Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: peptidoglycan, glycopeptide
Contained glycoepitopes: IEDB_135813,IEDB_136017,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_1635957,IEDB_241115,IEDB_423183,IEDB_885814

• Article ID: 2673
  Dziarski R, Gupta D "Heparin, sulfated heparinoids, and lipoteichoic acids bind to the 70-kDa peptidoglycan/lipopolysaccharide receptor protein on lymphocytes" - Journal of Biological Chemistry 269 (1994) 2100-2110
  

  The same 70-kDa protein, present on the surface of mouse lymphocytes, served as the predominant binding site for heparin, heparinoids, and bacterial lipoteichoic acids, as well as peptidoglycan and lipopolysaccharides. This conclusion was supported by the following results: (a) all of these compounds photoaffinity cross-linked to one major 70-kDa 6.5-7.0 pI protein that co-migrated on two-dimensional polyacrylamide gel electrophoresis; (b) peptide maps of the 70-kDa proteins digested with chymotrypsin, subtilisin, protease V, or papain yielded the same peptides for heparin-, lipoteichoic acid-, peptidoglycan-, and lipopolysaccharide-binding proteins; (c) cross-linking of peptidoglycan, lipopolysaccharide, lipoteichoic acid, and heparin was competitively inhibited by the same compounds with the same order of potency, i.e. carboxyl-reduced sulfated heparin > peptidoglycan > pentosan polysulfate > heparin > chitin > dextran sulfate > trestatin sulfate > polyanetholesulfonate > fucoidan > beta-cyclodextrin tetradecasulfate > heparan sulfate > carrageenan lambda > lipoteichoic acids > Re-lipopolysaccharide > lipopolysaccharide > lipid A > polygalacturonic acid; and (d) cross-linking of each of these ligands was not inhibited by carboxyl-reduced heparin, dextran, beta-cyclodextrin, trestatin, carrageenan kappa, chondroitin 4-sulfate, chondroitin 6-sulfate, beta-D-glucan, carboxy-methylcellulose, levan, alpha-D-mannan, and glycogen. The minimum size of the molecule that bound was 7-9 glycan residues, whereas, di- and trisaccharides did not bind. There was a logarithmic linear relationship between the strength of the binding and the length of the polymer (up to > 1500 glycan residues), which indicates an avidity effect of the cooperative binding of one polymeric molecule to several receptor molecules on the cell surface. The 70-kDa receptor, therefore, has a broad, but limited specificity of binding for non-charged (peptidoglycan and chitin), highly negatively charged (heparin and heparinoids), and weakly negatively charged (lipoteichoic acids, lipopolysaccharides, and lipid A) ligands.

  NCBI PubMed ID: 8294463
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Institutions: Northwest Center for Medical Education, Indiana University School of Medicine, Gary 46408
  
   
  
  Staphylococcus aureus
  CSDB ID 136965 (all data & tools)
• Article ID: 4298
  Fujimoto Y, Pradipta AR, Inohara N, Fukase K "Peptidoglycan as Nod1 ligand; fragment structures in the environment, chemical synthesis, and their innate immunostimulation" - Natural Product Reports 29(5) (2012) 568-579
  

  Covering: up to 2011. This review focuses on the recent revealing of the immunostimulatory bacterial cell wall peptidoglycan (PGN) fragments as Nod1 ligands, especially a newly developed chemical synthesis of the partial structures, fragment structures in the environment and bacterial supernatant, and the immunostimulatory activities of the Nod1 ligands.

  synthesis, cell, bacteria, cell wall, immunostimulatory, Nod1 Signaling Adaptor Protein, Nod2 Signaling Adaptor Protein, peptidoglycan structure

  NCBI PubMed ID: 22370813
  Publication DOI: 10.1039/c2np00091a
  Journal NLM ID: 8502408
  Publisher: London: Royal Society of Chemistry
  Correspondence: yukarif@chem.sci.osaka-u.ac.jp
  Institutions: Department of Chemistry, Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560-0043, Japan
  
   
  
  Staphylococcus aureus
  CSDB ID 27155 (all data & tools)
• Article ID: 5590
  Shah NJ "Reversing resistance: The next generation antibacterials" - Indian Journal of Pharmacology 47(3) (2015) 248-255
  

  Irrational antibiotic usage has led to vast spread resistance to available antibiotics, but we refuse to slide back to "preantibiotic era". The threat is serious with the "Enterococcus, Staphylococcous, Klebsiella, Acinetobacter, Pseudomonas and Enterobacter" organisms causing nosocomial infections that are difficult to treat because of the production of extended spectrum β-lactamases, carbapenamases and metallo-β-lactamases. Facing us is a situation where soon multidrug resistance would have spread across the globe with no antibiotics to withstand it. The infectious disease society of America and Food and Drug Administration have taken initiatives like the 10 × '20 where they plan to develop 10 new antibiotics by the year 2020. Existing classes of antibiotics against resistant bacteria include the carbapenems, oxazolidinones, glycopeptides, monobactams, streptogramins and daptomycin. Newer drugs in existing classes of antibiotics such as cephalosporins, aminoglycosides, tetracyclines, glycopeptides and β-lactamase inhibitors continue to get synthesized. The situation demands newer targets against bacterial machinery. Some of them include the peptidoglycantransferase, outer membrane protein of Pseudomonas, tRNA synthase, fatty acid synthase and mycobacterial ATP synthase. To curb the irrational and excessive usage of presently available antibiotics should be a priority if they are still to be kept in usage for the future

  Food and Drug Administration safety and innovation act, new antibiotics, new carbapenems, new glycopeptides, new quinolones

  NCBI PubMed ID: 26069360
  Publication DOI: 10.4103/0253-7613.157109
  Journal NLM ID: 7902477
  Publisher: Mumbai: Medknow Publications
  Correspondence: neel.lakshya@gmail.com
  Institutions: Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
  
   
  
  (bacteria)
  CSDB ID 47445 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: peptidoglycan
Contained glycoepitopes: IEDB_135813,IEDB_136017,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_1635957,IEDB_885814

• Article ID: 3225
  Courtin P, Miranda G, Guillot A, Wessner F, Merzange C, Domakova E, Kulakauskas S, Chapot-Chartier M "Peptidoglycan Structure Analysis of Lactococcus lactis Reveals the Presence of an L,D-Carboxypeptidase Involved inPeptidoglycan Maturation" - Journal of Bacteriology 188(14) (2006) 5293-5298
  

  Detailed structural analysis of Lactococcus lactis peptidoglycan was achieved by identification of its constituent muropeptides separated by reverse phase high-performance liquid chromatography. Modification of the classical elution buffer allowed direct and sensitive analysis of the purified muropeptides by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The structures of 45 muropeptides were assigned for L. lactis strain MG1363. Analysis of the muropeptide composition of an MG1363 dacB mutant showed that the dacB-encoded protein has l,d-carboxypeptidase activity and is involved in peptidoglycan maturation.

  structure, Lactococcus lactis, Lactococcus, peptidoglycan, bacteriology

  NCBI PubMed ID: 16816203
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: Marie-Pierre.Chapot@jouy.inra.fr
  Institutions: Institut National de la Recherche Agronomique, Unite de Biochimie Bacterienne, Unite Bacteries Lactiques et Pathogenes Opportunistes, 78352 Jouy-en-Josas Cedex, France
  Methods: MALDI-MS
  
   
  
  Lactococcus lactis MG1363
  CSDB ID 20018 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: glycolipid
Contained glycoepitopes: IEDB_135813,IEDB_136017,IEDB_137340,IEDB_141807,IEDB_151531

• Article ID: 5590
  Shah NJ "Reversing resistance: The next generation antibacterials" - Indian Journal of Pharmacology 47(3) (2015) 248-255
  

  Irrational antibiotic usage has led to vast spread resistance to available antibiotics, but we refuse to slide back to "preantibiotic era". The threat is serious with the "Enterococcus, Staphylococcous, Klebsiella, Acinetobacter, Pseudomonas and Enterobacter" organisms causing nosocomial infections that are difficult to treat because of the production of extended spectrum β-lactamases, carbapenamases and metallo-β-lactamases. Facing us is a situation where soon multidrug resistance would have spread across the globe with no antibiotics to withstand it. The infectious disease society of America and Food and Drug Administration have taken initiatives like the 10 × '20 where they plan to develop 10 new antibiotics by the year 2020. Existing classes of antibiotics against resistant bacteria include the carbapenems, oxazolidinones, glycopeptides, monobactams, streptogramins and daptomycin. Newer drugs in existing classes of antibiotics such as cephalosporins, aminoglycosides, tetracyclines, glycopeptides and β-lactamase inhibitors continue to get synthesized. The situation demands newer targets against bacterial machinery. Some of them include the peptidoglycantransferase, outer membrane protein of Pseudomonas, tRNA synthase, fatty acid synthase and mycobacterial ATP synthase. To curb the irrational and excessive usage of presently available antibiotics should be a priority if they are still to be kept in usage for the future

  Food and Drug Administration safety and innovation act, new antibiotics, new carbapenems, new glycopeptides, new quinolones

  NCBI PubMed ID: 26069360
  Publication DOI: 10.4103/0253-7613.157109
  Journal NLM ID: 7902477
  Publisher: Mumbai: Medknow Publications
  Correspondence: neel.lakshya@gmail.com
  Institutions: Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
  
   
  
  (bacteria)
  CSDB ID 47447 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Trivial name: peptidoglycan
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_1635957,IEDB_241115,IEDB_423183,IEDB_885814

• Article ID: 5871
  Yakovlieva L, Walvoort MTC "Processivity in Bacterial Glycosyltransferases" - ACS Chemical Biology 15(1) (2020) 3-16
  

  Extracellular polysaccharides and glycoproteins of pathogenic bacteria assist in adherence, autoaggregation, biofilm formation, and host immune system evasion. As a result, considerable research in the field of glycobiology is dedicated to study the composition and function of glycans associated with virulence, as well as the enzymes involved in their biosynthesis with the aim to identify novel antibiotic targets. Especially, insights into the enzyme mechanism, substrate binding, and transition-state structures are valuable as a starting point for rational inhibitor design. An intriguing aspect of enzymes that generate or process polysaccharides and glycoproteins is the level of processivity. The existence of enzymatic processivity reflects the need for regulation of the final glycan/glycoprotein length and structure, depending on the role they perform. In this Review, we describe the currently reported examples of various processive enzymes involved in polymerization and transfer of sugar moieties, predominantly in bacterial pathogens, with a focus on the biochemical methods, to showcase the importance of studying processivity for understanding the mechanism.

  processivity, Apparent processivity, Distributivity, Hyperglycosylation, Intrinsic processivity, Semiprocessive

  NCBI PubMed ID: 31750644
  Publication DOI: 10.1021/acschembio.9b00619
  Journal NLM ID: 101282906
  Publisher: Washington, DC: American Chemical Society
  Correspondence: m.t.c.walvoort@rug.nl
  Institutions: Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
  
   
  
  (bacteria)
  CSDB ID 32237 (all data & tools)

Show legend Show as text

Structure type: cyclic polymer repeating unit ; 1388.7577 [M+H]+
C₆₆H₁₀₅N₁₁O₂₁
Trivial name: desmamides A
Compound class: lipoglycopeptide
Contained glycoepitopes: IEDB_114701,IEDB_150900

• Article ID: 6224
  Freitas S, Castelo-Branco R, Wenzel-Storjohann A, Vasconcelos VM, Tasdemir D, Leão PN "Structure and Biosynthesis of Desmamides A-C, Lipoglycopeptides from the Endophytic Cyanobacterium Desmonostoc muscorum LEGE 12446" - Journal of Natural Products 85(7) (2022) 1704-1714
  

  Certain cyanobacteria of the secondary metabolite-rich order Nostocales can establish permanent symbioses with a large number of cycads, by accumulating in their coralloid roots and shifting their metabolism to dinitrogen fixation. Here, we report the discovery of two new lipoglycopeptides, desmamides A (1) and B (2), together with their aglycone desmamide C (3), from the nostocalean cyanobacterium Desmonostoc muscorum LEGE 12446 isolated from a cycad (Cycas revoluta) coralloid root. The chemical structures of the compounds were elucidated using a combination of 1D and 2D NMR spectroscopy and mass spectrometry. The desmamides are decapeptides featuring O-glycosylation of tyrosine (in 1 and 2) and an unusual 3,5-dihydroxy-2-methyldecanoic acid residue. The biosynthesis of the desmamides was studied by substrate incubation experiments and bioinformatics. We describe herein the dsm biosynthetic gene cluster and propose it to be associated with desmamide production. The discovery of this class of very abundant (>1.5% d.w.) bacterial lipoglycopeptides paves the way for exploration of their potential role in root endosymbiosis.

  structure, NMR spectroscopy, mass spectrometry, cyanobacteria, marine, lipoglycopeptides, Desmonostoc muscorum

  NCBI PubMed ID: 35793792
  Publication DOI: 10.1021/acs.jnatprod.2c00162
  Journal NLM ID: 7906882
  Publisher: American Society of Pharmacognosy
  Correspondence: P.N. Leão
  Institutions: Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal, Department of Biology, Faculty of Sciences, University of Porto Rua do Campo Alegre, Porto, Portugal, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106 Kiel, Germany, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
  Methods: 13C NMR, 1H NMR, NMR-2D, FTIR, HPLC, extraction, optical rotation measurement, bioinformatic analysis, HR-ESI-MS, antibacterial assay, cell viability assay, flash chromatography, genome sequencing, Marfey’s method, LC-HR-ESI-MS
  
   
  
  Desmonostoc muscorum LEGE 12446
  CSDB ID 8455 (all data & tools)

Show legend Show as text

Structure type: cyclic polymer repeating unit ; 1430.7666 [M+H]+
C₆₈H₁₀₈N₁₁O₂₂
Trivial name: desmamides B
Compound class: lipoglycopeptide
Contained glycoepitopes: IEDB_114701,IEDB_150900

• Article ID: 6224
  Freitas S, Castelo-Branco R, Wenzel-Storjohann A, Vasconcelos VM, Tasdemir D, Leão PN "Structure and Biosynthesis of Desmamides A-C, Lipoglycopeptides from the Endophytic Cyanobacterium Desmonostoc muscorum LEGE 12446" - Journal of Natural Products 85(7) (2022) 1704-1714
  

  Certain cyanobacteria of the secondary metabolite-rich order Nostocales can establish permanent symbioses with a large number of cycads, by accumulating in their coralloid roots and shifting their metabolism to dinitrogen fixation. Here, we report the discovery of two new lipoglycopeptides, desmamides A (1) and B (2), together with their aglycone desmamide C (3), from the nostocalean cyanobacterium Desmonostoc muscorum LEGE 12446 isolated from a cycad (Cycas revoluta) coralloid root. The chemical structures of the compounds were elucidated using a combination of 1D and 2D NMR spectroscopy and mass spectrometry. The desmamides are decapeptides featuring O-glycosylation of tyrosine (in 1 and 2) and an unusual 3,5-dihydroxy-2-methyldecanoic acid residue. The biosynthesis of the desmamides was studied by substrate incubation experiments and bioinformatics. We describe herein the dsm biosynthetic gene cluster and propose it to be associated with desmamide production. The discovery of this class of very abundant (>1.5% d.w.) bacterial lipoglycopeptides paves the way for exploration of their potential role in root endosymbiosis.

  structure, NMR spectroscopy, mass spectrometry, cyanobacteria, marine, lipoglycopeptides, Desmonostoc muscorum

  NCBI PubMed ID: 35793792
  Publication DOI: 10.1021/acs.jnatprod.2c00162
  Journal NLM ID: 7906882
  Publisher: American Society of Pharmacognosy
  Correspondence: P.N. Leão
  Institutions: Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal, Department of Biology, Faculty of Sciences, University of Porto Rua do Campo Alegre, Porto, Portugal, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106 Kiel, Germany, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
  Methods: 13C NMR, 1H NMR, NMR-2D, FTIR, HPLC, extraction, optical rotation measurement, bioinformatic analysis, HR-ESI-MS, antibacterial assay, cell viability assay, flash chromatography, genome sequencing, Marfey’s method, LC-HR-ESI-MS
  
   
  
  Desmonostoc muscorum LEGE 12446
  CSDB ID 20935 (all data & tools)