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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Koatale P, Welling MM, Ndlovu H, Kgatle M, Mdanda S, Mdlophane A, Okem A, Takyi-Williams J, Sathekge MM, Ebenhan T. Insights into Peptidoglycan-Targeting Radiotracers for Imaging Bacterial Infections: Updates, Challenges, and Future Perspectives. ACS Infect Dis 2024; 10:270-286. [PMID: 38290525 PMCID: PMC10862554 DOI: 10.1021/acsinfecdis.3c00443] [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: 08/28/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 02/01/2024]
Abstract
The unique structural architecture of the peptidoglycan allows for the stratification of bacteria as either Gram-negative or Gram-positive, which makes bacterial cells distinguishable from mammalian cells. This classification has received attention as a potential target for diagnostic and therapeutic purposes. Bacteria's ability to metabolically integrate peptidoglycan precursors during cell wall biosynthesis and recycling offers an opportunity to target and image pathogens in their biological state. This Review explores the peptidoglycan biosynthesis for bacteria-specific targeting for infection imaging. Current and potential radiolabeled peptidoglycan precursors for bacterial infection imaging, their development status, and their performance in vitro and/or in vivo are highlighted. We conclude by providing our thoughts on how to shape this area of research for future clinical translation.
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Affiliation(s)
- Palesa
C. Koatale
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mick M. Welling
- Interventional
Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Honest Ndlovu
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Mankgopo Kgatle
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Sipho Mdanda
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Amanda Mdlophane
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Ambrose Okem
- Department
of Anaesthesia, School of Clinical Medicine, University of Witwatersrand, 2050 Johannesburg, South Africa
| | - John Takyi-Williams
- Pharmacokinetic
and Mass Spectrometry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mike M. Sathekge
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
| | - Thomas Ebenhan
- Department
of Nuclear Medicine, University of Pretoria, 0001 Pretoria, South Africa
- Nuclear
Medicine Research Infrastructure (NuMeRI) NPC, 0001 Pretoria, South Africa
- DSI/NWU Pre-clinical
Drug Development Platform, North West University, 2520 Potchefstroom, South Africa
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3
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Karak M, Cloonan CR, Baker BR, Cochrane RVK, Cochrane SA. Optimizations of lipid II synthesis: an essential glycolipid precursor in bacterial cell wall synthesis and a validated antibiotic target. Beilstein J Org Chem 2024; 20:220-227. [PMID: 38352069 PMCID: PMC10862138 DOI: 10.3762/bjoc.20.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Lipid II is an essential glycolipid found in bacteria. Accessing this valuable cell wall precursor is important both for studying cell wall synthesis and for studying/identifying novel antimicrobial compounds. Herein, we describe optimizations to the modular chemical synthesis of lipid II and unnatural analogues. In particular, the glycosylation step, a critical step in the formation of the central disaccharide unit (GlcNAc-MurNAc), was optimized. This was achieved by employing the use of glycosyl donors with diverse leaving groups. The key advantage of this approach lies in its adaptability, allowing for the generation of a wide array of analogues through the incorporation of alternative building blocks at different stages of synthesis.
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Affiliation(s)
- Milandip Karak
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Cian R Cloonan
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Brad R Baker
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Rachel V K Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
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4
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Wu C, Lower BA, Moreira R, Dorantes D, Le T, Giurgiu C, Shi Y, van der Donk WA. Investigation into the mechanism of action of the antimicrobial peptide epilancin 15X. Front Microbiol 2023; 14:1247222. [PMID: 38029153 PMCID: PMC10652874 DOI: 10.3389/fmicb.2023.1247222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Addressing the current antibiotic-resistance challenge would be aided by the identification of compounds with novel mechanisms of action. Epilancin 15X, a lantibiotic produced by Staphylococcus epidermidis 15 × 154, displays antimicrobial activity in the submicromolar range against a subset of pathogenic Gram-positive bacteria. S. epidermidis is a common member of the human skin or mucosal microbiota. We here investigated the mechanism of action of epilancin 15X. The compound is bactericidal against Staphylococcus carnosus as well as Bacillus subtilis and appears to kill these bacteria by membrane disruption. Structure-activity relationship studies using engineered analogs show that its conserved positively charged residues and dehydroamino acids are important for bioactivity, but the N-terminal lactyl group is tolerant of changes. Epilancin 15X treatment negatively affects fatty acid synthesis, RNA translation, and DNA replication and transcription without affecting cell wall biosynthesis. The compound appears localized to the surface of bacteria and is most potent in disrupting the membranes of liposomes composed of negatively charged membrane lipids in a lipid II independent manner. Epilancin 15X does not elicit a LiaRS response in B. subtilis but did upregulate VraRS in S. carnosus. Treatment of S. carnosus or B. subtilis with epilancin 15X resulted in an aggregation phenotype in microscopy experiments. Collectively these studies provide new information on epilancin 15X activity.
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Affiliation(s)
- Chunyu Wu
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Champaign, IL, United States
| | - B. Alexis Lower
- Department of Chemistry, The Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Champaign, IL, United States
| | - Ryan Moreira
- Department of Chemistry, The Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Champaign, IL, United States
| | - Darian Dorantes
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Champaign, IL, United States
| | - Tung Le
- Department of Chemistry, The Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Champaign, IL, United States
| | - Constantin Giurgiu
- Department of Chemistry, The Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Champaign, IL, United States
| | - Yanxiang Shi
- Department of Chemistry, The Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Champaign, IL, United States
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Champaign, IL, United States
- Department of Chemistry, The Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Champaign, IL, United States
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5
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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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6
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Zheng Y, Zhang J, Meisner J, Li W, Luo Y, Wei F, Wen L. Cofactor-Driven Cascade Reactions Enable the Efficient Preparation of Sugar Nucleotides. Angew Chem Int Ed Engl 2022; 61:e202115696. [PMID: 35212445 DOI: 10.1002/anie.202115696] [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: 11/17/2021] [Indexed: 12/14/2022]
Abstract
Glycosylation is catalyzed by glycosyltransferases using sugar nucleotides or occasionally lipid-linked phosphosugars as donors. However, only very few common sugar nucleotides that occur in humans can be obtained readily, while the majority of sugar nucleotides that exist in bacteria, plants, archaea, or viruses cannot be synthesized in sufficient quantities by either enzymatic or chemical synthesis. The limited availability of such rare sugar nucleotides is one of the major obstacles that has greatly hampered progress in glycoscience. Herein we describe a general cofactor-driven cascade conversion strategy for the efficient synthesis of sugar nucleotides. The described strategy allows the large-scale preparation of rare sugar nucleotides from common sugars in high yields and without the need for tedious purification processes.
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Affiliation(s)
- Yuan Zheng
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiabin Zhang
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China.,Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Zhongshan, Guangdong, 528400, China
| | | | - Wanjin Li
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yawen Luo
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangyu Wei
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Oluwole AO, Corey RA, Brown CM, Hernández-Rocamora VM, Stansfeld PJ, Vollmer W, Bolla JR, Robinson CV. Peptidoglycan biosynthesis is driven by lipid transfer along enzyme-substrate affinity gradients. Nat Commun 2022; 13:2278. [PMID: 35477938 PMCID: PMC9046198 DOI: 10.1038/s41467-022-29836-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 03/31/2022] [Indexed: 01/02/2023] Open
Abstract
Maintenance of bacterial cell shape and resistance to osmotic stress by the peptidoglycan (PG) renders PG biosynthetic enzymes and precursors attractive targets for combating bacterial infections. Here, by applying native mass spectrometry, we elucidate the effects of lipid substrates on the PG membrane enzymes MraY, MurG, and MurJ. We show that dimerization of MraY is coupled with binding of the carrier lipid substrate undecaprenyl phosphate (C55-P). Further, we demonstrate the use of native MS for biosynthetic reaction monitoring and find that the passage of substrates and products is controlled by the relative binding affinities of the different membrane enzymes. Overall, we provide a molecular view of how PG membrane enzymes convey lipid precursors through favourable binding events and highlight possible opportunities for intervention. Bacterial cell wall enzymes and their precursors are critical targets for antibiotic development. Here, the authors investigate several biosynthetic enzymes with their substrates and show that the passage of substrates and products in the pathway is controlled by their relative binding affinities.
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Affiliation(s)
- Abraham O Oluwole
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.,The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Chelsea M Brown
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Victor M Hernández-Rocamora
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Jani R Bolla
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU, UK. .,Department of Plant Sciences/Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK. .,The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU, UK.
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8
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Wen L, Zheng Y, Zhang J, Meisner J, Li W, Luo Y, Wei F. Cofactor‐Driven Cascade Reactions Enable the Efficient Preparation of Sugar Nucleotides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Liuqing Wen
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Chemistry 501 Haike Road 30303 shanghai CHINA
| | - Yuan Zheng
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Carbohydrate-based drug research center CHINA
| | - Jiabinq Zhang
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Carbohydrate-based drug research center CHINA
| | | | - Wanjin Li
- Shanghai Institute of Materia Medica Chinese Academy of Sciences carbohydrate-based drug research center CHINA
| | - Yawen Luo
- Shanghai Institute of Materia Medica Chinese Academy of Sciences cArbohydrate-based drug research center CHINA
| | - Fangyu Wei
- Shanghai Institute of Materia Medica Chinese Academy of Sciences carbohydrate-based drug research center CHINA
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9
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Banahene N, Kavunja HW, Swarts BM. Chemical Reporters for Bacterial Glycans: Development and Applications. Chem Rev 2022; 122:3336-3413. [PMID: 34905344 PMCID: PMC8958928 DOI: 10.1021/acs.chemrev.1c00729] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacteria possess an extraordinary repertoire of cell envelope glycans that have critical physiological functions. Pathogenic bacteria have glycans that are essential for growth and virulence but are absent from humans, making them high-priority targets for antibiotic, vaccine, and diagnostic development. The advent of metabolic labeling with bioorthogonal chemical reporters and small-molecule fluorescent reporters has enabled the investigation and targeting of specific bacterial glycans in their native environments. These tools have opened the door to imaging glycan dynamics, assaying and inhibiting glycan biosynthesis, profiling glycoproteins and glycan-binding proteins, and targeting pathogens with diagnostic and therapeutic payload. These capabilities have been wielded in diverse commensal and pathogenic Gram-positive, Gram-negative, and mycobacterial species─including within live host organisms. Here, we review the development and applications of chemical reporters for bacterial glycans, including peptidoglycan, lipopolysaccharide, glycoproteins, teichoic acids, and capsular polysaccharides, as well as mycobacterial glycans, including trehalose glycolipids and arabinan-containing glycoconjugates. We cover in detail how bacteria-targeting chemical reporters are designed, synthesized, and evaluated, how they operate from a mechanistic standpoint, and how this information informs their judicious and innovative application. We also provide a perspective on the current state and future directions of the field, underscoring the need for interdisciplinary teams to create novel tools and extend existing tools to support fundamental and translational research on bacterial glycans.
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10
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Zhu S, Gao B, Umetsu Y, Peigneur S, Li P, Ohki S, Tytgat J. Adaptively evolved human oral actinomyces-sourced defensins show therapeutic potential. EMBO Mol Med 2021; 14:e14499. [PMID: 34927385 PMCID: PMC8819291 DOI: 10.15252/emmm.202114499] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
The development of eukaryote‐derived antimicrobial peptides as systemically administered drugs has proven a challenging task. Here, we report the first human oral actinomyces‐sourced defensin—actinomycesin—that shows promise for systemic therapy. Actinomycesin and its homologs are only present in actinobacteria and myxobacteria, and share similarity with a group of ancient invertebrate‐type defensins reported in fungi and invertebrates. Signatures of natural selection were detected in defensins from the actinomyces colonized in human oral cavity and ruminant rumen and dental plaque, highlighting their role in adaptation to complex multispecies bacterial communities. Consistently, actinomycesin exhibited potent antibacterial activity against oral bacteria and clinical isolates of Staphylococcus and synergized with two classes of human salivary antibacterial factors. Actinomycesin specifically inhibited bacterial peptidoglycan synthesis and displayed weak immunomodulatory activity and low toxicity on human and mammalian cells and ion channels in the heart and central nervous system. Actinomycesin was highly efficient in mice infected with Streptococcus pneumoniae and mice with MRSA‐induced experimental peritoneal infection. This work identifies human oral bacteria as a new source of systemic anti‐infective drugs.
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Affiliation(s)
- Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yoshitaka Umetsu
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Nomi, Japan
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven, Leuven, Belgium
| | - Ping Li
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), National Center for Nanoscience and Technology, Beijing, China
| | - Shinya Ohki
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Nomi, Japan
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven, Leuven, Belgium
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11
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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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12
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Baker BR, Ives CM, Bray A, Caffrey M, Cochrane SA. Undecaprenol kinase: Function, mechanism and substrate specificity of a potential antibiotic target. Eur J Med Chem 2020; 210:113062. [PMID: 33310291 DOI: 10.1016/j.ejmech.2020.113062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
The bifunctional undecaprenol kinase/phosphatase (UdpK) is a small, prokaryotic, integral membrane kinase, homologous with Escherichia coli diacylglycerol kinase and expressed by the dgkA gene. In Gram-positive bacteria, UdpK is involved in the homeostasis of the bacterial undecaprenoid pool, where it converts undecaprenol to undecaprenyl phosphate (C55P) and also catalyses the reverse process. C55P is the universal lipid carrier and critical to numerous glycopolymer and glycoprotein biosynthetic pathways in bacteria. DgkA gene expression has been linked to facilitating bacterial growth and survival in response to environmental stressors, as well being implicated as a resistance mechanism to the topical antibiotic bacitracin, by providing an additional route to C55P. Therefore, identification of UdpK inhibitors could lead to novel antibiotic treatments. A combination of homology modelling and mutagenesis experiments on UdpK have been used to identify residues that may be involved in kinase/phosphatase activity. In this review, we will summarise recent work on the mechanism and substrate specificity of UdpK.
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Affiliation(s)
- Brad R Baker
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Callum M Ives
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland; Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Ashley Bray
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland.
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK.
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13
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Affiliation(s)
- Yuan Xu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences Nanyang Technological University Singapore
| | - Xue‐Wei Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences Nanyang Technological University Singapore
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14
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Assembly of Peptidoglycan Fragments-A Synthetic Challenge. Pharmaceuticals (Basel) 2020; 13:ph13110392. [PMID: 33203094 PMCID: PMC7696421 DOI: 10.3390/ph13110392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/19/2022] Open
Abstract
Peptidoglycan (PGN) is a major constituent of most bacterial cell walls that is recognized as a primary target of the innate immune system. The availability of pure PGN molecules has become key to different biological studies. This review aims to (1) provide an overview of PGN biosynthesis, focusing on the main biosynthetic intermediates; (2) focus on the challenges for chemical synthesis posed by the unique and complex structure of PGN; and (3) cover the synthetic routes of PGN fragments developed to date. The key difficulties in the synthesis of PGN molecules mainly involve stereoselective glycosylation involving NAG derivatives. The complex synthesis of the carbohydrate backbone commonly involves multistep sequences of chemical reactions to install the lactyl moiety at the O-3 position of NAG derivatives and to control enantioselective glycosylation. Recent advances are presented and synthetic routes are described according to the main strategy used: (i) based on the availability of starting materials such as glucosamine derivatives; (ii) based on a particular orthogonal synthesis; and (iii) based on the use of other natural biopolymers as raw materials.
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15
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Wingen LM, Rausch M, Schneider T, Menche D. Modular Total Synthesis of Farnesyl Analogues of Cell Wall Precursors Lipid I and II Containing the Staphylococcus aureus Pentaglycine Bridge Modification. J Org Chem 2020; 85:10206-10215. [PMID: 32571025 DOI: 10.1021/acs.joc.0c01004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A scalable and modular total synthesis of 3-lipid I and 3-lipid II was accomplished by a novel route involving an efficient solid phase synthesis of the peptide fragment and an effective chemoenzymatic attachment of the second sugar moiety. The generality of this route was further documented by the synthesis of an analogue bearing the pentaglycine interpeptidic bridge modification characteristic for the human pathogen Staphylococcus aureus.
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Affiliation(s)
- Lukas M Wingen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany
| | - Marvin Rausch
- Institute for Pharmaceutical Microbiology, University Clinic Bonn, University of Bonn, 53115 Bonn, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Clinic Bonn, University of Bonn, 53115 Bonn, Germany
| | - Dirk Menche
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany
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16
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Mitachi K, Yun HG, Gillman CD, Skorupinska-Tudek K, Swiezewska E, Clemons WM, Kurosu M. Substrate Tolerance of Bacterial Glycosyltransferase MurG: Novel Fluorescence-Based Assays. ACS Infect Dis 2020; 6:1501-1516. [PMID: 31769280 DOI: 10.1021/acsinfecdis.9b00242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MurG (uridine diphosphate-N-acetylglucosamine/N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase) is an essential bacterial glycosyltransferase that catalyzes the N-acetylglucosamine (GlcNAc) transformation of lipid I to lipid II during peptidoglycan biosynthesis. Park's nucleotide has been a convenient biochemical tool to study the function of MraY (phospho-MurNAc-(pentapeptide) translocase) and MurG; however, no fluorescent probe has been developed to differentiate individual processes in the biotransformation of Park's nucleotide to lipid II via lipid I. Herein, we report a robust assay of MurG using either the membrane fraction of a M. smegmatis strain or a thermostable MraY and MurG of Hydrogenivirga sp. as enzyme sources, along with Park's nucleotide or Park's nucleotide-Nε-C6-dansylthiourea and uridine diphosphate (UDP)-GlcN-C6-FITC as acceptor and donor substrates. Identification of both the MraY and MurG products can be performed simultaneously by HPLC in dual UV mode. Conveniently, the generated lipid II fluorescent analogue can also be quantitated via UV-Vis spectrometry without the separation of the unreacted lipid I derivative. The microplate-based assay reported here is amenable to high-throughput MurG screening. A preliminary screening of a collection of small molecules has demonstrated the robustness of the assays and resulted in rediscovery of ristocetin A as a strong antimycobacterial MurG and MraY inhibitor.
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Hyun Gi Yun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Cody D. Gillman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Karolina Skorupinska-Tudek
- Department of Lipid Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Ewa Swiezewska
- Department of Lipid Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - William M. Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
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17
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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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18
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He JX, Le Mai Hoang K, Kho SH, Guo Z, Zhong W, Venkata Thappeta KR, Zamudio-Vázquez R, Hoo SN, Xiong Q, Duan H, Yang L, Chan-Park MB, Liu XW. Synthetic biohybrid peptidoglycan oligomers enable pan-bacteria-specific labeling and imaging: in vitro and in vivo. Chem Sci 2020; 11:3171-3179. [PMID: 34122822 PMCID: PMC8157403 DOI: 10.1039/c9sc06345e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Peptidoglycan is the core component of the bacterial cell wall, which makes it an attractive target for the development of bacterial targeting agents. Intercepting its enzymatic assembly with synthetic substrates allows for labeling and engineering of live bacterial cells. Over the past two decades, small-molecule-based labeling agents, such as antibiotics, d-amino acids or monosaccharides have been developed for probing biological processes in bacteria. Herein, peptidoglycan oligomers, substrates for transglycosylation, are prepared for the first time using a top-down approach, which starts from chitosan as a cheap feedstock. A high efficiency of labeling has been observed in all bacterial strains tested using micromolar substrates. In contrast, uptake into mammalian cells was barely observable. Additional mechanistic studies support a hypothesis of bacteria-specific metabolic labeling rather than non-specific binding to the bacterial surface. Eventually, its practicality in bacterial targeting capability is demonstrated in resistant strain detection and in vivo infection models.
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Affiliation(s)
- Jing-Xi He
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore .,School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Kim Le Mai Hoang
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
| | - Shu Hui Kho
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore .,NTU Institute for Health Technologies, Nanyang Technological University Singapore
| | - Zhong Guo
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
| | - Wenbin Zhong
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Kishore Reddy Venkata Thappeta
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Rubí Zamudio-Vázquez
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Sin Ni Hoo
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
| | - Qirong Xiong
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Hongwei Duan
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology Shenzhen 518055 China
| | - Mary B Chan-Park
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Xue-Wei Liu
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
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19
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Do T, Page JE, Walker S. Uncovering the activities, biological roles, and regulation of bacterial cell wall hydrolases and tailoring enzymes. J Biol Chem 2020; 295:3347-3361. [PMID: 31974163 DOI: 10.1074/jbc.rev119.010155] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteria account for 1000-fold more biomass than humans. They vary widely in shape and size. The morphological diversity of bacteria is due largely to the different peptidoglycan-based cell wall structures that encase bacterial cells. Although the basic structure of peptidoglycan is highly conserved, consisting of long glycan strands that are cross-linked by short peptide chains, the mature cell wall is chemically diverse. Peptidoglycan hydrolases and cell wall-tailoring enzymes that regulate glycan strand length, the degree of cross-linking, and the addition of other modifications to peptidoglycan are central in determining the final architecture of the bacterial cell wall. Historically, it has been difficult to biochemically characterize these enzymes that act on peptidoglycan because suitable peptidoglycan substrates were inaccessible. In this review, we discuss fundamental aspects of bacterial cell wall synthesis, describe the regulation and diverse biochemical and functional activities of peptidoglycan hydrolases, and highlight recently developed methods to make and label defined peptidoglycan substrates. We also review how access to these substrates has now enabled biochemical studies that deepen our understanding of how bacterial cell wall enzymes cooperate to build a mature cell wall. Such improved understanding is critical to the development of new antibiotics that disrupt cell wall biogenesis, a process essential to the survival of bacteria.
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Affiliation(s)
- Truc Do
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Julia E Page
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115.
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20
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Cochrane RVK, Alexander FM, Boland C, Fetics SK, Caffrey M, Cochrane SA. From plant to probe: semi-synthesis of labelled undecaprenol analogues allows rapid access to probes for antibiotic targets. Chem Commun (Camb) 2020; 56:8603-8606. [DOI: 10.1039/d0cc03388j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Extraction of undecaprenol from bay leaves followed by synthetic modification is a convenient method to obtain novel chemical probes.
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Affiliation(s)
| | | | - Coilín Boland
- School of Medicine and School of Biochemistry and Immunology
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Susan K. Fetics
- School of Medicine and School of Biochemistry and Immunology
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Stephen A. Cochrane
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast
- UK
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21
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Taguchi A, Kahne D, Walker S. Chemical tools to characterize peptidoglycan synthases. Curr Opin Chem Biol 2019; 53:44-50. [PMID: 31466035 DOI: 10.1016/j.cbpa.2019.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 02/02/2023]
Abstract
The peptidoglycan cell wall is a unique macromolecular structure in bacteria that defines their shape and confers protection from the surrounding environment. Decades of research has focused on understanding the peptidoglycan synthesis pathway and exploiting its essentiality for antibiotic development. Recently, a new class of peptidoglycan polymerases known as the SEDS (shape, elongation, division and sporulation) proteins were identified; these polytopic membrane proteins function together with the better-known penicillin-binding proteins (PBPs) to build the cell wall. In this review, we will highlight recent developments in chemical tools and methods to label the bacterial cell wall and discuss how these developments are leading to a better understanding of peptidoglycan synthases and their cellular roles.
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Affiliation(s)
- Atsushi Taguchi
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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22
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Abstract
The translation of biological glycosylation in humans to the clinical applications involves systematic studies using homogeneous samples of oligosaccharides and glycoconjugates, which could be accessed by chemical, enzymatic or other biological methods. However, the structural complexity and wide-range variations of glycans and their conjugates represent a major challenge in the synthesis of this class of biomolecules. To help navigate within many methods of oligosaccharide synthesis, this Perspective offers a critical assessment of the most promising synthetic strategies with an eye on the therapeutically relevant targets.
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Affiliation(s)
- Larissa Krasnova
- Department of Chemistry , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States
| | - Chi-Huey Wong
- Department of Chemistry , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States.,Genomics Research Center, Academia Sinica , Taipei 115 , Taiwan
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23
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Fonvielle M, Bouhss A, Hoareau C, Patin D, Mengin-Lecreulx D, Iannazzo L, Sakkas N, El Sagheer A, Brown T, Ethève-Quelquejeu M, Arthur M. Synthesis of Lipid-Carbohydrate-Peptidyl-RNA Conjugates to Explore the Limits Imposed by the Substrate Specificity of Cell Wall Enzymes on the Acquisition of Drug Resistance. Chemistry 2018; 24:14911-14915. [PMID: 30020544 DOI: 10.1002/chem.201802360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/16/2018] [Indexed: 01/10/2023]
Abstract
Conjugation of RNA with multiple partners to obtain mimics of complex biomolecules is limited by the identification of orthogonal reactions. Here, lipid-carbohydrate-peptidyl-RNA conjugates were obtained by post-functionalization reactions, solid-phase synthesis, and enzymatic steps, to generate molecules mimicking the substrates of FmhB, an essential peptidoglycan synthesis enzyme of Staphylococcus aureus. Mimics of Gly-tRNAGly and lipid intermediate II (undecaprenyl-diphospho-disaccharide-pentapeptide) were combined in a single "bi-substrate" inhibitor (IC50 =56 nm). The synthetic route was exploited to generate substrates and inhibitors containing d-lactate residue (d-Lac) instead of d-Ala at the C-terminus of the pentapeptide stem, a modification responsible for vancomycin resistance in the enterococci. The substitution impaired recognition of peptidoglycan precursors by FmhB. The associated fitness cost may account for limited dissemination of vancomycin resistance genes in S. aureus.
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Affiliation(s)
- Matthieu Fonvielle
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06;, 'Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Ahmed Bouhss
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Present address: Laboratoire Structure-Activité des Biomolécules, Normales et Pathologiques (SABNP), Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Coralie Hoareau
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06;, 'Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Nicolas Sakkas
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Affaf El Sagheer
- Chemistry Branch, Dept. of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt.,Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Michel Arthur
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06;, 'Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, 75006, Paris, France
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24
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Pertel SS, Seryi SA, Kakayan ES. A new approach to the synthesis of lactams of muramic, isomuramic and normuramic acids via intramolecular O-alkylation: Stereochemical features of the intramolecular nucleophilic substitution. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.07.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Wang X, Krasnova L, Wu KB, Wu WS, Cheng TJ, Wong CH. Towards new antibiotics targeting bacterial transglycosylase: Synthesis of a Lipid II analog as stable transition-state mimic inhibitor. Bioorg Med Chem Lett 2018; 28:2708-2712. [PMID: 29602680 PMCID: PMC6182773 DOI: 10.1016/j.bmcl.2018.03.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
Abstract
Described here is the asymmetric synthesis of iminosugar 2b, a Lipid II analog, designed to mimic the transition state of transglycosylation catalyzed by the bacterial transglycosylase. The high density of functional groups, together with a rich stereochemistry, represents an extraordinary challenge for chemical synthesis. The key 2,6-anti- stereochemistry of the iminosugar ring was established through an iridium-catalyzed asymmetric allylic amination. The developed synthetic route is suitable for the synthesis of focused libraries to enable the structure-activity relationship study and late-stage modification of iminosugar scaffold with variable lipid, peptide and sugar substituents. Compound 2b showed 70% inhibition of transglycosylase from Acinetobacter baumannii, providing a basis for further improvement.
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Affiliation(s)
- Xiaolei Wang
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA
| | - Larissa Krasnova
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA
| | - Kevin Binchia Wu
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA
| | - Wei-Shen Wu
- Genomics Research Center, Academia Sinica, 128 Sec 2 Academia Road, Taipei, Nankang 115, Taiwan
| | - Ting-Jen Cheng
- Genomics Research Center, Academia Sinica, 128 Sec 2 Academia Road, Taipei, Nankang 115, Taiwan
| | - Chi-Huey Wong
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92122, USA; Genomics Research Center, Academia Sinica, 128 Sec 2 Academia Road, Taipei, Nankang 115, Taiwan.
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26
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Kawakami N, Fujisaki S. Undecaprenyl phosphate metabolism in Gram-negative and Gram-positive bacteria. Biosci Biotechnol Biochem 2018; 82:940-946. [DOI: 10.1080/09168451.2017.1401915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Undecaprenyl phosphate (UP) is essential for the biosynthesis of bacterial extracellular polysaccharides. UP is produced by the dephosphorylation of undecaprenyl diphosphate (UPP) via de novo synthetic and recycling pathways. Gram-positive bacteria contain remarkable amounts of undecaprenol (UOH), which is phosphorylated to UP, although UOH has not been found in Gram-negative bacteria. Here, current knowledge about UPP phosphatase and UOH kinase is reviewed. Dephosphorylation of UPP is catalyzed by a BacA homologue and a type-2 phosphatidic acid phosphatase (PAP2) homologue. The presence of one of these UPP phosphatases is essential for bacterial growth. The catalytic center of both types of enzyme is located outside the cytoplasmic membrane. In Gram-positive bacteria, an enzyme homologous to DgkA, which is the diacylglycerol kinase of Escherichia coli, catalyzes UOH phosphorylation. The possible role of UOH and the significance of systematic construction of Staphylococcus aureus mutants to determine UP metabolism are discussed.
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Affiliation(s)
- Naoki Kawakami
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Shingo Fujisaki
- Faculty of Science, Department of Biomolecular Science, Toho University, Funabashi, Japan
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27
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Ngadjeua F, Braud E, Saidjalolov S, Iannazzo L, Schnappinger D, Ehrt S, Hugonnet JE, Mengin-Lecreulx D, Patin D, Ethève-Quelquejeu M, Fonvielle M, Arthur M. Critical Impact of Peptidoglycan Precursor Amidation on the Activity ofl,d-Transpeptidases fromEnterococcus faeciumandMycobacterium tuberculosis. Chemistry 2018; 24:5743-5747. [DOI: 10.1002/chem.201706082] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Flora Ngadjeua
- INSERM UMRS 1138; Sorbonne Universités UPMC Univ Paris 06
- Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot
- Centre de Recherche des Cordeliers; 75006 Paris France
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie, Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris 75005 France
- CNRS UMR 8601; Paris 75006 France
| | - Saidbakhrom Saidjalolov
- Laboratoire de Chimie et de Biochimie, Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris 75005 France
- CNRS UMR 8601; Paris 75006 France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie, Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris 75005 France
- CNRS UMR 8601; Paris 75006 France
| | - Dirk Schnappinger
- Department of Microbiology and Immunology; Weill Cornell Medical College; New York NY 10021 USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology; Weill Cornell Medical College; New York NY 10021 USA
| | - Jean-Emmanuel Hugonnet
- INSERM UMRS 1138; Sorbonne Universités UPMC Univ Paris 06
- Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot
- Centre de Recherche des Cordeliers; 75006 Paris France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie, Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris 75005 France
- CNRS UMR 8601; Paris 75006 France
| | - Matthieu Fonvielle
- INSERM UMRS 1138; Sorbonne Universités UPMC Univ Paris 06
- Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot
- Centre de Recherche des Cordeliers; 75006 Paris France
| | - Michel Arthur
- INSERM UMRS 1138; Sorbonne Universités UPMC Univ Paris 06
- Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot
- Centre de Recherche des Cordeliers; 75006 Paris France
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28
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Lee M, Hesek D, Zajíček J, Fisher JF, Mobashery S. Synthesis and shift-reagent-assisted full NMR assignment of bacterial (Z 8,E 2,ω)-undecaprenol. Chem Commun (Camb) 2017; 53:12774-12777. [PMID: 29139490 PMCID: PMC5749266 DOI: 10.1039/c7cc06781j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The repeating isoprene unit is a fundamental biosynthetic motif. The repetitive structure presents challenges both for synthesis and for structural characterization. In this synthesis of the (Z8,E2,ω)-undecaprenol of prokaryotic glycobiology, we exemplify solutions to these challenges. Allylation of sulfone-derived carbanions controlled the stereochemistry, and its proof-of-structure was secured by Eu(hfc)3 complexation to disperse the overlaid resonances of its 1H NMR spectrum.
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Affiliation(s)
- Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.
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29
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Huang LY, Wang SC, Cheng TJR, Wong CH. Undecaprenyl Phosphate Phosphatase Activity of Undecaprenol Kinase Regulates the Lipid Pool in Gram-Positive Bacteria. Biochemistry 2017; 56:5417-5427. [PMID: 28872301 DOI: 10.1021/acs.biochem.7b00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria cell walls contain many repeating glycan structures, such as peptidoglycans, lipopolysaccharides, teichoic acids, and capsular polysaccharides. Their synthesis starts in the cytosol, and they are constructed from a glycan lipid carrier, undecaprenyl phosphate (C55P), which is essential for cell growth and survival. The lipid derivative undecaprenol (C55OH) is predominant in many Gram-positive bacteria but has not been detected in Gram-negative bacteria; its origin and role have thus remained unknown. Recently, a homologue of diacylglycerol kinase (DgkA) in Escherichia coli (E. coli) was demonstrated to be an undecaprenol kinase (UK) in the Gram-positive bacterium Streptococcus mutans (S. mutans). In this study, we found that S. mutans UK was not only an undecaprenol kinase but also a Mg-ADP-dependent undecaprenyl phosphate phosphatase (UpP), catalyzing the hydrolysis of C55P to C55OH and a free inorganic phosphate. Furthermore, the naturally undetectable C55OH was observed in E. coli cells expressing S. mutans dgkA, supporting the phosphatase activity of UK/UpP in vivo. These two activities were indispensable to each other and utilized identical essential residues binding to their substrates, suggesting that both activities share the same active site and might involve a direct phosphoryl transfer mechanism. This study revealed a unique membrane enzyme displaying bifunctional activities determined by substrate binding and C55OH production. The reciprocal conversion of C55P and the undecaprenol pool efficiently regulate cell wall synthesis, especially in Gram-positive bacteria.
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Affiliation(s)
- Lin-Ya Huang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
| | - Shih-Chi Wang
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
| | | | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University , Taipei 112, Taiwan
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30
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Srisuknimit V, Qiao Y, Schaefer K, Kahne D, Walker S. Peptidoglycan Cross-Linking Preferences of Staphylococcus aureus Penicillin-Binding Proteins Have Implications for Treating MRSA Infections. J Am Chem Soc 2017; 139:9791-9794. [PMID: 28691491 PMCID: PMC5613940 DOI: 10.1021/jacs.7b04881] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infections are a global public health problem. MRSA strains have acquired a non-native penicillin-binding protein called PBP2a that cross-links peptidoglycan when the native S. aureus PBPs are inhibited by β-lactams. It has been proposed that the native S. aureus PBPs can use cell wall precursors having different glycine branch lengths (penta-, tri-, or monoglycine), while PBP2a can only cross-link peptidoglycan strands bearing a complete pentaglycine branch. This hypothesis has never been tested because the necessary substrates have not been available. Here, we compared the ability of PBP2a and two native S. aureus transpeptidases to cross-link peptidoglycan strands bearing different glycine branches. We show that purified PBP2a can cross-link glycan strands bearing penta- and triglycine, but not monoglycine, and experiments in cells provide support for these findings. Because PBP2a cannot cross-link peptidoglycan containing monoglycine, this study implicates the enzyme (FemA) that extends the monoglycine branch to triglycine on Lipid II as an ideal target for small molecules that restore sensitivity of MRSA to β-lactams.
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Affiliation(s)
- Veerasak Srisuknimit
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Yuan Qiao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, 02138, United States
| | - Kaitlin Schaefer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, 02138, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Suzanne Walker
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, 02138, United States
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31
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Qiao Y, Srisuknimit V, Rubino F, Schaefer K, Ruiz N, Walker S, Kahne D. Lipid II overproduction allows direct assay of transpeptidase inhibition by β-lactams. Nat Chem Biol 2017; 13:793-798. [PMID: 28553948 PMCID: PMC5478438 DOI: 10.1038/nchembio.2388] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/13/2017] [Indexed: 01/07/2023]
Abstract
Peptidoglycan is an essential crosslinked polymer that surrounds bacteria and protects them from osmotic lysis. Beta-lactam antibiotics target the final stages of peptidoglycan biosynthesis by inhibiting the transpeptidases that crosslink glycan strands to complete cell wall assembly. Characterization of transpeptidases and their inhibition by beta-lactams has been hampered by lack of access to substrate. We describe a general approach to accumulate Lipid II in bacteria and to obtain large quantities of this cell wall precursor. We demonstrate utility by isolating Staphylococcus aureus Lipid II and reconstituting the synthesis of crosslinked peptidoglycan by the essential penicillin-binding protein 2, PBP2, which catalyzes both glycan polymerization and transpeptidation. We also show that we can compare the potencies of different beta-lactams by directly monitoring transpeptidase inhibition. The methods reported here will enable a better understanding of cell wall biosynthesis and facilitate studies of next-generation transpeptidase inhibitors.
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Affiliation(s)
- Yuan Qiao
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Veerasak Srisuknimit
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Frederick Rubino
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Kaitlin Schaefer
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Natividad Ruiz
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Suzanne Walker
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
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32
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Wohnig S, Spork AP, Koppermann S, Mieskes G, Gisch N, Jahn R, Ducho C. Total Synthesis of Dansylated Park's Nucleotide for High-Throughput MraY Assays. Chemistry 2016; 22:17813-17819. [PMID: 27791327 DOI: 10.1002/chem.201604279] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 11/11/2022]
Abstract
The membrane protein translocase I (MraY) is a key enzyme in bacterial peptidoglycan biosynthesis. It is therefore frequently discussed as a target for the development of novel antibiotics. The screening of compound libraries for the identification of MraY inhibitors is enabled by an established fluorescence-based MraY assay. However, this assay requires a dansylated derivative of the bacterial biosynthetic intermediate Park's nucleotide as the MraY substrate. Isolation of Park's nucleotide from bacteria and subsequent dansylation only furnishes limited amounts of this substrate, thus hampering the high-throughput screening for MraY inhibitors. Accordingly, the efficient provision of dansylated Park's nucleotide is a major bottleneck in the exploration of this promising drug target. In this work, we present the first total synthesis of dansylated Park's nucleotide, affording an unprecedented amount of the target compound for high-throughput MraY assays.
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Affiliation(s)
- Stephanie Wohnig
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Anatol P Spork
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany.,Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Gottfried Mieskes
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, 23845, Borstel, Germany
| | - Reinhard Jahn
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
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33
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Structural Investigation of Park's Nucleotide on Bacterial Translocase MraY: Discovery of Unexpected MraY Inhibitors. Sci Rep 2016; 6:31579. [PMID: 27531195 PMCID: PMC4987650 DOI: 10.1038/srep31579] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/26/2016] [Indexed: 11/17/2022] Open
Abstract
Systematic structural modifications of the muramic acid, peptide, and nucleotide moieties of Park’s nucleotide were performed to investigate the substrate specificity of B. subtilis MraY (MraYBS). It was found that the simplest analogue of Park’s nucleotide only bearing the first two amino acids, l-alanine-iso-d-glutamic acid, could function as a MraYBS substrate. Also, the acid group attached to the Cα of iso-d-glutamic acid was found to play an important role for substrate activity. Epimerization of the C4-hydroxyl group of muramic acid and modification at the 5-position of the uracil in Park’s nucleotide were both found to dramatically impair their substrate activity. Unexpectedly, structural modifications on the uracil moiety changed the parent molecule from a substrate to an inhibitor, blocking the MraYBS translocation. One unoptimized inhibitor was found to have a Ki value of 4 ± 1 μM against MraYBS, more potent than tunicamycins.
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34
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Ng V, Chan WC. New Found Hope for Antibiotic Discovery: Lipid II Inhibitors. Chemistry 2016; 22:12606-16. [PMID: 27388768 DOI: 10.1002/chem.201601315] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/14/2022]
Abstract
Research into antibacterial agents has recently gathered pace in light of the disturbing crisis of antimicrobial resistance. The development of modern tools offers the opportunity of reviving the fallen era of antibacterial discovery through uncovering novel lead compounds that target vital bacterial cell components, such as lipid II. This paper provides a summary of the role of lipid II as well as an overview and insight into the structural features of macrocyclic peptides that inhibit this bacterial cell wall component. The recent discovery of teixobactin, a new class of lipid II inhibitor has generated substantial research interests. As such, the significant progress that has been achieved towards its development as a promising antibacterial agent is discussed.
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Affiliation(s)
- Vivian Ng
- School of Pharmacy, Centre of Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Weng C Chan
- School of Pharmacy, Centre of Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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35
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Li L, Woodward RL, Han W, Qu J, Song J, Ma C, Wang PG. Chemoenzymatic synthesis of the bacterial polysaccharide repeating unit undecaprenyl pyrophosphate and its analogs. Nat Protoc 2016; 11:1280-98. [PMID: 27336706 DOI: 10.1038/nprot.2016.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polysaccharides are essential and immunologically relevant components of bacterial cell walls. These biomolecules can be found covalently attached to lipids (e.g., O-polysaccharide (PS) contains undecaprenyl and lipopolysaccharide (LPS) contains lipid A) or noncovalently associated with cell wells (e.g., capsular PS (CPS)). Although extensive genetic studies have indicated that the Wzy-dependent biosynthetic pathway is primarily responsible for producing such polysaccharides, in vitro biochemical studies are needed to determine, for example, which gene product is responsible for catalyzing each step in the pathway, and to reveal molecular details about the Wzx translocase, Wzy polymerase and O-PS chain-length determinant. Many of these biochemical studies require access to a structurally well-defined PS repeating unit undecaprenyl pyrophosphate (RU-PP-Und), the key building block in this pathway. We describe herein the chemoenzymatic synthesis of Escherichia coli (serotype O157) RU-PP-Und. This involves (i) chemical synthesis of precursor N-acetyl-D-galactosamine (GalNAc)-PP-Und (2 weeks) and (ii) enzymatic extension of the precursor to produce RU-PP-Und (2 weeks). Undecaprenyl phosphate and peracetylated GalNAc-1-phosphate are prepared from commercially available undecaprenol and peracetylated GalNAc. The chemical coupling of these two products, followed by structural confirmation (mass spectrometry and NMR) and deprotection, generates GalNAc-PP-Und. This compound is then sequentially modified by enzymes in the E. coli serotype O157 (E. coli O157) O-PS biosynthetic pathway. Three glycosyltransferases (GTs) are involved (WbdN, WbdO and WbdP) and they transfer glucose (Glc), L-fucose (L-Fuc) and N-acetylperosamine (PerNAc) onto GalNAc-PP-Und to form the intact RU-PP-Und in a stepwise manner. Final compounds and intermediates are confirmed by mass spectrometry. The procedure can be adapted to the synthesis of analogs with different PS or lipid moieties.
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Affiliation(s)
- Lei Li
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Robert L Woodward
- Department of Chemistry and Biochemistry, University of Mount Union, Alliance, Ohio, USA
| | - Weiqing Han
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Jingyao Qu
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Jing Song
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Cheng Ma
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Peng G Wang
- Department of Chemistry and Center for Diagnostics &Therapeutics, Georgia State University, Atlanta, Georgia, USA
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36
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Krasnova L, Wong CH. Understanding the Chemistry and Biology of Glycosylation with Glycan Synthesis. Annu Rev Biochem 2016; 85:599-630. [DOI: 10.1146/annurev-biochem-060614-034420] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Larissa Krasnova
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037;
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037;
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, 115
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37
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Liu Y, Rodrigues JPGLM, Bonvin AMJJ, Zaal EA, Berkers CR, Heger M, Gawarecka K, Swiezewska E, Breukink E, Egmond MR. New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies. J Biol Chem 2016; 291:15057-68. [PMID: 27226570 DOI: 10.1074/jbc.m116.717884] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Indexed: 01/01/2023] Open
Abstract
Phospho-MurNAc-pentapeptide translocase (MraY) catalyzes the synthesis of Lipid I, a bacterial peptidoglycan precursor. As such, MraY is essential for bacterial survival and therefore is an ideal target for developing novel antibiotics. However, the understanding of its catalytic mechanism, despite the recently determined crystal structure, remains limited. In the present study, the kinetic properties of Bacillus subtilis MraY (BsMraY) were investigated by fluorescence enhancement using dansylated UDP-MurNAc-pentapeptide and heptaprenyl phosphate (C35-P, short-chain homolog of undecaprenyl phosphate, the endogenous substrate of MraY) as second substrate. Varying the concentrations of both of these substrates and fitting the kinetics data to two-substrate models showed that the concomitant binding of both UDP-MurNAc-pentapeptide-DNS and C35-P to the enzyme is required before the release of the two products, Lipid I and UMP. We built a model of BsMraY and performed docking studies with the substrate C35-P to further deepen our understanding of how MraY accommodates this lipid substrate. Based on these modeling studies, a novel catalytic role was put forward for a fully conserved histidine residue in MraY (His-289 in BsMraY), which has been experimentally confirmed to be essential for MraY activity. Using the current model of BsMraY, we propose that a small conformational change is necessary to relocate the His-289 residue, such that the translocase reaction can proceed via a nucleophilic attack of the phosphate moiety of C35-P on bound UDP-MurNAc-pentapeptide.
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Affiliation(s)
- Yao Liu
- From Institute of Biomembranes, Department of Membrane Biochemistry and Biophysics, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | | | | | - Esther A Zaal
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Celia R Berkers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Michal Heger
- the Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands, and
| | - Katarzyna Gawarecka
- the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Ewa Swiezewska
- the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Eefjan Breukink
- From Institute of Biomembranes, Department of Membrane Biochemistry and Biophysics, Utrecht University, 3584 CH, Utrecht, the Netherlands,
| | - Maarten R Egmond
- From Institute of Biomembranes, Department of Membrane Biochemistry and Biophysics, Utrecht University, 3584 CH, Utrecht, the Netherlands
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38
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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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39
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Henrich E, Ma Y, Engels I, Münch D, Otten C, Schneider T, Henrichfreise B, Sahl HG, Dötsch V, Bernhard F. Lipid Requirements for the Enzymatic Activity of MraY Translocases and in Vitro Reconstitution of the Lipid II Synthesis Pathway. J Biol Chem 2015; 291:2535-46. [PMID: 26620564 DOI: 10.1074/jbc.m115.664292] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 12/19/2022] Open
Abstract
Screening of new compounds directed against key protein targets must continually keep pace with emerging antibiotic resistances. Although periplasmic enzymes of bacterial cell wall biosynthesis have been among the first drug targets, compounds directed against the membrane-integrated catalysts are hardly available. A promising future target is the integral membrane protein MraY catalyzing the first membrane associated step within the cytoplasmic pathway of bacterial peptidoglycan biosynthesis. However, the expression of most MraY homologues in cellular expression systems is challenging and limits biochemical analysis. We report the efficient production of MraY homologues from various human pathogens by synthetic cell-free expression approaches and their subsequent characterization. MraY homologues originating from Bordetella pertussis, Helicobacter pylori, Chlamydia pneumoniae, Borrelia burgdorferi, and Escherichia coli as well as Bacillus subtilis were co-translationally solubilized using either detergent micelles or preformed nanodiscs assembled with defined membranes. All MraY enzymes originating from Gram-negative bacteria were sensitive to detergents and required nanodiscs containing negatively charged lipids for obtaining a stable and functionally folded conformation. In contrast, the Gram-positive B. subtilis MraY not only tolerates detergent but is also less specific for its lipid environment. The MraY·nanodisc complexes were able to reconstitute a complete in vitro lipid I and lipid II forming pipeline in combination with the cell-free expressed soluble enzymes MurA-F and with the membrane-associated protein MurG. As a proof of principle for future screening platforms, we demonstrate the inhibition of the in vitro lipid II biosynthesis with the specific inhibitors fosfomycin, feglymycin, and tunicamycin.
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Affiliation(s)
- Erik Henrich
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany
| | - Yi Ma
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany, the School of Bioscience and Bioengineering, South China University of Technology, 510006 Guangzhou, China,
| | - Ina Engels
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and the German Centre for Infection Research (DZIF), partner site Cologne-Bonn, 53115 Bonn, Germany
| | - Daniela Münch
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and
| | - Christian Otten
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and
| | - Tanja Schneider
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and the German Centre for Infection Research (DZIF), partner site Cologne-Bonn, 53115 Bonn, Germany
| | - Beate Henrichfreise
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and
| | - Hans-Georg Sahl
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and the German Centre for Infection Research (DZIF), partner site Cologne-Bonn, 53115 Bonn, Germany
| | - Volker Dötsch
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany
| | - Frank Bernhard
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany,
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40
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Gale RT, Brown ED. New chemical tools to probe cell wall biosynthesis in bacteria. Curr Opin Microbiol 2015; 27:69-77. [PMID: 26291270 DOI: 10.1016/j.mib.2015.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/23/2015] [Accepted: 07/30/2015] [Indexed: 12/25/2022]
Abstract
Some of the most successful drugs in the antibiotic pharmacopeia are those that inhibit bacterial cell wall biosynthesis. However, the worldwide spread of bacterial antibiotic resistance has eroded the clinical efficacy of these drugs and the antibiotic pipeline continues to be lean as drug discovery programs struggle to bring new agents to the clinic. Nevertheless, cell wall biogenesis remains a high interest and celebrated target. Recent advances in the preparation of chemical probes and biosynthetic intermediates provide the tools necessary to better understand cell wall assembly. Likewise, these tools offer new opportunities to identify and evaluate novel biosynthetic inhibitors. This review aims to highlight these advancements and to provide context for their utility as innovative new tools to study cell wall biogenesis and for antibacterial drug discovery.
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Affiliation(s)
- Robert T Gale
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Eric D Brown
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5.
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