Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531

• Article ID: 653
  Gorshkova RP, Nazarenko EL, Zubkov VA, Shashkov AS, Knirel YA, Paramonov NA, Meshkov SV, Ivanova EP "Structure of the capsular polysaccharide from Alteromonas nigrifaciens IAM 13010T containing 2-acetamido-2,6-dideoxy-L-talose and 3-deoxy-D-manno-octulosonic acid" - Carbohydrate Research 299 (1997) 69-76
  

  A capsular polysaccharide was obtained from Alteromonas nigrifaciens IAM 13010T by saline extraction. On the basis of 1H and 13C NMR spectroscopy, including one-dimensional (1D) NOE spectroscopy, 2D rotating-frame NOE spectroscopy (ROESY), and 1H-detected heteronuclear 1H,13C multiple-quantum coherence (HMQC), it was concluded that the polysaccharide contained inter alia an acidic sugar, 3-deoxy-D-manno-octulosonic acid (Kdo), and a rare amino sugar, 2-acetamido-2,6-dideoxy-L-talose (L6dTalNAc, N-acetylpneumosamine), and has a pentasaccharide repeating unit of the following structure: [equation: see text]

  structure, capsular, polysaccharide, acid, capsular polysaccharide, 2-acetamido-2, 3-deoxy-D-manno-octulosonic acid, Alteromonas, 6-dideoxy-L-galactose, 6-dideoxy-L-talose, Alteromonas nigrifaciens

  NCBI PubMed ID: 9129296
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: N.D.Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russian Federation, Service Center of the Physico-Chemical Methods of the Russian Foundation for Basic Research, Moscow, Russian Federation
  Methods: NMR-2D, NMR
  
   
  
  Alteromonas nigrifaciens IAM 13010T
  CSDB ID 428 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531

• Article ID: 653
  Gorshkova RP, Nazarenko EL, Zubkov VA, Shashkov AS, Knirel YA, Paramonov NA, Meshkov SV, Ivanova EP "Structure of the capsular polysaccharide from Alteromonas nigrifaciens IAM 13010T containing 2-acetamido-2,6-dideoxy-L-talose and 3-deoxy-D-manno-octulosonic acid" - Carbohydrate Research 299 (1997) 69-76
  

  A capsular polysaccharide was obtained from Alteromonas nigrifaciens IAM 13010T by saline extraction. On the basis of 1H and 13C NMR spectroscopy, including one-dimensional (1D) NOE spectroscopy, 2D rotating-frame NOE spectroscopy (ROESY), and 1H-detected heteronuclear 1H,13C multiple-quantum coherence (HMQC), it was concluded that the polysaccharide contained inter alia an acidic sugar, 3-deoxy-D-manno-octulosonic acid (Kdo), and a rare amino sugar, 2-acetamido-2,6-dideoxy-L-talose (L6dTalNAc, N-acetylpneumosamine), and has a pentasaccharide repeating unit of the following structure: [equation: see text]

  structure, capsular, polysaccharide, acid, capsular polysaccharide, 2-acetamido-2, 3-deoxy-D-manno-octulosonic acid, Alteromonas, 6-dideoxy-L-galactose, 6-dideoxy-L-talose, Alteromonas nigrifaciens

  NCBI PubMed ID: 9129296
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: N.D.Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russian Federation, Service Center of the Physico-Chemical Methods of the Russian Foundation for Basic Research, Moscow, Russian Federation
  Methods: NMR-2D, NMR
  
   
  
  Alteromonas nigrifaciens IAM 13010T
  CSDB ID 558 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_423153,IEDB_983931,SB_192

• Article ID: 1347
  Abeygunawardana C, Williams TC, Sumner JS, Hennessey JP "Development and validation of an NMR-based identity assay for bacterial polysaccharides" - Analytical Biochemistry 279(2) (2000) 226-240
  

  A method utilizing NMR spectroscopy has been developed to confirm the identity of bacterial polysaccharides used to formulate a polyvalent pneumococcal polysaccharide vaccine. The method is based on 600 MHz proton NMR spectra of individual serotype-specific polysaccharides. A portion of the anomeric region of each spectrum (5.89 to 4.64 ppm) is compared to spectra generated for designated reference samples for each polysaccharide of interest. The selected region offers a spectral window that is unique to a given polysaccharide and is sensitive to any structural alteration of the repeating units. The similarity of any two spectral profiles is evaluated using a correlation coefficient (rho), where rho >/= 0.95 between a sample and reference profile indicates a positive identification of the sample polysaccharide. This method has been shown to be extremely selective in its ability to discriminate between serotype-specific polysaccharides, some of which differ by no more than a single glycosidic linkage. Furthermore, the method is rapid and does not require extensive sample manipulations or pretreatments. The method was validated as a qualitative identity assay and will be incorporated into routine quality control testing of polysaccharide powders to be used in preparation of the polyvalent pneumococcal vaccine PNEUMOVAX 23. The specificity and reproducibility of the NMR-based identity assay is superior to the currently used colorimetric assays and can be readily adapted for use with other bacterial polysaccharide preparations as well.

  NMR, Bacterial, polysaccharide, Bacterial polysaccharide, polysaccharides, bacterial polysaccharides, assay, development, identity assay, method development, validation

  NCBI PubMed ID: 10706792
  Publication DOI: 10.1006/abio.1999.447
  Journal NLM ID: 0370535
  Publisher: Academic Press
  Correspondence: abey@merck.com
  Institutions: Bioprocess and Bioanalytical Research, Merck Research Laboratories, West Point, Pensylvania, USA
  Methods: NMR
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 6398 (all data & tools)
• Article ID: 4554
  Kokoulin MS, Kalinovsky AI, Komandrova NA, Tovarchi VE, Tomshich SV, Nedashkovskaya OI, Vaskovsky VE "The structure of the O-specific polysaccharide from marine bacterium Litorimonas taeanensis G5 containing 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-D-quinovose and 2-acetamido-2,6-dideoxy-L-xylo-hexos-4-ulose" - Carbohydrate Research 375 (2013) 105-111
  

  The O-polysaccharide was isolated from the lipopolysaccharide of Litorimonas taeanensis G5T and studied by chemical methods along with 1H and 13C NMR spectroscopy, including 1H, 1H COSY, 1D and 2D TOCSY, NOESY, 1H, 13C HSQC, HMBC, and H2BC experiments. The following new structure of the O-polysaccharide of L. taeanensis G5T containing 2-acetamido-2-deoxy-d-galacturonic acid (d-GalNAcA), 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-d-quinovose (d-QuiNAc4NR), and 2-acetamido-2,6-dideoxy-l-xylo-hexos-4-ulose (l-Sug) was established: where R is (3S,5S)-3,5-dihydroxyhexanoic acid.

  O-specific polysaccharide, 2-acetamido-2, 6-dideoxy-L-xylo-hexos-4-ulose, 2-Acetamido-4-((3S, 5S)-3, 5-dihydroxyhexanamido)-2, 4-dideoxy-D-quinovose, Litorimonas taeanensis

  NCBI PubMed ID: 23694711
  Publication DOI: 10.1016/j.carres.2013.04.004
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: maxchem@mail.ru
  Institutions: G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
  Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, NMR-1D, triflic acid solvolysis, borohydride reduction
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 29616 (all data & tools)
• Article ID: 4828
  Geno KA, Gilbert GL, Song JY, Skovsted IC, Klugman KP, Jones C, Konradsen HB, Nahm MH "Pneumococcal Capsules and Their Types: Past, Present, and Future" - Clinical Microbiology Reviews 28(3) (2015) 871-899
  

  Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.

  serotype, Streptococcus pneumoniae, vaccines, Pneumococcal Capsules

  NCBI PubMed ID: 26085553
  Publication DOI: 10.1128/CMR.00024-15
  Journal NLM ID: 8807282
  Publisher: Washington, DC: American Society for Microbiology
  Correspondence: Moon H. Nahm
  Institutions: Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA, Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Wentworthville, New South Wales, Australia, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia, Division of Infectious Disease, Department of Internal Medicine, Korea University Guro Hospital, Seoul, South Korea, SSI Diagnostica, Division of Microbiology and Diagnostics, Statens Serum Institut, Copenhagen, Denmark, Pneumonia Program Strategy Team, Bill & Melinda Gates Foundation, Seattle, Washington, USA, Laboratory for Molecular Structure, NIBSC, South Mimms, Herts, United Kingdom, Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 31007 (all data & tools)
• Article ID: 4836
  Berti F, Ravenscroft N "Characterization of Carbohydrate Vaccines by NMR Spectroscopy" - Methods in Molecular Biology 1331 (2015) 189-209
  

  Physicochemical techniques are a powerful tool for the structural characterization of carbohydrate-based vaccines. High-field Nuclear Magnetic Resonance (NMR) spectroscopy has been established as an extremely useful and robust method for tracking the industrial manufacturing process of these vaccines from polysaccharide bulk antigen through to the final formulation. Here, we describe the use of proton NMR for structural identity and conformity testing of carbohydrate-based vaccines.

  carbohydrates, capsular polysaccharide, antigens, nuclear magnetic resonance spectroscopy, vaccines

  NCBI PubMed ID: 26169742
  Publication DOI: 10.1007/978-1-4939-2874-3_12
  Journal NLM ID: 9214969
  Publisher: Springer
  Correspondence: francesco.x.berti@gsk.com
  Institutions: Research, GSK Vaccines, Via Fiorentina 1, 53100, Siena, Italy
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 11097 (all data & tools)
• Article ID: 5093
  Lisboa MP, Khan N, Martin C, Xu FF, Reppe K, Geissner A, Govindan S, Witzenrath M, Pereira CL, Seeberger PH "Semisynthetic glycoconjugate vaccine candidate against Streptococcus pneumoniae serotype 5" - Proceedings of the National Academy of Sciences of the USA 114(42) (2017) 11063-11068
  

  Glycoconjugate vaccines based on isolated capsular polysaccharide (CPS) save millions of lives annually by preventing invasive pneumococcal disease caused by Streptococcus pneumoniae Some components of the S. pneumoniae glycoconjugate vaccine Prevnar13 that contains CPS antigens from 13 serotypes undergo modifications or degradation during isolation and conjugation, resulting in production problems and lower efficacy. We illustrate how stable, synthetic oligosaccharide analogs of labile CPS induce a specific protective immune response against native CPS using S. pneumoniae serotype 5 (ST-5), a problematic CPS component of Prevnar13. The rare aminosugar l-PneuNAc and a branched l-FucNAc present in the natural repeating unit (RU) are essential for antibody recognition and avidity. The epitope responsible for specificity differs from the part of the antigen that is stabilized by chemical modification. Glycoconjugates containing stable, monovalent synthetic oligosaccharide analogs of ST-5 CPS RU induced long-term memory and protective immune responses in rabbits superior to those elicited by the ST-5 CPS component in multivalent Prevnar13.

  vaccine, glycoconjugate, S. pneumoniae, carbohydrate chemistry, serotype 5

  NCBI PubMed ID: 28973947
  Publication DOI: 10.1073/pnas.1706875114
  Journal NLM ID: 7505876
  Publisher: National Academy of Sciences
  Correspondence: claney.pereira@vaxxilon.com; peter.seeberger@mpikg.mpg.de
  Institutions: Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, D-14424 Potsdam, Germany, Department of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany, Department of Infectious Diseases and Pulmonary Medicine, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
  Methods: 13C NMR, 1H NMR, NMR-2D, IR, SDS-PAGE, TLC, ELISA, chemical synthesis, biological assays, glycosylation, optical rotation measurement, statistical analysis, immunization, conjugation, HR-ESI-MS, microarray analysis, flow cytometry, microarray binding assays
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 12025 (all data & tools)
• Article ID: 5473
  Zou W, Li J, Vinogradov E, Cox A "Removal of cell wall polysaccharide in pneumococcal capsular polysaccharides by selective degradation via deamination" - Carbohydrate Polymers 218 (2019) 199-207
  

  Pneumococcal cell wall polysaccharide (C-PS), a contaminant in pneumococcal capsular polysaccharide (Pn-PS) vaccines is degraded by mild deamination of the 4-amino-2-acetamido-2,4,6-tri-deoxy-galactose (AAT) in C-PS, which was carried out by addition of 5% aqueous sodium nitrite to a solution of polysaccharide in 5% aqueous acetic acid. Glycosidic linkage and functional groups such as O-acetates, phosphodiesters, and pyruvates were preserved under the conditions. The small fragments from degraded C-PS were removed by ultrafiltration or dialysis to provide essentially C-PS free Pn-PS. Because of the presence of AAT in its structure the deamination is not suitable for the purification of type 1 Pn-PS. Meanwhile, the mass and NMR spectroscopic analysis on the deamination products suggests that both type 1 Pn-PS and C-PS degraded following a major pathway of 5,4-hydride shift, cleavage of AAT O5-C1 bond, C1 hemiacetal formation, and its hydrolysis to release neighboring GalA- in type 1 Pn-PS and GalNAc(6-O-PCho)- in C-PS

  mechanism, degradation, deamination, cell wall polysaccharide, pneumococcal capsular polysaccharide

  NCBI PubMed ID: 31221321
  Publication DOI: 10.1016/j.carbpol.2019.03.070
  Journal NLM ID: 8307156
  Publisher: Elsevier
  Correspondence: W. Zou
  Institutions: Human Health Therapeutic Research Center, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
  Methods: 13C NMR, 1H NMR, gel filtration, sugar analysis, MS/MS, MS, dialysis, SEC-HPLC, ultrafiltration, mild deamination
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 1947 (all data & tools)
• Article ID: 5791
  Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" - Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
  

  Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.

  polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component

  Publication DOI: 10.1016/B978-0-12-819475-1.00005-5
  Publisher: Elsevier
  Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
  Editors: Barchi J, Kamerling H
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 7031 (all data & tools)
• Article ID: 6058
  Genning M, Kurbatova EA, Nifantiev NE "Synthetic Analogs of Streptococcus pneumoniae Capsular Polysaccharides and Immunogenic Activities of Glycoconjugates" - Russian Journal of Bioorganic Chemistry 47(1) (2021) 1-25
  

  treptococcus pneumoniae is a Gram-positive bacterium (pneumococcus) that causes severe diseases in adults and children. It was established that some capsular polysaccharides of the clinically significant serotypes of S. pneumoniae in the composition of commercial pneumococcal polysaccharide or conjugate vaccines exhibit low immunogenicity. The review considers production methods and structural features of the synthetic oligosaccharides from the problematic pneumococcal serotypes that are characterized with low immunogenicity due to destruction or detrimental modification occurring in the process of their preparation and purification. Bacterial serotypes that cause severe pneumococcal diseases as well as serotypes not included in the composition of the pneumococcal conjugate vaccines are also discussed. It is demonstrated that the synthetic oligosaccharides corresponding to protective glycotopes of the capsular polysaccharides of various pneumococcal serotypes are capable of inducing formation of the protective opsonizing antibodies and immunological memory. Optimal constructs of oligosaccharides from the epidemiologically significant pneumococcal serotypes are presented that can be used for designing synthetic pneumococcal vaccines, as well as test systems for diagnosis of S. pneumoniae infections and monitoring of vaccination efficiency.

  oligosaccharide, antibodies, ligand, vaccine, immunogen, Opsonophagocytosis, protective activity, pneumococci

  NCBI PubMed ID: 33776393
  Publication DOI: 10.1134/S1068162021010076
  Journal NLM ID: 9420101
  Publisher: Springer Science and Business Media
  Correspondence: nen@ioc.ac.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 7973 (all data & tools)
• Article ID: 6073
  Javed J, Mandal PK "Bacterial surface capsular polysaccharides from Streptococcus pneumoniae: A systematic review on structures, syntheses, and glycoconjugate vaccines" - Carbohydrate Research 502 (2021) 108277
  

  The polysaccharide capsule of Streptococcus pneumoniae constitutes the outermost surface structure of the organism and plays a critical role in virulence. The capsule is the target of current pneumococcal vaccines and glycoconjugates and has important medical and industrial applications. Widespread use of these vaccines is driving changes in serotype prevalence in disease. A massive array of sugars and glycosidic linkages experienced with complete diversity of potential polysaccharide structures. However, it is impossible to collect a sufficient quantity of glycan antigens for the preparation of CPS-based glycoconjugate vaccines from natural sources with high purity and for thorough biological evaluation. So nowadays, the development of a chemical synthetic strategy and their conjugation with a carrier protein to form synthetic glycoconjugate vaccines has been used to gain access on a large scale. This review provides a comprehensive summary of structures, synthesis as well as recent development of synthetic glycoconjugate vaccines, which will support research and may benefit the glycochemical and medical sciences.

  synthesis, Streptococcus pneumoniae, glycoconjugate vaccines, polysaccharides, Pneumococcal Infections

  NCBI PubMed ID: 33743443
  Publication DOI: 10.1016/j.carres.2021.108277
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: P.K. Mandal
  Institutions: Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow, 226 031, India, Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 5809 (all data & tools)
• Article ID: 6461
  Shende N, Karale A, Bore P, Bhagade S, Gulhane A, Mallya AD, Dhere RM "Evaluation of structural modification induced activation of pneumococcal polysaccharide by GC-MS for the conjugate vaccine" - Carbohydrate Research 531 (2023) 108878
  

  Polysaccharide (Ps) activation evaluation is an imperative quality attribute in a conjugate vaccine. Pneumococcal polysaccharide (PnPs) serotypes 5, 6B, 14, 19A and 23F were cyanylated for 3 and 8 min. The cyanylated and non-cyanylated polysaccharides were methanolysed and derivatized to assess the activation of each sugar by GC-MS. The activation of 22 and 27% serotype 6B and 11 and 36% in serotype 23 F Ps at 3 and 8 min respectively showed controlled conjugation kinetics with CRM197 carrier protein estimated by SEC-HPLC and optimal absolute molar mass by SEC-MALS. The Glc and Gal are the most commonly activated sugars of all PnPs serotypes while N-acetyl sugars PneuNAc, GalNAc and Rha in serotypes 5, 14 and 19A respectively showed >50% activation which contributes to conjugate aggregate formation at 8 min compared to 3 min cyanylation. The GC-MS analysis of structural modifications at functional groups entails important information to characterize the activated polysaccharide for consistent conjugate vaccine manufacturing.

  activation, conjugate vaccine, pneumococcal polysaccharide, GC-MS, cyanylation, SEC-HPLC, SEC-MALS

  NCBI PubMed ID: 37390792
  Publication DOI: 10.1016/j.carres.2023.108878
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: A.D. Mallya
  Institutions: Research and Development Department, Serum Institute of India Pvt. Ltd, Hadapsar, Pune, Maharashtra, 411028, India
  Methods: GC-MS, methanolysis, SEC-MALS, conjugation, SEC-HPLC, CDAP-cyanylation, quantification
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 22313 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_423153,IEDB_983931,SB_192

• Article ID: 1520
  Jones C "NMR assays for carbohydrate-based vaccines" - Journal of Pharmaceutical and Biomedical Analysis 38(5) (2005) 840-850
  

  Antibodies against the cell surface carbohydrates of many microbial pathogens protect against infection. This was initially exploited by the development of purified polysaccharide vaccines, but glycoconjugate vaccines, in which the cell surface carbohydrate of a microbial pathogen is covalently attached to an appropriate carrier protein, are proving the most effective means to generate this protective immunity. Carbohydrate-based vaccines against Haemophilus influenzae Type b, Neisseria meningitidis, Streptococcus pneumoniae and Salmonella enterica serotype Typhi (S. Typhi) are already licensed, and many similar products are in various stages of development. For many of these vaccines, biological assays are not available or are inappropriate and NMR spectroscopy is proving a valuable tool for the characterisation and quality control of existing and novel products. This review highlights some of the areas in which NMR spectroscopy is currently used, and where further developments may be expected.

  capsular polysaccharide, O-acetylation, pneumonia, glycoconjugate, meningitis, carbohydrate-based vaccines, identity, typhoid

  NCBI PubMed ID: 16087046
  Publication DOI: 10.1016/j.jpba.2005.01.044
  Journal NLM ID: 8309336
  Publisher: London: Elsevier
  Institutions: Laboratory for Molecular Structure, National Institute for Biological Standards and Control, South Mimms, UK
  Methods: NMR
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 10371 (all data & tools)
• Article ID: 6386
  Gaikwad WK, Dhere RM, Jana SK, Mallya AD, Soni DJ, Gholap M, Ravenscroft N, Kodam KM "Effect of trifluoroacetic acid on the antigenicity of capsular polysaccharides obtained from various Streptococcus pneumoniae serotypes" - Carbohydrate Polymers 320 (2023) 121204
  

  Determining the safety, antigenicity, and immunogenicity by in vitro and in vivo studies is a prerequisite for the development of new vaccines. And this study investigated it for a vaccine made from Streptococcus pneumoniae serotypes 2, 5, 12F, 18C, and 22F. The crude CPS was purified and partially depolymerized by conventional and trifluoroacetic acid methods. 1H NMR analysis confirmed the identity of the depolymerized CPS which gave similar profiles to reference polysaccharides, except for serotype 18C which was de-O-acetylated during TFA treatment. The antigenicity of the depolymerized CPS prepared by either method was comparable to that of the native CPS for serotypes 2, 5, 18C, and 22F based on multiplex bead based competitive inhibition assay. This study demonstrated a relationship between antigenicity and immunogenicity, which offers more suitable candidates for conjugation. It was found that after partial depolymerization process, the CPS with optimal molecular size resulted in higher antigenicity. The immunogenicity of S. pneumoniae serotype 2 conjugates in mice was evaluated by opsonophagocytic assay and a multiplex bead-based assay, wherein on day 42 after immunization, the total and functional IgG titer was found to be increased by 32-fold.

  Streptococcus pneumoniae, immunogenicity, antigenicity, CRM197, pneumococcal conjugate vaccine, trifluoroacetic acid

  NCBI PubMed ID: 37659807
  Publication DOI: 10.1016/j.carbpol.2023.121204
  Journal NLM ID: 8307156
  Publisher: Elsevier
  Correspondence: R.M. Dhere ; K.M. Kodam
  Institutions: Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa, Department of Technology, Savitribai Phule Pune University, Pune 411007, India, Division of Biochemistry, Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India, Research and Development Department, Serum Institute of India Pvt. Ltd, Hadapsar, Pune 411028, India
  Methods: 1H NMR, chemical analysis, inhibition studies, partial depolymerization, immunization, conjugation, fermentation, SEC-HPLC, opsonophagocytic assay
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 10694 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_423153,IEDB_983931,SB_192

• Article ID: 2950
  Jansson PE, Lindberg B, Lindquist U "Structural studies of the capsular polysaccharide from Streptococcus pneumoniae type 5" - Carbohydrate Research 140 (1985) 101-110
  

  The structure of the capsular polysaccharide (S5) elaborated by Streptococcus pneumoniae type 5 has been investigated by using n.m.r. spectroscopy, methylation analysis, and various specific degradations. It is concluded that the polysaccharide is composed of pentasaccharide repeating-units having the following structure: (Formula: see text) In this structure, L-PneNAc stands for 2-acetamido-2,6-dideoxy-L-talose (pneumosamine) and D-Sug for 2-acetamido-2,6-dideoxy-D-xylo-hexos-4-ulose. The latter sugar accounts for the lability of S5 towards alkali. N.m.r. spectra indicate heterogeneity in S5, most probably associated with the hexosyl-4-ulose residue.

  NCBI PubMed ID: 4053092
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Methods: 13C NMR, 1H NMR, methylation, acid hydrolysis, GLC, Smith degradation, borohydride reduction
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 114428 (all data & tools)

Show legend Show as text

Structure type: monomer
Trivial name: UDP-2-acetamido-2,6-dideoxy-L-talose

• Article ID: 3506
  Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Wang Q, Reeves P, Wang L "Structure and genetics of Shigella O antigens" - FEMS Microbiology Reviews 32(4) (2008) 627-653
  

  This review covers the O antigens of the 46 serotypes of Shigella, but those of most Shigella flexneri are variants of one basic structure, leaving 34 Shigella distinct O antigens to review, together with their gene clusters. Several of the structures and gene clusters are reported for the first time and this is the first such group for which structures and DNA sequences have been determined for all O antigens. Shigella strains are in effect Escherichia coli with a specific mode of pathogenicity, and 18 of the 34 O antigens are also found in traditional E. coli. Three are very similar to E. coli O antigens and 13 are unique to Shigella strains. The O antigen of Shigella sonnei is quite atypical for E. coli and is thought to have transferred from Plesiomonas. The other 12 O antigens unique to Shigella strains have structures that are typical of E. coli, but there are considerably more anomalies in their gene clusters, probably reflecting recent modification of the structures. Having the complete set of structures and genes opens the way for experimental studies on the role of this diversity in pathogenicity.

  structure, O antigen, Shigella, O antigen gene cluster, O antigen diversity

  NCBI PubMed ID: 18422615
  Publication DOI: 10.1111/j.1574-6976.2008.00114.x
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: wanglei@nankai.edu.cn
  Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China.
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, serological methods, genetic methods, biochemical methods
  
   
  
  Shigella
  CSDB ID 23089 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide

• Article ID: 3589
  Pieretti G, Corsaro MM, Lanzetta R, Parrilli M, Canals R, Merino S, Tomas JM "Structural studies of the O-chain polysaccharide from Plesiomonas shigelloides strain 302-73 (serotype O1)" - European Journal of Organic Chemistry (18) (2008) 3149-3155
  

  Plesiomonas shigelloides is a Gram-negative bacterium belonging to the Enterobacteriaceae family. It has been found in an aquatic environment in the tropical and subtropical regions and is responsible for many gastrointestinal infections in humans, which take place from drinking untreated water or eating uncooked shellfish. Plesiomonas shigelloides has also been reported to provoke extraintestinal infections such as meningitis and bacteremia in immunocompromised adults and neonates. Despite the emerging importance of this pathogenic microorganism, only three different O-antigens have been characterised so far. The structure of the O-chain of the lipopolysaccharide (LPS) from Plesiomonasshigelloides strain 302–73 (serotype O1) was determined by chemical analysis, 1D and 2D NMR spectroscopy and MALDI-TOF mass spectrometry. The polysaccharide was constituted by a linear pentasaccharidic repeating unit as follows: →3)-α-L-PneNAc4OAc(1→4)-α-L-FucNAc(1→4)-α-L-FucNAc(1→4)-α-L-FucNAc(1→3)-β-D-QuiNAc4NHb(1→ (PneNAc = 2-acetamido-2,6-dideoxy-talose, Hb = (S)-3-hydroxybutanoyl) PneNAc O-acetylation was not stoichiometric and was found to be about 75 %. The position of the O-acetyl group and the amount of acetylation were deduced by NMR spectroscopic analysis. All the monosaccharides included in the repeating unit were deoxyamino sugars, which most probably, together with the presence of O-acetyl groups, were responsible for the recovery of the LPS in the phenol layer of the phenol/water extract of dried bacteria cells.

  Lipopolysaccharide, NMR spectroscopy, structure elucidation, Plesiomonas shigelloides, Pneumosamine

  Publication DOI: 10.1002/ejoc.200800198
  Journal NLM ID: 9805750
  Publisher: Wiley-VCH
  Correspondence: corsaro@unina.it
  Institutions: Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, 23845 Borstel (Germany), Fax: (+49) 4537-188745
  Methods: 13C NMR, 1H NMR, methylation, NMR-2D, GC-MS, SDS-PAGE, sugar analysis, acid hydrolysis, alkaline degradation, MALDI-TOF MS
  
   
  
  Plesiomonas shigelloides 302-73
  CSDB ID 23417 (all data & tools)
• Article ID: 4359
  Nazarenko EL, Crawford RJ, Ivanova EP "The structural diversity of carbohydrate antigens of selected Gram-negative marine bacteria" - Marine Drugs 9(10) (2011) 1914-1954
  

  Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens) found in cell walls of gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobacteria phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria.

  O-specific polysaccharides, carbohydrate antigens, marine microorganisms

  NCBI PubMed ID: 22073003
  Publication DOI: 10.3390/md9101914
  Journal NLM ID: 101213729
  Publisher: Basel, Switzerland: Molecular Diversity Preservation International
  Correspondence: elnaz@piboc.dvo.ru
  Institutions: Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia, Faculty of Life and Social Sciences, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
  Methods: 13C NMR, 1H NMR, methylation, periodate oxidation, NMR-2D, FAB-MS, partial acid hydrolysis, NMR, HF solvolysis, sugar analysis, 31P NMR, ESI-MS, acid hydrolysis, mild acid hydrolysis, HPAEC, ESI-ICR-MS, Smith degradation, chemical methods, MALDI-TOF MS, MS, de-O-acetylation, NMR-1D, GPC, alkaline hydrolysis, CE-ESI-MS, CE-MS, hydrazinolysis
  
   
  
  Plesiomonas shigelloides O1 302-73
  CSDB ID 28482 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen

• Article ID: 3763
  Pieretti G, Corsaro MM, Lanzetta R, Parrilli M, Vilehes S, Merino S, Tomas JM "Structure of the core region from the lipopolysaceharide of Plesiomonas shigelloides strain 302-73 (serotype Ol)" - European Journal of Organic Chemistry (9) (2009) 1365-1371
  

  Plesiomonas shigelloides is a Gram-negative pathogenic bacterium belonging to the Enterobacteriaceae family. To date, only few lipopolysaccharide (LPS) structures from P. shigelloides strains are known. In particular, three core oligosaccharides have been found. Recently, we elucidated the structure of the O-antigen of P. shigelloides 302-73 (serotype O1) and in this paper we present the characterization of the core structure from the LPS of the same strain. The LPS was hydrolyzed under both alkaline and mildly acidic conditions. In both cases, a mixture of oligosaccharides was obtained, which was purified by gel filtration and HPAEC. The oligosaccharides were characterized by chemical analysis, 2D NMR spectroscopy and MALDI-TOF mass spectrometry. A new core structure was found for P. shigelloides. In particular, from the analysis of the acid hydrolysed product it was possible to reveal the presence of a of D-glycero-D-talo-2-octulopyranosonic acid (Ko) residue, which substitutes in part the terminal 3-doxy-D-manno-oct-2-ulosonic acid (Kdo) unit. The Ko residue is not frequently found in core structures.

  Oligosaccharides, NMR spectroscopy, structure elucidation, sequence determination

  Publication DOI: 10.1002/ejoc.200801200
  Journal NLM ID: 9805750
  Publisher: Wiley-VCH
  Correspondence: corsaro@unina.it
  Institutions: Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli, Italy, Fax: +39-081-674393, Departamento Microbiología, Universidad de Barcelona, Diagonal 645, 08071 Barcelona, Spain
  Methods: 13C NMR, 1H NMR, methylation, NMR-2D, GC-MS, de-O-acylation, SDS-PAGE, sugar analysis, acid hydrolysis, alkaline degradation, MALDI-TOF MS, NMR-1D, HPAEC-PAD
  
   
  
  Plesiomonas shigelloides 302-73
  CSDB ID 23816 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: repeating unit oligosaccharide
Contained glycoepitopes: IEDB_130650

• Article ID: 3931
  Pieretti G, Carillo S, Lindner B, Lanzetta R, Parrilli M, Jimenez N, Regue M, Tomas JM, Corsaro MM "The complete structure of the core of the LPS from Plesiomonas shigelloides 302-73 and the identification of its O-antigen biological repeating unit" - Carbohydrate Research 345(17) (2010) 2523-2528
  

  Plesiomonas shigelloides is a Gram-negative opportunistic pathogen associated with gastrointestinal and extraintestinal infections, which especially invades immunocompromised patients and neonates. The lipopolysaccharides are one of the major virulence determinants in Gram-negative bacteria and are structurally composed of three different domains: the lipid A, the core oligosaccharide and the O-antigen polysaccharide. In the last few years we elucidated the structures of the O-chain and the core oligosaccharide from the P. shigelloides strain 302-73. In this paper we now report the characterization of the linkage between the core and the O-chain. The LPS obtained after PCP extraction contained a small number of O-chain repeating units. The product obtained by hydrazinolysis was analysed by FTICR-ESIMS and suggested the presence of an additional Kdo in the core oligosaccharide. Furthermore, the LPS was hydrolysed under mild acid conditions and a fraction that contained one O-chain repeating unit linked to a Kdo residue was isolated and characterized by FTICR-ESIMS and NMR spectroscopy. Moreover, after an alkaline reductive hydrolysis, a disaccharide α-Kdo-(2→6)-GlcNol was isolated and characterized. The data obtained proved the presence of an α-Kdo in the outer core and allowed the identification of the O-antigen biological repeating unit as well as its linkage with the core oligosaccharide.

  NMR spectroscopy, structure elucidation, Plesiomonas, outer-core Kdo, reductive hydrolysis

  NCBI PubMed ID: 20933222
  Publication DOI: 10.1016/j.carres.2010.09.007
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: corsaro@unina.it
  Institutions: Dipartimento di Chimica Organica e Biochimica, Universita di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli, Italy, Departamento Microbiología, Universidad de Barcelona, Diagonal 645, 08071 Barcelona, Spain, Division of Immunochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 10, 23845 Borstel, Germany
  Methods: 13C NMR, 1H NMR, NMR-2D, de-O-acylation, sugar analysis, 31P NMR, mild acid hydrolysis, ESI-ICR-MS, MALDI-TOF MS, NMR-1D, hydrazinolysis, alkaline reductive hydrolysis
  
   
  
  Plesiomonas shigelloides 302-73
  CSDB ID 25397 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531

• Article ID: 4050
  Knirel YA, Shevelev SD, Perepelov AV "Higher aldulosonic acids: components of bacterial glycans" - Mendeleev Communications 21(4) (2011) 173-182
  

  Recent data on the natural occurrence, chemistry, and biochemistry of C8 and C9 aldulosonic acids (3-deoxy-d-manno-oct-2-ulosonic acid, sialic acids, N-acyl derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids, and some others) as well as on the structures and biological significance of bacterial glycans containing these higher acidic monosaccharides are summarized.

  structure, Bacterial, glycan, aldulosonic acid, higher acidic monosaccharides, sialic acids

  Publication DOI: 10.1016/j.mencom.2011.07.001
  Journal NLM ID: 9425965
  Publisher: Moscow: Academy of Sciences of the USSR; Cambridge,UK : Royal Society of Chemistry
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Pseudoalteromonas nigrifaciens IAM 13010
  CSDB ID 26786 (all data & tools)
• Article ID: 4435
  Nazarenko EL, Komandrova NA, Gorshkova RP, Tomshich SV, Zubkov VA, Kilcoyne M, Savage AV "Structures of polysaccharides and oligosaccharides of some Gram-negative marine Proteobacteria" - Carbohydrate Research 338(23) (2003) 2449-2457
  

  The chemical structures of polysaccharides and LPS core oligosaccharides, isolated from various Gram-negative marine bacteria from the genera Pseudoalteromonas and Shewanella belonging to the Alteromonadaceae family and gamma-subclass of Proteobacteria, are reviewed. The polysaccharides are distinguished by the acidic character (e.g., due to the presence of hexuronic and aldulosonic acids and their derivatives) and the occurrence of unusual sugars, including N-acyl derivatives of 6-deoxyamino sugars, such as N-acetyl-D-quinovosamine, N-acetyl-L-fucosamine and N-acetyl-6-deoxy-L-talosamine, and higher sugars like 2,6-dideoxy-2-acetamido-4-C-(3'-carboxamide-2',2'-dihydroxypropyl)-D-galac topyranose (shewanellose). Many constituent sugars have various uncommon non-sugar substituents, such as alanine, formic, lactic and hydroxybutyric acids, sulfate, phosphate, and 2-aminopropane-1,3-diol.

  Lipopolysaccharide, oligosaccharide structure, O-antigen, polysaccharide structure, Shewanella, Pseudoalteromonas, Proteobacteria

  NCBI PubMed ID: 14670708
  Publication DOI: 10.1016/j.carres.2003.06.004
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: A.V. Savage
  Institutions: Department of Chemistry, National University of Ireland, Galway, Ireland, Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russian Federation
  
   
  
  Pseudoalteromonas nigrifaciens IAM 13010T
  CSDB ID 28832 (all data & tools)
• Article ID: 4926
  Sanapala SR, Kulkarni SS "Expedient Route To Access Rare Deoxy Amino L-Sugar Building Blocks for the Assembly of Bacterial Glycoconjugates" - Journal of the American Chemical Society 138(14) (2016) 4938-4947
  

  Bacterial glycoproteins and oligosaccharides contain several rare deoxy amino l-sugars which are virtually absent in the human cells. This structural difference between the bacterial and host cell surface glycans can be exploited for the development of carbohydrate based vaccines and target specific drugs. However, the unusual deoxy amino l-sugars present in the bacterial glycoconjugates are not available from natural sources. Thus, procurement of orthogonally protected rare l-sugar building blocks through efficient chemical synthesis is a crucial step toward the synthesis of structurally well-defined and homogeneous complex glycans. Herein, we report a general and expedient methodology to access a variety of unusual deoxy amino l-sugars starting from readily available l-rhamnose and l-fucose via highly regioselective, one-pot double serial and double parallel displacements of the corresponding 2,4-bistriflates using azide and nitrite anions as nucleophiles. Alternatively, regioselective monotriflation at O2, O3, and O4 of l-rhamnose/l-fucose allowed selective inversions at respective positions leading to diverse rare sugars. The orthogonally protected deoxy amino l-sugar building blocks could be stereoselectively assembled to obtain biologically relevant bacterial O-glycans, as exemplified by the first total synthesis of the amino linker-attached, conjugation-ready tetrasaccharide of O-PS of Yersinia enterocolitica O:50 strain 3229 and the trisaccharide of Pseudomonas chlororaphis subsp. aureofaciens strain M71.

  trisaccharide, Pseudomonas, glycoconjugates, vaccines, L-rhamnose, L-fucose, Yersinia enterocolitica, chemical synthesis, O-glycans

  NCBI PubMed ID: 27002789
  Publication DOI: 10.1021/jacs.6b01823
  Journal NLM ID: 7503056
  Publisher: American Chemical Society
  Correspondence: suvarn@chem.iitb.ac.in
  Institutions: Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
  Methods: 13C NMR, 1H NMR, TLC, GLC, chemical synthesis, chemical methods, MS, glycosylation
  
   
  
  Alteromonas nigrifaciens IAM 13010T
  CSDB ID 11735 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen

• Article ID: 4329
  Knirel YA "Structure of O-antigens" - Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
  

  The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.

  Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis

  Publication DOI: 10.1007/978-3-7091-0733-1_3
  Publisher: Springer
  Correspondence: knirel@ioc.ac.ru
  Editors: Knirel YA, Valvano MA
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Plesiomonas shigelloides O1
  CSDB ID 27655 (all data & tools)
• Article ID: 4926
  Sanapala SR, Kulkarni SS "Expedient Route To Access Rare Deoxy Amino L-Sugar Building Blocks for the Assembly of Bacterial Glycoconjugates" - Journal of the American Chemical Society 138(14) (2016) 4938-4947
  

  Bacterial glycoproteins and oligosaccharides contain several rare deoxy amino l-sugars which are virtually absent in the human cells. This structural difference between the bacterial and host cell surface glycans can be exploited for the development of carbohydrate based vaccines and target specific drugs. However, the unusual deoxy amino l-sugars present in the bacterial glycoconjugates are not available from natural sources. Thus, procurement of orthogonally protected rare l-sugar building blocks through efficient chemical synthesis is a crucial step toward the synthesis of structurally well-defined and homogeneous complex glycans. Herein, we report a general and expedient methodology to access a variety of unusual deoxy amino l-sugars starting from readily available l-rhamnose and l-fucose via highly regioselective, one-pot double serial and double parallel displacements of the corresponding 2,4-bistriflates using azide and nitrite anions as nucleophiles. Alternatively, regioselective monotriflation at O2, O3, and O4 of l-rhamnose/l-fucose allowed selective inversions at respective positions leading to diverse rare sugars. The orthogonally protected deoxy amino l-sugar building blocks could be stereoselectively assembled to obtain biologically relevant bacterial O-glycans, as exemplified by the first total synthesis of the amino linker-attached, conjugation-ready tetrasaccharide of O-PS of Yersinia enterocolitica O:50 strain 3229 and the trisaccharide of Pseudomonas chlororaphis subsp. aureofaciens strain M71.

  trisaccharide, Pseudomonas, glycoconjugates, vaccines, L-rhamnose, L-fucose, Yersinia enterocolitica, chemical synthesis, O-glycans

  NCBI PubMed ID: 27002789
  Publication DOI: 10.1021/jacs.6b01823
  Journal NLM ID: 7503056
  Publisher: American Chemical Society
  Correspondence: suvarn@chem.iitb.ac.in
  Institutions: Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
  Methods: 13C NMR, 1H NMR, TLC, GLC, chemical synthesis, chemical methods, MS, glycosylation
  
   
  
  Plesiomonas shigelloides O1
  CSDB ID 11732 (all data & tools)
• Article ID: 6301
  Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" - Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
  

  Bacterial surface glycans perform a diverse and important set of biological roles, and have been widely used in the treatment of bacterial infectious diseases. The majority of bacterial surface glycans are decorated with diverse rare functional groups, including amido, acetamidino, carboxamido and pyruvate groups. These functional groups are thought to be important constituents for the biological activities of glycans. Chemical synthesis of glycans bearing these functional groups or their variants is essential for the investigation of structure-activity relationships by a medicinal chemistry approach. To date, a broad choice of synthetic methods is available for targeting the different rare functional groups in bacterial surface glycans. This article reviews the structures of naturally occurring rare functional groups in bacterial surface glycans, and the chemical methods used for installation of these groups.

  chemical synthesis, acetamidino group, amido group, bacterial surface glycan, carboxamido group, pyruvyl ketal

  NCBI PubMed ID: 35750381
  Publication DOI: 10.1016/S1875-5364(22)60177-8
  Journal NLM ID: 101504416
  Publisher: Beijing: Science Press; Elsevier
  Correspondence: J. Yin
  Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
  
   
  
  Plesiomonas shigelloides O1
  CSDB ID 21148 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_423153,IEDB_983931,SB_192

• Article ID: 4431
  Ovodov YS "Bacterial capsular antigens. Structural patterns of capsular antigens" - Biochemistry (Moscow) 71(9) (2006) 937-954
  

  Structural patterns of bacterial capsular antigens including capsular polysaccharides and exoglycans are given in this review. In addition, the immunological activity of capsular antigens and their role in type specificity of bacteria are discussed.

  structure, capsular polysaccharides, bacterial capsular antigens, bacterial exoglycans, immunological activity, type specificity

  NCBI PubMed ID: 17009947
  Publication DOI: 10.1134/S000629790609001X
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: ovoys@physiol.komisc.ru
  Institutions: Institute of Physiology, Komi Science Center, Urals Branch of the Russian Academy of Sciences, Syktyvkar 167982, Russia
  
   
  
  Streptococcus pneumoniae type 5
  CSDB ID 28706 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-antigen

• Article ID: 4479
  Aquilini E, Merino S, Tomas JM "The Plesiomonas shigelloides wb gene cluster and the role of O1-antigen LPS in pathogenicity" - Microbial Pathogenesis 63 (2013) 1-7
  

  The Plesiomonas shigelloides 302-73 strain (serotype O1) wb gene cluster encodes 15 proteins which are consistent with the chemical structure of the O1-antigen lypopolysaccharide (LPS) previously described for this strain. The P. shigelloides O1-antigen LPS export uses the Wzy-dependent pathway as correspond to heteropolysaccharides structures. By the isolation of two mutants lacking this O1-antigen LPS, we could establish that the presence of the O1-antigen LPS is crucial for to survive in serum mainly to become resistant to complement. Also, it is an important factor in the bacterial adhesion and invasion to some eukaryotic cells, and in the ability to form biofilms. This is the first report on the genetics from a P. shigelloides O-antigen LPS cluster (wb) not shared by Shigella like P. shigelloides O17, the only one reported until now.

  Pathogenesis, Plesiomonas shigelloides, O1-antigen LPS, wb cluster

  NCBI PubMed ID: 23727162
  Publication DOI: 10.1016/j.micpath.2013.05.010
  Journal NLM ID: 8606191
  Publisher: Academic Press
  Correspondence: J.M. Tomas
  Institutions: Departamento de Microbiologia, Facultad de Biologia, Universidad de Barcelona, Diagonal 643, 08071 Barcelona, Spain
  Methods: SDS-PAGE, genetic methods, Southern blotting
  
   
  
  Plesiomonas shigelloides O1
  CSDB ID 29907 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: spacer-CRM197 protein
Trivial name: glycan epitope (glycotope)
Compound class: CPS, glycoconjugate
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_423153,IEDB_983931,SB_192

• Article ID: 6170
  Zaslona ME, Downey AM, Seeberger PH, Moscovitz O "Semi- and fully synthetic carbohydrate vaccines against pathogenic bacteria: recent developments" - Biochemical Society Transactions 49(5) (2021) 2411-2429
  

  The importance of vaccine-induced protection was repeatedly demonstrated over the last three decades and emphasized during the recent COVID-19 pandemic as the safest and most effective way of preventing infectious diseases. Vaccines have controlled, and in some cases, eradicated global viral and bacterial infections with high efficiency and at a relatively low cost. Carbohydrates form the capsular sugar coat that surrounds the outer surface of human pathogenic bacteria. Specific surface-exposed bacterial carbohydrates serve as potent vaccine targets that broadened our toolbox against bacterial infections. Since first approved for commercial use, antibacterial carbohydrate-based vaccines mostly rely on inherently complex and heterogenous naturally derived polysaccharides, challenging to obtain in a pure, safe, and cost-effective manner. The introduction of synthetic fragments identical with bacterial capsular polysaccharides provided well-defined and homogenous structures that resolved many challenges of purified polysaccharides. The success of semisynthetic glycoconjugate vaccines against bacterial infections, now in different phases of clinical trials, opened up new possibilities and encouraged further development towards fully synthetic antibacterial vaccine solutions. In this mini-review, we describe the recent achievements in semi- and fully synthetic carbohydrate vaccines against a range of human pathogenic bacteria, focusing on preclinical and clinical studies.

  carbohydrates, capsular polysaccharides, bacteria, vaccines, synthetic carbohydrate, antibacterial vaccines

  NCBI PubMed ID: 34495299
  Publication DOI: 10.1042/BST20210766
  Journal NLM ID: 7506897
  Correspondence: Oren Moscovitz
  Institutions: Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 10427 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: spacer-CRM197
Trivial name: repeating unit conjugate
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_423153,IEDB_983931,SB_192

• Article ID: 6211
  Del Bino L, Osterlid KE, Wu DY, Nonne F, Romano MR, Codée J, Adamo R "Synthetic Glycans to Improve Current Glycoconjugate Vaccines and Fight Antimicrobial Resistance" - Chemical Reviews 122(20) (2022) 15672-15716
  

  Antimicrobial resistance (AMR) is emerging as the next potential pandemic. Different microorganisms, including the bacteria Acinetobacter baumannii, Clostridioides difficile, Escherichia coli, Enterococcus faecium, Klebsiella pneumoniae, Neisseria gonorrhoeae, Pseudomonas aeruginosa, non-typhoidal Salmonella, and Staphylococcus aureus, and the fungus Candida auris, have been identified by the WHO and CDC as urgent or serious AMR threats. Others, such as group A and B Streptococci, are classified as concerning threats. Glycoconjugate vaccines have been demonstrated to be an efficacious and cost-effective measure to combat infections against Haemophilus influenzae, Neisseria meningitis, Streptococcus pneumoniae, and, more recently, Salmonella typhi. Recent times have seen enormous progress in methodologies for the assembly of complex glycans and glycoconjugates, with developments in synthetic, chemoenzymatic, and glycoengineering methodologies. This review analyzes the advancement of glycoconjugate vaccines based on synthetic carbohydrates to improve existing vaccines and identify novel candidates to combat AMR. Through this literature survey we built an overview of structure-immunogenicity relationships from available data and identify gaps and areas for further research to better exploit the peculiar role of carbohydrates as vaccine targets and create the next generation of synthetic carbohydrate-based vaccines.

  carbohydrates, glycan, glycoconjugate vaccine

  NCBI PubMed ID: 35608633
  Publication DOI: 10.1021/acs.chemrev.2c00021
  Journal NLM ID: 2985134R
  Publisher: Chem Rev
  Correspondence: J. Codée ; R. Adamo
  Institutions: GSK, R&D, 53100 Siena, Italy, Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
  
   
  
  Streptococcus pneumoniae 5
  CSDB ID 20877 (all data & tools)