1
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Hsu TW, Fang JM. Advances and prospects of analytic methods for bacterial transglycosylation and inhibitor discovery. Analyst 2024; 149:2204-2222. [PMID: 38517346 DOI: 10.1039/d3an01968c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
The cell wall is essential for bacteria to maintain structural rigidity and withstand external osmotic pressure. In bacteria, the cell wall is composed of peptidoglycan. Lipid II is the basic unit for constructing highly cross-linked peptidoglycan scaffolds. Transglycosylase (TGase) is the initiating enzyme in peptidoglycan synthesis that catalyzes the ligation of lipid II moieties into repeating GlcNAc-MurNAc polysaccharides, followed by transpeptidation to generate cross-linked structures. In addition to the transglycosylases in the class-A penicillin-binding proteins (aPBPs), SEDS (shape, elongation, division and sporulation) proteins are also present in most bacteria and play vital roles in cell wall renewal, elongation, and division. In this review, we focus on the latest analytical methods including the use of radioactive labeling, gel electrophoresis, mass spectrometry, fluorescence labeling, probing undecaprenyl pyrophosphate, fluorescence anisotropy, ligand-binding-induced tryptophan fluorescence quenching, and surface plasmon resonance to evaluate TGase activity in cell wall formation. This review also covers the discovery of TGase inhibitors as potential antibacterial agents. We hope that this review will give readers a better understanding of the chemistry and basic research for the development of novel antibiotics.
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Affiliation(s)
- Tse-Wei Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
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2
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Mitchell SL, Kearns DB, Carlson EE. Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock. Appl Environ Microbiol 2024; 90:e0054823. [PMID: 38126750 PMCID: PMC10807460 DOI: 10.1128/aem.00548-23] [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: 04/03/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape maintenance, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Apparently-redundant proteins can be important for enabling an organism to cope with environmental stressors. In this study, we evaluated the consequence of environmental pH on PBP enzymatic activity in Bacillus subtilis. Our data show that a subset of PBPs in B. subtilis change activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are favored for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed in Streptococcus pneumoniae, implying that it may be generalizable across additional bacterial species and further emphasizing the evolutionary benefit of maintaining many, seemingly-redundant periplasmic enzymes.IMPORTANCEMicrobes adapt to ever-changing environments and thrive over a vast range of conditions. While bacterial genomes are relatively small, significant portions encode for "redundant" functions. Apparent redundancy is especially pervasive in bacterial proteins that reside outside of the inner membrane. While conditions within the cytoplasm are carefully controlled, those of the periplasmic space are largely determined by the cell's exterior environment. As a result, proteins within this environmentally exposed region must be capable of functioning under a vast array of conditions, and/or there must be several similar proteins that have evolved to function under a variety of conditions. This study examines the activity of a class of enzymes that is essential in cell wall construction to determine if individual proteins might be adapted for activity under particular growth conditions. Our results indicate that a subset of these proteins are preferred for growth under alkaline conditions, while others are readily dispensable.
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Affiliation(s)
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
- Departments of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, United States
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3
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Nygaard R, Graham CLB, Belcher Dufrisne M, Colburn JD, Pepe J, Hydorn MA, Corradi S, Brown CM, Ashraf KU, Vickery ON, Briggs NS, Deering JJ, Kloss B, Botta B, Clarke OB, Columbus L, Dworkin J, Stansfeld PJ, Roper DI, Mancia F. Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex. Nat Commun 2023; 14:5151. [PMID: 37620344 PMCID: PMC10449877 DOI: 10.1038/s41467-023-40483-8] [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: 11/11/2022] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Peptidoglycan (PG) is an essential structural component of the bacterial cell wall that is synthetized during cell division and elongation. PG forms an extracellular polymer crucial for cellular viability, the synthesis of which is the target of many antibiotics. PG assembly requires a glycosyltransferase (GT) to generate a glycan polymer using a Lipid II substrate, which is then crosslinked to the existing PG via a transpeptidase (TP) reaction. A Shape, Elongation, Division and Sporulation (SEDS) GT enzyme and a Class B Penicillin Binding Protein (PBP) form the core of the multi-protein complex required for PG assembly. Here we used single particle cryo-electron microscopy to determine the structure of a cell elongation-specific E. coli RodA-PBP2 complex. We combine this information with biochemical, genetic, spectroscopic, and computational analyses to identify the Lipid II binding sites and propose a mechanism for Lipid II polymerization. Our data suggest a hypothesis for the movement of the glycan strand from the Lipid II polymerization site of RodA towards the TP site of PBP2, functionally linking these two central enzymatic activities required for cell wall peptidoglycan biosynthesis.
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Affiliation(s)
- Rie Nygaard
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Chris L B Graham
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Meagan Belcher Dufrisne
- Department of Chemistry and Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22904, USA
| | - Jonathan D Colburn
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Joseph Pepe
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Molly A Hydorn
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Silvia Corradi
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome, Italy
| | - Chelsea M Brown
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Khuram U Ashraf
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Owen N Vickery
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Nicholas S Briggs
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - John J Deering
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027, USA
| | - Bruno Botta
- Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome, Italy
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Linda Columbus
- Department of Chemistry and Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22904, USA.
| | - Jonathan Dworkin
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Phillip J Stansfeld
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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4
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Park Y, Taguchi A, Baidin V, Kahne D, Walker S. A Time-Resolved FRET Assay Identifies a Small Molecule that Inhibits the Essential Bacterial Cell Wall Polymerase FtsW. Angew Chem Int Ed Engl 2023; 62:e202301522. [PMID: 37099323 PMCID: PMC10330507 DOI: 10.1002/anie.202301522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/10/2023] [Accepted: 04/26/2023] [Indexed: 04/27/2023]
Abstract
The peptidoglycan cell wall is essential for bacterial survival. To form the cell wall, peptidoglycan glycosyltransferases (PGTs) polymerize Lipid II to make glycan strands and then those strands are crosslinked by transpeptidases (TPs). Recently, the SEDS (for shape, elongation, division, and sporulation) proteins were identified as a new class of PGTs. The SEDS protein FtsW, which produces septal peptidoglycan during cell division, is an attractive target for novel antibiotics because it is essential in virtually all bacteria. Here, we developed a time-resolved Förster resonance energy transfer (TR-FRET) assay to monitor PGT activity and screened a Staphylococcus aureus lethal compound library for FtsW inhibitors. We identified a compound that inhibits S. aureus FtsW in vitro. Using a non-polymerizable Lipid II derivative, we showed that this compound competes with Lipid II for binding to FtsW. The assays described here will be useful for discovering and characterizing other PGT inhibitors.
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Affiliation(s)
- Youngseon Park
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Atsushi Taguchi
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
- (Current location) SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Vadim Baidin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
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5
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Mitchell SL, Kearns DB, Carlson EE. Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533529. [PMID: 36993441 PMCID: PMC10055284 DOI: 10.1101/2023.03.20.533529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Seemingly redundant proteins can be important for enabling an organism to cope with environmental stressors. We sought to evaluate the consequence of environmental pH on PBP enzymatic activity in Bacillus subtilis. Our data show that a subset of B. subtilis PBPs change activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are preferred for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed in Streptococcus pneumoniae, implying that it may be generalizable across additional bacterial species and further emphasizing the evolutionary benefit of maintaining many, seemingly redundant periplasmic enzymes.
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Affiliation(s)
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Departments of Medicinal Chemistry, Biochemistry, Molecular Biology and Biophysics, and Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
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6
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Kwan JMC, Qiao Y. Mechanistic Insights into the Activities of Major Families of Enzymes in Bacterial Peptidoglycan Assembly and Breakdown. Chembiochem 2023; 24:e202200693. [PMID: 36715567 DOI: 10.1002/cbic.202200693] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 01/31/2023]
Abstract
Serving as an exoskeletal scaffold, peptidoglycan is a polymeric macromolecule that is essential and conserved across all bacteria, yet is absent in mammalian cells; this has made bacterial peptidoglycan a well-established excellent antibiotic target. In addition, soluble peptidoglycan fragments derived from bacteria are increasingly recognised as key signalling molecules in mediating diverse intra- and inter-species communication in nature, including in gut microbiota-host crosstalk. Each bacterial species encodes multiple redundant enzymes for key enzymatic activities involved in peptidoglycan assembly and breakdown. In this review, we discuss recent findings on the biochemical activities of major peptidoglycan enzymes, including peptidoglycan glycosyltransferases (PGT) and transpeptidases (TPs) in the final stage of peptidoglycan assembly, as well as peptidoglycan glycosidases, lytic transglycosylase (LTs), amidases, endopeptidases (EPs) and carboxypeptidases (CPs) in peptidoglycan turnover and metabolism. Biochemical characterisation of these enzymes provides valuable insights into their substrate specificity, regulation mechanisms and potential modes of inhibition.
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Affiliation(s)
- Jeric Mun Chung Kwan
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), 21 Nanyang Link, Singapore, 637371, Singapore.,LKC School of Medicine, Nanyang Technological University (NTU) Singapore, 11 Mandalay Road, Singapore, Singapore, 208232, Singapore
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology (CCEB), Nanyang Technological University (NTU), Singapore, 21 Nanyang Link, Singapore, 637371, Singapore
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7
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Vacariu CM, Tanner ME. Recent Advances in the Synthesis and Biological Applications of Peptidoglycan Fragments. Chemistry 2022; 28:e202200788. [PMID: 35560956 DOI: 10.1002/chem.202200788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Indexed: 11/09/2022]
Abstract
The biosynthesis, breakdown, and modification of peptidoglycan (PG) play vital roles in both bacterial viability and in the response of human physiology to bacterial infection. Studies on PG biochemistry are hampered by the fact that PG is an inhomogeneous insoluble macromolecule. Chemical synthesis is therefore an important means to obtain PG fragments that may serve as enzyme substrates and elicitors of the human immune response. This review outlines the recent advances in the synthesis and biochemical studies of PG fragments, PG biosynthetic intermediates (such as Park's nucleotides and PG lipids), and PG breakdown products (such as muramyl dipeptides and anhydro-muramic acid-containing fragments). A rich variety of synthetic approaches has been applied to preparing such compounds since carbohydrate, peptide, and phospholipid chemical methodologies must all be applied.
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Affiliation(s)
- Condurache M Vacariu
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
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8
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Xu Y, Hernández-Rocamora VM, Lorent JH, Cox R, Wang X, Bao X, Stel M, Vos G, van den Bos RM, Pieters RJ, Gray J, Vollmer W, Breukink E. Metabolic labeling of the bacterial peptidoglycan by functionalized glucosamine. iScience 2022; 25:104753. [PMID: 35942089 PMCID: PMC9356107 DOI: 10.1016/j.isci.2022.104753] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/09/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
N-Acetylglucosamine (GlcNAc) is an essential monosaccharide required in almost all organisms. Fluorescent labeling of the peptidoglycan (PG) on N-acetylglucosamine has been poorly explored. Here, we report on the labeling of the PG with a bioorthogonal handle on the GlcNAc. We developed a facile one-step synthesis of uridine diphosphate N-azidoacetylglucosamine (UDP-GlcNAz) using the glycosyltransferase OleD, followed by in vitro incorporation of GlcNAz into the peptidoglycan precursor Lipid II and fluorescent labeling of the azido group via click chemistry. In a PG synthesis assay, fluorescent GlcNAz-labeled Lipid II was incorporated into peptidoglycan by the DD-transpeptidase activity of bifunctional class A penicillin-binding proteins. We further demonstrate the incorporation of GlcNAz into the PG layer of OleD-expressed bacteria by feeding with 2-chloro-4-nitrophenyl GlcNAz (GlcNAz-CNP). Hence, our labeling method using the heterologous expression of OleD is useful to study PG synthesis and possibly other biological processes involving GlcNAc metabolism in vivo. Peptidoglycan consists of N-acetylglucosamine, N-acetylmuramic acid, and amino acids We developed a one-step synthesis of azide-labeled UDP-N-acetylglucosamine In vivo generated azide-labeled UDP-N-acetylglucosamine gets incorporated into peptidoglycan Bacteria were fluorescently labeled on N-acetylglucosamine of peptidoglycan
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Affiliation(s)
- Yang Xu
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | | | - Joseph H. Lorent
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Ruud Cox
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Xue Bao
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Marjon Stel
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 Utrecht, the Netherlands
| | - Gaël Vos
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 Utrecht, the Netherlands
| | - Ramon M. van den Bos
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Roland J. Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 Utrecht, the Netherlands
| | - Joe Gray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
- Corresponding author
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9
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Hsu TW, Fang JM. Effective assay of bacterial transglycosylation by molecular turn-on sensing and a second-order scattering effect. Analyst 2021; 146:5843-5847. [PMID: 34570849 DOI: 10.1039/d1an00941a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Instead of using the lipid II substrate that requires prior labelling with a radioactive isotope or fluorophore to probe the formation of peptidoglycan in bacterial transglycosylation, the released undecaprenyl pyrophosphate (UPP) product is quantitatively measured either using a terpyridine-zinc fluorescence turn-on sensor or simply by the second-order scattering effect of the in situ formed UPP-calcium complex. Both the assay methods are utilized to identify moenomycin A as a potent transglycosylase inhibitor with a consistent IC50 value.
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Affiliation(s)
- Tse-Wei Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan. .,The Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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10
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Wang Y, Liang Z, Zheng Y, Leung ASL, Yan SC, So PK, Leung YC, Wong WL, Wong KY. Rational structural modification of the isatin scaffold to develop new and potent antimicrobial agents targeting bacterial peptidoglycan glycosyltransferase. RSC Adv 2021; 11:18122-18130. [PMID: 35480164 PMCID: PMC9033243 DOI: 10.1039/d1ra02119b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
A series of isatin derivatives bearing three different substituent groups at the N-1, C-3 and C-5 positions of the isatin scaffold were systematically designed and synthesized to study the structure-activity relationship of their inhibition of bacterial peptidoglycan glycosyltransferase (PGT) activity and antimicrobial susceptibility against S. aureus, E. coli and methicillin-resistant Staphylococcus aureus (MRSA (BAA41)) strains. The substituents at these sites are pointing towards three different directions from the isatin scaffold to interact with the amino acid residues in the binding pocket of PGT. Comparative studies of their structure-activity relationship allow us to gain better understanding of the direction of the substituents that contribute critical interactions leading to inhibition activity against the bacterial enzyme. Our results indicate that the modification of these sites is able to maximize the antimicrobial potency and inhibitory action against the bacterial enzyme. Two compounds show good antimicrobial potency (MIC = 3 μg mL-1 against S. aureus and MRSA; 12-24 μg mL-1 against E. coli). Results of the inhibition study against the bacterial enzyme (E. coli PBP 1b) reveal that some compounds are able to achieve excellent in vitro inhibitions of bacterial enzymatic activity (up to 100%). The best half maximal inhibitory concentration (IC50) observed among the new compounds is 8.9 μM.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Zhiguang Liang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Yuanyuan Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Alan Siu-Lun Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Siu-Cheong Yan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Pui-Kin So
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Yun-Chung Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hunghom Kowloon Hong Kong P. R. China
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11
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Hernández-Rocamora VM, Baranova N, Peters K, Breukink E, Loose M, Vollmer W. Real-time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin-binding proteins. eLife 2021; 10:61525. [PMID: 33625355 PMCID: PMC7943195 DOI: 10.7554/elife.61525] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.
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Affiliation(s)
- Víctor M Hernández-Rocamora
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Natalia Baranova
- Institute for Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Utrecht, Netherlands
| | - Martin Loose
- Institute for Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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12
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Lipoteichoic acid polymer length is determined by competition between free starter units. Proc Natl Acad Sci U S A 2020; 117:29669-29676. [PMID: 33172991 DOI: 10.1073/pnas.2008929117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Carbohydrate polymers exhibit incredible chemical and structural diversity, yet are produced by polymerases without a template to guide length and composition. As the length of carbohydrate polymers is critical for their biological functions, understanding the mechanisms that determine polymer length is an important area of investigation. Most Gram-positive bacteria produce anionic glycopolymers called lipoteichoic acids (LTA) that are synthesized by lipoteichoic acid synthase (LtaS) on a diglucosyl-diacylglycerol (Glc2DAG) starter unit embedded in the extracellular leaflet of the cell membrane. LtaS can use phosphatidylglycerol (PG) as an alternative starter unit, but PG-anchored LTA polymers are significantly longer, and cells that make these abnormally long polymers exhibit major defects in cell growth and division. To determine how LTA polymer length is controlled, we reconstituted Staphylococcus aureus LtaS in vitro. We show that polymer length is an intrinsic property of LtaS that is directly regulated by the identity and concentration of lipid starter units. Polymerization is processive, and the overall reaction rate is substantially faster for the preferred Glc2DAG starter unit, yet the use of Glc2DAG leads to shorter polymers. We propose a simple mechanism to explain this surprising result: free starter units terminate polymerization by displacing the lipid anchor of the growing polymer from its binding site on the enzyme. Because LtaS is conserved across most Gram-positive bacteria and is important for survival, this reconstituted system should be useful for characterizing inhibitors of this key cell envelope enzyme.
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13
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Hsu TW, Hsu HC, Chan HY, Fang JM. A Terpyridine Zinc Complex for Selective Detection of Lipid Pyrophosphates: A Model System for Monitoring Bacterial O- and N-Transglycosylations. J Org Chem 2020; 85:12747-12753. [PMID: 32885656 DOI: 10.1021/acs.joc.0c01252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To develop an effective method for probing O- and N-glycosyltransfer reactions that are accompanied by the release of undecaprenyl pyrophosphate, solanesyl pyrophosphate (SPP) is used as a surrogate to bind a terpyridine zinc complex (Tpy-Zn), forming a fluorescent [Tpy-Zn]-SPP complex (Kass 106,000 M-1 in EtOH-CHCl3) with 5.8 μM LOD in HEPES buffer (10 mM, pH 7.4) containing 10 mM CaCl2 and 0.08% decyl PEG, which is similar to the bioassay conditions for lipid II polymerization.
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Affiliation(s)
- Tse-Wei Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hsin-Chuan Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hsin-Yu Chan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.,The Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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14
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Goossens K, Neves RP, Fernandes PA, De Winter H. A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes. J Chem Inf Model 2020; 60:5513-5528. [PMID: 32786224 DOI: 10.1021/acs.jcim.0c00377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacterial glycosyltransferases of the GT51 family are key enzymes in bacterial cell wall synthesis. Inhibiting cell wall synthesis is a very effective approach for development of antibiotics, as this can lead to either bacteriostatic or bactericidal effects. Even though the existence of this family has been known for over 50 years, only one potent inhibitor exists, which is an analog of the lipid IV product and derived from a natural product. Drug development focused on bacterial transglycosylase has been hampered due to little being know about its structure and reaction mechanism. In this study, Staphylococcus aureus monoglycosyltransferase was investigated at an atomistic level using computational methods. Classical molecular dynamics simulations were used to reveal information about the large-scale dynamics of the enzyme-substrate complex and the importance of magnesium in structure and function of the protein, while mixed mode quantum mechanics/molecular mechanics calculations unveiled a novel hypothesis for the reaction mechanism. From these results, we present a new model for the binding mode of lipid II and the reaction mechanism of the GT51 glycosyltransferases. A metal-bound hydroxide catalyzed reaction mechanism yields an estimated free energy barrier of 16.1 ± 1.0 kcal/mol, which is in line with experimental values. The importance of divalent cations is also further discussed. These findings could significantly aid targeted drug design, particularly the efficient development of transition state analogues as potential inhibitors for the GT51 glycosyltransferases.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Rui Pp Neves
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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15
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Boes A, Brunel JM, Derouaux A, Kerff F, Bouhss A, Touze T, Breukink E, Terrak M. Squalamine and Aminosterol Mimics Inhibit the Peptidoglycan Glycosyltransferase Activity of PBP1b. Antibiotics (Basel) 2020; 9:antibiotics9070373. [PMID: 32630634 PMCID: PMC7400108 DOI: 10.3390/antibiotics9070373] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Peptidoglycan (PG) is an essential polymer of the bacterial cell wall and a major antibacterial target. Its synthesis requires glycosyltransferase (GTase) and transpeptidase enzymes that, respectively, catalyze glycan chain elongation and their cross-linking to form the protective sacculus of the bacterial cell. The GTase domain of bifunctional penicillin-binding proteins (PBPs) of class A, such as Escherichia coli PBP1b, belong to the GTase 51 family. These enzymes play an essential role in PG synthesis, and their specific inhibition by moenomycin was shown to lead to bacterial cell death. In this work, we report that the aminosterol squalamine and mimic compounds present an unexpected mode of action consisting in the inhibition of the GTase activity of the model enzyme PBP1b. In addition, selected compounds were able to specifically displace the lipid II from the active site in a fluorescence anisotropy assay, suggesting that they act as competitive inhibitors.
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Affiliation(s)
- Adrien Boes
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
| | - Jean Michel Brunel
- UMR_MD1, U-1261, Aix Marseille Univ, INSERM, SSA, MCT, 13385 Marseille, France;
| | - Adeline Derouaux
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
| | - Frédéric Kerff
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
| | - Ahmed Bouhss
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (A.B.); (T.T.)
- Laboratoire Structure-Activite des Biomolecules Normales et Pathologiques (SABNP), Univ Evry, INSERM U1204, Universite Paris-Saclay, 91025 Evry, France
| | - Thierry Touze
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (A.B.); (T.T.)
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Mohammed Terrak
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
- Correspondence: ; Tel.: +33-4366-3332
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16
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Wang Y, Cheong WL, Liang Z, So LY, Chan KF, So PK, Chen YW, Wong WL, Wong KY. Hydrophobic substituents on isatin derivatives enhance their inhibition against bacterial peptidoglycan glycosyltransferase activity. Bioorg Chem 2020; 97:103710. [DOI: 10.1016/j.bioorg.2020.103710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
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17
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Abstract
Extracellular polysaccharides and glycoproteins of pathogenic bacteria assist in adherence, autoaggregation, biofilm formation, and host immune system evasion. As a result, considerable research in the field of glycobiology is dedicated to study the composition and function of glycans associated with virulence, as well as the enzymes involved in their biosynthesis with the aim to identify novel antibiotic targets. Especially, insights into the enzyme mechanism, substrate binding, and transition-state structures are valuable as a starting point for rational inhibitor design. An intriguing aspect of enzymes that generate or process polysaccharides and glycoproteins is the level of processivity. The existence of enzymatic processivity reflects the need for regulation of the final glycan/glycoprotein length and structure, depending on the role they perform. In this Review, we describe the currently reported examples of various processive enzymes involved in polymerization and transfer of sugar moieties, predominantly in bacterial pathogens, with a focus on the biochemical methods, to showcase the importance of studying processivity for understanding the mechanism.
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Affiliation(s)
- Liubov Yakovlieva
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Marthe T. C. Walvoort
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
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18
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Welsh MA, Schaefer K, Taguchi A, Kahne D, Walker S. Direction of Chain Growth and Substrate Preferences of Shape, Elongation, Division, and Sporulation-Family Peptidoglycan Glycosyltransferases. J Am Chem Soc 2019; 141:12994-12997. [PMID: 31386359 PMCID: PMC6738341 DOI: 10.1021/jacs.9b06358] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The bacterial cell wall is composed of peptidoglycan, and its biosynthesis is an established target for antibiotics. Peptidoglycan is assembled from a glycopeptide precursor, Lipid II, that is polymerized by peptidoglycan glycosyltransferases into glycan strands that are subsequently cross-linked to form the mature cell wall. For decades bacteria were thought to contain only one family of enzymes that polymerize Lipid II, but recently, the ubiquitous Shape, Elongation, Division, and Sporulation (SEDS)-family proteins RodA and FtsW were shown to be peptidoglycan polymerases. Because RodA and FtsW are essential in nearly all bacteria, these enzymes are promising targets for new antibiotics. However, almost nothing is known about the mechanisms of these polymerases. Here, we report that SEDS proteins synthesize peptidoglycan by adding new Lipid II monomers to the reducing end of the growing glycan chain. Using substrates that can only react at the reducing end, we also show that the glycosyl donor and acceptor in the polymerization reaction have distinct lipid requirements. These findings provide the first fundamental insights into the mechanism of SEDS-family polymerases and lay the groundwork for future biochemical and structural studies.
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Affiliation(s)
- Michael A. Welsh
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Kaitlin Schaefer
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Atsushi Taguchi
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
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19
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Song HW, Yoo G, Bong JH, Kang MJ, Lee SS, Pyun JC. Surface display of sialyltransferase on the outer membrane of Escherichia coli and ClearColi. Enzyme Microb Technol 2019; 128:1-8. [PMID: 31186105 DOI: 10.1016/j.enzmictec.2019.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 01/03/2023]
Abstract
α2,3-Sialyltransferase from Pasteurella multocida (PmST1) is an enzyme that transfers a sialyl group of donor substrates to an acceptor substrate called N-acetyl-d-lactosamine (LacNAc). In this study PmST1 was expressed on the outer membrane of wildtype Escherichia coli (BL21) with lipopolysaccharide (LPS) and ClearColi with no LPS, and then the enzyme activity and expression level of PmST1 were compared. As the first step, the expression levels of PmST1 on the outer membranes of wildtype E. coli (BL21) and ClearColi were compared according to the IPTG induction time, and the absolute amount of surface-displayed PmST1 was calculated using densitometry of SDS-PAGE. As the next step, the influence of LPS on the PmST1 activity was estimated by analyzing Michaelis-Menten plot. The enzyme activity of PmST1 was analyzed by measuring the concentration of CMP, which was a by-product after the transfer of the sialyl group of donor compounds to the acceptor compounds. From a Michaelis-Menten plot, the enzyme activity of the surface-displayed PmST1 and the maximum rate (Vmax) of ClearColi were higher than those of wildtype E. coli (BL21). However, the KM value, which represented the concentration of substrate to reach half the maximum rate (Vmax), was similar for both enzymes. These results represented such a difference in enzyme activity was occurred from the interference of LPS on the mass transport of the donor and acceptor to PmST1 for the sialyl group transfer.
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Affiliation(s)
- Hyun-Woo Song
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seo-dae-mun-gu, Seoul, 03722, Republic of Korea
| | - Gu Yoo
- School of Chemistry & Institute for Life Sciences, FNES, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Ji-Hong Bong
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seo-dae-mun-gu, Seoul, 03722, Republic of Korea
| | - Min-Jung Kang
- Korea Institute of Science and Technology (KIST), Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Seung Seo Lee
- School of Chemistry & Institute for Life Sciences, FNES, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seo-dae-mun-gu, Seoul, 03722, Republic of Korea.
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20
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Regulation of the Peptidoglycan Polymerase Activity of PBP1b by Antagonist Actions of the Core Divisome Proteins FtsBLQ and FtsN. mBio 2019; 10:mBio.01912-18. [PMID: 30622193 PMCID: PMC6325244 DOI: 10.1128/mbio.01912-18] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Peptidoglycan (PG) is an essential constituent of the bacterial cell wall. During cell division, PG synthesis localizes at midcell under the control of a multiprotein complex, the divisome, allowing the safe formation of two new cell poles and separation of daughter cells. Genetic studies in Escherichia coli pointed out that FtsBLQ and FtsN participate in the regulation of septal PG (sPG) synthesis; however, the underlying molecular mechanisms remained largely unknown. Here we show that FtsBLQ subcomplex directly interacts with the PG synthase PBP1b and with the subcomplex FtsW-PBP3, mainly via FtsW. Strikingly, we discovered that FtsBLQ inhibits the glycosyltransferase activity of PBP1b and that this inhibition was antagonized by the PBP1b activators FtsN and LpoB. The same results were obtained in the presence of FtsW-PBP3. Moreover, using a simple thioester substrate (S2d), we showed that FtsBLQ also inhibits the transpeptidase domain of PBP3 but not of PBP1b. As the glycosyltransferase and transpeptidase activities of PBP1b are coupled and PBP3 activity requires nascent PG substrate, the results suggest that PBP1b inhibition by FtsBLQ will block sPG synthesis by these enzymes, thus maintaining cell division as repressed until the maturation of the divisome is signaled by the accumulation of FtsN, which triggers sPG synthesis and the initiation of cell constriction. These results confirm that PBP1b plays an important role in E. coli cell division and shed light on the specific role of FtsN, which seems to counterbalance the inhibitory effect of FtsBLQ to restore PBP1b activity.IMPORTANCE Bacterial cell division is governed by a multiprotein complex called divisome, which facilitates a precise cell wall synthesis at midcell and daughter cell separation. Protein-protein interactions and activity studies using different combinations of the septum synthesis core of the divisome revealed that the glycosyltransferase activity of PBP1b is repressed by FtsBLQ and that the presence of FtsN or LpoB suppresses this inhibition. Moreover, FtsBLQ also inhibits the PBP3 activity on a thioester substrate. These results provide enzymatic evidence of the regulation of the peptidoglycan synthase PBP1b and PBP3 within the divisome. The results confirm that PBP1b plays an important role in E. coli cell division and shed light on the specific role of FtsN, which functions to relieve the repression on PBP1b by FtsBLQ and to initiate septal peptidoglycan synthesis.
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21
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Punekar AS, Samsudin F, Lloyd AJ, Dowson CG, Scott DJ, Khalid S, Roper DI. The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization. Cell Surf 2018; 2:54-66. [PMID: 30046666 PMCID: PMC6053601 DOI: 10.1016/j.tcsw.2018.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/27/2022] Open
Abstract
Bacterial peptidoglycan glycosyltransferases (PGT) catalyse the essential polymerization of lipid II into linear glycan chains required for peptidoglycan biosynthesis. The PGT domain is composed of a large head subdomain and a smaller jaw subdomain and can be potently inhibited by the antibiotic moenomycin A (MoeA). We present an X-ray structure of the MoeA-bound Staphylococcus aureus monofunctional PGT enzyme, revealing electron density for a second MoeA bound to the jaw subdomain as well as the PGT donor site. Isothermal titration calorimetry confirms two drug-binding sites with markedly different affinities and positive cooperativity. Hydrophobic cluster analysis suggests that the membrane-interacting surface of the jaw subdomain has structural and physicochemical properties similar to amphipathic cationic α -helical antimicrobial peptides for lipid II recognition and binding. Furthermore, molecular dynamics simulations of the drug-free and -bound forms of the enzyme demonstrate the importance of the jaw subdomain movement for lipid II selection and polymerization process and provide molecular-level insights into the mechanism of peptidoglycan biosynthesis by PGTs.
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Affiliation(s)
- Avinash S. Punekar
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Adrian J. Lloyd
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - David J. Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
- ISIS Neutron and Muon Spallation Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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22
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Yu JY, Cheng HJ, Wu HR, Wu WS, Lu JW, Cheng TJ, Wu YT, Fang JM. Structure-based design of bacterial transglycosylase inhibitors incorporating biphenyl, amine linker and 2-alkoxy-3-phosphorylpropanoate moieties. Eur J Med Chem 2018; 150:729-741. [PMID: 29574202 DOI: 10.1016/j.ejmech.2018.03.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 01/28/2023]
Abstract
Transglycosylase (TGase) is essential to biosynthesis of peptidoglycan for formation of bacterial cell wall. Moenomycin is a potent TGase inhibitor, but not used in clinic treatment due to its poor pharmacokinetics. The E-F disaccharide, phosphoglycerate and lipid tail in moenomycin are crucial elements for TGase inhibition and antibacterial activity. Based on this scaffold, a series of truncated mimics comprising biphenyl, amine linker and 2-alkoxy-3-phosphorylpropanoate moieties were designed to test their TGase inhibitory activity. In this design, the phosphorylpropanoate group is a surrogate of phosphoglycerate with improved stability. A library of lipid tails can be constructed by a straightforward approach using Cu(I)-catalyzed (3 + 2) cycloaddition reactions, and the as-synthesized triazole ring can provide additional hydrogen bonds in the TGase active site. Our molecular docking experiments reveal that the biphenyl group provides π-π and π-cation interactions to act as a simplified alternative of the C-E disaccharide in moenomycin. To play the role of the oxonium transition state in transglycosylation, the amine linker exists as a positively charged species in physiological condition to attain electrostatic interactions with acidic residues. In this study, two biphenyl-linked 2-alkoxy-3-phosphorylpropanoate compounds (8 and 10) are found to exhibit modest inhibitory activity (IC50 ≈ 150 μM) against the TGase of Acinetobacter baumannii and good antibacterial activity against Staphylococcus aureus (MIC = 6.3 μM).
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Affiliation(s)
- Jui-Yin Yu
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Hsiu-Jung Cheng
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Huei-Ru Wu
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Wei-Shen Wu
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Jui-Wen Lu
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Ting-Jen Cheng
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Ying-Ta Wu
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan, ROC; The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC.
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23
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Guo T, Yang Y, Liu R, Li X. Enhanced removal of intracellular organic matters (IOM) from Microcystic aeruginosa by aluminum coagulation. Sep Purif Technol 2017. [DOI: 10.1016/j.seppur.2017.06.066] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Ngo M, Suits MDL. Methods for Determining Glycosyltransferase Kinetics. Methods Mol Biol 2017; 1588:59-70. [PMID: 28417361 DOI: 10.1007/978-1-4939-6899-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Glycosyltransferases are a class of biosynthetic enzymes that transfer individual activated monosaccharide units to specific acceptors. Colorimetric assays using the detection of released products such as para-nitrophenol and coupled assays for inorganic phosphate detection allow for convenient and quantifiable kinetic characterization. These techniques may be applied to determine the enzymatic activity of glycosyltransferases by indirectly measuring the transfer of nucleotide-activated donor carbohydrate units to various cognate acceptor molecules. In addition to an overview of these methods, the protocol for quantifying the glycosyltransferase activity used for the characterization of penicillin-binding proteins (PBPs) involving the transfer of lipid II to form elongated murein chains during bacterial cell wall synthesis is described herein.
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Affiliation(s)
- Maria Ngo
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada, N2L 3C5
| | - Michael D L Suits
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada, N2L 3C5.
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25
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Interplay between Penicillin-binding proteins and SEDS proteins promotes bacterial cell wall synthesis. Sci Rep 2017; 7:43306. [PMID: 28233869 PMCID: PMC5324115 DOI: 10.1038/srep43306] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/06/2017] [Indexed: 11/14/2022] Open
Abstract
Bacteria utilize specialized multi-protein machineries to synthesize the essential peptidoglycan (PG) cell wall during growth and division. The divisome controls septal PG synthesis and separation of daughter cells. In E. coli, the lipid II transporter candidate FtsW is thought to work in concert with the PG synthases penicillin-binding proteins PBP3 and PBP1b. Yet, the exact molecular mechanisms of their function in complexes are largely unknown. We show that FtsW interacts with PBP1b and lipid II and that PBP1b, FtsW and PBP3 co-purify suggesting that they form a trimeric complex. We also show that the large loop between transmembrane helices 7 and 8 of FtsW is important for the interaction with PBP3. Moreover, we found that FtsW, but not the other flippase candidate MurJ, impairs lipid II polymerization and peptide cross-linking activities of PBP1b, and that PBP3 relieves these inhibitory effects. All together the results suggest that FtsW interacts with lipid II preventing its polymerization by PBP1b unless PBP3 is also present, indicating that PBP3 facilitates lipid II release and/or its transfer to PBP1b after transport across the cytoplasmic membrane. This tight regulatory mechanism is consistent with the cell’s need to ensure appropriate use of the limited pool of lipid II.
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26
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King DT, Wasney GA, Nosella M, Fong A, Strynadka NCJ. Structural Insights into Inhibition of Escherichia coli Penicillin-binding Protein 1B. J Biol Chem 2016; 292:979-993. [PMID: 27899450 DOI: 10.1074/jbc.m116.718403] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli, the peptidoglycan cell wall is synthesized by bifunctional penicillin-binding proteins such as PBP1b that have both transpeptidase and transglycosylase activities. The PBP1b transpeptidase domain is a major target of β-lactams, and therefore it is important to attain a detailed understanding of its inhibition. The peptidoglycan glycosyltransferase domain of PBP1b is also considered an excellent antibiotic target yet is not exploited by any clinically approved antibacterials. Herein, we adapt a pyrophosphate sensor assay to monitor PBP1b-catalyzed glycosyltransfer and present an improved crystallographic model for inhibition of the PBP1b glycosyltransferase domain by the potent substrate analog moenomycin. We elucidate the structure of a previously disordered region in the glycosyltransferase active site and discuss its implications with regards to peptidoglycan polymerization. Furthermore, we solve the crystal structures of E. coli PBP1b bound to multiple different β-lactams in the transpeptidase active site and complement these data with gel-based competition assays to provide a detailed structural understanding of its inhibition. Taken together, these biochemical and structural data allow us to propose new insights into inhibition of both enzymatic domains in PBP1b.
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Affiliation(s)
- Dustin T King
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Gregory A Wasney
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Michael Nosella
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Anita Fong
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Natalie C J Strynadka
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
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27
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Blanchaert B, Palabiyik IM, Gökbulut A, Wang MJ, Dai Z, Wei F, Ma SC, Adams E, Van Schepdael A. Bioanalytical LC/MS study of potential bacterial transglycosylation inhibitors. J Pharm Biomed Anal 2016; 127:123-8. [PMID: 26782294 DOI: 10.1016/j.jpba.2015.12.050] [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: 10/20/2015] [Revised: 12/14/2015] [Accepted: 12/24/2015] [Indexed: 11/24/2022]
Abstract
Bacterial transglycosylation is an interesting target in antibiotic drug development. An in vitro transglycosylation assay was developed and used to search for possible inhibitors of Staphylococcus aureus Penicillin Binding Protein 2-mediated transglycosylation. Since the substrate, Lipid II, has no UV-chromophore, the assay relies on LC coupled to MS for analysis of the incubation mixtures. Extracts from Thymus sipyleus, Salvia verticillata, Salvia virgata and Oolong tea were tested, as well as epigallocatechin gallate and ursolic acid, which are chemical compounds derived from plants. Matrix effects hampered Lipid II quantification in samples treated with very high concentrations of extracts. None of these extracts or isolated compounds appeared to have inhibitory activities towards the transglycosylation function of Penicillin Binding Protein 2.
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Affiliation(s)
- Bart Blanchaert
- KU Leuven-University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ismail Murat Palabiyik
- University of Ankara, Faculty of Pharmacy, Department of Analytical Chemistry, 06100 Tandogan, Ankara, Turkey
| | - Alper Gökbulut
- University of Ankara, Faculty of Pharmacy, Department of Pharmacognosy, 06100 Tandogan, Ankara, Turkey
| | - Ming-Juan Wang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Zhong Dai
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Feng Wei
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Shuang-Cheng Ma
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Erwin Adams
- KU Leuven-University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ann Van Schepdael
- KU Leuven-University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium.
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28
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Yamatsugu K, Splain RA, Kiessling LL. Fidelity and Promiscuity of a Mycobacterial Glycosyltransferase. J Am Chem Soc 2016; 138:9205-11. [PMID: 27302377 DOI: 10.1021/jacs.6b04481] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Members of the genus Mycobacterium cause devastating human diseases, including tuberculosis. Mycobacterium tuberculosis can resist some antibiotics because of its durable and impermeable cell envelope. This barrier is assembled from saccharide building blocks not found in mammals, including galactofuranose (Galf). Within the cell envelope, Galf residues are linked together to afford an essential polysaccharide, termed the galactan. The formation of this polymer is catalyzed by the glycosyltransferase GlfT2, a processive carbohydrate polymerase, which generates a sequence-specific polysaccharide with alternating regioisomeric β(1-5) and β(1-6) Galf linkages. GlfT2 exhibits high fidelity in linkage formation, as it will terminate polymerization rather than deviate from its linkage pattern. These findings suggest that GlfT2 would prefer an acceptor with a canonical alternating β(1-5) and β(1-6) Galf sequence. To test this hypothesis, we devised a synthetic route to assemble oligosaccharides with natural and non-natural sequences. GlfT2 could elongate each of these acceptors, even those with non-natural linkage patterns. These data indicate that the glycosyltransferase is surprisingly promiscuous in its substrate preferences. However, GlfT2 did favor some substrates: it preferentially acted on those in which the lipid-bearing Galf residue was connected to the sequence by a β(1-6) glycosidic linkage. The finding that the relative positioning of the lipid and the non-reducing end of the acceptor influences substrate selectivity is consistent with a role for the lipid in acceptor binding. The data also suggest that the fidelity of GlfT2 for generating an alternating β(1-5) and β(1-6) pattern of Galf residues arises not from preferential substrate binding but during processive elongation. These observations suggest that inhibiting the action of GlfT2 will afford changes in cell wall structure.
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Affiliation(s)
- Kenzo Yamatsugu
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Rebecca A Splain
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Laura L Kiessling
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States.,Department of Biochemistry, University of Wisconsin-Madison , 433 Babcock Drive, Madison, Wisconsin 53706, United States
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29
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Glycosyltransferases and Transpeptidases/Penicillin-Binding Proteins: Valuable Targets for New Antibacterials. Antibiotics (Basel) 2016; 5:antibiotics5010012. [PMID: 27025527 PMCID: PMC4810414 DOI: 10.3390/antibiotics5010012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/27/2016] [Accepted: 02/03/2016] [Indexed: 12/29/2022] Open
Abstract
Peptidoglycan (PG) is an essential macromolecular sacculus surrounding most bacteria. It is assembled by the glycosyltransferase (GT) and transpeptidase (TP) activities of multimodular penicillin-binding proteins (PBPs) within multiprotein complex machineries. Both activities are essential for the synthesis of a functional stress-bearing PG shell. Although good progress has been made in terms of the functional and structural understanding of GT, finding a clinically useful antibiotic against them has been challenging until now. In contrast, the TP/PBP module has been successfully targeted by β-lactam derivatives, but the extensive use of these antibiotics has selected resistant bacterial strains that employ a wide variety of mechanisms to escape the lethal action of these antibiotics. In addition to traditional β-lactams, other classes of molecules (non-β-lactams) that inhibit PBPs are now emerging, opening new perspectives for tackling the resistance problem while taking advantage of these valuable targets, for which a wealth of structural and functional knowledge has been accumulated. The overall evidence shows that PBPs are part of multiprotein machineries whose activities are modulated by cofactors. Perturbation of these systems could lead to lethal effects. Developing screening strategies to take advantage of these mechanisms could lead to new inhibitors of PG assembly. In this paper, we present a general background on the GTs and TPs/PBPs, a survey of recent issues of bacterial resistance and a review of recent works describing new inhibitors of these enzymes.
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30
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Egan AJF, Vollmer W. Continuous Fluorescence Assay for Peptidoglycan Glycosyltransferases. Methods Mol Biol 2016; 1440:171-84. [PMID: 27311672 DOI: 10.1007/978-1-4939-3676-2_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bacterial cell wall peptidoglycan is synthesized from its precursor lipid II by two enzymatic reactions. First, glycosyltransferases polymerize the glycan strands and second, DD-transpeptidases form cross-links between peptides of neighboring strands. Most bacteria possess bifunctional peptidoglycan synthesis enzymes capable of catalyzing both reactions. Here, we describe a continuous fluorescence glycosyltransferase assay using Dansyl-labeled lipid II as substrate. Progression of the reaction is monitored by the reduction in fluorescence over time. The assay is suitable to investigate the effect of protein interaction partners on the glycan strand synthesis activity of peptidoglycan polymerases.
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Affiliation(s)
- Alexander J F Egan
- Institute for Cell and Molecular Biosciences, The Centre for Bacterial Cell Biology, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
| | - Waldemar Vollmer
- Institute for Cell and Molecular Biosciences, The Centre for Bacterial Cell Biology, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
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31
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Sosič I, Anderluh M, Sova M, Gobec M, Mlinarič Raščan I, Derouaux A, Amoroso A, Terrak M, Breukink E, Gobec S. Structure-Activity Relationships of Novel Tryptamine-Based Inhibitors of Bacterial Transglycosylase. J Med Chem 2015; 58:9712-21. [PMID: 26588190 DOI: 10.1021/acs.jmedchem.5b01482] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Penicillin-binding proteins represent well-established, validated, and still very promising targets for the design and development of new antibacterial agents. The transglycosylase domain of penicillin-binding proteins is especially important, as it catalyzes polymerization of glycan chains, using the peptidoglycan precursor lipid II as a substrate. On the basis of the previous discovery of a noncovalent small-molecule inhibitor of transglycosylase activity, we systematically explored the structure-activity relationships of these tryptamine-based inhibitors. The main aim was to reduce the nonspecific cytotoxic properties of the initial hit compound and concurrently to retain the mode of its inhibition. A focused library of tryptamine-based compounds was synthesized, characterized, and evaluated biochemically. The results presented here show the successful reduction of the nonspecific cytotoxicity, and the retention of the inhibition of transglycosylase enzymatic activity, as well as the ability of these compounds to bind to lipid II and to have antibacterial actions.
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Affiliation(s)
- Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Irena Mlinarič Raščan
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Adeline Derouaux
- Centre d'Ingénierie des Protéines, Université de Liège , Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Ana Amoroso
- Centre d'Ingénierie des Protéines, Université de Liège , Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Mohammed Terrak
- Centre d'Ingénierie des Protéines, Université de Liège , Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Eefjan Breukink
- Department Biochemistry of Membranes, Bijvoet Centre, Institute of Biomembranes, Utrecht University , Utrecht 3584 CH, The Netherlands
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
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32
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Mesleh MF, Rajaratnam P, Conrad M, Chandrasekaran V, Liu CM, Pandya BA, Hwang YS, Rye PT, Muldoon C, Becker B, Zuegg J, Meutermans W, Moy TI. Targeting Bacterial Cell Wall Peptidoglycan Synthesis by Inhibition of Glycosyltransferase Activity. Chem Biol Drug Des 2015; 87:190-9. [PMID: 26358369 DOI: 10.1111/cbdd.12662] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 08/20/2015] [Accepted: 08/27/2015] [Indexed: 11/25/2022]
Abstract
Synthesis of bacterial cell wall peptidoglycan requires glycosyltransferase enzymes that transfer the disaccharide-peptide from lipid II onto the growing glycan chain. The polymerization of the glycan chain precedes cross-linking by penicillin-binding proteins and is essential for growth for key bacterial pathogens. As such, bacterial cell wall glycosyltransferases are an attractive target for antibiotic drug discovery. However, significant challenges to the development of inhibitors for these targets include the development of suitable assays and chemical matter that is suited to the nature of the binding site. We developed glycosyltransferase enzymatic activity and binding assays using the natural products moenomycin and vancomycin as model inhibitors. In addition, we designed a library of disaccharide compounds based on the minimum moenomycin fragment with peptidoglycan glycosyltransferase inhibitory activity and based on a more drug-like and synthetically versatile disaccharide building block. A subset of these disaccharide compounds bound and inhibited the glycosyltransferase enzymes, and these compounds could serve as chemical entry points for antibiotic development.
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Affiliation(s)
- Michael F Mesleh
- Cubist Pharmaceuticals, a wholly-owned subsidiary of Merck & Co. Inc., 65 Hayden Avenue, Lexington, MA, 02421, USA
| | - Premraj Rajaratnam
- Alchemia Limited, 3 Hi-Tech Court, Eight Mile Plains, Brisbane Technology Park, Qld, 4113, Australia
| | - Mary Conrad
- Cubist Pharmaceuticals, a wholly-owned subsidiary of Merck & Co. Inc., 65 Hayden Avenue, Lexington, MA, 02421, USA
| | - Vasu Chandrasekaran
- Cubist Pharmaceuticals, a wholly-owned subsidiary of Merck & Co. Inc., 65 Hayden Avenue, Lexington, MA, 02421, USA
| | - Christopher M Liu
- Cubist Pharmaceuticals, a wholly-owned subsidiary of Merck & Co. Inc., 65 Hayden Avenue, Lexington, MA, 02421, USA
| | - Bhaumik A Pandya
- Cubist Pharmaceuticals, a wholly-owned subsidiary of Merck & Co. Inc., 65 Hayden Avenue, Lexington, MA, 02421, USA
| | - You Seok Hwang
- Cubist Pharmaceuticals, a wholly-owned subsidiary of Merck & Co. Inc., 65 Hayden Avenue, Lexington, MA, 02421, USA
| | - Peter T Rye
- Agilent Technologies, Inc., 11 Audubon Road, Wakefield, MA, 01880, USA
| | - Craig Muldoon
- Alchemia Limited, 3 Hi-Tech Court, Eight Mile Plains, Brisbane Technology Park, Qld, 4113, Australia
| | - Bernd Becker
- Alchemia Limited, 3 Hi-Tech Court, Eight Mile Plains, Brisbane Technology Park, Qld, 4113, Australia
| | - Johannes Zuegg
- Alchemia Limited, 3 Hi-Tech Court, Eight Mile Plains, Brisbane Technology Park, Qld, 4113, Australia
| | - Wim Meutermans
- Alchemia Limited, 3 Hi-Tech Court, Eight Mile Plains, Brisbane Technology Park, Qld, 4113, Australia
| | - Terence I Moy
- Cubist Pharmaceuticals, a wholly-owned subsidiary of Merck & Co. Inc., 65 Hayden Avenue, Lexington, MA, 02421, USA
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33
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Egan AJF, Biboy J, van't Veer I, Breukink E, Vollmer W. Activities and regulation of peptidoglycan synthases. Philos Trans R Soc Lond B Biol Sci 2015; 370:20150031. [PMID: 26370943 PMCID: PMC4632607 DOI: 10.1098/rstb.2015.0031] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2015] [Indexed: 12/22/2022] Open
Abstract
Peptidoglycan (PG) is an essential component in the cell wall of nearly all bacteria, forming a continuous, mesh-like structure, called the sacculus, around the cytoplasmic membrane to protect the cell from bursting by its turgor. Although PG synthases, the penicillin-binding proteins (PBPs), have been studied for 70 years, useful in vitro assays for measuring their activities were established only recently, and these provided the first insights into the regulation of these enzymes. Here, we review the current knowledge on the glycosyltransferase and transpeptidase activities of PG synthases. We provide new data showing that the bifunctional PBP1A and PBP1B from Escherichia coli are active upon reconstitution into the membrane environment of proteoliposomes, and that these enzymes also exhibit DD-carboxypeptidase activity in certain conditions. Both novel features are relevant for their functioning within the cell. We also review recent data on the impact of protein-protein interactions and other factors on the activities of PBPs. As an example, we demonstrate a synergistic effect of multiple protein-protein interactions on the glycosyltransferase activity of PBP1B, by its cognate lipoprotein activator LpoB and the essential cell division protein FtsN.
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Affiliation(s)
- Alexander J F Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Inge van't Veer
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 Utrecht, The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 Utrecht, The Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
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34
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Carbohydrate scaffolds as glycosyltransferase inhibitors with in vivo antibacterial activity. Nat Commun 2015; 6:7719. [PMID: 26194781 PMCID: PMC4530474 DOI: 10.1038/ncomms8719] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/05/2015] [Indexed: 02/08/2023] Open
Abstract
The rapid rise of multi-drug-resistant bacteria is a global healthcare crisis, and new antibiotics are urgently required, especially those with modes of action that have low-resistance potential. One promising lead is the liposaccharide antibiotic moenomycin that inhibits bacterial glycosyltransferases, which are essential for peptidoglycan polymerization, while displaying a low rate of resistance. Unfortunately, the lipophilicity of moenomycin leads to unfavourable pharmacokinetic properties that render it unsuitable for systemic administration. In this study, we show that using moenomycin and other glycosyltransferase inhibitors as templates, we were able to synthesize compound libraries based on novel pyranose scaffold chemistry, with moenomycin-like activity, but with improved drug-like properties. The novel compounds exhibit in vitro inhibition comparable to moenomycin, with low toxicity and good efficacy in several in vivo models of infection. This approach based on non-planar carbohydrate scaffolds provides a new opportunity to develop new antibiotics with low propensity for resistance induction.
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35
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Bury D, Dahmane I, Derouaux A, Dumbre S, Herdewijn P, Matagne A, Breukink E, Mueller-Seitz E, Petz M, Terrak M. Positive cooperativity between acceptor and donor sites of the peptidoglycan glycosyltransferase. Biochem Pharmacol 2014; 93:141-50. [PMID: 25462814 DOI: 10.1016/j.bcp.2014.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/07/2014] [Accepted: 11/07/2014] [Indexed: 12/01/2022]
Abstract
The glycosyltransferases of family 51 (GT51) catalyze the polymerization of lipid II to form linear glycan chains, which, after cross linking by the transpeptidases, form the net-like peptidoglycan macromolecule. The essential function of the GT makes it an attractive antimicrobial target; therefore a better understanding of its function and its mechanism of interaction with substrates could help in the design and the development of new antibiotics. In this work, we have used a surface plasmon resonance Biacore(®) biosensor, based on an amine derivative of moenomycin A immobilized on a sensor chip surface, to investigate the mechanism of binding of substrate analogous inhibitors to the GT. Addition of increasing concentrations of moenomycin A to the Staphylococcus aureus MtgA led to reduced binding of the protein to the sensor chip as expected. Remarkably, in the presence of low concentrations of the most active disaccharide inhibitors, binding of MtgA to immobilized moenomycin A was found to increase; in contrast competition with moenomycin A occurred only at high concentrations. This finding suggests that at low concentrations, the lipid II analogs bind to the acceptor site and induce a cooperative binding of moenomycin A to the donor site. Our results constitute the first indication of the existence of a positive cooperativity between the acceptor and the donor sites of peptidoglycan GTs. In addition, our study indicates that a modification of two residues (L119N and F120S) within the hydrophobic region of MtgA can yield monodisperse forms of the protein with apparently no change in its secondary structure content, but this is at the expense of the enzyme function.
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Affiliation(s)
- Daniel Bury
- Department of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaussstr. 20, 42119 Wuppertal, Germany.
| | - Ismahene Dahmane
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Adeline Derouaux
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Shrinivas Dumbre
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - André Matagne
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Erika Mueller-Seitz
- Department of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaussstr. 20, 42119 Wuppertal, Germany
| | - Michael Petz
- Department of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaussstr. 20, 42119 Wuppertal, Germany
| | - Mohammed Terrak
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium.
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36
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Braddick D, Sandhu S, Roper DI, Chappell MJ, Bugg TDH. Observation of the time-course for peptidoglycan lipid intermediate II polymerization by Staphylococcus aureus monofunctional transglycosylase. MICROBIOLOGY-SGM 2014; 160:1628-1636. [PMID: 24858082 DOI: 10.1099/mic.0.079442-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The polymerization of lipid intermediate II by the transglycosylase activity of penicillin-binding proteins (PBPs) represents an important target for antibacterial action, but limited methods are available for quantitative assay of this reaction, or screening potential inhibitors. A new labelling method for lipid II polymerization products using Sanger's reagent (fluoro-2,4-dinitrobenzene), followed by gel permeation HPLC analysis, has permitted the observation of intermediate polymerization products for Staphylococcus aureus monofunctional transglycosylase MGT. Peak formation is inhibited by 6 µM ramoplanin or enduracidin. Characterization by mass spectrometry indicates the formation of tetrasaccharide and octasaccharide intermediates, but not a hexasaccharide intermediate, suggesting a dimerization of a lipid-linked tetrasaccharide. Numerical modelling of the time-course data supports a kinetic model involving addition to lipid-linked tetrasaccharide of either lipid II or lipid-linked tetrasaccharide. Observation of free octasaccharide suggests that hydrolysis of the undecaprenyl diphosphate lipid carrier occurs at this stage in peptidoglycan transglycosylation.
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Affiliation(s)
- Darren Braddick
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Sandeep Sandhu
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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37
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Galley NF, O'Reilly AM, Roper DI. Prospects for novel inhibitors of peptidoglycan transglycosylases. Bioorg Chem 2014; 55:16-26. [PMID: 24924926 PMCID: PMC4126109 DOI: 10.1016/j.bioorg.2014.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/12/2014] [Accepted: 05/12/2014] [Indexed: 01/07/2023]
Abstract
We examine key aspects of transglycosylase inhibitor design. Low to high throughput assays suitable for transglycosylase drug discovery. Existing chemical start points for transglycosylase active site targeting.
The lack of novel antimicrobial drugs under development coupled with the increasing occurrence of resistance to existing antibiotics by community and hospital acquired infections is of grave concern. The targeting of biosynthesis of the peptidoglycan component of the bacterial cell wall has proven to be clinically valuable but relatively little therapeutic development has been directed towards the transglycosylase step of this process. Advances towards the isolation of new antimicrobials that target transglycosylase activity will rely on the development of the enzymological tools required to identify and characterise novel inhibitors of these enzymes. Therefore, in this article, we review the assay methods developed for transglycosylases and review recent novel chemical inhibitors discovered in relation to both the lipidic substrates and natural product inhibitors of the transglycosylase step.
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Affiliation(s)
- Nicola F Galley
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Amy M O'Reilly
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
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38
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Bacterial cell division proteins as antibiotic targets. Bioorg Chem 2014; 55:27-38. [PMID: 24755375 DOI: 10.1016/j.bioorg.2014.03.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 11/21/2022]
Abstract
Proteins involved in bacterial cell division often do not have a counterpart in eukaryotic cells and they are essential for the survival of the bacteria. The genetic accessibility of many bacterial species in combination with the Green Fluorescence Protein revolution to study localization of proteins and the availability of crystal structures has increased our knowledge on bacterial cell division considerably in this century. Consequently, bacterial cell division proteins are more and more recognized as potential new antibiotic targets. An international effort to find small molecules that inhibit the cell division initiating protein FtsZ has yielded many compounds of which some are promising as leads for preclinical use. The essential transglycosylase activity of peptidoglycan synthases has recently become accessible to inhibitor screening. Enzymatic assays for and structural information on essential integral membrane proteins such as MraY and FtsW involved in lipid II (the peptidoglycan building block precursor) biosynthesis have put these proteins on the list of potential new targets. This review summarises and discusses the results and approaches to the development of lead compounds that inhibit bacterial cell division.
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Function and localization dynamics of bifunctional penicillin-binding proteins in Caulobacter crescentus. J Bacteriol 2014; 196:1627-39. [PMID: 24532768 DOI: 10.1128/jb.01194-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The peptidoglycan cell wall of bacteria is a complex macromolecule composed of glycan strands that are cross-linked by short peptide bridges. Its biosynthesis involves a conserved group of enzymes, the bifunctional penicillin-binding proteins (bPBPs), which contain both a transglycosylase and a transpeptidase domain, thus being able to elongate the glycan strands and, at the same time, generate the peptide cross-links. The stalked model bacterium Caulobacter crescentus possesses five bPBP paralogs, named Pbp1A, PbpC, PbpX, PbpY, and PbpZ, whose function is still incompletely understood. In this study, we show that any of these proteins except for PbpZ is sufficient for growth and normal morphogenesis when expressed at native or elevated levels, whereas inactivation of all five paralogs is lethal. Growth analyses indicate a central role of PbpX in the resistance of C. crescentus against the noncanonical amino acid d-alanine. Moreover, we show that PbpX and PbpY localize to the cell division site. Their recruitment to the divisome is dependent on the essential cell division protein FtsN and likely involves interactions with FtsL and the putative peptidoglycan hydrolase DipM. The same interaction pattern is observed for Pbp1A and PbpC, although these proteins do not accumulate at midcell. Our findings demonstrate that the bPBPs of C. crescentus are, to a large extent, redundant and have retained the ability to interact with the peptidoglycan biosynthetic machineries responsible for cell elongation, cytokinesis, and stalk growth. Nevertheless, they may preferentially act in specific peptidoglycan biosynthetic complexes, thereby facilitating the independent regulation of distinct growth processes.
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Lupoli TJ, Lebar MD, Markovski M, Bernhardt T, Kahne D, Walker S. Lipoprotein activators stimulate Escherichia coli penicillin-binding proteins by different mechanisms. J Am Chem Soc 2013; 136:52-5. [PMID: 24341982 DOI: 10.1021/ja410813j] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In Escherichia coli , the bifunctional penicillin-binding proteins (PBPs), PBP1A and PBP1B, play critical roles in the final stage of peptidoglycan (PG) biosynthesis. These synthetic enzymes each possess a PG glycosyltransferase (PGT) domain and a transpeptidase (TP) domain. Recent genetic experiments have shown that PBP1A and PBP1B each require an outer membrane lipoprotein, LpoA and LpoB, respectively, to function properly in vivo. Here, we use complementary assays to show that LpoA and LpoB each increase the PGT and TP activities of their cognate PBPs, albeit by different mechanisms. LpoA directly increases the rate of the PBP1A TP reaction, which also results in enhanced PGT activity; in contrast, LpoB directly affects PGT domain activity, resulting in enhanced TP activity. These studies demonstrate bidirectional coupling of PGT and TP domain function. Additionally, the transpeptidation assay described here can be applied to study other activators or inhibitors of the TP domain of PBPs, which are validated drug targets.
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Affiliation(s)
- Tania J Lupoli
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
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Huang SH, Wu WS, Huang LY, Huang WF, Fu WC, Chen PT, Fang JM, Cheng WC, Cheng TJR, Wong CH. New continuous fluorometric assay for bacterial transglycosylase using Förster resonance energy transfer. J Am Chem Soc 2013; 135:17078-89. [PMID: 24131464 DOI: 10.1021/ja407985m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The emergence of antibiotic resistance has prompted scientists to search for new antibiotics. Transglycosylase (TGase) is an attractive target for new antibiotic discovery due to its location on the outer membrane of bacteria and its essential role in peptidoglycan synthesis. Though there have been a few molecules identified as TGase inhibitors in the past thirty years, none of them have been developed into antibiotics for humans. The slow pace of development is perhaps due to the lack of continuous, quantitative, and high-throughput assay available for the enzyme. Herein, we report a new continuous fluorescent assay based on Förster resonance energy transfer, using lipid II analogues with a dimethylamino-azobenzenesulfonyl quencher in the lipid chain and a coumarin fluorophore in the peptide chain. During the process of transglycosylation, the quencher-appended polyprenol is released and the fluorescence of coumarin can be detected. Using this system, the substrate specificity and affinity of lipid II analogues bearing various numbers and configurations of isoprene units were investigated. Moreover, the inhibition constants of moenomycin and two previously identified small molecules were also determined. In addition, a high-throughput screening using the new assay was conducted to identify potent TGase inhibitors from a 120,000 compound library. This new continuous fluorescent assay not only provides an efficient and convenient way to study TGase activities, but also enables the high-throughput screening of potential TGase inhibitors for antibiotic discovery.
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Affiliation(s)
- Shih-Hsien Huang
- Genomics Research Center, Academia Sinica , 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan
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Derouaux A, Sauvage E, Terrak M. Peptidoglycan glycosyltransferase substrate mimics as templates for the design of new antibacterial drugs. Front Immunol 2013; 4:78. [PMID: 23543824 PMCID: PMC3608906 DOI: 10.3389/fimmu.2013.00078] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 03/13/2013] [Indexed: 12/02/2022] Open
Abstract
Peptidoglycan (PG) is an essential net-like macromolecule that surrounds bacteria, gives them their shape, and protects them against their own high osmotic pressure. PG synthesis inhibition leads to bacterial cell lysis, making it an important target for many antibiotics. The final two reactions in PG synthesis are performed by penicillin-binding proteins (PBPs). Their glycosyltransferase (GT) activity uses the lipid II precursor to synthesize glycan chains and their transpeptidase (TP) activity catalyzes the cross-linking of two glycan chains via the peptide side chains. Inhibition of either of these two reactions leads to bacterial cell death. β-lactam antibiotics target the transpeptidation reaction while antibiotic therapy based on inhibition of the GTs remains to be developed. Ongoing research is trying to fill this gap by studying the interactions of GTs with inhibitors and substrate mimics and utilizing the latter as templates for the design of new antibiotics. In this review we present an updated overview on the GTs and describe the structure-activity relationship of recently developed synthetic ligands.
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Affiliation(s)
- Adeline Derouaux
- Centre d'Ingénierie des Protéines, University of Liège Liège, Belgium
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Gampe CM, Tsukamoto H, Doud EH, Walker S, Kahne D. Tuning the moenomycin pharmacophore to enable discovery of bacterial cell wall synthesis inhibitors. J Am Chem Soc 2013; 135:3776-9. [PMID: 23448584 DOI: 10.1021/ja4000933] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antibiotic drugs need to be identified to address rapidly developing resistance of bacterial pathogens to common antibiotics. The natural antibiotic moenomycin A is the prototype for compounds that bind to bacterial peptidoglycan glycosyltransferases (PGTs) and inhibit cell wall biosynthesis, but it cannot be used as a drug. Here we report the chemoenzymatic synthesis of a fluorescently labeled, truncated analogue of moenomycin based on the minimal pharmacophore. This probe, which has optimized enzyme binding properties compared to moenomycin, was designed to identify low-micromolar inhibitors that bind to conserved features in PGT active sites. We demonstrate its use in displacement assays using PGTs from S. aureus, E. faecalis, and E. coli. 110,000 compounds were screened against S. aureus SgtB, and we identified a non-carbohydrate based compound that binds to all PGTs tested. We also show that the compound inhibits in vitro formation of peptidoglycan chains by several different PGTs. Thus, this assay enables the identification of small molecules that target PGT active sites, and may provide lead compounds for development of new antibiotics.
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Affiliation(s)
- Christian M Gampe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Abstract
Bacterial cell wall peptidoglycan is synthesized from lipid II precursor by two reactions. Glycosyltransferases polymerize the glycan chains and transpeptidases form the peptide cross-links. The bifunctional class A penicillin-binding proteins catalyze both of these reactions. Here, we describe an in vitro peptidoglycan synthesis assay utilizing radiolabeled lipid II substrate to monitor simultaneously peptidoglycan glycosyltransferase and transpeptidase activities. The products of the reaction are separated by high-pressure liquid chromatography and quantified by flow-through scintillation counting.
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Shih HW, Chang YF, Li WJ, Meng FC, Huang CY, Ma C, Cheng TJR, Wong CH, Cheng WC. Effect of the Peptide Moiety of Lipid II on Bacterial Transglycosylase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Shih HW, Chang YF, Li WJ, Meng FC, Huang CY, Ma C, Cheng TJR, Wong CH, Cheng WC. Effect of the peptide moiety of Lipid II on bacterial transglycosylase. Angew Chem Int Ed Engl 2012; 51:10123-6. [PMID: 22952114 DOI: 10.1002/anie.201204038] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Hao-Wei Shih
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Taipei 115, Taiwan
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Banzhaf M, van den Berg van Saparoea B, Terrak M, Fraipont C, Egan A, Philippe J, Zapun A, Breukink E, Nguyen-Distèche M, den Blaauwen T, Vollmer W. Cooperativity of peptidoglycan synthases active in bacterial cell elongation. Mol Microbiol 2012; 85:179-94. [PMID: 22606933 DOI: 10.1111/j.1365-2958.2012.08103.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Growth of the bacterial cell wall peptidoglycan sacculus requires the co-ordinated activities of peptidoglycan synthases, hydrolases and cell morphogenesis proteins, but the details of these interactions are largely unknown. We now show that the Escherichia coli peptidoglycan glycosyltrasferase-transpeptidase PBP1A interacts with the cell elongation-specific transpeptidase PBP2 in vitro and in the cell. Cells lacking PBP1A are thinner and initiate cell division later in the cell cycle. PBP1A localizes mainly to the cylindrical wall of the cell, supporting its role in cell elongation. Our in vitro peptidoglycan synthesis assays provide novel insights into the cooperativity of peptidoglycan synthases with different activities. PBP2 stimulates the glycosyltransferase activity of PBP1A, and PBP1A and PBP2 cooperate to attach newly synthesized peptidoglycan to sacculi. PBP2 has peptidoglycan transpeptidase activity in the presence of active PBP1A. Our data also provide a possible explanation for the depletion of lipid II precursors in penicillin-treated cells.
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Affiliation(s)
- Manuel Banzhaf
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
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Helassa N, Vollmer W, Breukink E, Vernet T, Zapun A. The membrane anchor of penicillin-binding protein PBP2a from Streptococcus pneumoniae influences peptidoglycan chain length. FEBS J 2012; 279:2071-81. [DOI: 10.1111/j.1742-4658.2012.08592.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism. Proc Natl Acad Sci U S A 2012; 109:6496-501. [PMID: 22493270 DOI: 10.1073/pnas.1203900109] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial transpeptidase and transglycosylase on the surface are essential for cell wall synthesis, and many antibiotics have been developed to target the transpeptidase; however, the problem of antibiotic resistance has arisen and caused a major threat in bacterial infection. The transglycosylase has been considered to be another excellent target, but no antibiotics have been developed to target this enzyme. Here, we determined the crystal structure of the Staphylococcus aureus membrane-bound transglycosylase, monofunctional glycosyltransferase, in complex with a lipid II analog to 2.3 Å resolution. Our results showed that the lipid II-contacting residues are not only conserved in WT and drug-resistant bacteria but also significant in enzymatic activity. Mechanistically, we proposed that K140 and R148 in the donor site, instead of the previously proposed E156, are used to stabilize the pyrophosphate-leaving group of lipid II, and E100 in the acceptor site acts as general base for the 4-OH of GlcNAc to facilitate the transglycosylation reaction. This mechanism, further supported by mutagenesis study and the structure of monofunctional glycosyltransferase in complex with moenomycin in the donor site, provides a direction for antibacterial drugs design.
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Shih HW, Chen KT, Cheng TJR, Wong CH, Cheng WC. A new synthetic approach toward bacterial transglycosylase substrates, Lipid II and Lipid IV. Org Lett 2011; 13:4600-3. [PMID: 21797279 DOI: 10.1021/ol201806d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new synthetic approach toward the bacterial transglycosylase substrates, Lipid II (1) and Lipid IV (2), is described. The key disaccharide was synthesized using the concept of relative reactivity value (RRV) and elaborated to Lipid II and Lipid IV by conjugation with the appropriate oligopeptides and pyrophosphate lipids. Interestingly, the results from our HPLC-based functional TGase assay suggested Lipid IV has a higher affinity for the enzyme than Lipid II.
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Affiliation(s)
- Hao-Wei Shih
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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