1
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Gannon HG, Riaz-Bradley A, Cann MJ. A Non-Functional Carbon Dioxide-Mediated Post-Translational Modification on Nucleoside Diphosphate Kinase of Arabidopsis thaliana. Int J Mol Sci 2024; 25:898. [PMID: 38255974 PMCID: PMC10815852 DOI: 10.3390/ijms25020898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
The carbamate post-translational modification (PTM), formed by the nucleophilic attack of carbon dioxide by a dissociated lysine epsilon-amino group, is proposed as a widespread mechanism for sensing this biologically important bioactive gas. Here, we demonstrate the discovery and in vitro characterization of a carbamate PTM on K9 of Arabidopsis nucleoside diphosphate kinase (AtNDK1). We demonstrate that altered side chain reactivity at K9 is deleterious for AtNDK1 structure and catalytic function, but that CO2 does not impact catalysis. We show that nucleotide substrate removes CO2 from AtNDK1, and the carbamate PTM is functionless within the detection limits of our experiments. The AtNDK1 K9 PTM is the first demonstration of a functionless carbamate. In light of this finding, we speculate that non-functionality is a possible feature of the many newly identified carbamate PTMs.
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Affiliation(s)
- Harry G. Gannon
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (H.G.G.)
| | - Amber Riaz-Bradley
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (H.G.G.)
| | - Martin J. Cann
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK; (H.G.G.)
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
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2
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Zhou Q, Catalán P, Bell H, Baumann P, Cooke R, Evans R, Yang J, Zhang Z, Zappalà D, Zhang Y, Blackburn GM, He Y, Jin Y. An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity. ACS CENTRAL SCIENCE 2023; 9:2339-2349. [PMID: 38161376 PMCID: PMC10755735 DOI: 10.1021/acscentsci.3c00609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 01/03/2024]
Abstract
Antibiotic-resistant Enterobacterales that produce oxacillinase (OXA)-48-like Class D β-lactamases are often linked to increased clinical mortality. Though the catalytic mechanism of OXA-48 is known, the molecular origin of its biphasic kinetics has been elusive. We here identify selective chloride binding rather than decarbamylation of the carbamylated lysine as the source of biphasic kinetics, utilizing isothermal titration calorimetry (ITC) to monitor the complete reaction course with the OXA-48 variant having a chemically stable N-acetyl lysine. Further structural investigation enables us to capture an unprecedented inactive acyl intermediate wedged in place by a halide ion paired with a conserved active site arginine. Supported by mutagenesis and mathematical simulation, we identify chloride as a "Janus effector" that operates by allosteric activation of the burst phase and by inhibition of the steady state in kinetic assays of β-lactams. We show that chloride-induced biphasic kinetics directly affects antibiotic efficacy and facilitates the differentiation of clinical isolates encoding Class D from Class A and B carbapenemases. As chloride is present in laboratory and clinical procedures, our discovery greatly expands the roles of chloride in modulating enzyme catalysis and highlights its potential impact on the pharmacokinetics and efficacy of antibiotics during in vivo treatment.
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Affiliation(s)
- Qi Zhou
- Key
Laboratory of Synthetic and Natural Functional Molecule, College of
Chemistry and Materials Science, Northwest
University, Xi’an 710127, P. R. China
| | - Pablo Catalán
- Grupo
Interdisciplinar de Sistemas Complejos, Departamento de Matemáticas, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - Helen Bell
- School
of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Patrick Baumann
- School
of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rebekah Cooke
- School
of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Rhodri Evans
- School
of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jianhua Yang
- Key
Laboratory of Synthetic and Natural Functional Molecule, College of
Chemistry and Materials Science, Northwest
University, Xi’an 710127, P. R. China
| | - Zhen Zhang
- Key
Laboratory of Synthetic and Natural Functional Molecule, College of
Chemistry and Materials Science, Northwest
University, Xi’an 710127, P. R. China
- School
of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Davide Zappalà
- School
of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
| | - Ye Zhang
- Key
Laboratory of Synthetic and Natural Functional Molecule, College of
Chemistry and Materials Science, Northwest
University, Xi’an 710127, P. R. China
| | - George Michael Blackburn
- School
of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Yuan He
- Key
Laboratory of Synthetic and Natural Functional Molecule, College of
Chemistry and Materials Science, Northwest
University, Xi’an 710127, P. R. China
| | - Yi Jin
- School
of Chemistry, Cardiff University, Cardiff, CF10 3AT, United Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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3
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Abstract
Background Identifying CO2-binding proteins is vital for our knowledge of CO2-regulated molecular processes. The carbamate post-translational modification is a reversible CO2-mediated adduct that can form on neutral N-terminal α-amino or lysine ε-amino groups. Methods We have developed triethyloxonium ion (TEO) as a chemical proteomics tool to trap the carbamate post-translational modification on protein covalently. We use 13C-NMR and TEO and identify ubiquitin as a plant CO2-binding protein. Results We observe the carbamate post-translational modification on the Arabidopsis thaliana ubiquitin ε-amino groups of lysines 6, 33, and 48. We show that biologically relevant near atmospheric PCO2 levels increase ubiquitin conjugation dependent on lysine 6. We further demonstrate that CO2 increases the ubiquitin E2 ligase (AtUBC5) charging step via the transthioesterification reaction in which Ub is transferred from the E1 ligase active site to the E2 active site. Conclusions and general significance Therefore, plant ubiquitin is a CO2-binding protein, and the carbamate post-translational modification represents a potential mechanism through which plant cells can respond to fluctuating PCO2.
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Affiliation(s)
- Harry G Gannon
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Martin J Cann
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
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4
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Affiliation(s)
- Vaishali Thakkur
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Chandan Kumar Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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5
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King DT, Zhu S, Hardie DB, Serrano-Negrón JE, Madden Z, Kolappan S, Vocadlo DJ. Chemoproteomic identification of CO 2-dependent lysine carboxylation in proteins. Nat Chem Biol 2022; 18:782-791. [PMID: 35710617 DOI: 10.1038/s41589-022-01043-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 04/15/2022] [Indexed: 01/09/2023]
Abstract
Carbon dioxide is an omnipresent gas that drives adaptive responses within organisms from all domains of life. The molecular mechanisms by which proteins serve as sensors of CO2 are, accordingly, of great interest. Because CO2 is electrophilic, one way it can modulate protein biochemistry is by carboxylation of the amine group of lysine residues. However, the resulting CO2-carboxylated lysines spontaneously decompose, giving off CO2, which makes studying this modification difficult. Here we describe a method to stably mimic CO2-carboxylated lysine residues in proteins. We leverage this method to develop a quantitative approach to identify CO2-carboxylated lysines of proteins and explore the lysine 'carboxylome' of the CO2-responsive cyanobacterium Synechocystis sp. We uncover one CO2-carboxylated lysine within the effector binding pocket of the metabolic signaling protein PII. CO2-carboxylatation of this lysine markedly lowers the affinity of PII for its regulatory effector ligand ATP, illuminating a negative molecular control mechanism mediated by CO2.
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Affiliation(s)
- Dustin T King
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sha Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Darryl B Hardie
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Jesús E Serrano-Negrón
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Zarina Madden
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Subramania Kolappan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - David J Vocadlo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. .,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
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6
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Avci FG, Tastekil I, Jaisi A, Ozbek Sarica P, Sariyar Akbulut B. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens. Pathog Glob Health 2022; 117:219-234. [PMID: 35758005 PMCID: PMC10081068 DOI: 10.1080/20477724.2022.2088496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Turkey
| | - Ilgaz Tastekil
- Bioengineering Department, Marmara University, Kadikoy, 34722, Turkey
| | - Amit Jaisi
- Drug and Cosmetics Excellence Center, School of Pharmacy, Walailak University, 80160, Nakhon Si Thammarat, Thailand
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7
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Fröhlich C, Chen JZ, Gholipour S, Erdogan AN, Tokuriki N. Evolution of β-lactamases and enzyme promiscuity. Protein Eng Des Sel 2021; 34:6294778. [PMID: 34100551 DOI: 10.1093/protein/gzab013] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 11/14/2022] Open
Abstract
β-Lactamases represent one of the most prevalent resistance mechanisms against β-lactam antibiotics. Beyond their clinical importance, they have also become key models in enzymology and evolutionary biochemistry. A global understanding of their evolution and sequence and functional diversity can therefore aid a wide set of different disciplines. Interestingly, β-lactamases have evolved multiple times from distinct evolutionary origins, with ancestries that reach back billions of years. It is therefore no surprise that these enzymes exhibit diverse structural features and enzymatic mechanisms. In this review, we provide a bird's eye view on the evolution of β-lactamases within the two enzyme superfamilies-i.e. the penicillin-binding protein-like and metallo-β-lactamase superfamily-through phylogenetics. We further discuss potential evolutionary origins of each β-lactamase class by highlighting signs of evolutionary connections in protein functions between β-lactamases and other enzymes, especially cases of enzyme promiscuity.
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Affiliation(s)
- Christopher Fröhlich
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - John Z Chen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Sevan Gholipour
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ayse N Erdogan
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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8
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Structural Investigations of the Inhibition of Escherichia coli AmpC β-Lactamase by Diazabicyclooctanes. Antimicrob Agents Chemother 2021; 65:AAC.02073-20. [PMID: 33199391 PMCID: PMC7849013 DOI: 10.1128/aac.02073-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/12/2020] [Indexed: 12/24/2022] Open
Abstract
β-Lactam antibiotics are presently the most important treatments for infections by pathogenic Escherichia coli, but their use is increasingly compromised by β-lactamases, including the chromosomally encoded class C AmpC serine-β-lactamases (SBLs). The diazabicyclooctane (DBO) avibactam is a potent AmpC inhibitor; the clinical success of avibactam combined with ceftazidime has stimulated efforts to optimize the DBO core. We report kinetic and structural studies, including four high-resolution crystal structures, concerning inhibition of the AmpC serine-β-lactamase from E. coli (AmpC EC ) by clinically relevant DBO-based inhibitors: avibactam, relebactam, nacubactam, and zidebactam. Kinetic analyses and mass spectrometry-based assays were used to study their mechanisms of AmpC EC inhibition. The results reveal that, under our assay conditions, zidebactam manifests increased potency (apparent inhibition constant [K iapp], 0.69 μM) against AmpC EC compared to that of the other DBOs (K iapp = 5.0 to 7.4 μM) due to an ∼10-fold accelerated carbamoylation rate. However, zidebactam also has an accelerated off-rate, and with sufficient preincubation time, all the DBOs manifest similar potencies. Crystallographic analyses indicate a greater conformational freedom of the AmpC EC -zidebactam carbamoyl complex compared to those for the other DBOs. The results suggest the carbamoyl complex lifetime should be a consideration in development of DBO-based SBL inhibitors for the clinically important class C SBLs.
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9
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Shapiro AB, Gao N. Interactions of the Diazabicyclooctane Serine β-Lactamase Inhibitor ETX1317 with Target Enzymes. ACS Infect Dis 2021; 7:114-122. [PMID: 33300345 PMCID: PMC7837508 DOI: 10.1021/acsinfecdis.0c00656] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
ETX0282
is an orally bioavailable prodrug of the diazabicyclooctane
serine β-lactamase inhibitor ETX1317. The combination of ETX0282
with cefpodoxime proxetil is in clinical trials as an oral therapy
for complicated urinary tract infections caused by Enterobacterales. Earlier diazabicyclooctane β-lactamase inhibitors, such as
avibactam and durlobactam, contain a sulfate moiety as the essential
anionic group and are administered intravenously. In contrast, ETX1317
contains a fluoroacetate moiety, which is esterified with an isopropyl
group in ETX0282 to provide high oral bioavailability. Previous studies
of avibactam and durlobactam showed that covalent inhibition of certain
β-lactamases is reversible due to the ability of the ring-opened
inhibitors to recyclize and dissociate in their original form. We
investigated the interaction of ETX1317 with several β-lactamases
commonly found in relevant bacterial pathogens, including CTX-M-15,
KPC-2, SHV-5, and TEM-1 from Ambler Class A; Pseudomonas aeruginosa AmpC and Enterobacter cloacae P99 from Class C,
and OXA-48 from Class D. The second-order rate constants for inhibition
(kinact/Ki) of these enzymes show that ETX1317 is intermediate in potency between
durlobactam and avibactam. The partition ratios were all approximately
1, indicating that the inhibitor is not also a substrate of these
enzymes. The rate constants for dissociation of the covalent complex
(koff) were similar to those for durlobactam
and avibactam. Acylation exchange experiments demonstrated that ETX1317
dissociated in its original form. No loss of mass from the inhibitor
was observed in the covalent inhibitor-enzyme complexes.
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Affiliation(s)
- Adam B. Shapiro
- Entasis Therapeutics, Waltham, Massachusetts 02451, United States
| | - Ning Gao
- AstraZeneca R&D Boston, Waltham, Massachusetts 02451, United States
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10
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Aertker KMJ, Chan HTH, Lohans CT, Schofield CJ. Analysis of β-lactone formation by clinically observed carbapenemases informs on a novel antibiotic resistance mechanism. J Biol Chem 2020; 295:16604-16613. [PMID: 32963107 PMCID: PMC7864059 DOI: 10.1074/jbc.ra120.014607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/07/2020] [Indexed: 01/18/2023] Open
Abstract
An important mechanism of resistance to β-lactam antibiotics is via their β-lactamase-catalyzed hydrolysis. Recent work has shown that, in addition to the established hydrolysis products, the reaction of the class D nucleophilic serine β-lactamases (SBLs) with carbapenems also produces β-lactones. We report studies on the factors determining β-lactone formation by class D SBLs. We show that variations in hydrophobic residues at the active site of class D SBLs (i.e. Trp105, Val120, and Leu158, using OXA-48 numbering) impact on the relative levels of β-lactones and hydrolysis products formed. Some variants, i.e. the OXA-48 V120L and OXA-23 V128L variants, catalyze increased β-lactone formation compared with the WT enzymes. The results of kinetic and product studies reveal that variations of residues other than those directly involved in catalysis, including those arising from clinically observed mutations, can alter the reaction outcome of class D SBL catalysis. NMR studies show that some class D SBL variants catalyze formation of β-lactones from all clinically relevant carbapenems regardless of the presence or absence of a 1β-methyl substituent. Analysis of reported crystal structures for carbapenem-derived acyl-enzyme complexes reveals preferred conformations for hydrolysis and β-lactone formation. The observation of increased β-lactone formation by class D SBL variants, including the clinically observed carbapenemase OXA-48 V120L, supports the proposal that class D SBL-catalyzed rearrangement of β-lactams to β-lactones is important as a resistance mechanism.
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Affiliation(s)
| | - H T Henry Chan
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Christopher T Lohans
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom; Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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11
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Leiros HKS, Thomassen AM, Samuelsen Ø, Flach CF, Kotsakis SD, Larsson DGJ. Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10. FEBS Open Bio 2020; 10:1821-1832. [PMID: 32683794 PMCID: PMC7459404 DOI: 10.1002/2211-5463.12935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/17/2020] [Accepted: 07/15/2020] [Indexed: 11/17/2022] Open
Abstract
Carbapenemases are the main cause of carbapenem resistance in Gram‐negative bacteria. How β‐lactamases with weak carbapenemase activity, such as the OXA‐10‐type class D β‐lactamases, contribute to anti‐bacterial drug resistance is unclear. OXA‐655 is a T26M and V117L OXA‐10 variant, recently identified from hospital wastewater. Despite exhibiting stronger carbapenemase activity towards ertapenem (ETP) and meropenem (MEM) in Escherichia coli, OXA‐655 exhibits reduced activity towards oxyimino‐substituted β‐lactams like ceftazidime. Here, we have solved crystal structures of OXA‐10 in complex with imipenem (IPM) and ETP, and OXA‐655 in complex with MEM in order to unravel the structure–function relationship and the impact of residue 117 in enzyme catalysis. The new crystal structures show that L117 is situated at a critical position with enhanced Van der Waals interactions to L155 in the omega loop. This restricts the movements of L155 and could explain the reduced ability for OXA‐655 to bind a bulky oxyimino group. The V117L replacement in OXA‐655 makes the active site S67 and the carboxylated K70 more water exposed. This could affect the supply of new deacylation water molecules required for hydrolysis and possibly the carboxylation rate of K70. But most importantly, L117 leaves more space for binding of the hydroxyethyl group in carbapenems. In summary, the crystal structures highlight the importance of residue 117 in OXA‐10 variants for carbapenemase activity. This study also illustrates the impact of a single amino acid substitution on the substrate profile of OXA‐10 and the evolutionary potential of new OXA‐10 variants.
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Affiliation(s)
- Hanna-Kirsti S Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ane Molden Thomassen
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.,Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Stathis D Kotsakis
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
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12
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Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam. Proc Natl Acad Sci U S A 2020; 117:5818-5825. [PMID: 32123084 DOI: 10.1073/pnas.1922203117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Gram-negative bacteria expressing class A β-lactamases pose a serious health threat due to their ability to inactivate all β-lactam antibiotics. The acyl-enzyme intermediate is a central milestone in the hydrolysis reaction catalyzed by these enzymes. However, the protonation states of the catalytic residues in this complex have never been fully analyzed experimentally due to inherent difficulties. To help unravel the ambiguity surrounding class A β-lactamase catalysis, we have used ultrahigh-resolution X-ray crystallography and the recently approved β-lactamase inhibitor avibactam to trap the acyl-enzyme complex of class A β-lactamase CTX-M-14 at varying pHs. A 0.83-Å-resolution CTX-M-14 complex structure at pH 7.9 revealed a neutral state for both Lys73 and Glu166. Furthermore, the avibactam hydroxylamine-O-sulfonate group conformation varied according to pH, and this conformational switch appeared to correspond to a change in the Lys73 protonation state at low pH. In conjunction with computational analyses, our structures suggest that Lys73 has a perturbed acid dissociation constant (pKa) compared with acyl-enzyme complexes with β-lactams, hindering its function to deprotonate Glu166 and the initiation of the deacylation reaction. Further NMR analysis demonstrated Lys73 pKa to be ∼5.2 to 5.6. Together with previous ultrahigh-resolution crystal structures, these findings enable us to follow the proton transfer process of the entire acylation reaction and reveal the critical role of Lys73. They also shed light on the stability and reversibility of the avibactam carbamoyl acyl-enzyme complex, highlighting the effect of substrate functional groups in influencing the protonation states of catalytic residues and subsequently the progression of the reaction.
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13
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Tselepis L, Langley GW, Aboklaish AF, Widlake E, Jackson DE, Walsh TR, Schofield CJ, Brem J, Tyrrell JM. In vitro efficacy of imipenem-relebactam and cefepime-AAI101 against a global collection of ESBL-positive and carbapenemase-producing Enterobacteriaceae. Int J Antimicrob Agents 2020; 56:105925. [PMID: 32084512 DOI: 10.1016/j.ijantimicag.2020.105925] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 01/03/2020] [Accepted: 02/11/2020] [Indexed: 01/04/2023]
Abstract
OBJECTIVES To evaluate the potential clinical in vitro efficacy of novel β-lactam/β-lactamase-inhibitor combinations - including imipenem-relebactam (IPM-REL) and cefepime-AAI101 (enmetazobactam) (FEP-AAI) - against contemporary multidrug-resistant (MDR) Enterobacteriaceae. METHODS Agar-based MIC screening against MDR Enterobacteriaceae (n = 264) was used to evaluate the in vitro efficacy of IPM-REL and FEP-AAI, to compare the results with established combinations, and to investigate alternative β-lactam partners for relebactam (REL) and enmetazobactam (AAI). The inhibition activities of REL, AAI and the comparators avibactam (AVI) and tazobactam, against isolated recombinant β-lactamases covering representatives from all four Ambler classes of β-lactamases, were tested using a fluorescence-based assay. RESULTS Using recombinant proteins, all four inhibitors were highly active against the tested class A serine β-lactamases (SBLs). REL and AVI showed moderate activity against the Class C AmpC from Pseudomonas aeruginosa and the Class D OXA-10/-48 SBLs, but outperformed tazobactam and AAI. All tested inhibitors lacked activity against Class B metallo-β-lactamases (MBLs). In the presence of REL and IPM, but not AAI, susceptibility increased against Klebsiella pnuemoniae carbapenemase (KPC)-positive and OXA-48-positive isolates. Both aztreonam-AVI and ceftolozane-tazobactam were more effective than IPM-REL. In all the tested combinations, AAI was a more effective inhibitor of class A β-lactamases (ESBLs) than the established inhibitors. CONCLUSION The results lead to the proposal of alternative combination therapies involving REL and AAI to potentiate the use of β-lactams against clinical Gram-negative isolates expressing a variety of lactamases. They highlight the potential of novel combinations for combating strains not covered by existing therapies.
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Affiliation(s)
- Lucas Tselepis
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Gareth W Langley
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom; Charles River Laboratories, Chesterford Research Park, Saffron Walden, United Kingdom
| | - Ali F Aboklaish
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Emma Widlake
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Dana E Jackson
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom
| | - Chris J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom.
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff, United Kingdom; School of Cellular & Molecular Medicine, Biomedical Sciences Building, University Walk, Bristol, United Kingdom.
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14
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 453] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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15
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van Groesen E, Lohans CT, Brem J, Aertker KMJ, Claridge TDW, Schofield CJ. 19 F NMR Monitoring of Reversible Protein Post-Translational Modifications: Class D β-Lactamase Carbamylation and Inhibition. Chemistry 2019; 25:11837-11841. [PMID: 31310409 PMCID: PMC6771976 DOI: 10.1002/chem.201902529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/11/2019] [Indexed: 11/05/2022]
Abstract
Bacterial production of β‐lactamases with carbapenemase activity is a global health threat. The active sites of class D carbapenemases such as OXA‐48, which is of major clinical importance, uniquely contain a carbamylated lysine residue which is essential for catalysis. Although there is significant interest in characterizing this post‐translational modification, and it is a promising inhibition target, protein carbamylation is challenging to monitor in solution. We report the use of 19F NMR spectroscopy to monitor the carbamylation state of 19F‐labelled OXA‐48. This method was used to investigate the interactions of OXA‐48 with clinically used serine β‐lactamase inhibitors, including avibactam and vaborbactam. Crystallographic studies on 19F‐labelled OXA‐48 provide a structural rationale for the sensitivity of the 19F label to active site interactions. The overall results demonstrate the use of 19F NMR to monitor reversible covalent post‐translational modifications.
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Affiliation(s)
- Emma van Groesen
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Christopher T Lohans
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.,Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
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16
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Langley GW, Cain R, Tyrrell JM, Hinchliffe P, Calvopiña K, Tooke CL, Widlake E, Dowson CG, Spencer J, Walsh TR, Schofield CJ, Brem J. Profiling interactions of vaborbactam with metallo-β-lactamases. Bioorg Med Chem Lett 2019; 29:1981-1984. [PMID: 31171422 PMCID: PMC6593178 DOI: 10.1016/j.bmcl.2019.05.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 11/20/2022]
Abstract
β-Lactams are the most successful antibacterials, yet their use is threatened by resistance, importantly as caused by β-lactamases. β-Lactamases fall into two mechanistic groups: the serine β-lactamases that utilise a covalent acyl-enzyme mechanism and the metallo β-lactamases that utilise a zinc-bound water nucleophile. Achieving simultaneous inhibition of both β-lactamase classes remains a challenge in the field. Vaborbactam is a boronate-based inhibitor that reacts with serine-β-lactamases to form covalent complexes that mimic tetrahedral intermediates in catalysis. Vaborbactam has recently been approved for clinical use in combination with the carbapenem meropenem. Here we show that vaborbactam moderately inhibits metallo-β-lactamases from all 3 subclasses (B1, B2 and B3), with a potency of around 20-100 fold below that by which it inhibits its current clinical targets, the Class A serine β-lactamases. This result contrasts with recent investigations of bicyclic boronate inhibitors, which potently inhibit subclass B1 MBLs but which presently lack activity against B2 and B3 enzymes. These findings indicate that cyclic boronate scaffolds have the potential to inhibit the full range of β-lactamases and justify further work on the development of boronates as broad-spectrum β-lactamase inhibitors.
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Affiliation(s)
- Gareth W Langley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom; Current address: Charles River Laboratories, Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom
| | - Ricky Cain
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Karina Calvopiña
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Catherine L Tooke
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Emma Widlake
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Christopher G Dowson
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease, Institute of Infection & Immunity, UHW Main Building, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
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17
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van den Akker F, Bonomo RA. Exploring Additional Dimensions of Complexity in Inhibitor Design for Serine β-Lactamases: Mechanistic and Intra- and Inter-molecular Chemistry Approaches. Front Microbiol 2018; 9:622. [PMID: 29675000 PMCID: PMC5895744 DOI: 10.3389/fmicb.2018.00622] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/19/2018] [Indexed: 01/14/2023] Open
Abstract
As a bacterial resistance strategy, serine β-lactamases have evolved from cell wall synthesizing enzymes known as penicillin-binding proteins (PBP), by not only covalently binding β-lactam antibiotics but, also acquiring mechanisms of deacylating these antibiotics. This critical deacylation step leads to release of hydrolyzed and inactivated β-lactams, thereby providing resistance for the bacteria against these antibiotics targeting the cell wall. To combat β-lactamase-mediated antibiotic resistance, numerous β-lactamase inhibitors were developed that utilize various strategies to inactivate the β-lactamase. Most of these compounds are “mechanism-based” inhibitors that in some manner mimic the β-lactam substrate, having a carbonyl moiety and a negatively charged carboxyl or sulfate group. These compounds form a covalent adduct with the catalytic serine via an initial acylation step. To increase the life-time of the inhibitory covalent adduct intermediates, a remarkable array of different strategies was employed to improve inhibition potency. Such approaches include post-acylation intra- and intermolecular chemical rearrangements as well as affecting the deacylation water. These approaches transform the inhibitor design process from a 3-dimensional problem (i.e., XYZ coordinates) to one with additional dimensions of complexity as the reaction coordinate and time spent at each chemical state need to be taken into consideration. This review highlights the mechanistic intricacies of the design efforts of the β-lactamase inhibitors which so far have resulted in the development of “two generations” and 5 clinically available inhibitors.
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Affiliation(s)
- Focco van den Akker
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Robert A Bonomo
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States.,Medicine, Pharmacology, Molecular Biology and Microbiology, Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, United States.,Medical Service and Geriatric Research, Education, and Clinical Centers (GRECC), Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States.,Case Western Reserve University-VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, United States
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18
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Akhter S, Lund BA, Ismael A, Langer M, Isaksson J, Christopeit T, Leiros HKS, Bayer A. A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design. Eur J Med Chem 2017; 145:634-648. [PMID: 29348071 DOI: 10.1016/j.ejmech.2017.12.085] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/24/2017] [Accepted: 12/26/2017] [Indexed: 01/05/2023]
Abstract
β-Lactam antibiotics are of utmost importance when treating bacterial infections in the medical community. However, currently their utility is threatened by the emergence and spread of β-lactam resistance. The most prevalent resistance mechanism to β-lactam antibiotics is expression of β-lactamase enzymes. One way to overcome resistance caused by β-lactamases, is the development of β-lactamase inhibitors and today several β-lactamase inhibitors e.g. avibactam, are approved in the clinic. Our focus is the oxacillinase-48 (OXA-48), an enzyme reported to spread rapidly across the world and commonly identified in Escherichia coli and Klebsiella pneumoniae. To guide inhibitor design, we used diversely substituted 3-aryl and 3-heteroaryl benzoic acids to probe the active site of OXA-48 for useful enzyme-inhibitor interactions. In the presented study, a focused fragment library containing 49 3-substituted benzoic acid derivatives were synthesised and biochemically characterized. Based on crystallographic data from 33 fragment-enzyme complexes, the fragments could be classified into R1 or R2 binders by their overall binding conformation in relation to the binding of the R1 and R2 side groups of imipenem. Moreover, binding interactions attractive for future inhibitor design were found and their usefulness explored by the rational design and evaluation of merged inhibitors from orthogonally binding fragments. The best inhibitors among the resulting 3,5-disubstituted benzoic acids showed inhibitory potential in the low micromolar range (IC50 = 2.9 μM). For these inhibitors, the complex X-ray structures revealed non-covalent binding to Arg250, Arg214 and Tyr211 in the active site and the interactions observed with the mono-substituted fragments were also identified in the merged structures.
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Affiliation(s)
- Sundus Akhter
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Bjarte Aarmo Lund
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Aya Ismael
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Manuel Langer
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Tony Christopeit
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Hanna-Kirsti S Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Annette Bayer
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway.
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