1
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Au SX, Mohd Padzil A, Muhd Noor ND, Matsumura H, Raja Abdul Rahman RNZ, Normi YM. Probing the substrate binding modes and catalytic mechanisms of BLEG-1, a promiscuous B3 metallo-β-lactamase with glyoxalase II properties. PLoS One 2023; 18:e0291012. [PMID: 37672512 PMCID: PMC10482274 DOI: 10.1371/journal.pone.0291012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/19/2023] [Indexed: 09/08/2023] Open
Abstract
BLEG-1 from Bacillus lehensis G1 is an evolutionary divergent B3 metallo-β-lactamase (MBL) that exhibited both β-lactamase and glyoxalase II (GLXII) activities. Sequence, phylogeny, biochemical and structural relatedness of BLEG-1 to B3 MBL and GLXII suggested BLEG-1 might be an intermediate in the evolutionary path of B3 MBL from GLXII. The unique active site cavity of BLEG-1 that recognizes both β-lactam antibiotics and S-D-lactoylglutathione (SLG) had been postulated as the key factor for its dual activity. In this study, dynamic ensembles of BLEG-1 and its substrate complexes divulged conformational plasticity and binding modes of structurally distinct substrates to the enzyme, providing better insights into its structure-to-function relationship and enzymatic promiscuity. Our results highlight the flexible nature of the active site pocket of BLEG-1, which is governed by concerted loop motions involving loop7+α3+loop8 and loop12 around the catalytic core, thereby moulding the binding pocket and facilitate interactions of BLEG-1 with both ampicillin and SLG. The distribution of (i) predominantly hydrophobic amino acids in the N-terminal domain, and (ii) flexible amino acids with polar and/or charged side chains in both N- and C-termini provide additional advantages to BLEG-1 in confining the aromatic group of ampicillin, and polar groups of SLG, respectively. The importance of these residues for substrates binding was further confirmed by the reduction in MBL and GLXII activities upon alanine substitutions of Ile-10, Phe-57, Arg-94, Leu-95, and Arg-159. Based on molecular dynamics simulation, mutational, and biochemical data presented herein, the catalytic mechanisms of BLEG-1 toward the hydrolysis of β-lactams and SLG were proposed.
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Affiliation(s)
- Shaw Xian Au
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Azyyati Mohd Padzil
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hiroyoshi Matsumura
- College of Life Sciences, Ritsumeikan University, Noji-Higashi, Kusatsu, Japan
| | - Raja Noor Zaliha Raja Abdul Rahman
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M. Normi
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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2
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Kurz JL, Pedroso MM, Richard E, McGeary RP, Schenk G. Inhibitors for metallo-β-lactamases from the B1 and B3 subgroups provide an avenue to combat a major mechanism of antibiotic resistance. Bioorg Med Chem Lett 2023; 92:129387. [PMID: 37369333 DOI: 10.1016/j.bmcl.2023.129387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/12/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023]
Abstract
Metallo-β-lactamases (MBLs) are a group of Zn(II)-dependent enzymes that pose a major threat to global health. They are linked to an increasing number of multi-drug resistant bacterial pathogens, but no clinically useful inhibitor is yet available. Since β-lactam antibiotics, which are inactivated by MBLs, constitute ∼65% of all antibiotics used to treat infections, the search for clinically relevant MBL inhibitors is urgent. Here, derivatives of a 2-amino-1-benzyl-4,5-diphenyl-1H-pyrrole-3-carbonitrile (1a) were synthesised and their inhibitory effects assessed against prominent representatives of the MBL family. Several compounds are potent inhibitors of each MBL tested, making them promising candidates for the development of broad-spectrum drug leads. In particular, compound 5f is highly potent across the MBL family, with Ki values in the low µM range. Furthermore, this compound also appears to display synergy in combination with antibiotics such as penicillin G, cefuroxime or meropenem. This molecule thus represents a promising starting point to develop new drugs to inhibit a major mechanism of antibiotic resistance.
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Affiliation(s)
- Julia L Kurz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Emmanuelle Richard
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD 4072, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia; Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD 4072, Australia.
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3
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Krco S, Davis SJ, Joshi P, Wilson LA, Monteiro Pedroso M, Douw A, Schofield CJ, Hugenholtz P, Schenk G, Morris MT. Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup-emerging targets to combat antibiotic resistance. Front Chem 2023; 11:1196073. [PMID: 37408556 PMCID: PMC10318434 DOI: 10.3389/fchem.2023.1196073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
β-Lactams are the most widely employed antibiotics in clinical settings due to their broad efficacy and low toxicity. However, since their first use in the 1940s, resistance to β-lactams has proliferated to the point where multi-drug resistant organisms are now one of the greatest threats to global human health. Many bacteria use β-lactamases to inactivate this class of antibiotics via hydrolysis. Although nucleophilic serine-β-lactamases have long been clinically important, most broad-spectrum β-lactamases employ one or two metal ions (likely Zn2+) in catalysis. To date, potent and clinically useful inhibitors of these metallo-β-lactamases (MBLs) have not been available, exacerbating their negative impact on healthcare. MBLs are categorised into three subgroups: B1, B2, and B3 MBLs, depending on their sequence similarities, active site structures, interactions with metal ions, and substrate preferences. The majority of MBLs associated with the spread of antibiotic resistance belong to the B1 subgroup. Most characterized B3 MBLs have been discovered in environmental bacteria, but they are increasingly identified in clinical samples. B3-type MBLs display greater diversity in their active sites than other MBLs. Furthermore, at least one of the known B3-type MBLs is inhibited by the serine-β-lactamase inhibitor clavulanic acid, an observation that may promote the design of derivatives active against a broader range of MBLs. In this Mini Review, recent advances in structure-function relationships of B3-type MBLs will be discussed, with a view to inspiring inhibitor development to combat the growing spread of β-lactam resistance.
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Affiliation(s)
- Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Samuel J. Davis
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Pallav Joshi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Liam A. Wilson
- Chemistry Research Laboratory, Department of Chemistry, The Ineos Oxford Institute for Antimicrobial Research, Oxford University, Oxford, United Kingdom
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew Douw
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, The Ineos Oxford Institute for Antimicrobial Research, Oxford University, Oxford, United Kingdom
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Marc T. Morris
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
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4
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Jayasinghe-Arachchige VM, Serafim LF, Hu Q, Ozen C, Moorkkannur SN, Schenk G, Prabhakar R. Elucidating the Roles of Distinct Chemical Factors in the Hydrolytic Activities of Hetero- and Homonuclear Synthetic Analogues of Binuclear Metalloenzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
| | - Leonardo F. Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Qiaoyu Hu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Cihan Ozen
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Sreerag N. Moorkkannur
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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5
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Stroek R, Wilson L, Goracke W, Kang T, Vermue F, Krco S, Mendels Y, Douw A, Morris M, Knaven EG, Mitić N, Gutierrez MCR, Schenk EB, Clark A, Garcia D, Monteiro Pedroso M, Schenk G. LAM-1 from Lysobacter antibioticus: A potent zinc-dependent activity that inactivates β-lactam antibiotics. J Inorg Biochem 2021; 226:111637. [PMID: 34749064 DOI: 10.1016/j.jinorgbio.2021.111637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022]
Abstract
Resistance to β-lactam antibiotics, including the "last-resort" carbapenems, has emerged as a major threat to global health. A major resistance mechanism employed by pathogens involves the use of metallo-β-lactamases (MBLs), zinc-dependent enzymes that inactivate most of the β-lactam antibiotics used to treat infections. Variants of MBLs are frequently discovered in clinical environments. However, an increasing number of such enzymes have been identified in microorganisms that are less impacted by human activities. Here, an MBL from Lysobacter antibioticus, isolated from the rhizosphere, has been shown to be highly active toward numerous β-lactam antibiotics. Its activity is higher than that of some of the most effective MBLs linked to hospital-acquired antibiotic resistance and thus poses an interesting system to investigate evolutionary pressures that drive the emergence of such biocatalysts.
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Affiliation(s)
- Rozanne Stroek
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Liam Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - William Goracke
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Taeuk Kang
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Febe Vermue
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yonatan Mendels
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Andrew Douw
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Marc Morris
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Esmee G Knaven
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Nataša Mitić
- Department of Chemistry, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Maria C R Gutierrez
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Elaine B Schenk
- School of Mathematics and Physics, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Alice Clark
- Sustainable Minerals Institute, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - David Garcia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia; Sustainable Minerals Institute, The University of Queensland, St. Lucia, Queensland 4072, Australia.
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia; Sustainable Minerals Institute, The University of Queensland, St. Lucia, Queensland 4072, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia.
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6
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Kinetic and Structural Characterization of the First B3 Metallo-β-Lactamase with an Active Site Glutamic Acid. Antimicrob Agents Chemother 2021; 65:e0093621. [PMID: 34310207 DOI: 10.1128/aac.00936-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structural diversity in metallo-β-lactamases (MBLs), especially in the vicinity of the active site, has been a major hurdle in the development of clinically effective inhibitors. Representatives from three variants of the B3 MBL subclass, containing either the canonical HHH/DHH active site motif (present in the majority of MBLs in this subclass) or the QHH/DHH (B3-Q) or HRH/DQK (B3-RQK) variations were reported previously. Here, we describe the structure and kinetic properties of the first example (SIE-1) of a fourth variant containing the EHH/DHH active site motif (B3-E). SIE-1 was identified in the hexachlorocyclohexane-degrading bacterium Sphingobium indicum, and kinetic analyses demonstrate that although it is active against a wide range of antibiotics its efficiency is lower than that of other B3 MBLs, but with improved efficiency towards cephalosporins relative to other β-lactam substrates. The overall fold of SIE-1 is characteristic of the MBLs; the notable variation is observed in the Zn1 site due to the replacement of the canonical His116 by a glutamate. The unusual preference of SIE-1 for cephalosporins and its occurrence in a widespread environmental organism suggests scope for increased MBL-mediated β-lactam resistance. It is thus relevant to include SIE-1 into MBL inhibitor design studies to widen the therapeutic scope of much needed anti-resistance drugs.
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7
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Selleck C, Pedroso MM, Wilson L, Krco S, Knaven EG, Miraula M, Mitić N, Larrabee JA, Brück T, Clark A, Guddat LW, Schenk G. Structure and mechanism of potent bifunctional β-lactam- and homoserine lactone-degrading enzymes from marine microorganisms. Sci Rep 2020; 10:12882. [PMID: 32732933 PMCID: PMC7392888 DOI: 10.1038/s41598-020-68612-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/26/2020] [Indexed: 11/11/2022] Open
Abstract
Genes that confer antibiotic resistance can rapidly be disseminated from one microorganism to another by mobile genetic elements, thus transferring resistance to previously susceptible bacterial strains. The misuse of antibiotics in health care and agriculture has provided a powerful evolutionary pressure to accelerate the spread of resistance genes, including those encoding β-lactamases. These are enzymes that are highly efficient in inactivating most of the commonly used β-lactam antibiotics. However, genes that confer antibiotic resistance are not only associated with pathogenic microorganisms, but are also found in non-pathogenic (i.e. environmental) microorganisms. Two recent examples are metal-dependent β-lactamases (MBLs) from the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans. Previous studies have demonstrated that their β-lactamase activity is comparable to those of well-known MBLs from pathogenic sources (e.g. NDM-1, AIM-1) but that they also possess efficient lactonase activity, an activity associated with quorum sensing. Here, we probed the structure and mechanism of these two enzymes using crystallographic, spectroscopic and fast kinetics techniques. Despite highly conserved active sites both enzymes demonstrate significant variations in their reaction mechanisms, highlighting both the extraordinary ability of MBLs to adapt to changing environmental conditions and the rather promiscuous acceptance of diverse substrates by these enzymes.
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Affiliation(s)
- Christopher Selleck
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Liam Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Esmée Gianna Knaven
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Manfredi Miraula
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Department of Chemistry, Maynooth University, Maynooth, County Kildare, Ireland
| | - Nataša Mitić
- Department of Chemistry, Maynooth University, Maynooth, County Kildare, Ireland
| | - James A Larrabee
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748, Garching, Germany
| | - Alice Clark
- Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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8
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Raczynska JE, Imiolczyk B, Komorowska M, Sliwiak J, Czyrko-Horczak J, Brzezinski K, Jaskolski M. Flexible loops of New Delhi metallo-β-lactamase modulate its activity towards different substrates. Int J Biol Macromol 2020; 158:104-115. [PMID: 32353499 DOI: 10.1016/j.ijbiomac.2020.04.219] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/26/2022]
Abstract
Two accessory loop regions that are present in numerous variants of New Delhi metallo-β-lactamases (NDM) are important for the enzymatic activity. The first one is a flexible loop L3 that is located near the active site and is thought to play an important role in the catalytic process. The second region, Ω loop is located close to a structural element that coordinates two essential zinc ions. Both loops are not involved in any specific interactions with a substrate. Herein, we investigated how the length and hydrophobicity of loop L3 influence the enzymatic activity of NDMs, by analyzing mutants of NDM-1 with various deletions/point mutations within the L3 loop. We also investigated NDM variants with sequence variations/artificial deletions within the Ω loop. For all these variants we determined kinetic parameters for the hydrolysis of ampicillin, imipenem, and a chromogenic cephalosporin (CENTA). None of the mutations in the L3 loop completely abolished the enzymatic activity of NDM-1. Our results suggest that various elements of the loop play different roles in the hydrolysis of different substrates and the flexibility of the loop seems necessary to fulfill the requirements imposed by various substrates. Deletions within the Ω loop usually enhanced the enzymatic activity, particularly for the hydrolysis of ampicillin and imipenem. However, the exact role of the Ω loop in the catalytic reaction remains unclear. In our kinetic tests, the NDM enzymes were inhibited in the β-lactamase reaction by the CENTA substrate. We also present the X-ray crystal structures of the NDM-1, NDM-9 and NDM-12 proteins.
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Affiliation(s)
- Joanna E Raczynska
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Imiolczyk
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marlena Komorowska
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Justyna Czyrko-Horczak
- Laboratory of Biochemistry and Structural Biology, Faculty of Chemistry, University of Bialystok, Poland
| | - Krzysztof Brzezinski
- Laboratory of Biochemistry and Structural Biology, Faculty of Chemistry, University of Bialystok, Poland.
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
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9
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Djenadi K, Zhang L, Murray AK, Gaze WH. Carbapenem resistance in bacteria isolated from soil and water environments in Algeria. J Glob Antimicrob Resist 2018; 15:262-267. [DOI: 10.1016/j.jgar.2018.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/25/2022] Open
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10
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Biochemical and genetic characterization of a novel metallo-β-lactamase from marine bacterium Erythrobacter litoralis HTCC 2594. Sci Rep 2018; 8:803. [PMID: 29339760 PMCID: PMC5770381 DOI: 10.1038/s41598-018-19279-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/12/2017] [Indexed: 11/09/2022] Open
Abstract
Metallo-β-lactamases (MBLs) are a group of enzymes that can inactivate most commonly used β-lactam-based antibiotics. Among MBLs, New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an urgent threat to public health as evidenced by its success in rapidly disseminating worldwide since its first discovery. Here we report the biochemical and genetic characteristics of a novel MBL, ElBla2, from the marine bacterium Erythrobacter litoralis HTCC 2594. This enzyme has a higher amino acid sequence similarity to NDM-1 (56%) than any previously reported MBL. Enzymatic assays and secondary structure alignment also confirmed the high similarity between these two enzymes. Whole genome comparison of four Erythrobacter species showed that genes located upstream and downstream of elbla2 were highly conserved, which may indicate that elbla2 was lost during evolution. Furthermore, we predicted two prophages, 13 genomic islands and 25 open reading frames related to insertion sequences in the genome of E. litoralis HTCC 2594. However, unlike NDM-1, the chromosome encoded ElBla2 did not locate in or near these mobile genetic elements, indicating that it cannot transfer between strains. Finally, following our phylogenetic analysis, we suggest a reclassification of E. litoralis HTCC 2594 as a novel species: Erythrobacter sp. HTCC 2594.
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11
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Hou CFD, Liu JW, Collyer C, Mitić N, Pedroso MM, Schenk G, Ollis DL. Insights into an evolutionary strategy leading to antibiotic resistance. Sci Rep 2017; 7:40357. [PMID: 28074907 PMCID: PMC5225480 DOI: 10.1038/srep40357] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/05/2016] [Indexed: 12/13/2022] Open
Abstract
Metallo-β-lactamases (MBLs) with activity towards a broad-spectrum of β-lactam antibiotics have become a major threat to public health, not least due to their ability to rapidly adapt their substrate preference. In this study, the capability of the MBL AIM-1 to evade antibiotic pressure by introducing specific mutations was probed by two alternative methods, i.e. site-saturation mutagenesis (SSM) of active site residues and in vitro evolution. Both approaches demonstrated that a single mutation in AIM-1 can greatly enhance a pathogen's resistance towards broad spectrum antibiotics without significantly compromising the catalytic efficiency of the enzyme. Importantly, the evolution experiments demonstrated that relevant amino acids are not necessarily in close proximity to the catalytic centre of the enzyme. This observation is a powerful demonstration that MBLs have a diverse array of possibilities to adapt to new selection pressures, avenues that cannot easily be predicted from a crystal structure alone.
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Affiliation(s)
- Chun-Feng D Hou
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia
| | - Jian-Wei Liu
- CSIRO Entomology, Black Mountain, ACT 2601, Australia
| | - Charles Collyer
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia
| | - Nataša Mitić
- Department of Chemistry, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David L Ollis
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia
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12
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Pedroso MM, Selleck C, Enculescu C, Harmer JR, Mitić N, Craig WR, Helweh W, Hugenholtz P, Tyson GW, Tierney DL, Larrabee JA, Schenk G. Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community. Metallomics 2017; 9:1157-1168. [DOI: 10.1039/c7mt00195a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microorganisms in the permafrost contain a potent mechanism to inactivate antibiotics.
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13
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Selleck C, Larrabee JA, Harmer J, Guddat LW, Mitić N, Helweh W, Ollis DL, Craig WR, Tierney DL, Monteiro Pedroso M, Schenk G. AIM-1: An Antibiotic-Degrading Metallohydrolase That Displays Mechanistic Flexibility. Chemistry 2016; 22:17704-17714. [DOI: 10.1002/chem.201602762] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher Selleck
- School of Chemistry and Molecular Biosciences; The University of Queensland; St. Lucia Queensland 4072 Australia
| | - James A. Larrabee
- Department of Chemistry and Biochemistry; Middlebury College; Middlebury Vermont 05753 USA
| | - Jeffrey Harmer
- Centre for Advanced Imaging; The University of Queensland; St. Lucia Queensland 4072 Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences; The University of Queensland; St. Lucia Queensland 4072 Australia
| | - Nataša Mitić
- Department of Chemistry; Maynooth University; Maynooth, Co. Kildare Ireland
| | - Waleed Helweh
- Department of Chemistry and Biochemistry; Middlebury College; Middlebury Vermont 05753 USA
| | - David L. Ollis
- Research School of Chemistry; Australian National University of Canberra; ACT 0200 Australia
| | - Whitney R. Craig
- Department of Chemistry and Biochemistry; Miami University, Oxford; Ohio 45056 USA
| | - David L. Tierney
- Department of Chemistry and Biochemistry; Miami University, Oxford; Ohio 45056 USA
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences; The University of Queensland; St. Lucia Queensland 4072 Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences; The University of Queensland; St. Lucia Queensland 4072 Australia
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14
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Promiscuous metallo-β-lactamases: MIM-1 and MIM-2 may play an essential role in quorum sensing networks. J Inorg Biochem 2016; 162:366-375. [DOI: 10.1016/j.jinorgbio.2015.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/04/2015] [Accepted: 12/16/2015] [Indexed: 11/21/2022]
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