplasm, and functional in both K. pneumoniae and Escherichia coli. Sequence analysis revealed the presence of an unusual signal peptide with a twin arginine motif and a duplicated hydrophobic region. Biochemical assays showed this signal peptide directs BKC-1 for translocation by both Sec and Tat translocons. This is one of the few descriptions of a periplasmic protein that is functionally translocated by both export pathways in the same organism, and we suggest it represents a snapshot of evolution for a β-lactamase adapting to functionality in a new host.
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10
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Structural Basis and Binding Kinetics of Vaborbactam in Class A β-Lactamase Inhibition. Antimicrob Agents Chemother 2020; 64:AAC.00398-20. [PMID: 32778546 DOI: 10.1128/aac.00398-20] [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] [Received: 03/03/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022] Open
Abstract
Class A β-lactamases are a major cause of β-lactam resistance in Gram-negative bacteria. The recently FDA-approved cyclic boronate vaborbactam is a reversible covalent inhibitor of class A β-lactamases, including CTX-M extended-spectrum β-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity for these two enzymes, despite their similarity. A 1.0-Å crystal structure of CTX-M-14 demonstrated that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25-Å crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, as well as alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the β3 strand on the inactivation rate, as well as the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved β-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.
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11
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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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12
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Targeting the Class A Carbapenemase GES-5 via Virtual Screening. Biomolecules 2020; 10:biom10020304. [PMID: 32075131 PMCID: PMC7072645 DOI: 10.3390/biom10020304] [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: 01/14/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/29/2022] Open
Abstract
The worldwide spread of β-lactamases able to hydrolyze last resort carbapenems contributes to the antibiotic resistance problem and menaces the successful antimicrobial treatment of clinically relevant pathogens. Class A carbapenemases include members of the KPC and GES families. While drugs against KPC-type carbapenemases have recently been approved, for GES-type enzymes, no inhibitors have yet been introduced in therapy. Thus, GES carbapenemases represent important drug targets. Here, we present an in silico screening against the most prevalent GES carbapenemase, GES-5, using a lead-like compound library of commercially available compounds. The most promising candidates were selected for in vitro validation in biochemical assays against recombinant GES-5 leading to four derivatives active as high micromolar competitive inhibitors. For the best inhibitors, the ability to inhibit KPC-2 was also evaluated. The discovered inhibitors constitute promising starting points for hit to lead optimization.
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13
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Oueslati S, Tlili L, Exilie C, Bernabeu S, Iorga B, Bonnin RA, Dortet L, Naas T. Different phenotypic expression of KPC β-lactamase variants and challenges in their detection. J Antimicrob Chemother 2019; 75:769-771. [DOI: 10.1093/jac/dkz508] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Saoussen Oueslati
- EA7361 ‘Structure, dynamic, function and expression of broad spectrum β-lactamases’, Faculty of Medicine Université Paris-Sud, LabEx LERMIT, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Linda Tlili
- EA7361 ‘Structure, dynamic, function and expression of broad spectrum β-lactamases’, Faculty of Medicine Université Paris-Sud, LabEx LERMIT, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Cynthia Exilie
- EA7361 ‘Structure, dynamic, function and expression of broad spectrum β-lactamases’, Faculty of Medicine Université Paris-Sud, LabEx LERMIT, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Sandrine Bernabeu
- EA7361 ‘Structure, dynamic, function and expression of broad spectrum β-lactamases’, Faculty of Medicine Université Paris-Sud, LabEx LERMIT, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Bogdan Iorga
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, Gif-sur-Yvette, France
| | - Rémy A Bonnin
- EA7361 ‘Structure, dynamic, function and expression of broad spectrum β-lactamases’, Faculty of Medicine Université Paris-Sud, LabEx LERMIT, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- EA7361 ‘Structure, dynamic, function and expression of broad spectrum β-lactamases’, Faculty of Medicine Université Paris-Sud, LabEx LERMIT, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- EA7361 ‘Structure, dynamic, function and expression of broad spectrum β-lactamases’, Faculty of Medicine Université Paris-Sud, LabEx LERMIT, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
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14
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Philippon A, Jacquier H, Ruppé E, Labia R. Structure-based classification of class A beta-lactamases, an update. Curr Res Transl Med 2019; 67:115-122. [PMID: 31155436 DOI: 10.1016/j.retram.2019.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023]
Abstract
Beta-lactamase (EC 3.5.2.6) synthesis, particularly in Gram-negative bacilli, is a major mechanism of natural and acquired resistance to beta-lactams, sometimes accompanied by impermeability and/or active efflux. These enzymes have been classified into four molecular classes (A-D). The serine enzymes of class A, which may be encoded by the bacterial chromosome or transferable elements and are susceptible to clinically available inhibitors (clavulanic acid, sulbactam, tazobactam, avibactam), are prevalent considering other molecular classes (B,C,D). The continual rapid development of genomic approaches and tremendous progress in automatic sequencer technology have resulted in the accumulation of massive amounts of data. A structure-based classification of class A beta-lactamases based on specific conserved motifs involved in catalytic mechanisms and/or substrate binding (S70XXK, S130DN, K234TG), together with E166 (Ambler numbering) and at least 24 other amino-acid residues or analogs such as G45, F66, V80, L81, L91, L101, P107, A134, L138, G143, G144, G156, L169, T181, T182, P183, was validated on 700 amino-acid sequences, including 132 representative types, but mostly probable enzyme sequences, many produced by environmental bacteria. Two subclasses (A1, A2), six major clusters or groups (e.g. natural limited-spectrum beta-lactamases (LSBL), wider spectrum beta-lactamases (WSBL), and various other clusters were identified on the basis of conserved (> 90%) and specific motifs, and residues such as S70TFKAL, S130DNTAANL, R164XEXXLN, V231GDKTG for subclass A1, S70VFKFH, S130DNNACDI,E166XXM, and V231AHKTG for subclass A2, a probable disulfide bridge C77-C123 and G236, A237, G238, and R244 for the LSBL group. This great diversity of primary structures was used as the basis for a structure-based and phylogenetic classification.
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Affiliation(s)
- Alain Philippon
- Faculté de Médecine Paris Descartes, Service de Bactériologie, Paris, France.
| | - Hervé Jacquier
- AP-HP, Hôpital Lariboisière, Laboratoire de Bactériologie, Paris, France; INSERM, IAME, UMR 1137, Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, France
| | - Etienne Ruppé
- INSERM, IAME, UMR 1137, Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | - Roger Labia
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, 6 Rue de l'Université, Quimper, France
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15
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 432] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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16
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Molecular Basis for the Potent Inhibition of the Emerging Carbapenemase VCC-1 by Avibactam. Antimicrob Agents Chemother 2019; 63:AAC.02112-18. [PMID: 30782990 DOI: 10.1128/aac.02112-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/18/2019] [Indexed: 11/20/2022] Open
Abstract
In 2016, we identified a new class A carbapenemase, VCC-1, in a nontoxigenic Vibrio cholerae strain that had been isolated from retail shrimp imported into Canada for human consumption. Shortly thereafter, seven additional VCC-1-producing V. cholerae isolates were recovered along the German coastline. These isolates appear to have acquired the VCC-1 gene (bla VCC-1) independently from the Canadian isolate, suggesting that bla VCC-1 is mobile and widely distributed. VCC-1 hydrolyzes penicillins, cephalothin, aztreonam, and carbapenems and, like the broadly disseminated class A carbapenemase KPC-2, is only weakly inhibited by clavulanic acid or tazobactam. Although VCC-1 has yet to be observed in the clinic, its encroachment into aquaculture and other areas with human activity suggests that the enzyme may be emerging as a public health threat. To preemptively address this threat, we examined the structural and functional biology of VCC-1 against the FDA-approved non-β-lactam-based inhibitor avibactam. We found that avibactam restored the in vitro sensitivity of V. cholerae to meropenem, imipenem, and ertapenem. The acylation efficiency was lower for VCC-1 than for KPC-2 and akin to that of Pseudomonas aeruginosa PAO1 AmpC (k 2/Ki = 3.0 × 103 M-1 s-1). The tertiary structure of VCC-1 is similar to that of KPC-2, and they bind avibactam similarly; however, our analyses suggest that VCC-1 may be unable to degrade avibactam, as has been found for KPC-2. Based on our prior genomics-based surveillance, we were able to target VCC-1 for detailed molecular studies to gain early insights that could be used to combat this carbapenemase in the future.
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17
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Spyrakis F, Bellio P, Quotadamo A, Linciano P, Benedetti P, D'Arrigo G, Baroni M, Cendron L, Celenza G, Tondi D. First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase. J Comput Aided Mol Des 2019; 33:295-305. [PMID: 30603820 DOI: 10.1007/s10822-018-0182-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
Abstract
The worldwide spread of beta-lactamases with hydrolytic activity extended to last resort carbapenems is aggravating the antibiotic resistance problem and endangers the successful antimicrobial treatment of clinically relevant pathogens. As recently highlighted by the World Health Organization, new strategies to contain antimicrobial resistance are urgently needed. Class A carbapenemases include members of the KPC, GES and SFC families. These enzymes have the ability to hydrolyse penicillins, cephalosporins and carbapenems, while also being less susceptible to available beta-lactam inhibitors, such as clavulanic acid. The KPC family is the most prevalent. It is mostly found on plasmids in Klebsiella pneumoniae, meaning that great amounts of attention, in terms of inhibitor design and structural biology, have been dedicated to it, whereas no efforts have yet been dedicated to GES-type enzymes, despite their ability to rapidly and horizontally disseminate. We herein report the first in silico screening against GES-5, which is the most dangerous GES-type beta-lactamase, using a library of 800K commercially available candidates that all share drug-like properties, such as their MW, logP, rotatable bonds and HBA/HBD atoms. The best screening results were filtered to enrich the number of different chemotypes, and then submitted to molecular docking. The 34 most promising candidates were selected for in vitro validation in biochemical assays against recombinant GES-5. Six hits acted as inhibitors, in the high micromolar range, towards GES-5 and led to the identification of the first, novel chemotypes with inhibitory activity against this clinically relevant carbapenemase.
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Affiliation(s)
- Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125, Turin, Italy.
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100, L'Aquila, Italy
| | - Antonio Quotadamo
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Paolo Benedetti
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS), Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Giulia D'Arrigo
- Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125, Turin, Italy
| | - Massimo Baroni
- Molecular Discovery Limited, U.501 Centennial Park, Centennial Ave, Elstree, Borehamwood, Hertfordshire, WD6 3FG, UK
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121, Padua, Italy
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100, L'Aquila, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy.
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18
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Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans. Sci Rep 2018; 8:8181. [PMID: 29802257 PMCID: PMC5970244 DOI: 10.1038/s41598-018-26079-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 05/04/2018] [Indexed: 01/24/2023] Open
Abstract
The development of antibiotic resistance during treatment is a threat to patients and their environment. Insight in the mechanisms of resistance development is important for appropriate therapy and infection control. Here, we describe how through the application of mass spectrometry-based proteomics, a novel beta-lactamase Axc was identified as an indicator of acquired carbapenem resistance in a clinical isolate of Achromobacter xylosoxidans. Comparative proteomic analysis of consecutively collected susceptible and resistant isolates from the same patient revealed that high Axc protein levels were only observed in the resistant isolate. Heterologous expression of Axc in Escherichia coli significantly increased the resistance towards carbapenems. Importantly, direct Axc mediated hydrolysis of imipenem was demonstrated using pH shift assays and 1H-NMR, confirming Axc as a legitimate carbapenemase. Whole genome sequencing revealed that the susceptible and resistant isolates were remarkably similar. Together these findings provide a molecular context for the fast development of meropenem resistance in A. xylosoxidans during treatment and demonstrate the use of mass spectrometric techniques in identifying novel resistance determinants.
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19
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P174E Substitution in GES-1 and GES-5 β-Lactamases Improves Catalytic Efficiency toward Carbapenems. Antimicrob Agents Chemother 2018; 62:AAC.01851-17. [PMID: 29507065 DOI: 10.1128/aac.01851-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 02/07/2018] [Indexed: 12/27/2022] Open
Abstract
GES-type β-lactamases are a group of enzymes that have evolved their hydrolytic activity against carbapenems. In this study, the role of residue 174 inside the Ω-loop of GES-1 and GES-5 was investigated. GES-1P174E and GES-5P174E mutants, selected by site saturation mutagenesis, were purified and kinetically characterized. In comparison with GES-1 and GES-5 wild-type enzymes, GES-1P174E and GES-5P174E mutants exhibited lower kcat and kcat/Km values for cephalosporins and penicillins. Concerning carbapenems, GES-1P174E shared higher kcat values but lower Km values than those calculated for GES-1. The GES-1P174E and GES-5P174E mutants showed high hydrolytic efficiency for imipenem, with kcat/Km values 100- and 660-fold higher, respectively, than those of GES-1. Clavulanic acid and tazobactam are good inhibitors for both GES-1P174E and GES-5P174E Molecular dynamic (MD) simulations carried out for GES-1, GES-5, GES-1P174E, and GES-5P174E complexed with imipenem and meropenem have shown that mutation at position 174 induces a drastic increase of enzyme flexibility, in particular in the Ω-loop. The circular dichroism (CD) spectroscopy spectra of the four enzymes indicate that the P174E substitution in GES-1 and GES-5 does not affect the secondary structural content of the enzymes.
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20
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Marathe NP, Janzon A, Kotsakis SD, Flach CF, Razavi M, Berglund F, Kristiansson E, Larsson DGJ. Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste. ENVIRONMENT INTERNATIONAL 2018; 112:279-286. [PMID: 29316517 DOI: 10.1016/j.envint.2017.12.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/21/2017] [Accepted: 12/24/2017] [Indexed: 05/28/2023]
Abstract
Evolution has provided environmental bacteria with a plethora of genes that give resistance to antibiotic compounds. Under anthropogenic selection pressures, some of these genes are believed to be recruited over time into pathogens by horizontal gene transfer. River sediment polluted with fluoroquinolones and other drugs discharged from bulk drug production in India constitute an environment with unprecedented, long-term antibiotic selection pressures. It is therefore plausible that previously unknown resistance genes have evolved and/or are promoted here. In order to search for novel resistance genes, we therefore analyzed such river sediments by a functional metagenomics approach. DNA fragments providing resistance to different antibiotics in E. coli were sequenced using Sanger and PacBio RSII platforms. We recaptured the majority of known antibiotic resistance genes previously identified by open shot-gun metagenomics sequencing of the same samples. In addition, seven novel resistance gene candidates (six beta-lactamases and one amikacin resistance gene) were identified. Two class A beta-lactamases, blaRSA1 and blaRSA2, were phylogenetically close to clinically important ESBLs like blaGES, blaBEL and blaL2, and were further characterized for their substrate spectra. The blaRSA1 protein, encoded as an integron gene cassette, efficiently hydrolysed penicillins, first generation cephalosporins and cefotaxime, while blaRSA2 was an inducible class A beta-lactamase, capable of hydrolyzing carbapenems albeit with limited efficiency, similar to the L2 beta-lactamase from Stenotrophomonas maltophilia. All detected novel genes were associated with plasmid mobilization proteins, integrons, and/or other resistance genes, suggesting a potential for mobility. This study provides insight into a resistome shaped by an exceptionally strong and long-term antibiotic selection pressure. An improved knowledge of mobilized resistance factors in the external environment may make us better prepared for the resistance challenges that we may face in clinics in the future.
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Affiliation(s)
- Nachiket P Marathe
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Anders Janzon
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Stathis D Kotsakis
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden.
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21
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Godoy CA. New Strategy for the Immobilization of Lipases on Glyoxyl-Agarose Supports: Production of Robust Biocatalysts for Natural Oil Transformation. Int J Mol Sci 2017; 18:ijms18102130. [PMID: 29023423 PMCID: PMC5666812 DOI: 10.3390/ijms18102130] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/08/2017] [Accepted: 10/09/2017] [Indexed: 01/18/2023] Open
Abstract
Immobilization on Glyoxyl–agarose support (Gx) is one of the best strategies to stabilize enzymes. However, the strategy is difficult to apply at neutral pH when most enzymes are stable and, even when possible, produces labile derivatives. This work contributes to overcoming this hurdle through a strategy that combines solid-phase amination, presence of key additives, and derivative basification. To this end, aminated industrial lipases from Candida artarctica (CAL), Thermomyces lunuginosus (TLL), and the recombinant Geobacillus thermocatenulatus (BTL2) were immobilized on Gx for the first time at neutral pH using anthranilic acid (AA) or DTT as additives (immobilization yields >70%; recovered activities 37.5–76.7%). The spectroscopic evidence suggests nucleophilic catalysis and/or adsorption as the initial lipase immobilization events. Subsequent basification drastically increases the stability of BTL2–glyoxyl derivatives under harsh conditions (t1/2, from 2.1–54.5 h at 70 °C; from 10.2 h–140 h in 80% dioxane). The novel BTL2-derivatives were active and selective in fish oil hydrolysis (1.0–1.8 μmol of polyunsaturated fatty acids (PUFAs) min−1·g−1) whereas the selected TLL-derivative was as active and stable in biodiesel production (fatty ethyl esters, EE) as the commercial Novozyme®-435 after ten reaction cycles (~70% EE). Therefore, the potential of the proposed strategy in producing suitable biocatalysts for industrial processes was demonstrated.
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Affiliation(s)
- César A Godoy
- Departamento de Química (LIBB), Grupo de Investigación en Ingeniería de los Procesos Agroalimentarios y Biotecnológicos (GIPAB), Universidad del Valle, C.P. 76001 Cali, Colombia.
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22
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Sabatini A, Brisdelli F, Celenza G, Marcoccia F, Colapietro M, Tavío MM, Piccirilli A, Amicosante G, Perilli M. Interaction of carbapenems and β-lactamase inhibitors towards CTX-M-15 and CTX-M-15 G238C mutant. J Glob Antimicrob Resist 2017; 10:95-100. [PMID: 28711560 DOI: 10.1016/j.jgar.2017.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/30/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVES The aim of this study was to evaluate the role of residue 238 in CTX-M-15 and CTX-M-15G238C mutant with respect to carbapenems and various β-lactamase inhibitors. METHODS A CTX-M-15G238C laboratory mutant was generated by site-directed mutagenesis from CTX-M-15 enzyme by replacing glycine 238 with cysteine. Thiol titration and p-chloromercuribenzoate (PCMB) inactivation assays were used to ascertain the presence of a disulfide bridge in the active site of CTX-M-15G238C. Kinetic parameters were determined both for CTX-M-15 and CTX-M-15G238C enzymes by analysing either the complete hydrolysis time courses or under initial rate conditions. RESULTS In CTX-M-15G238C mutant, the two cysteines (C69 and C238) located in the enzyme active site were unable to form a disulfide bridge. CTX-M-15 and thermostable CTX-M-15G238C were used to study the kinetic interaction with carbapenems, which behaved as poor substrates for both enzymes. Meropenem and ertapenem acted as transient inactivators for CTX-M-15 and CTX-M-15G238C, and for these compounds the variation of kobs versus the inactivator concentration was linear. Imipenem behaved as a transient inactivator for CTX-M-15 and as an inactivator (with k+3=0) for CTX-M-15G238C. In any case, the k+2/K values for CTX-M-15G238C were higher than those for CTX-M-15. CONCLUSIONS Compared with CTX-M-15, CTX-M-15G238C mutant appears to have a more favourable conformation for carbapenem acylation and higher activity against cefotaxime, which could be due to the presence of free -SH groups in the enzyme active site.
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Affiliation(s)
- Alessia Sabatini
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell'Aquila, L'Aquila, Italy
| | - Fabrizia Brisdelli
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell'Aquila, L'Aquila, Italy
| | - Giuseppe Celenza
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell'Aquila, L'Aquila, Italy
| | - Francesca Marcoccia
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell'Aquila, L'Aquila, Italy
| | - Martina Colapietro
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell'Aquila, L'Aquila, Italy
| | - María M Tavío
- Microbiology, Clinical Science Department, University of Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Alessandra Piccirilli
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell'Aquila, L'Aquila, Italy
| | - Gianfranco Amicosante
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell'Aquila, L'Aquila, Italy
| | - Mariagrazia Perilli
- Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell'Aquila, L'Aquila, Italy.
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