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Sękowska A. In Vitro Activity of "Old" and "New" Antimicrobials against the Klebsiella pneumoniae Complex. Antibiotics (Basel) 2024; 13:126. [PMID: 38391512 PMCID: PMC10886291 DOI: 10.3390/antibiotics13020126] [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: 12/19/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024] Open
Abstract
The Klebsiella pneumoniae complex is a commonly isolated bacteria in human infections. These opportunistic pathogens pose a serious threat to public health due to their potential transmission to the human population. Resistance to carbapenems is a significant antimicrobial resistance mechanism, leading to limited therapeutic options. Therefore, the aim of this study was to evaluate the in vitro activity of fosfomycin, colistin, ceftazidime-avibactam, and meropenem-vaborbactam against multidrug-resistant K. pneumoniae complex strains. This study involved 160 strains of Gram-negative rods, comprising 138 K. pneumoniae and 22 K. variicola. The minimal inhibitory concentration of fosfomycin was estimated using the agar dilution method, and for colistin, the microdilution method was employed. Susceptibility to ceftazidime-avibactam and meropenem-vaborbactam was determined using the gradient strip method. All analyzed K. pneumoniae complex isolates produced extended-spectrum β-lactamases, and 60.0% exhibited carbapenemases. The majority of the analyzed strains were susceptible to fosfomycin and colistin (62.5%). Among pandrug-resistant K. pneumoniae complex isolates, the highest susceptibility was observed with colistin (43.9%). Fosfomycin demonstrated good activity against ESβLs- and VIM-positive isolates from this complex. Colistin also exhibited satisfactory in vitro activity against VIM- and KPC-positive isolates from the K. pneumoniae complex. Ceftazidime-avibactam displayed good activity against K. pneumoniae complex strains producing ESβLs, KPC, and OXA enzymes. Additionally, meropenem-vaborbactam showed satisfactory in vitro activity against ESβLs- and KPC-positive isolates from this complex.
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Affiliation(s)
- Alicja Sękowska
- Microbiology Department, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 9 Maria Skłodowska-Curie St., 85-094 Bydgoszcz, Poland
- Clinical Microbiology Department, Dr. A. Jurasz University Hospital No. 1, 85-094 Bydgoszcz, Poland
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2
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Oelschlaeger P, Kaadan H, Dhungana R. Strategies to Name Metallo-β-Lactamases and Number Their Amino Acid Residues. Antibiotics (Basel) 2023; 12:1746. [PMID: 38136780 PMCID: PMC10740994 DOI: 10.3390/antibiotics12121746] [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: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Metallo-β-lactamases (MBLs), also known as class B β-lactamases (BBLs), are Zn(II)-containing enzymes able to inactivate a broad range of β-lactams, the most commonly used antibiotics, including life-saving carbapenems. They have been known for about six decades, yet they have only gained much attention as a clinical problem for about three decades. The naming conventions of these enzymes have changed over time and followed various strategies, sometimes leading to confusion. We are summarizing the naming strategies of the currently known MBLs. These enzymes are quite diverse on the amino acid sequence level but structurally similar. Problems trying to describe conserved residues, such as Zn(II) ligands and other catalytically important residues, which have different numbers in different sequences, have led to the establishment of a standard numbering scheme for BBLs. While well intended, the standard numbering scheme is not trivial and has not been applied consistently. We revisit this standard numbering scheme and suggest some strategies for how its implementation could be made more accessible to researchers. Standard numbering facilitates the comparison of different enzymes as well as their interaction with novel antibiotics and BBL inhibitors.
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Affiliation(s)
- Peter Oelschlaeger
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Heba Kaadan
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Rinku Dhungana
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
- Department of Biological Sciences, Kenneth P. Dietrich School of Arts & Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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3
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El-Khoury C, Mansour E, Yuliandra Y, Lai F, Hawkins BA, Du JJ, Sundberg EJ, Sluis-Cremer N, Hibbs DE, Groundwater PW. The role of adjuvants in overcoming antibacterial resistance due to enzymatic drug modification. RSC Med Chem 2022; 13:1276-1299. [PMID: 36439977 PMCID: PMC9667779 DOI: 10.1039/d2md00263a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/16/2022] [Indexed: 02/03/2023] Open
Abstract
Antibacterial resistance is a prominent issue with monotherapy often leading to treatment failure in serious infections. Many mechanisms can lead to antibacterial resistance including deactivation of antibacterial agents by bacterial enzymes. Enzymatic drug modification confers resistance to β-lactams, aminoglycosides, chloramphenicol, macrolides, isoniazid, rifamycins, fosfomycin and lincosamides. Novel enzyme inhibitor adjuvants have been developed in an attempt to overcome resistance to these agents, only a few of which have so far reached the market. This review discusses the different enzymatic processes that lead to deactivation of antibacterial agents and provides an update on the current and potential enzyme inhibitors that may restore bacterial susceptibility.
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Affiliation(s)
- Christy El-Khoury
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Elissar Mansour
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Yori Yuliandra
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Bryson A Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine Pittsburgh PA 15213 USA
| | - David E Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Paul W Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
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4
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Janin YL. On drug discovery against infectious diseases and academic medicinal chemistry contributions. Beilstein J Org Chem 2022; 18:1355-1378. [PMID: 36247982 PMCID: PMC9531561 DOI: 10.3762/bjoc.18.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022] Open
Abstract
This perspective is an attempt to document the problems that medicinal chemists are facing in drug discovery. It is also trying to identify relevant/possible, research areas in which academics can have an impact and should thus be the subject of grant calls. Accordingly, it describes how hit discovery happens, how compounds to be screened are selected from available chemicals and the possible reasons for the recurrent paucity of useful/exploitable results reported. This is followed by the successful hit to lead stories leading to recent and original antibacterials which are, or about to be, used in human medicine. Then, illustrated considerations and suggestions are made on the possible inputs of academic medicinal chemists. This starts with the observation that discovering a "good" hit in the course of a screening campaign still rely on a lot of luck - which is within the reach of academics -, that the hit to lead process requires a lot of chemistry and that if public-private partnerships can be important throughout these stages, they are absolute requirements for clinical trials. Concerning suggestions to improve the current hit success rate, one academic input in organic chemistry would be to identify new and pertinent chemical space, design synthetic accesses to reach these and prepare the corresponding chemical libraries. Concerning hit to lead programs on a given target, if no new hits are available, previously reported leads along with new structural data can be pertinent starting points to design, prepare and assay original analogues. In conclusion, this text is an actual plea illustrating that, in many countries, academic research in medicinal chemistry should be more funded, especially in the therapeutic area neglected by the industry. At the least, such funds would provide the intensive to secure series of hopefully relevant chemical entities which appears to often lack when considering the results of academic as well as industrial screening campaigns.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
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5
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Chen C, Oelschlaeger P, Wang D, Xu H, Wang Q, Wang C, Zhao A, Yang KW. Structure and Mechanism-Guided Design of Dual Serine/Metallo-Carbapenemase Inhibitors. J Med Chem 2022; 65:5954-5974. [PMID: 35420040 DOI: 10.1021/acs.jmedchem.2c00213] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Serine/metallo-carbapenemase-coproducing pathogens, often referred to as "superbugs", are a significant clinical problem. They hydrolyze nearly all available β-lactam antibiotics, especially carbapenems considered as last-resort antibiotics, seriously endangering efficacious antibacterial treatment. Despite the continuous global spread of carbapenem resistance, no dual-action inhibitors are available in therapy. This Perspective is the first systematic investigation of all chemotypes, modes of inhibition, and crystal structures of dual serine/metallo-carbapenemase inhibitors. An overview of the key strategy for designing dual serine/metallo-carbapenemase inhibitors and their mechanism of action is provided, as guiding rules for the development of clinically available dual inhibitors, coadministrated with carbapenems, to overcome the carbapenem resistance issue.
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Affiliation(s)
- Cheng Chen
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona 91766, California, United States
| | - Dongmei Wang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310030, P. R. China
| | - Qian Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University of Chinese Medicine, Jinshui District 450046, Zhengzhou, P. R. China
| | - Cheng Wang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Aiguo Zhao
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China
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6
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Detection and characterization of VIM-52, a new variant of VIM-1 from Klebsiella pneumoniae clinical isolate. Antimicrob Agents Chemother 2021; 65:e0266020. [PMID: 34370584 DOI: 10.1128/aac.02660-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Over the last two decades, antimicrobial resistance has become a global health problem. In Gram-negative bacteria, metallo-β-lactamases (MBLs), which inactivate virtually all β-lactams, increasingly contribute to this phenomenon. The aim of this study is to characterize VIM-52, a His224Arg variant of VIM-1, identified in a Klebsiella pneumoniae clinical isolate. VIM-52 conferred lower MICs to cefepime and ceftazidime as compared to VIM-1. These results were confirmed by steady state kinetic measurements, where VIM-52 yielded a lower activity towards ceftazidime and cefepime but not against carbapenems. Residue 224 is part of the L10 loop (residues 221-241), which borders the active site. As Arg 224 and Ser 228 are both playing an important and interrelated role in enzymatic activity, stability and substrate specificity for the MBLs, targeted mutagenesis at both positions were performed and further confirmed their crucial role for substrate specificity.
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7
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Reddy N, Shungube M, Arvidsson PI, Baijnath S, Kruger HG, Govender T, Naicker T. A 2018–2019 patent review of metallo beta-lactamase inhibitors. Expert Opin Ther Pat 2020; 30:541-555. [DOI: 10.1080/13543776.2020.1767070] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nakita Reddy
- Catalysis and Peptide Research Unit, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Mbongeni Shungube
- Catalysis and Peptide Research Unit, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Per I Arvidsson
- Catalysis and Peptide Research Unit, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
- Science for Life Laboratory, Karolinska Institutet, Stockhlom, Sweden
| | - Sooraj Baijnath
- Catalysis and Peptide Research Unit, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
| | | | - Tricia Naicker
- Catalysis and Peptide Research Unit, Westville Campus, University of KwaZulu-Natal, Durban, South Africa
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8
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Henry EJ, Bird SJ, Gowland P, Collins M, Cassella JP. Ferrocenyl chalcone derivatives as possible antimicrobial agents. J Antibiot (Tokyo) 2020; 73:299-308. [PMID: 31988484 DOI: 10.1038/s41429-020-0280-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 11/09/2022]
Abstract
The swift spread of infections caused by drug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), has quickly become a worldwide concern as infections spread from healthcare settings to the wider community. While ferrocenyl chalcones, which are chalcone derivatives with antimicrobial activity, have gained attention from researchers, further study is needed to assess their cytotoxicity. Ten newly developed chalcones, in which ring A was replaced with a ferrocenyl moiety and ring B contained increasing alkyl chain lengths from 1 to 10 carbons, were assessed. Using twofold broth microdilution, the minimum inhibitory concentration (MIC) of five of the ten compounds were lower against Gram-positive organisms (MICs from 0.008 mg ml-1 to 0.063 mg ml-1) than Gram-negative organisms (MICs = 0.125 mg ml-1). These novel ferrocenyl chalcone compounds were effective against three types of clinically isolated drug-resistant S. aureus, including an MRSA, and against other non-resistant clinically isolated and laboratory-adapted Gram-positive bacteria. The same compounds inhibited growth in non-resistant bacteria by potentially obstructing cellular respiration in Gram-positive bacteria. Images obtained through scanning electron microscopy revealed fully lysed bacterial cells once exposed to a selected compound that showed activity. The results indicate that these newly developed compounds could be important antimicrobial agents in the treatment of infections from clinically resistant bacteria.
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Affiliation(s)
- Elecia J Henry
- School of Life Sciences and Education, Staffordshire University, Stoke-on-Trent, Staffordshire, ST4 2DF, UK. .,Department of Food Production, University of the West Indies, Frank Stockdale Building, St. Augustine, Trinidad and Tobago.
| | - Susan J Bird
- School of Life Sciences and Education, Staffordshire University, Stoke-on-Trent, Staffordshire, ST4 2DF, UK
| | - Pauline Gowland
- School of Life Sciences and Education, Staffordshire University, Stoke-on-Trent, Staffordshire, ST4 2DF, UK
| | - Michael Collins
- Chesterfield Royal Hospital NHS Foundation Trust, Chesterfield Road, Calow, Chesterfield, Derbyshire, S44 5BL, UK
| | - John P Cassella
- School of Law, Policing and Forensics, Staffordshire University, Stoke-on-Trent, Staffordshire, ST4 2DF, UK
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9
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Mutation S115T in IMP-Type Metallo-β-Lactamases Compensates for Decreased Expression Levels Caused by Mutation S119G. Biomolecules 2019; 9:biom9110724. [PMID: 31718049 PMCID: PMC6920813 DOI: 10.3390/biom9110724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
(1) Background: Metallo-β-lactamases (MBLs) have raised concerns due to their ability to inactivate carbapenems and newer generation cephalosporins and the absence of clinically available MBL inhibitors. Their genes are often transferred horizontally, and the number of MBL variants has grown exponentially, with many newer variants showing enhanced enzyme activity or stability. In this study, we investigated a closely related group of variants from the IMP family that all contain the combination of mutations S115T and S119G relative to IMP-1. (2) Methods: The effects of each individual mutation and their combination in the IMP-1 sequence background in comparison to IMP-1 were investigated. Their ability to confer resistance and their in-cell expression levels were determined. All enzymes were purified, and their secondary structure and thermal stability were determined with circular dichroism. Their Zn(II) content and kinetic constants with a panel of β-lactam antibiotics were determined. (3) Results: All four enzymes were viable and conferred resistance to all antibiotics tested except aztreonam. However, the single-mutant enzymes were slightly deficient, IMP-1S115T due to decreased enzyme activity and IMP-1-S119G due to decreased thermal stability and expression, while the double mutant did not show these defects. (4) Conclusions: These observations suggest that S119G was acquired due to its increased enzyme activity and S115T to suppress the thermal stability and expression defect introduced by S119G.
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Proia L, Anzil A, Borrego C, Farrè M, Llorca M, Sanchis J, Bogaerts P, Balcázar JL, Servais P. Occurrence and persistence of carbapenemases genes in hospital and wastewater treatment plants and propagation in the receiving river. JOURNAL OF HAZARDOUS MATERIALS 2018; 358:33-43. [PMID: 29960932 DOI: 10.1016/j.jhazmat.2018.06.058] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/22/2018] [Accepted: 06/25/2018] [Indexed: 05/29/2023]
Abstract
This study aims to investigate the prevalence of clinically relevant carbapenemases genes (blaKPC, blaNDM and blaOXA-48) in water samples collected over one-year period from hospital (H), raw and treated wastewater of two wastewater treatment plants (WWTPs) as well as along the Zenne River (Belgium). The genes were quantified in both particle-attached (PAB) and free-living (FLB) bacteria. Our results showed that absolute abundances were the highest in H waters. Although absolute abundances were significantly reduced in WWTP effluents, the relative abundance (normalized per 16S rRNA) was never lowered through wastewater treatment. Particularly, for the PAB the relative abundances were significantly higher in the effluents respect to the influents of both WWTPs for all the genes. The absolute abundances along the Zenne River increased from upstream to downstream, peaking after the release of WWTPs effluents, in both fractions. Our results demonstrated that blaKPC, blaNDM and blaOXA-48 are widely distributed in the Zenne as a consequence of chronic discharge from WWTPs. To conclude, the levels of carbapenemases genes are significantly lower than other genes conferring resistance to more widely used antibiotics (analyzed in previous studies carried out at the same sites), but could raise up to the levels of high prevalent resistance genes.
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Affiliation(s)
- Lorenzo Proia
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Adriana Anzil
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Carles Borrego
- Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus de Montilivi, 17003, Girona, Spain
| | - Marinella Farrè
- Water and Soil Quality Research Group, Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Marta Llorca
- Water and Soil Quality Research Group, Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Josep Sanchis
- Water and Soil Quality Research Group, Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Pierre Bogaerts
- Laboratory of Clinical Microbiology, Belgian National Reference Center for Monitoring Antimicrobial Resistance in Gram-negative Bacteria, CHU UCL Avenue Docteur G. Thérasse, 1, 5530, Yvoir, Belgium
| | - Jose Luis Balcázar
- Catalan Institute for Water Research (ICRA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium
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Somboro AM, Osei Sekyere J, Amoako DG, Essack SY, Bester LA. Diversity and Proliferation of Metallo-β-Lactamases: a Clarion Call for Clinically Effective Metallo-β-Lactamase Inhibitors. Appl Environ Microbiol 2018; 84:e00698-18. [PMID: 30006399 PMCID: PMC6121990 DOI: 10.1128/aem.00698-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The worldwide proliferation of life-threatening metallo-β-lactamase (MBL)-producing Gram-negative bacteria is a serious concern to public health. MBLs are compromising the therapeutic efficacies of β-lactams, particularly carbapenems, which are last-resort antibiotics indicated for various multidrug-resistant bacterial infections. Inhibition of enzymes mediating antibiotic resistance in bacteria is one of the major promising means for overcoming bacterial resistance. Compounds having potential MBL-inhibitory activity have been reported, but none are currently under clinical trials. The need for developing safe and efficient MBL inhibitors (MBLIs) is obvious, particularly with the continuous spread of MBLs worldwide. In this review, the emergence and escalation of MBLs in Gram-negative bacteria are discussed. The relationships between different class B β-lactamases identified up to 2017 are represented by a phylogenetic tree and summarized. In addition, approved and/or clinical-phase serine β-lactamase inhibitors are recapitulated to reflect the successful advances made in developing class A β-lactamase inhibitors. Reported MBLIs, their inhibitory properties, and their purported modes of inhibition are delineated. Insights into structural variations of MBLs and the challenges involved in developing potent MBLIs are also elucidated and discussed. Currently, natural products and MBL-resistant β-lactam analogues are the most promising agents that can become clinically efficient MBLIs. A deeper comprehension of the mechanisms of action and activity spectra of the various MBLs and their inhibitors will serve as a bedrock for further investigations that can result in clinically useful MBLIs to curb this global menace.
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Affiliation(s)
- Anou M Somboro
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda A Bester
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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12
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Kang JS, Zhang AL, Faheem M, Zhang CJ, Ai N, Buynak JD, Welsh WJ, Oelschlaeger P. Virtual Screening and Experimental Testing of B1 Metallo-β-lactamase Inhibitors. J Chem Inf Model 2018; 58:1902-1914. [PMID: 30107123 DOI: 10.1021/acs.jcim.8b00133] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The global rise of metallo-β-lactamases (MBLs) is problematic due to their ability to inactivate most β-lactam antibiotics. MBL inhibitors that could be coadministered with and restore the efficacy of β-lactams are highly sought after. In this study, we employ virtual screening of candidate MBL inhibitors without thiols or carboxylates to avoid off-target effects using the Avalanche software package, followed by experimental validation of the selected compounds. As target enzymes, we chose the clinically relevant B1 MBLs NDM-1, IMP-1, and VIM-2. Among 32 compounds selected from an approximately 1.5 million compound library, 6 exhibited IC50 values less than 40 μM against NDM-1 and/or IMP-1. The most potent inhibitors of NDM-1, IMP-1, and VIM-2 had IC50 values of 19 ± 2, 14 ± 1, and 50 ± 20 μM, respectively. While chemically diverse, the most potent inhibitors all contain combinations of hydroxyl, ketone, ester, amide, or sulfonyl groups. Docking studies suggest that these electron-dense moieties are involved in Zn(II) coordination and interaction with protein residues. These novel scaffolds could serve as the basis for further development of MBL inhibitors. A procedure for renaming NDM-1 residues to conform to the class B β-lactamase (BBL) numbering scheme is also included.
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Affiliation(s)
- Joon S Kang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States.,Department of Biological Sciences , California State Polytechnic University , Pomona , California 91768-2557 , United States
| | - Antonia L Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Mohammad Faheem
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Charles J Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Ni Ai
- Pharmaceutical Informatics Institute, School of Pharmaceutical Sciences , Zhejiang University , Zhejiang 31005 , People's Republic of China
| | - John D Buynak
- Department of Chemistry , Southern Methodist University , Dallas , Texas 75275-0314 , United States
| | - William J Welsh
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, and Division of Chem Informatics, Biomedical Informatics Shared Resource, Rutgers-Cancer Institute of New Jersey , The State University of New Jersey , Piscataway , New Jersey 08854-8021 , United States
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
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13
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Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance. Sci Rep 2018; 8:12916. [PMID: 30150677 PMCID: PMC6110804 DOI: 10.1038/s41598-018-31176-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/13/2018] [Indexed: 11/08/2022] Open
Abstract
The rise of multi-drug resistance in bacterial pathogens is one of the grand challenges facing medical science. A major concern is the speed of development of β-lactamase-mediated resistance in Gram-negative species, thus putting at risk the efficacy of the most recently approved antibiotics and inhibitors, including carbapenems and avibactam, respectively. New strategies to overcome resistance are urgently required, which will ultimately be facilitated by a deeper understanding of the mechanisms that regulate the function of β-lactamases such as the Klebsiella Pneumoniae carbapenemases (KPCs). Using enhanced sampling computational methods together with site-directed mutagenesis, we report the identification of two “hydrophobic networks” in the KPC-2 enzyme, the integrity of which has been found to be essential for protein stability and corresponding resistance. Present throughout the structure, these networks are responsible for the structural integrity and allosteric signaling. Disruption of the networks leads to a loss of the KPC-2 mediated resistance phenotype, resulting in restored susceptibility to different classes of β-lactam antibiotics including carbapenems and cephalosporins. The ”hydrophobic networks” were found to be highly conserved among class-A β-lactamases, which implies their suitability for exploitation as a potential target for therapeutic intervention.
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14
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Mojica MF, Bonomo RA, Fast W. B1-Metallo-β-Lactamases: Where Do We Stand? Curr Drug Targets 2017; 17:1029-50. [PMID: 26424398 DOI: 10.2174/1389450116666151001105622] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 12/31/1969] [Accepted: 09/14/2015] [Indexed: 11/22/2022]
Abstract
Metallo-β-Lactamases (MBLs) are class Bβ-lactamases that hydrolyze almost all clinically-availableβ-lactam antibiotics. MBLs feature the distinctive αβ/βα sandwich fold of the metallo-hydrolase/oxidoreductase superfamily and possess a shallow active-site groove containing one or two divalent zinc ions, flanked by flexible loops. According to sequence identity and zinc ion dependence, MBLs are classified into three subclasses (B1, B2 and B3), of which the B1 subclass enzymes have emerged as the most clinically significant. Differences among the active site architectures, the nature of zinc ligands, and the catalytic mechanisms have limited the development of a common inhibitor. In this review, we will describe the molecular epidemiology and structural studies of the most prominent representatives of class B1 MBLs (NDM-1, IMP-1 and VIM-2) and describe the implications for inhibitor design to counter this growing clinical threat.
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Affiliation(s)
| | - Robert A Bonomo
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Blvd., Cleveland, OH 44106, USA.
| | - Walter Fast
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin TX, 78712, USA.
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15
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Sevaille L, Gavara L, Bebrone C, De Luca F, Nauton L, Achard M, Mercuri P, Tanfoni S, Borgianni L, Guyon C, Lonjon P, Turan-Zitouni G, Dzieciolowski J, Becker K, Bénard L, Condon C, Maillard L, Martinez J, Frère JM, Dideberg O, Galleni M, Docquier JD, Hernandez JF. 1,2,4-Triazole-3-thione Compounds as Inhibitors of Dizinc Metallo-β-lactamases. ChemMedChem 2017; 12:972-985. [DOI: 10.1002/cmdc.201700186] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/12/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Laurent Sevaille
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Carine Bebrone
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
- Present address: Symbiose Biomaterials S.A., GIGA Bât. B34; 1 avenue de l'Hôpital 4000 Liège Belgium
| | - Filomena De Luca
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Lionel Nauton
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR5075 CNRS, CEA; Université Joseph Fourier; 41 rue Jules Horowitz 38027 Grenoble cedex 1 France
- Present address: Institut de Chimie de Clermont-Ferrand, UMR6296 CNRS; Université Clermont Auvergne; 63000 Clermont-Ferrand France
| | - Maud Achard
- EMBL Outstation c/o DESY; Notkestrasse 85 22603 Hamburg Germany
- Present address: School of Chemistry and Molecular Bioscience; University of Queensland, St. Lucia; Brisbane QLD 4072 Australia
| | - Paola Mercuri
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
| | - Silvia Tanfoni
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Luisa Borgianni
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Carole Guyon
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Pauline Lonjon
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
- Present address: CERN, HSE/SEE/SI; 1211 Geneva 23 Switzerland
| | - Gülhan Turan-Zitouni
- Department of Pharmaceutical Chemistry; Anadolu University, Faculty of Pharmacy; 26470 Eskisehir Turkey
| | - Julia Dzieciolowski
- Chair of Biochemistry and Molecular Biology, Interdisciplinary Research Center; Justus Liebig University; Heinrich-Buff-Ring 26-32 35392 Giessen Germany
| | - Katja Becker
- Chair of Biochemistry and Molecular Biology, Interdisciplinary Research Center; Justus Liebig University; Heinrich-Buff-Ring 26-32 35392 Giessen Germany
| | - Lionel Bénard
- UMR8226, CNRS, Université Pierre et Marie Curie; Institut de Biologie Physico-Chimique; 13 rue Pierre et Marie Curie 75005 Paris France
| | - Ciaran Condon
- UMR8261, CNRS, Université Paris-Diderot; Institut de Biologie Physico-Chimique; 13 rue Pierre et Marie Curie 75005 Paris France
| | - Ludovic Maillard
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
| | - Jean-Marie Frère
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
| | - Otto Dideberg
- Institut de Biologie Structurale-Jean-Pierre Ebel, UMR5075 CNRS, CEA; Université Joseph Fourier; 41 rue Jules Horowitz 38027 Grenoble cedex 1 France
| | - Moreno Galleni
- Laboratoire de Macromolécules Biologiques, Centre d'Ingénierie des Protéines; Université de Liège; Allée du 6 août B6, Sart-Tilman 4000 Liège Belgium
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche; Università di Siena; 53100 Siena Italy
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS; Université de Montpellier, ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier cedex 5 France
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16
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Chang YN, Xiang Y, Zhang YJ, Wang WM, Chen C, Oelschlaeger P, Yang KW. Carbamylmethyl Mercaptoacetate Thioether: A Novel Scaffold for the Development of L1 Metallo-β-lactamase Inhibitors. ACS Med Chem Lett 2017; 8:527-532. [PMID: 28523105 DOI: 10.1021/acsmedchemlett.7b00058] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/24/2017] [Indexed: 12/30/2022] Open
Abstract
Given the clinical importance of metallo-β-lactamases (MβLs), a new scaffold, N-substituted carbamylmethyl mercaptoacetate thioether, was constructed. The obtained molecules 1-16 inhibited MβLs from all three subclasses, but preferentially L1 from subclass B3. Compound 9 with a p-carboxyphenyl substituent exhibited the broadest spectrum with at least 70% inhibition of enzymes from all subclasses at 100 μM, while compound 5 with a p-methylphenyl substituent was the most potent inhibitor of any individual enzyme, with 97% inhibition at 100 μM and an IC50 value of 0.41 μM against L1. Isothermal titration calorimetry assays corroborate findings from UV-vis spectrophotometric assays that the inhibition of L1 by 5 is dose-dependent. Docking studies suggest that the carboxyl group, the sulfide atom, and the carbonyl group of the carbamyl coordinate Zn2 in a chelating fashion. Using E. coli cells expressing L1, 6 and 8 were able to decrease cefazolin minimum inhibitory concentration 8-fold.
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Affiliation(s)
- Ya-Nan Chang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, Chemical Biology Innovation Laboratory,
College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Yang Xiang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, Chemical Biology Innovation Laboratory,
College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Yue-Juan Zhang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, Chemical Biology Innovation Laboratory,
College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Wen-Ming Wang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, Chemical Biology Innovation Laboratory,
College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Cheng Chen
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, Chemical Biology Innovation Laboratory,
College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Peter Oelschlaeger
- Department
of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona, California 91766, United States
| | - Ke-Wu Yang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, Chemical Biology Innovation Laboratory,
College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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17
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New Delhi metallo-β-lactamase-1: structure, inhibitors and detection of producers. Future Med Chem 2016; 8:993-1012. [PMID: 27253479 DOI: 10.4155/fmc-2016-0015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Since its discovery in 2008, New Delhi metallo-β-lactamase-1 (NDM-1)-producing Enterobacteriaceae have disseminated globally, facilitated predominantly by gut colonization and the spread of plasmids carrying the bla NDM-1 gene. With few effective antibiotics against NDM-1 producers, and resistance developing to those which remain, there is an urgent need to develop new treatments. To date, most drug design in this area has been focused on developing an NDM-1 inhibitor and has been aided by the wealth of structural and mechanistic information available from high resolution x-ray crystallography and molecular modeling. This review aims to summarize current knowledge regarding the detection of NDM-1 producers, the mechanism of action of NDM-1 and to highlight recent attempts toward the development of clinically useful inhibitors.
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18
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Montagner C, Nigen M, Jacquin O, Willet N, Dumoulin M, Karsisiotis AI, Roberts GCK, Damblon C, Redfield C, Matagne A. The Role of Active Site Flexible Loops in Catalysis and of Zinc in Conformational Stability of Bacillus cereus 569/H/9 β-Lactamase. J Biol Chem 2016; 291:16124-37. [PMID: 27235401 DOI: 10.1074/jbc.m116.719005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Indexed: 11/06/2022] Open
Abstract
Metallo-β-lactamases catalyze the hydrolysis of most β-lactam antibiotics and hence represent a major clinical concern. The development of inhibitors for these enzymes is complicated by the diversity and flexibility of their substrate-binding sites, motivating research into their structure and function. In this study, we examined the conformational properties of the Bacillus cereus β-lactamase II in the presence of chemical denaturants using a variety of biochemical and biophysical techniques. The apoenzyme was found to unfold cooperatively, with a Gibbs free energy of stabilization (ΔG(0)) of 32 ± 2 kJ·mol(-1) For holoBcII, a first non-cooperative transition leads to multiple interconverting native-like states, in which both zinc atoms remain bound in an apparently unaltered active site, and the protein displays a well organized compact hydrophobic core with structural changes confined to the enzyme surface, but with no catalytic activity. Two-dimensional NMR data revealed that the loss of activity occurs concomitantly with perturbations in two loops that border the enzyme active site. A second cooperative transition, corresponding to global unfolding, is observed at higher denaturant concentrations, with ΔG(0) value of 65 ± 1.4 kJ·mol(-1) These combined data highlight the importance of the two zinc ions in maintaining structure as well as a relatively well defined conformation for both active site loops to maintain enzymatic activity.
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Affiliation(s)
- Caroline Montagner
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Michaël Nigen
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Olivier Jacquin
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Nicolas Willet
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Mireille Dumoulin
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Andreas Ioannis Karsisiotis
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Gordon C K Roberts
- the Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom, and
| | - Christian Damblon
- Département de Chimie, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Christina Redfield
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - André Matagne
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
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19
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Prevalence and Fate of Carbapenemase Genes in a Wastewater Treatment Plant in Northern China. PLoS One 2016; 11:e0156383. [PMID: 27227329 PMCID: PMC4882038 DOI: 10.1371/journal.pone.0156383] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/15/2016] [Indexed: 01/09/2023] Open
Abstract
Carbapenemase-producing strains of bacteria, which were primarily found in the medical field, have increasingly been found in the environment, thus posing potential risks to public health. One possible way for carbapenemase genes to enter the environment is via wastewater. Therefore, the goal of this study was to determine the occurrence and fate of five high-risk carbapenemase genes in a wastewater treatment plant (WWTP) in northern China using real-time qPCR. Results showed that the blaKPC-2, blaGES-1, and blaIMP-1 genes prevailed throughout all processing stages (even in the chlorination disinfection unit) in the WWTP, whereas the blaVIM-2 and blaOXA-48 genes were not detected in all samples. Worryingly, considerable amounts of carbapenemase genes ((1.54 ± 0.61) × 103 copies/mL to (2.14± 0.41) × 105 copies/mL) were detected in WWTP effluent samples, while the majority of the carbapenemase genes were transported to the dewatered sludge with concentrations from (6.51 ± 0.14) × 109 copies/g to (6.18 ± 0.63) × 1010 copies/g dry weight. Furthermore, a total of 97 KPC-2-producing strains, belonging to 8 bacterial genera, were isolated from the WWTP. Sequencing of 16S rRNA revealed that most of KPC-2 producing isolates were opportunistic pathogens, including Klebsiella spp. (10.3%), Enterococcus spp. (11.3%), Acinetobacter spp. (19.6%), Escherichia spp. (12.4%), Shigella spp. (17.5%), Stenotrophomonas spp. (10.3%) and Wautersiella spp. (9.3%). Moreover, blaKPC-2 genes were identified for the first time in Paenibacillus spp. isolates (an indigenous bacteria), indicating an increased risk of horizontal transfer between clinical pathogens and environmental bacteria. Indeed, a conjugation experiment demonstrated transfer of the blaKPC-2 gene to an E.coli J53 strain from a Klebsiella strain isolated from the WWTP. To our knowledge, this is the first study to obtain Paenibacillus spp. isolates carrying the carbapenemase gene and to quantify the abundance of carbapenemase genes in the environment.
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20
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González MM, Vila AJ. An Elusive Task: A Clinically Useful Inhibitor of Metallo-β-Lactamases. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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21
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Elucidating the Role of Residue 67 in IMP-Type Metallo-β-Lactamase Evolution. Antimicrob Agents Chemother 2015; 59:7299-307. [PMID: 26369960 DOI: 10.1128/aac.01651-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/06/2015] [Indexed: 02/07/2023] Open
Abstract
Antibiotic resistance in bacteria is ever changing and adapting, as once-novel β-lactam antibiotics are losing their efficacy, primarily due to the production of β-lactamases. Metallo-β-lactamases (MBLs) efficiently inactivate a broad range of β-lactam antibiotics, including carbapenems, and are often coexpressed with other antibacterial resistance factors. The rapid dissemination of MBLs and lack of novel antibacterials pose an imminent threat to global health. In an effort to better counter these resistance-conferring β-lactamases, an investigation of their natural evolution and resulting substrate specificity was employed. In this study, we elucidated the effects of different amino acid substitutions at position 67 in IMP-type MBLs on the ability to hydrolyze and confer resistance to a range of β-lactam antibiotics. Wild-type β-lactamases IMP-1 and IMP-10 and mutants IMP-1-V67A and IMP-1-V67I were characterized biophysically and biochemically, and MICs for Escherichia coli cells expressing these enzymes were determined. We found that all variants exhibited catalytic efficiencies (kcat/Km) equal to or higher than that of IMP-1 against all tested β-lactams except penicillins, against which IMP-1 and IMP-1-V67I showed the highest kcat/Km values. The substrate-specific effects of the different amino acid substitutions at position 67 are discussed in light of their side chain structures and possible interactions with the substrates. Docking calculations were employed to investigate interactions between different side chains and an inhibitor used as a β-lactam surrogate. The differences in binding affinities determined experimentally and computationally seem to be governed by hydrophobic interactions between residue 67 and the inhibitor and, by inference, the β-lactam substrates.
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22
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Meropenem and chromacef intermediates observed in IMP-25 metallo-β-lactamase-catalyzed hydrolysis. Antimicrob Agents Chemother 2015; 59:4326-30. [PMID: 25918145 DOI: 10.1128/aac.04409-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 04/12/2015] [Indexed: 01/09/2023] Open
Abstract
Metallo-β-lactamases inactivate most β-lactam antibacterials, and much attention has been paid to their catalytic mechanism. One issue of controversy has been whether β-lactam hydrolysis generally proceeds through an anionic intermediate bound to the active-site Zn(II) ions or not. The formation of an intermediate has not been shown conclusively in imipenemase (IMP) enzymes to date. Here, we provide evidence that intermediates are formed during the hydrolysis of meropenem and chromacef catalyzed by the variant IMP-25 and, to a lesser degree, IMP-1.
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23
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Theoretical studies of the hydrolysis of antibiotics catalyzed by a metallo-β-lactamase. Arch Biochem Biophys 2015; 582:116-26. [PMID: 25622886 DOI: 10.1016/j.abb.2015.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 12/27/2022]
Abstract
In this paper, hybrid QM/MM molecular dynamics (MD) simulations have been performed to explore the mechanisms of hydrolysis of two antibiotics, Imipenen (IMI), an antibiotic belonging to the subgroup of carbapenems, and the Cefotaxime (CEF), a third-generation cephalosporin antibiotic, in the active site of a mono-nuclear β-lactamase, CphA from Aeromonas hydrophila. Significant different transition state structures are obtained for the hydrolysis of both antibiotics: while the TS of the CEF is an ionic species with negative charge on nitrogen, the IMI TS presents a tetrahedral-like character with negative charge on oxygen atom of the carbonyl group of the lactam ring. Thus, dramatic conformational changes can take place in the cavity of CphA to accommodate different substrates, which would be the origin of its substrate promiscuity. Since CphA shows only activity against carbapenem antibiotic, this study sheds some light into the origin of the selectivity of the different MbL and, as a consequence, into the discovery of specific and potent MβL inhibitors against a broad spectrum of bacterial pathogens. We have finally probed that a re-parametrization of semiempirical methods should be done to properly describe the behavior the metal cation in active site, Zn(2+), when used in QM/MM calculations.
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24
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Pegg KM, Liu EM, George AC, LaCuran AE, Bethel CR, Bonomo RA, Oelschlaeger P. Understanding the determinants of substrate specificity in IMP family metallo-β-lactamases: the importance of residue 262. Protein Sci 2014; 23:1451-60. [PMID: 25131397 DOI: 10.1002/pro.2530] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 11/11/2022]
Abstract
In Gram-negative bacteria, resistance to β-lactam antibacterials is largely due to β-lactamases and is a growing public health threat. One of the most concerning β-lactamases to evolve in bacteria are the Class B enzymes, the metallo-β-lactamases (MBLs). To date, penams and cephems resistant to hydrolysis by MBLs have not yet been found. As a result of this broad substrate specificity, a better understanding of the role of catalytically important amino acids in MBLs is necessary to design novel β-lactams and inhibitors. Two MBLs, the wild type IMP-1 with serine at position 262, and an engineered variant with valine at the same position (IMP-1-S262V), were previously found to exhibit very different substrate spectra. These findings compelled us to investigate the impact of a threonine at position 262 (IMP-1-S262T) on the substrate spectrum. Here, we explore MBL sequence-structure-activity relationships by predicting and experimentally validating the effect of the S262T substitution in IMP-1. Using site-directed mutagenesis, threonine was introduced at position 262, and the IMP-1-S262T enzyme, as well as the other two enzymes IMP-1 and IMP-1-S262V, were purified and kinetic constants were determined against a range of β-lactam antibacterials. Catalytic efficiencies (kcat /KM ) obtained with IMP-1-S262T and minimum inhibitory concentrations (MICs) observed with bacterial cells expressing the protein were intermediate or comparable to the corresponding values with IMP-1 and IMP-1-S262V, validating the role of this residue in catalysis. Our results reveal the important role of IMP residue 262 in β-lactam turnover and support this approach to predict activities of certain novel MBL variants.
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Affiliation(s)
- Kevin M Pegg
- Biological Sciences Department, College of Science, California State Polytechnic University, Pomona, California
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25
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Zhang YL, Yang KW, Zhou YJ, LaCuran AE, Oelschlaeger P, Crowder MW. Diaryl-Substituted Azolylthioacetamides: Inhibitor Discovery of New Delhi Metallo-β-Lactamase-1 (NDM-1). ChemMedChem 2014; 9:2445-8. [DOI: 10.1002/cmdc.201402249] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Indexed: 11/09/2022]
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26
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Widmann M, Pleiss J. Protein variants form a system of networks: microdiversity of IMP metallo-beta-lactamases. PLoS One 2014; 9:e101813. [PMID: 25013948 PMCID: PMC4094381 DOI: 10.1371/journal.pone.0101813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/10/2014] [Indexed: 12/29/2022] Open
Abstract
Genome and metagenome sequencing projects support the view that only a tiny portion of the total protein microdiversity in the biosphere has been sequenced yet, while the vast majority of existing protein variants is still unknown. By using a network approach, the microdiversity of 42 metallo-β-lactamases of the IMP family was investigated. In the networks, the nodes are formed by the variants, while the edges correspond to single mutations between pairs of variants. The 42 variants were assigned to 7 separate networks. By analyzing the networks and their relationships, the structure of sequence space was studied and existing, but still unknown, functional variants were predicted. The largest network consists of 10 variants with IMP-1 in its center and includes two ubiquitous mutations, V67F and S262G. By relating the corresponding pairs of variants, the networks were integrated into a single system of networks. The largest network also included a quartet of variants: IMP-1, two single mutants, and the respective double mutant. The existence of quartets indicates that if two mutations resulted in functional enzymes, the double mutant may also be active and stable. Therefore, quartet construction from triplets was applied to predict 15 functional variants. Further functional mutants were predicted by applying the two ubiquitous mutations in all networks. In addition, since the networks are separated from each other by 10-15 mutations on average, it is expected that a subset of the theoretical intermediates are functional, and therefore are supposed to exist in the biosphere. Finally, the network analysis helps to distinguish between epistatic and additive effects of mutations; while the presence of correlated mutations indicates a strong interdependency between the respective positions, the mutations V67F and S262G are ubiquitous and therefore background independent.
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Affiliation(s)
- Michael Widmann
- Institute of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail:
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27
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Shi H, Cheng Y, Lee KH, Luo RF, Banaei N, Rao J. Engineering the Stereochemistry of Cephalosporin for Specific Detection of Pathogenic Carbapenemase-Expressing Bacteria. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Shi H, Cheng Y, Lee KH, Luo RF, Banaei N, Rao J. Engineering the Stereochemistry of Cephalosporin for Specific Detection of Pathogenic Carbapenemase-Expressing Bacteria. Angew Chem Int Ed Engl 2014; 53:8113-6. [DOI: 10.1002/anie.201402012] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/25/2014] [Indexed: 01/19/2023]
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Blizzard TA, Chen H, Kim S, Wu J, Bodner R, Gude C, Imbriglio J, Young K, Park YW, Ogawa A, Raghoobar S, Hairston N, Painter RE, Wisniewski D, Scapin G, Fitzgerald P, Sharma N, Lu J, Ha S, Hermes J, Hammond ML. Discovery of MK-7655, a β-lactamase inhibitor for combination with Primaxin®. Bioorg Med Chem Lett 2014; 24:780-5. [DOI: 10.1016/j.bmcl.2013.12.101] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/20/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
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30
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31
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Drawz SM, Papp-Wallace KM, Bonomo RA. New β-lactamase inhibitors: a therapeutic renaissance in an MDR world. Antimicrob Agents Chemother 2013; 58:1835-46. [PMID: 24379206 PMCID: PMC4023773 DOI: 10.1128/aac.00826-13] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
As the incidence of Gram-negative bacterial infections for which few effective treatments remain increases, so does the contribution of drug-hydrolyzing β-lactamase enzymes to this serious clinical problem. This review highlights recent advances in β-lactamase inhibitors and focuses on agents with novel mechanisms of action against a wide range of enzymes. To this end, we review the β-lactamase inhibitors currently in clinical trials, select agents still in preclinical development, and older therapeutic approaches that are being revisited. Particular emphasis is placed on the activity of compounds at the forefront of the developmental pipeline, including the diazabicyclooctane inhibitors (avibactam and MK-7655) and the boronate RPX7009. With its novel reversible mechanism, avibactam stands to be the first new β-lactamase inhibitor brought into clinical use in the past 2 decades. Our discussion includes the importance of selecting the appropriate partner β-lactam and dosing regimens for these promising agents. This "renaissance" of β-lactamase inhibitors offers new hope in a world plagued by multidrug-resistant (MDR) Gram-negative bacteria.
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Affiliation(s)
- Sarah M. Drawz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Krisztina M. Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
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32
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van Berkel SS, Brem J, Rydzik AM, Salimraj R, Cain R, Verma A, Owens RJ, Fishwick CWG, Spencer J, Schofield CJ. Assay platform for clinically relevant metallo-β-lactamases. J Med Chem 2013; 56:6945-53. [PMID: 23898798 PMCID: PMC3910272 DOI: 10.1021/jm400769b] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Metallo-β-lactamases
(MBLs) are a growing threat to the use
of almost all clinically used β-lactam antibiotics. The identification
of broad-spectrum MBL inhibitors is hampered by the lack of a suitable
screening platform, consisting of appropriate substrates and a set
of clinically relevant MBLs. We report procedures for the preparation
of a set of clinically relevant metallo-β-lactamases (i.e.,
NDM-1 (New Delhi MBL), IMP-1 (Imipenemase), SPM-1 (São Paulo
MBL), and VIM-2 (Verona integron-encoded MBL)) and the identification
of suitable fluorogenic substrates (umbelliferone-derived cephalosporins).
The fluorogenic substrates were compared to chromogenic substrates
(CENTA, nitrocefin, and imipenem), showing improved sensitivity and
kinetic parameters. The efficiency of the fluorogenic substrates was
exemplified by inhibitor screening, identifying 4-chloroisoquinolinols
as potential pan MBL inhibitors.
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Affiliation(s)
- Sander S van Berkel
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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33
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Biochemical characterization of IMP-30, a metallo-β-lactamase with enhanced activity toward ceftazidime. Antimicrob Agents Chemother 2013; 57:5122-6. [PMID: 23836186 DOI: 10.1128/aac.02341-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
IMP-type enzymes constitute a clinically important family of metallo-β-lactamases that has grown dramatically in the past decade to its current 45 known members. Here, we report the biochemical characterization of IMP-30 in comparison to IMP-1, from which it deviates by a single E59K mutation. Kinetics, MIC assays, docking, and molecular dynamics simulations support a scenario in which Lys59 interacts with the ceftazidime R1 group, resulting in increased water access and enhanced turnover and MIC of ceftazidime.
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34
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Tilvawala R, Pratt RF. Covalent Inhibition of Serine β-Lactamases by Novel Hydroxamic Acid Derivatives. Biochemistry 2013; 52:3712-20. [DOI: 10.1021/bi4003887] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ronak Tilvawala
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut
06459, United States
| | - R. F. Pratt
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut
06459, United States
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35
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Bushnell G, Mitrani-Gold F, Mundy LM. Emergence of New Delhi metallo-β-lactamase type 1-producing Enterobacteriaceae and non-Enterobacteriaceae: global case detection and bacterial surveillance. Int J Infect Dis 2013; 17:e325-33. [DOI: 10.1016/j.ijid.2012.11.025] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 11/08/2012] [Accepted: 11/10/2012] [Indexed: 01/01/2023] Open
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36
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van der Kamp MW, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 2013; 52:2708-28. [PMID: 23557014 DOI: 10.1021/bi400215w] [Citation(s) in RCA: 402] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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37
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Thomas PW, Spicer T, Cammarata M, Brodbelt JS, Hodder P, Fast W. An altered zinc-binding site confers resistance to a covalent inactivator of New Delhi metallo-beta-lactamase-1 (NDM-1) discovered by high-throughput screening. Bioorg Med Chem 2013; 21:3138-46. [PMID: 23591260 DOI: 10.1016/j.bmc.2013.03.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/11/2013] [Accepted: 03/16/2013] [Indexed: 10/27/2022]
Abstract
Due to the global threat of antibiotic resistance mediated by New Delhi metallo-beta-lactamase-1 (NDM-1) and the lack of structurally diverse inhibitors reported for this enzyme, we developed screening and counter-screening assays for manual and automated formats. The manual assay is a trans-well absorbance-based endpoint assay in 96-well plates and has a Z' factor of 0.8. The automated assay is an epi-absorbance endpoint assay in 384-well plates, has a Z' factor of ≥0.8, good signal/baseline ratios (>3.8), and is likely scalable for high-throughput screening (HTS). A TEM-1-based counter-screen is also presented to eliminate false positives due to assay interference or off-target activities. A pilot screen of a pharmacologically characterized compound library identified two thiol-modifying compounds as authentic NDM-1 inhibitors: p-chloromecuribenzoate (p-CMB) and nitroprusside. Recombinant NDM-1 has one Cys residue that serves as a conserved active-site primary zinc ligand and is selectively modified by p-CMB as confirmed by LC-MS/MS. However a C208D mutation results in an enzyme that maintains almost full lactamase activity, yet is completely resistant to the inhibitor. These results predict that covalent targeting of the conserved active-site Cys residue may have drawbacks as a drug design strategy.
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Affiliation(s)
- Pei W Thomas
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
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38
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Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the hydrolysis reaction. PLoS One 2013; 8:e55136. [PMID: 23372827 PMCID: PMC3556986 DOI: 10.1371/journal.pone.0055136] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 12/18/2012] [Indexed: 11/26/2022] Open
Abstract
Background A general mechanism has been proposed for metallo β-lactamases (MβLs), in which deprotonation of a water molecule near the Zn ion(s) results in the formation of a hydroxide ion that attacks the carbonyl oxygen of the β-lactam ring. However, because of the absence of X-ray structures that show the exact position of the antibiotic in the reactant state (RS) it has been difficult to obtain a definitive validation of this mechanism. Methodology/Principal Findings We have employed a strategy to identify the RS, which does not rely on substrate docking and/or molecular dynamics. Starting from the X-ray structure of the enzyme:product complex (the product state, PS), a QM/MM scan was used to drive the reaction uphill from product back to reactant. Since in this process also the enzyme changes from PS to RS, we actually generate the enzyme:substrate complex from product and avoid the uncertainties associated with models of the reactant state. We used this strategy to study the reaction of biapenem hydrolysis by B2 MβL CphA. QM/MM simulations were carried out under 14 different ionization states of the active site, in order to generate potential energy surfaces (PESs) corresponding to a variety of possible reaction paths. Conclusions/Significance The calculations support a model for biapenem hydrolysis by CphA, in which the nucleophile that attacks the β-lactam ring is not the water molecule located in proximity of the active site Zn, but a second water molecule, hydrogen bonded to the first one, which is used up in the reaction, and thus is not visible in the X-ray structure of the enzyme:product complex.
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39
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Monti S, Corozzi A, Fristrup P, Joshi KL, Shin YK, Oelschlaeger P, van Duin ACT, Barone V. Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field. Phys Chem Chem Phys 2013; 15:15062-77. [DOI: 10.1039/c3cp51931g] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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The sequence-activity relationship between metallo-β-lactamases IMP-1, IMP-6, and IMP-25 suggests an evolutionary adaptation to meropenem exposure. Antimicrob Agents Chemother 2012; 56:6403-6. [PMID: 23006757 DOI: 10.1128/aac.01440-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Metallo-β-lactamases are important determinants of antibacterial resistance. In this study, we investigate the sequence-activity relationship between the closely related enzymes IMP-1, IMP-6, and IMP-25. While IMP-1 is the more efficient enzyme across the overall spectrum of tested β-lactam antibacterial agents, IMP-6 and IMP-25 seem to have evolved to specifically inactivate the newer carbapenem meropenem. Molecular modeling indicates that the G235S mutation distinguishing IMP-25 from IMP-1 and IMP-6 may affect enzyme activity via Asn233.
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41
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Chakraborty S, Asgeirsson B, Minda R, Salaye L, Frère JM, Rao BJ. Inhibition of a cold-active alkaline phosphatase by imipenem revealed by in silico
modeling of metallo-β-lactamase active sites. FEBS Lett 2012; 586:3710-5. [PMID: 22982109 DOI: 10.1016/j.febslet.2012.08.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 08/24/2012] [Accepted: 08/24/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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42
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Systematic analysis of metallo-β-lactamases using an automated database. Antimicrob Agents Chemother 2012; 56:3481-91. [PMID: 22547615 DOI: 10.1128/aac.00255-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Metallo-β-lactamases (MBLs) are enzymes that hydrolyze β-lactam antibiotics, resulting in bacterial resistance to these drugs. These proteins have caused concerns due to their facile transference, broad substrate spectra, and the absence of clinically useful inhibitors. To facilitate the classification, nomenclature, and analysis of MBLs, an automated database system was developed, the Metallo-β-Lactamase Engineering Database (MBLED) (http://www.mbled.uni-stuttgart.de). It contains information on MBLs retrieved from the NCBI peptide database while strictly following the nomenclature by Jacoby and Bush (http://www.lahey.org/Studies/) and the generally accepted class B β-lactamase (BBL) standard numbering scheme for MBLs. The database comprises 597 MBL protein sequences and enables systematic analyses of these sequences. A systematic analysis employing the database resulted in the generation of mutation profiles of assigned IMP- and VIM-type MBLs, the identification of five MBL protein entries from the NCBI peptide database that were inconsistent with the Jacoby and Bush nomenclature, and the identification of 15 new IMP candidates and 9 new VIM candidates. Furthermore, the database was used to identify residues with high mutation frequencies and variability (mutation hot spots) that were unexpectedly distant from the active site located in the ββ sandwich: positions 208 and 266 in the IMP family and positions 215 and 258 in the VIM family. We expect that the MBLED will be a valuable tool for systematically cataloguing and analyzing the increasing number of MBLs being reported.
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43
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Bush K, Fisher JF. Epidemiological expansion, structural studies, and clinical challenges of new β-lactamases from gram-negative bacteria. Annu Rev Microbiol 2012; 65:455-78. [PMID: 21740228 DOI: 10.1146/annurev-micro-090110-102911] [Citation(s) in RCA: 297] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
β-Lactamase evolution presents to the infectious disease community a major challenge in the treatment of infections caused by multidrug-resistant gram-negative bacteria. Because over 1,000 of these naturally occurring β-lactamases exist, attempts to correlate structure and function have become daunting. Although new enzymes in the extended-spectrum β-lactamase (ESBL) families are frequently identified, the older CTX-M-14 and CTX-M-15 enzymes have become the most prevalent ESBLs in global surveillance. Carbapenemases with either serine-based or zinc-facilitated hydrolysis mechanisms are posing some of the most critical problems. Most geographical regions now report KPC serine carbapenemases and the metallo-β-lactamases VIM, IMP, and NDM-1, even though NDM-1 was only recently identified. The rapid emergence of these newer enzymes, with multiple β-lactamases appearing in a single organism, makes the design of new β-lactamase inactivators or β-lactamase-stable β-lactams all the more difficult. Combination therapy will likely be required to counteract the continuing evolution of these insidious enzymes in multidrug-resistant pathogens.
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Affiliation(s)
- Karen Bush
- Biology Department, Indiana University, Bloomington, Indiana 47401, USA.
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44
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45
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Qi Q, Shen Q, Lü L. Polyfluoroalkylation of 2-Aminothiazoles: Unexpected sp3 CCl Substitution under Mild Conditions. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180439] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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46
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Griffin DH, Richmond TK, Sanchez C, Moller AJ, Breece RM, Tierney DL, Bennett B, Crowder MW. Structural and kinetic studies on metallo-β-lactamase IMP-1. Biochemistry 2011; 50:9125-34. [PMID: 21928807 DOI: 10.1021/bi200839h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In an effort to probe for metal binding to metallo-β-lactamase (MβL) IMP-1, the enzyme was overexpressed, purified, and characterized. The resulting enzyme was shown to bind 2 equiv of Zn(II), exhibit significant catalytic activity, and yield EXAFS results similar to crystallographic data previously reported. Rapid kinetic studies showed that IMP-1 does not stabilize a nitrocefin-derived reaction intermediate; rather, the enzyme follows a simple Michaelis mechanism to hydrolyze nitrocefin. Metal-substituted and metal-reconstituted analogues of IMP-1 were prepared by directly adding metal ion stocks to metal-free enzyme, which was generated by dialysis versus EDTA. UV-vis studies on IMP-1 containing 1 equiv of Co(II) showed a strong ligand-to-metal charge transition at 340 nm, and the intensity of this feature increased when the second equivalent of Co(II) was added to the enzyme. EXAFS fits on IMP-1 containing 1 equiv of Co(II) strongly suggest the presence of a metal-metal interaction, and EPR spectra of the IMP-1 containing 1 and 2 equiv of Co(II) are very similar. Taken together, steady-state kinetic and spectroscopic studies suggest that metal binding to metal-free IMP-1 follows a positive-cooperative mode.
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Affiliation(s)
- Dionne H Griffin
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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47
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Rotschafer JC, Ullman MA, Sullivan CJ. Optimal use of fluoroquinolones in the intensive care unit setting. Crit Care Clin 2011; 27:95-106. [PMID: 21144988 DOI: 10.1016/j.ccc.2010.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Fluoroquinolones have become a staple antimicrobial in a variety of settings for a wide spectrum of infectious diseases. Although fluoroquinolones have been associated with a broad spectrum of adverse events, the side effect profile is generally acceptable. Their use in the intensive care unit as empiric therapy is becoming compromised due to the development of multiple drug resistant gram negative pathogens and collateral damage with C difficile & MRSA. Fluoroquinolones should be used along with another antibiotic of different chemical structure, mechanism of action, and pharmacodynamic profile to ensure adequate initial antimicrobial coverage and maximize the likelihood of a favorable clinical and microbiologic response.
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Affiliation(s)
- John C Rotschafer
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, WDH 7-189, 308 Harvard Street SE, Minneapolis, MN 55455, USA.
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48
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Papp-Wallace KM, Taracila M, Wallace CJ, Hujer KM, Bethel CR, Hornick JM, Bonomo RA. Elucidating the role of Trp105 in the KPC-2 β-lactamase. Protein Sci 2011; 19:1714-27. [PMID: 20662006 DOI: 10.1002/pro.454] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The molecular basis of resistance to β-lactams and β-lactam-β-lactamase inhibitor combinations in the KPC family of class A enzymes is of extreme importance to the future design of effective β-lactam therapy. Recent crystal structures of KPC-2 and other class A β-lactamases suggest that Ambler position Trp105 may be of importance in binding β-lactam compounds. Based on this notion, we explored the role of residue Trp105 in KPC-2 by conducting site-saturation mutagenesis at this position. Escherichia coli DH10B cells expressing the Trp105Phe, -Tyr, -Asn, and -His KPC-2 variants possessed minimal inhibitory concentrations (MICs) similar to E. coli cells expressing wild type (WT) KPC-2. Interestingly, most of the variants showed increased MICs to ampicillin-clavulanic acid but not to ampicillin-sulbactam or piperacillin-tazobactam. To explain the biochemical basis of this behavior, four variants (Trp105Phe, -Asn, -Leu, and -Val) were studied in detail. Consistent with the MIC data, the Trp105Phe β-lactamase displayed improved catalytic efficiencies, k(cat)/K(m), toward piperacillin, cephalothin, and nitrocefin, but slightly decreased k(cat)/K(m) toward cefotaxime and imipenem when compared to WT β-lactamase. The Trp105Asn variant exhibited increased K(m)s for all substrates. In contrast, the Trp105Leu and -Val substituted enzymes demonstrated notably decreased catalytic efficiencies (k(cat)/K(m)) for all substrates. With respect to clavulanic acid, the K(i)s and partition ratios were increased for the Trp105Phe, -Asn, and -Val variants. We conclude that interactions between Trp105 of KPC-2 and the β-lactam are essential for hydrolysis of substrates. Taken together, kinetic and molecular modeling studies define the role of Trp105 in β-lactam and β-lactamase inhibitor discrimination.
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49
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Abstract
The celestial rise in antibiotic resistance among Gram-negative bacteria has challenged both the scientific and pharmaceutical sectors. The hallmark of this general increase is the unbridled dissemination of carbapenem resistance genes, namely KPC, OXA and metallo-β-lactamase variants. In particular, the media attention given to the NDM-1 metallo-β-lactamase has highlighted the global consequences of human behaviour on spreading antibiotic resistance.
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50
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Wu S, Xu D, Guo H. QM/MM studies of monozinc β-lactamase CphA suggest that the crystal structure of an enzyme-intermediate complex represents a minor pathway. J Am Chem Soc 2010; 132:17986-8. [PMID: 21138257 DOI: 10.1021/ja104241g] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
QM/MM studies of the hydrolysis of a β-lactam antibiotic molecule (biapenem) catalyzed by a monozinc β-lactamase (CphA) have revealed the complete reaction mechanism and shown that an experimentally determined enzyme-intermediate complex is a stable intermediate or product in a minor pathway.
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Affiliation(s)
- Shanshan Wu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
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