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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Della-Felice F, de Andrade Bartolomeu A, Pilli RA. The phosphate ester group in secondary metabolites. Nat Prod Rep 2022; 39:1066-1107. [PMID: 35420073 DOI: 10.1039/d1np00078k] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2000 to mid-2021The phosphate ester is a versatile, widespread functional group involved in a plethora of biological activities. Its presence in secondary metabolites, however, is relatively rare compared to other functionalities and thus is part of a rather unexplored chemical space. Herein, the chemistry of secondary metabolites containing the phosphate ester group is discussed. The text emphasizes their structural diversity, biological and pharmacological profiles, and synthetic approaches employed in the phosphorylation step during total synthesis campaigns, covering the literature from 2000 to mid-2021.
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Affiliation(s)
- Franco Della-Felice
- Institute of Chemistry, University of Campinas (UNICAMP), P.O. Box 6154, CEP 13083-970 Campinas, Sao Paulo, Brazil.,Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain.
| | | | - Ronaldo Aloise Pilli
- Institute of Chemistry, University of Campinas (UNICAMP), P.O. Box 6154, CEP 13083-970 Campinas, Sao Paulo, Brazil
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3
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Goossens K, Neves RP, Fernandes PA, De Winter H. A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes. J Chem Inf Model 2020; 60:5513-5528. [PMID: 32786224 DOI: 10.1021/acs.jcim.0c00377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacterial glycosyltransferases of the GT51 family are key enzymes in bacterial cell wall synthesis. Inhibiting cell wall synthesis is a very effective approach for development of antibiotics, as this can lead to either bacteriostatic or bactericidal effects. Even though the existence of this family has been known for over 50 years, only one potent inhibitor exists, which is an analog of the lipid IV product and derived from a natural product. Drug development focused on bacterial transglycosylase has been hampered due to little being know about its structure and reaction mechanism. In this study, Staphylococcus aureus monoglycosyltransferase was investigated at an atomistic level using computational methods. Classical molecular dynamics simulations were used to reveal information about the large-scale dynamics of the enzyme-substrate complex and the importance of magnesium in structure and function of the protein, while mixed mode quantum mechanics/molecular mechanics calculations unveiled a novel hypothesis for the reaction mechanism. From these results, we present a new model for the binding mode of lipid II and the reaction mechanism of the GT51 glycosyltransferases. A metal-bound hydroxide catalyzed reaction mechanism yields an estimated free energy barrier of 16.1 ± 1.0 kcal/mol, which is in line with experimental values. The importance of divalent cations is also further discussed. These findings could significantly aid targeted drug design, particularly the efficient development of transition state analogues as potential inhibitors for the GT51 glycosyltransferases.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Rui Pp Neves
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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4
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Chen X, Wong CH, Ma C. Targeting the Bacterial Transglycosylase: Antibiotic Development from a Structural Perspective. ACS Infect Dis 2019; 5:1493-1504. [PMID: 31283163 DOI: 10.1021/acsinfecdis.9b00118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
One of the major threats to human life nowadays is widespread antibiotic resistance. Antibiotics are used to treat bacterial infections by targeting their essential pathways, such as the biosynthesis of bacterial cell walls. Bacterial transglycosylase, particularly glycosyltransferase family 51 (GT51), is one critical player in the cell wall biosynthesis and has long been known as a promising yet challenging target for antibiotic development. Here, we review the structural studies of this protein and summarize recent progress in developing its specific inhibitors, including synthetic substrate analogs and novel compounds identified from high-throughput screens. A detailed analysis of the protein-ligand interface has also provided us with valuable insights into the future antibiotic development against the bacterial transglycosylase.
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Affiliation(s)
- Xiaorui Chen
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan
| | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan
| | - Che Ma
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Nangang District, Taipei 115, Taiwan
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5
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Yu JY, Cheng HJ, Wu HR, Wu WS, Lu JW, Cheng TJ, Wu YT, Fang JM. Structure-based design of bacterial transglycosylase inhibitors incorporating biphenyl, amine linker and 2-alkoxy-3-phosphorylpropanoate moieties. Eur J Med Chem 2018; 150:729-741. [PMID: 29574202 DOI: 10.1016/j.ejmech.2018.03.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 01/28/2023]
Abstract
Transglycosylase (TGase) is essential to biosynthesis of peptidoglycan for formation of bacterial cell wall. Moenomycin is a potent TGase inhibitor, but not used in clinic treatment due to its poor pharmacokinetics. The E-F disaccharide, phosphoglycerate and lipid tail in moenomycin are crucial elements for TGase inhibition and antibacterial activity. Based on this scaffold, a series of truncated mimics comprising biphenyl, amine linker and 2-alkoxy-3-phosphorylpropanoate moieties were designed to test their TGase inhibitory activity. In this design, the phosphorylpropanoate group is a surrogate of phosphoglycerate with improved stability. A library of lipid tails can be constructed by a straightforward approach using Cu(I)-catalyzed (3 + 2) cycloaddition reactions, and the as-synthesized triazole ring can provide additional hydrogen bonds in the TGase active site. Our molecular docking experiments reveal that the biphenyl group provides π-π and π-cation interactions to act as a simplified alternative of the C-E disaccharide in moenomycin. To play the role of the oxonium transition state in transglycosylation, the amine linker exists as a positively charged species in physiological condition to attain electrostatic interactions with acidic residues. In this study, two biphenyl-linked 2-alkoxy-3-phosphorylpropanoate compounds (8 and 10) are found to exhibit modest inhibitory activity (IC50 ≈ 150 μM) against the TGase of Acinetobacter baumannii and good antibacterial activity against Staphylococcus aureus (MIC = 6.3 μM).
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Affiliation(s)
- Jui-Yin Yu
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Hsiu-Jung Cheng
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Huei-Ru Wu
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan, ROC
| | - Wei-Shen Wu
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Jui-Wen Lu
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Ting-Jen Cheng
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Ying-Ta Wu
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan, ROC; The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan, ROC.
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6
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Blanchaert B, Palabiyik IM, Gökbulut A, Wang MJ, Dai Z, Wei F, Ma SC, Adams E, Van Schepdael A. Bioanalytical LC/MS study of potential bacterial transglycosylation inhibitors. J Pharm Biomed Anal 2016; 127:123-8. [PMID: 26782294 DOI: 10.1016/j.jpba.2015.12.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/14/2015] [Accepted: 12/24/2015] [Indexed: 11/24/2022]
Abstract
Bacterial transglycosylation is an interesting target in antibiotic drug development. An in vitro transglycosylation assay was developed and used to search for possible inhibitors of Staphylococcus aureus Penicillin Binding Protein 2-mediated transglycosylation. Since the substrate, Lipid II, has no UV-chromophore, the assay relies on LC coupled to MS for analysis of the incubation mixtures. Extracts from Thymus sipyleus, Salvia verticillata, Salvia virgata and Oolong tea were tested, as well as epigallocatechin gallate and ursolic acid, which are chemical compounds derived from plants. Matrix effects hampered Lipid II quantification in samples treated with very high concentrations of extracts. None of these extracts or isolated compounds appeared to have inhibitory activities towards the transglycosylation function of Penicillin Binding Protein 2.
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Affiliation(s)
- Bart Blanchaert
- KU Leuven-University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ismail Murat Palabiyik
- University of Ankara, Faculty of Pharmacy, Department of Analytical Chemistry, 06100 Tandogan, Ankara, Turkey
| | - Alper Gökbulut
- University of Ankara, Faculty of Pharmacy, Department of Pharmacognosy, 06100 Tandogan, Ankara, Turkey
| | - Ming-Juan Wang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Zhong Dai
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Feng Wei
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Shuang-Cheng Ma
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Erwin Adams
- KU Leuven-University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ann Van Schepdael
- KU Leuven-University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium.
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7
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Egan AJF, Biboy J, van't Veer I, Breukink E, Vollmer W. Activities and regulation of peptidoglycan synthases. Philos Trans R Soc Lond B Biol Sci 2015; 370:20150031. [PMID: 26370943 PMCID: PMC4632607 DOI: 10.1098/rstb.2015.0031] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2015] [Indexed: 12/22/2022] Open
Abstract
Peptidoglycan (PG) is an essential component in the cell wall of nearly all bacteria, forming a continuous, mesh-like structure, called the sacculus, around the cytoplasmic membrane to protect the cell from bursting by its turgor. Although PG synthases, the penicillin-binding proteins (PBPs), have been studied for 70 years, useful in vitro assays for measuring their activities were established only recently, and these provided the first insights into the regulation of these enzymes. Here, we review the current knowledge on the glycosyltransferase and transpeptidase activities of PG synthases. We provide new data showing that the bifunctional PBP1A and PBP1B from Escherichia coli are active upon reconstitution into the membrane environment of proteoliposomes, and that these enzymes also exhibit DD-carboxypeptidase activity in certain conditions. Both novel features are relevant for their functioning within the cell. We also review recent data on the impact of protein-protein interactions and other factors on the activities of PBPs. As an example, we demonstrate a synergistic effect of multiple protein-protein interactions on the glycosyltransferase activity of PBP1B, by its cognate lipoprotein activator LpoB and the essential cell division protein FtsN.
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Affiliation(s)
- Alexander J F Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Inge van't Veer
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 Utrecht, The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 Utrecht, The Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
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8
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The sweet tooth of bacteria: common themes in bacterial glycoconjugates. Microbiol Mol Biol Rev 2015; 78:372-417. [PMID: 25184559 DOI: 10.1128/mmbr.00007-14] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Humans have been increasingly recognized as being superorganisms, living in close contact with a microbiota on all their mucosal surfaces. However, most studies on the human microbiota have focused on gaining comprehensive insights into the composition of the microbiota under different health conditions (e.g., enterotypes), while there is also a need for detailed knowledge of the different molecules that mediate interactions with the host. Glycoconjugates are an interesting class of molecules for detailed studies, as they form a strain-specific barcode on the surface of bacteria, mediating specific interactions with the host. Strikingly, most glycoconjugates are synthesized by similar biosynthesis mechanisms. Bacteria can produce their major glycoconjugates by using a sequential or an en bloc mechanism, with both mechanistic options coexisting in many species for different macromolecules. In this review, these common themes are conceptualized and illustrated for all major classes of known bacterial glycoconjugates, with a special focus on the rather recently emergent field of glycosylated proteins. We describe the biosynthesis and importance of glycoconjugates in both pathogenic and beneficial bacteria and in both Gram-positive and -negative organisms. The focus lies on microorganisms important for human physiology. In addition, the potential for a better knowledge of bacterial glycoconjugates in the emerging field of glycoengineering and other perspectives is discussed.
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9
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Wang Y, Chan FY, Sun N, Lui HK, So PK, Yan SC, Chan KF, Chiou J, Chen S, Abagyan R, Leung YC, Wong KY. Structure-based design, synthesis, and biological evaluation of isatin derivatives as potential glycosyltransferase inhibitors. Chem Biol Drug Des 2014; 84:685-96. [PMID: 24890564 DOI: 10.1111/cbdd.12361] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 11/28/2022]
Abstract
Peptidoglycan glycosyltransferase (PGT) has been shown to be an important pharmacological target for the inhibition of bacterial cell wall biosynthesis. Structure-based virtual screening of about 3,000,000 commercially available compounds against the crystal structure of the glycosyltransferase (GT) domain of the Staphylococcus aureus penicillin-binding protein 2 (S. aureus PBP2) resulted in identification of an isatin derivative, 2-(3-(2-carbamimidoylhydrazono)-2-oxoindolin-1-yl)-N-(m-tolyl)acetamide (4) as a novel potential GT inhibitor. A series of 4 derivatives were synthesized. Several compounds showed more active antimicrobial activity than the initial hit compound 4, in particular 2-(3-(2-carbamimidoylhydrazono)-2-oxoindolin-1-yl)-N-(3-nitrophenyl)acetamide (4l), against Gram-positive Bacillus subtilis and S. aureus with MIC values of 24 and 48 μg/mL, respectively. Saturation transfer difference (STD) NMR study revealed that there is a binding contact between 4l and the GT domain of S. aureus PBP2. Competitive STD-NMR further proved that 4l and moenomycin A bind to GT domain in a competitive manner. Molecular docking study suggests a potential binding pocket of 4l in the GT domain of S. aureus PBP2. Taken together, compound 4l would provide a new scaffold for further development of potent GT inhibitors.
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Affiliation(s)
- Yong Wang
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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10
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Galley NF, O'Reilly AM, Roper DI. Prospects for novel inhibitors of peptidoglycan transglycosylases. Bioorg Chem 2014; 55:16-26. [PMID: 24924926 PMCID: PMC4126109 DOI: 10.1016/j.bioorg.2014.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/12/2014] [Accepted: 05/12/2014] [Indexed: 01/07/2023]
Abstract
We examine key aspects of transglycosylase inhibitor design. Low to high throughput assays suitable for transglycosylase drug discovery. Existing chemical start points for transglycosylase active site targeting.
The lack of novel antimicrobial drugs under development coupled with the increasing occurrence of resistance to existing antibiotics by community and hospital acquired infections is of grave concern. The targeting of biosynthesis of the peptidoglycan component of the bacterial cell wall has proven to be clinically valuable but relatively little therapeutic development has been directed towards the transglycosylase step of this process. Advances towards the isolation of new antimicrobials that target transglycosylase activity will rely on the development of the enzymological tools required to identify and characterise novel inhibitors of these enzymes. Therefore, in this article, we review the assay methods developed for transglycosylases and review recent novel chemical inhibitors discovered in relation to both the lipidic substrates and natural product inhibitors of the transglycosylase step.
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Affiliation(s)
- Nicola F Galley
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Amy M O'Reilly
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
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11
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Rebets Y, Lupoli T, Qiao Y, Schirner K, Villet R, Hooper D, Kahne D, Walker S. Moenomycin resistance mutations in Staphylococcus aureus reduce peptidoglycan chain length and cause aberrant cell division. ACS Chem Biol 2014; 9:459-67. [PMID: 24255971 DOI: 10.1021/cb4006744] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Staphylococcus aureus is a Gram-positive pathogen with an unusual mode of cell division in that it divides in orthogonal rather than parallel planes. Through selection using moenomycin, an antibiotic proposed to target peptidoglycan glycosyltransferases (PGTs), we have generated resistant mutants containing a single point mutation in the active site of the PGT domain of an essential peptidoglycan (PG) biosynthetic enzyme, PBP2. Using cell free polymerization assays, we show that this mutation alters PGT activity so that much shorter PG chains are made. The same mutation in another S. aureus PGT, SgtB, has a similar effect on glycan chain length. Moenomycin-resistant S. aureus strains containing mutated PGTs that make only short glycan polymers display major cell division defects, implicating PG chain length in determining bacterial cell morphology and division site placement.
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Affiliation(s)
- Yuriy Rebets
- Department
of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tania Lupoli
- Department
of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yuan Qiao
- Department
of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Kathrin Schirner
- Department
of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Regis Villet
- Division
of Infectious Diseases and Medical Services, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - David Hooper
- Division
of Infectious Diseases and Medical Services, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Daniel Kahne
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Suzanne Walker
- Department
of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
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12
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Gampe CM, Tsukamoto H, Doud EH, Walker S, Kahne D. Tuning the moenomycin pharmacophore to enable discovery of bacterial cell wall synthesis inhibitors. J Am Chem Soc 2013; 135:3776-9. [PMID: 23448584 DOI: 10.1021/ja4000933] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antibiotic drugs need to be identified to address rapidly developing resistance of bacterial pathogens to common antibiotics. The natural antibiotic moenomycin A is the prototype for compounds that bind to bacterial peptidoglycan glycosyltransferases (PGTs) and inhibit cell wall biosynthesis, but it cannot be used as a drug. Here we report the chemoenzymatic synthesis of a fluorescently labeled, truncated analogue of moenomycin based on the minimal pharmacophore. This probe, which has optimized enzyme binding properties compared to moenomycin, was designed to identify low-micromolar inhibitors that bind to conserved features in PGT active sites. We demonstrate its use in displacement assays using PGTs from S. aureus, E. faecalis, and E. coli. 110,000 compounds were screened against S. aureus SgtB, and we identified a non-carbohydrate based compound that binds to all PGTs tested. We also show that the compound inhibits in vitro formation of peptidoglycan chains by several different PGTs. Thus, this assay enables the identification of small molecules that target PGT active sites, and may provide lead compounds for development of new antibiotics.
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Affiliation(s)
- Christian M Gampe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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13
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Lovering AL, Safadi SS, Strynadka NCJ. Structural perspective of peptidoglycan biosynthesis and assembly. Annu Rev Biochem 2012; 81:451-78. [PMID: 22663080 DOI: 10.1146/annurev-biochem-061809-112742] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The peptidoglycan biosynthetic pathway is a critical process in the bacterial cell and is exploited as a target for the design of antibiotics. This pathway culminates in the production of the peptidoglycan layer, which is composed of polymerized glycan chains with cross-linked peptide substituents. This layer forms the major structural component of the protective barrier known as the cell wall. Disruption in the assembly of the peptidoglycan layer causes a weakened cell wall and subsequent bacterial lysis. With bacteria responsible for both properly functioning human health (probiotic strains) and potentially serious illness (pathogenic strains), a delicate balance is necessary during clinical intervention. Recent research has furthered our understanding of the precise molecular structures, mechanisms of action, and functional interactions involved in peptidoglycan biosynthesis. This research is helping guide our understanding of how to capitalize on peptidoglycan-based therapeutics and, at a more fundamental level, of the complex machinery that creates this critical barrier for bacterial survival.
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Affiliation(s)
- Andrew L Lovering
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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14
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Dumbre S, Derouaux A, Lescrinier E, Piette A, Joris B, Terrak M, Herdewijn P. Synthesis of Modified Peptidoglycan Precursor Analogues for the Inhibition of Glycosyltransferase. J Am Chem Soc 2012; 134:9343-51. [DOI: 10.1021/ja302099u] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shrinivas Dumbre
- Laboratory of Medicinal Chemistry,
Rega Institute for Medical Research, University of Leuven (KU Leuven), Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Adeline Derouaux
- Centre d’Ingénierie
des Protéines, Université de Liège, Allée de la chimie, B6a, B-4000, Sart Tilman, Liège,
Belgium
| | - Eveline Lescrinier
- Laboratory of Medicinal Chemistry,
Rega Institute for Medical Research, University of Leuven (KU Leuven), Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - André Piette
- Centre d’Ingénierie
des Protéines, Université de Liège, Allée de la chimie, B6a, B-4000, Sart Tilman, Liège,
Belgium
| | - Bernard Joris
- Centre d’Ingénierie
des Protéines, Université de Liège, Allée de la chimie, B6a, B-4000, Sart Tilman, Liège,
Belgium
| | - Mohammed Terrak
- Centre d’Ingénierie
des Protéines, Université de Liège, Allée de la chimie, B6a, B-4000, Sart Tilman, Liège,
Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry,
Rega Institute for Medical Research, University of Leuven (KU Leuven), Minderbroedersstraat 10, 3000 Leuven, Belgium
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15
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Naidoo KJ. Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association. Phys Chem Chem Phys 2012; 14:9026-36. [DOI: 10.1039/c2cp23802k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Gampe CM, Tsukamoto H, Wang TSA, Walker S, Kahne D. Modular synthesis of diphospholipid oligosaccharide fragments of the bacterial cell wall and their use to study the mechanism of moenomycin and other antibiotics. Tetrahedron 2011; 67:9771-9778. [PMID: 22505780 PMCID: PMC3322638 DOI: 10.1016/j.tet.2011.09.114] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a flexible, modular route to GlcNAc-MurNAc-oligosaccharides that can be readily converted into peptidoglycan (PG) fragments to serve as reagents for the study of bacterial enzymes that are targets for antibiotics. Demonstrating the utility of these synthetic PG substrates, we show that the tetrasaccharide substrate lipid IV (3), but not the disaccharide substrate lipid II (2), significantly increases the concentration of moenomycin A required to inhibit a prototypical PG-glycosyltransferase (PGT). These results imply that lipid IV and moenomycin A bind to the same site on the enzyme. We also show the moenomycin A inhibits the formation of elongated polysaccharide product but does not affect length distribution. We conclude that moenomycin A blocks PG-strand initiation rather than elongation or chain termination. Synthetic access to diphospholipid oligosaccharides will enable further studies of bacterial cell wall synthesis with the long-term goal of identifying novel antibiotics.
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Affiliation(s)
- Christian M. Gampe
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Hirokazu Tsukamoto
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Tsung-Shing Andrew Wang
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Suzanne Walker
- Harvard Medical School, Department of Microbiology and Molecular Genetics, Boston, Massachusetts 02115, USA
| | - Daniel Kahne
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol 2010; 31:295-336. [PMID: 21091161 DOI: 10.3109/07388551.2010.525498] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
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Affiliation(s)
- Ankur Gautam
- Department of Biotechnology, Panjab University, Chandigarh, India
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18
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Ostash B, Walker S. Moenomycin family antibiotics: chemical synthesis, biosynthesis, and biological activity. Nat Prod Rep 2010; 27:1594-617. [PMID: 20730219 PMCID: PMC2987538 DOI: 10.1039/c001461n] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The review (with 214 references cited) is devoted to moenomycins, the only known group of antibiotics that directly inhibit bacterial peptidoglycan glycosytransferases. Naturally occurring moenomycins and chemical and biological approaches to their derivatives are described. The biological properties of moenomycins and plausible mechanisms of bacterial resistance to them are also covered here, portraying a complete picture of the chemistry and biology of these fascinating natural products
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Affiliation(s)
- Bohdan Ostash
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave., Armenise Bldg. 2, Rm 630, Boston, MA 02115, USA
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Assembly of the type II secretion system: identification of ExeA residues critical for peptidoglycan binding and secretin multimerization. J Bacteriol 2010; 193:197-204. [PMID: 20971903 DOI: 10.1128/jb.00882-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aeromonas hydrophila secretes a number of protein toxins across the outer membrane via the type II secretion system (T2SS). Assembly of the secretion channel ExeD secretin into the outer membrane is dependent on the peptidoglycan binding domain of ExeA. In this study, the peptidoglycan binding domain PF01471 family members were divided into a prokaryotic group and a eukaryotic group. By comparison of their sequence conservation profiles and their representative crystal structures, we found the prokaryotic members to have a highly conserved pocket(s) that is not present in the eukaryotic members. Substitution mutations of nine amino acids of the pocket were constructed in ExeA. Five of the substitution derivatives showed greatly decreased lipase secretion, accompanied by defects in secretin assembly. In addition, using in vivo cross-linking and in vitro cosedimentation assays, we showed that these mutations decreased ExeA-peptidoglycan interactions. These results suggest that the highly conserved pocket in ExeA is the binding site for its peptidoglycan ligand and identify residues critical for this binding.
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20
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Global transcriptome analysis of the Escherichia coli O157 response to Houttuynia Cordata Thunb. BIOCHIP JOURNAL 2010. [DOI: 10.1007/s13206-010-4312-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Offant J, Terrak M, Derouaux A, Breukink E, Nguyen-Distèche M, Zapun A, Vernet T. Optimization of conditions for the glycosyltransferase activity of penicillin-binding protein 1a from Thermotoga maritima. FEBS J 2010; 277:4290-8. [DOI: 10.1111/j.1742-4658.2010.07817.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Frantom PA, Coward JK, Blanchard JS. UDP-(5F)-GlcNAc acts as a slow-binding inhibitor of MshA, a retaining glycosyltransferase. J Am Chem Soc 2010; 132:6626-7. [PMID: 20411981 DOI: 10.1021/ja101231a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycosyltransferase enzymes play important roles in numerous cellular pathways. Despite their participation in many therapeutically relevant pathways, there is a paucity of information on how to effectively inhibit this class of enzymes. Here we report that UDP-(5F)-GlcNAc acts as a slow-binding, competitive inhibitor of the retaining glycosyltransferase MshA from Corynebacterium glutamicum (K(i) approximately 1.6 muM). The kinetic data are consistent with a single-step inhibition mechanism whose equilibration is slow relative to catalysis. We believe that this is the first slow-onset inhibitor to be reported for the glycosyltransferase family of enzymes. The potent inhibition of the enzyme by the fluoro-substituted substrate is consistent with the involvement of an oxocarbenium transition-state structure, which has been previously proposed for this family of enzymes. Additionally, although several members of the GT-B enzyme family, including MshA, have been shown to undergo a conformational change upon UDP-GlcNAc binding, the kinetic data are inconsistent with a two-step inhibition mechanism. This suggests that there may be other conformations of the enzyme that are useful for the design of inhibitors against the large family of GT-B glycosyltransferase enzymes.
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Affiliation(s)
- Patrick A Frantom
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
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Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli. Proc Natl Acad Sci U S A 2009; 106:8824-9. [PMID: 19458048 DOI: 10.1073/pnas.0904030106] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Drug-resistant bacteria have caused serious medical problems in recent years, and the need for new antibacterial agents is undisputed. Transglycosylase, a multidomain membrane protein essential for cell wall synthesis, is an excellent target for the development of new antibiotics. Here, we determined the X-ray crystal structure of the bifunctional transglycosylase penicillin-binding protein 1b (PBP1b) from Escherichia coli in complex with its inhibitor moenomycin to 2.16-A resolution. In addition to the transglycosylase and transpeptidase domains, our structure provides a complete visualization of this important antibacterial target, and reveals a domain for protein-protein interaction and a transmembrane helix domain essential for substrate binding, enzymatic activity, and membrane orientation.
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