PolysacDB: A comprehensive database of microbial polysaccharide antigens and their antibodies

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Citation: Aithal A, Sharma A, Joshi S, Raghava GPS, Varshney GC (2012) PolysacDB: A Database of Microbial Polysaccharide Antigens and Their Antibodies. PLoS ONE 7(4): e34613. doi:10.1371/journal.pone.0034613
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PolysacDB ID1995
Carbohydrate NameCapsular polysaccharide   (Drugpedia)
Carbohydrate ClassCapsular polysaccharide
Microbe NameStreptococcus pneumoniae serotype 6B   (NCBI Taxonomy)   (Drugpedia)
Basic StructureThe capsular polysaccharide consists of the following residues : -2)-α-D-Galp-(1-->3)-α-D-Glcp-(1-->3)-α-L-Rhap-(1-->4)-D-Rib-ol-(5-P-
BCSDB Structure5205
Proposed FunctionN/A
Antigenic NatureGlycoconjugates
Carrier NameDiphtheria toxin mutant (CRM197)
Conjugate MethodN/A
AntibodiesMab Hyp6BM17
Antibody Type ClassIgM
Assay SystemSandwich ELISA, opsonization assays
Cross ReactivityThis Mab cross-reacted with strain 6A
Proposed EpitopeN/A
IEDB EpitopeN/A
Proposed UtilityThis Mab had opsonophagocytic activity
Curator IDAA + AS
Date of Curation13-12-2010
ReferencesPMC97888

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PolysacDB ID1996
Carbohydrate NameCapsular polysaccharide   (Drugpedia)
Carbohydrate ClassCapsular polysaccharide
Microbe NameStreptococcus pneumoniae serotype 6B   (NCBI Taxonomy)   (Drugpedia)
Basic StructureThe capsular polysaccharide consists of the following residues : -2)-α-D-Galp-(1-->3)-α-D-Glcp-(1-->3)-α-L-Rhap-(1-->4)-D-Rib-ol-(5-P-
BCSDB Structure5205
Proposed FunctionN/A
Antigenic NatureGlycoconjugates
Carrier NameDiphtheria toxin mutant (CRM197)
Conjugate MethodN/A
AntibodiesMab Hyp6BG6
Antibody Type ClassIgG2b
Assay SystemSandwich ELISA, opsonization assays
Cross ReactivityThis Mab cross-reacted with strain 6A
Proposed EpitopeN/A
IEDB EpitopeN/A
Proposed UtilityThis Mab had opsonophagocytic activity
Curator IDAA + AS
Date of Curation13-12-2010
ReferencesPMC97888

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PolysacDB ID1997
Carbohydrate NameCapsular polysaccharide   (Drugpedia)
Carbohydrate ClassCapsular polysaccharide
Microbe NameStreptococcus pneumoniae serotype 6B   (NCBI Taxonomy)   (Drugpedia)
Basic StructureThe capsular polysaccharide consists of the following residues : -2)-α-D-Galp-(1-->3)-α-D-Glcp-(1-->3)-α-L-Rhap-(1-->4)-D-Rib-ol-(5-P-
BCSDB Structure5205
Proposed FunctionN/A
Antigenic NatureGlycoconjugates
Carrier NameDiphtheria toxin mutant (CRM197)
Conjugate MethodN/A
AntibodiesMab Hyp6BG7
Antibody Type ClassIgG1
Assay SystemSandwich ELISA, opsonization assays
Cross ReactivityThis Mab cross-reacted with strain 6A
Proposed EpitopeN/A
IEDB EpitopeN/A
Proposed UtilityThis Mab had opsonophagocytic activity
Curator IDAA + AS
Date of Curation14-12-2010
ReferencesPMC97888

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PolysacDB ID1998
Carbohydrate NameCapsular polysaccharide   (Drugpedia)
Carbohydrate ClassCapsular polysaccharide
Microbe NameStreptococcus pneumoniae serotype 6B   (NCBI Taxonomy)   (Drugpedia)
Basic StructureThe capsular polysaccharide consists of the following residues : -2)-α-D-Galp-(1-->3)-α-D-Glcp-(1-->3)-α-L-Rhap-(1-->4)-D-Rib-ol-(5-P-
BCSDB Structure5205
Proposed FunctionN/A
Antigenic NatureGlycoconjugates
Carrier NameDiphtheria toxin mutant (CRM197)
Conjugate MethodN/A
AntibodiesMab Hyp6BG8
Antibody Type ClassIgG1
Assay SystemSandwich ELISA, opsonization assays
Cross ReactivityThis Mab cross-reacted with strain 6A
Proposed EpitopeN/A
IEDB EpitopeN/A
Proposed UtilityThis Mab had opsonophagocytic activity
Curator IDAA + AS
Date of Curation14-12-2010
ReferencesPMC97888

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PolysacDB ID2435
Carbohydrate NameTrisaccharide part of Streptococcus pneumoniae type 3 polysaccharide   (Drugpedia)
Carbohydrate ClassCapsular polysaccharide
Microbe NameStreptococcus pneumoniae Type 3   (NCBI Taxonomy)   (Drugpedia)
Basic StructureN/A
BCSDB StructureN/A
Proposed FunctionN/A
Antigenic NatureGlycoconjugates
Carrier NameDiphtheria toxin mutant (CRM197)
Conjugate MethodThe saccharide fragments described above were conjugated to CRM197 using diethyl squarate as linker. Elongation of the saccharides with diethyl squarate was performed in ethanol/0.1M sodium phosphate (pH 6.9). The reaction products were purified by solid-phase extraction and coupled to protein in 0.1m sodium borate buffer at pH 9.5
AntibodiesAntisera
Antibody Type ClassN/A
Assay SystemEnzyme-linked immunosorbent assay and in-vitro phagocytosis assay
Cross ReactivityN/A
Proposed Epitopeβ-d-Glcp-(1-->3)-β-d-GlcpA-(1-->4)-β-d-Glcp
IEDB EpitopeN/A
Proposed UtilityThis antisera provided full protection against challenge with pneumococcal type 3 bacteria
Curator IDAA + AS
Date of Curation13-05-2011
ReferencesPMC308892

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PolysacDB ID2466
Carbohydrate NamePneumococcal vaccine PP   (Drugpedia)
Carbohydrate ClassLipopolysaccharide
Microbe NameStreptococcus pneumoniae   (NCBI Taxonomy)   (Drugpedia)
Basic StructureThis vaccine includes the polysaccharides of 6B, 14, 19F, 18C, 23F serotypes
BCSDB StructureN/A
Proposed FunctionN/A
Antigenic NatureGlycoconjugates
Carrier NameDiphtheria toxin mutant (CRM197)
Conjugate MethodThe oligosaccharide-CRM197 conjugates were synthesized by either first hydrolysing the native oligosaccharide [PS] to smaller fragments and then subjecting the fragments to limited periodate oxidation or by oxidizing the native PS and then hydrolyzing it into smaller fragments. The PS-CRM197 conjugates were synthesized by oxidizing native pneumococcal PS with sodium metaperiodate to introduce random aldehyde functional groups. Oxidized OS or PS fragments were coupled to CRM197 in the presence of sodium cyanoborohydride
AntibodiesHuman Antisera
Antibody Type ClassN/A
Assay SystemELISA, Opsonophagocytic killing assay
Cross ReactivityThe antisera reacted with 6B serotype, showed good opsonophagocytic activity for 19F serotype. This antisera also cross-reacted with 6A serotype but did not react with 19A serotype
Proposed EpitopeN/A
IEDB EpitopeN/A
Proposed UtilityThe findings suggest that some conjugate vaccines may elicit cross-protection against related polysaccharides better than others
Curator IDAA + AS
Date of Curation26-05-2011
References10515817

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PolysacDB ID2467
Carbohydrate NamePneumococcal vaccine OP   (Drugpedia)
Carbohydrate ClassLipopolysaccharide
Microbe NameStreptococcus pneumoniae   (NCBI Taxonomy)   (Drugpedia)
Basic StructureThis vaccine includes oligosaccharides of 6B, 14, 19F, 18C, 23F serotypes
BCSDB StructureN/A
Proposed FunctionN/A
Antigenic NatureGlycoconjugates
Carrier NameDiphtheria toxin mutant (CRM197)
Conjugate MethodThe oligosaccharide-CRM197 conjugates were synthesized by either first hydrolysing the native oligosaccharide [PS] to smaller fragments and then subjecting the fragments to limited periodate oxidation or by oxidizing the native PS and then hydrolyzing it into smaller fragments. The PS-CRM197 conjugates were synthesized by oxidizing native pneumococcal PS with sodium metaperiodate to introduce random aldehyde functional groups. Oxidized OS or PS fragments were coupled to CRM197 in the presence of sodium cyanoborohydride
AntibodiesHuman Antisera
Antibody Type ClassN/A
Assay SystemELISA, Opsonophagocytic killing assay
Cross ReactivityThe antisera reacted with 6B serotype, showed poor opsonophagocytic activity for 19F serotype. This antisera also cross-reacted with 6A serotype but did not react with 19A serotype
Proposed EpitopeN/A
IEDB EpitopeN/A
Proposed UtilityThe findings suggest that some conjugate vaccines may elicit cross-protection against related polysaccharides better than others
Curator IDAA + AS
Date of Curation26-05-2011
References10515817

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PolysacDB ID2468
Carbohydrate NamePneumococcal vaccine MK   (Drugpedia)
Carbohydrate ClassLipopolysaccharide
Microbe NameStreptococcus pneumoniae   (NCBI Taxonomy)   (Drugpedia)
Basic StructureThis vaccine includes oligosaccharides of 6B, 14, 19F, 18C, 23F, 4 and 9V serotypes
BCSDB StructureN/A
Proposed FunctionN/A
Antigenic NatureGlycoconjugates
Carrier NameDiphtheria toxin mutant (CRM197)
Conjugate MethodThe oligosaccharide-CRM197 conjugates were synthesized by either first hydrolysing the native oligosaccharide [PS] to smaller fragments and then subjecting the fragments to limited periodate oxidation or by oxidizing the native PS and then hydrolyzing it into smaller fragments. The PS-CRM197 conjugates were synthesized by oxidizing native pneumococcal PS with sodium metaperiodate to introduce random aldehyde functional groups. Oxidized OS or PS fragments were coupled to CRM197 in the presence of sodium cyanoborohydride
AntibodiesHuman Antisera
Antibody Type ClassN/A
Assay SystemELISA, Opsonophagocytic killing assay
Cross ReactivityThe antisera reacted with 6B serotype, showed good opsonophagocytic activity for 19F serotype. This antisera also cross-reacted with 6A serotype and 19A serotype
Proposed EpitopeN/A
IEDB EpitopeN/A
Proposed UtilityThe findings suggest that some conjugate vaccines may elicit cross-protection against related polysaccharides better than others
Curator IDAA + AS
Date of Curation27-05-2011
References10515817

Bioinformatics Centre, Institute of Microbial Technology, Sec - 39A, Chandigarh, India - 160036