Found 51 structures.
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1. Compound ID: 5845
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a-L-2,6dlyxHexp3Me4Ac-(1-4)-b-L-Digp3Me-(1-3)-L-1,5daraHex4Me-ol
Dig = 2,6-deoxy-ribo-Hexose (digitoxose) |
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Structure type: oligomer
The structure is contained in the following publication(s):
- Article ID: 2571
Carter GT, Phillipson DW, Goodman JJ, Dunne TS, Borders DB "LL-E19020 α and β, novel growth promoting agents: isolation, characterization and structures" -
The Journal of Antibiotics 41 (1988) 1511-1514
No abstract available
NCBI PubMed ID: 3192501Publication DOI: 10.7164/antibiotics.41.1511Journal NLM ID: 0151115Publisher: London: Nature Publishing Group
Institutions: American Cyanamid Company, Medical Research Division, Lederle Laboratories, Pearl River, NY, USA
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2. Compound ID: 9776
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a-D-Xylp-(1-3)-+
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Fuc-(1-?)-a-D-Galp4Me-(1-2)-+ |
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b-D-ManpNAcA4Me6NH2-(1-3)-+ | | b-Digp-(1-2)-+
| | | |
Gc-(1-7)-Psep5Am-(2-4)-b-D-ManpNAcA-(1-4)-a-D-Fucp-(1-4)-b-D-GlcpA-(1-3)-a-D-Galp-(1--/(1->3)Ser/Thr of S-layer protein/ |
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Structure type: oligomer
Aglycon: (1->3)Ser/Thr of S-layer protein
Compound class: S-layer glycan
Contained glycoepitopes: IEDB_114701,IEDB_115015,IEDB_115136,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_149135,IEDB_151528,IEDB_152214,IEDB_153553,IEDB_174333,IEDB_190606,IEDB_423153,SB_154,SB_7,SB_86
The structure is contained in the following publication(s):
- Article ID: 4098
Posch G, Pabst M, Brecker L, Altmann F, Messner P, Schäffer C "Characterization and scope of S-layer protein O-glycosylation in Tannerella forsythia" -
Journal of Biological Chemistry 286(44) (2011) 38714-38724
Cell surface glycosylation is an important element in defining the life of pathogenic bacteria. Tannerella forsythia is a Gram-negative, anaerobic periodontal pathogen inhabiting the subgingival plaque biofilms. It is completely covered by a two-dimensional crystalline surface layer (S-layer) composed of two glycoproteins. Although the S-layer has previously been shown to delay the bacterium's recognition by the innate immune system, we characterize here the S-layer protein O-glycosylation as a potential virulence factor. The T. forsythia S-layer glycan was elucidated by a combination of electrospray ionization-tandem mass spectrometry and nuclear magnetic resonance spectroscopy as an oligosaccharide with the structure 4-Me-β-ManpNAcCONH(2)-(1→3)-[Pse5Am7Gc-(2→4)-]-β-ManpNAcA-(1→4)-[4-Me-α-Galp-(1→2)-]-α-Fucp-(1→4)-[-α-Xylp-(1→3)-]-β-GlcpA-(1→3)-[-β-Digp-(1→2)-]-α-Galp, which is O-glycosidically linked to distinct serine and threonine residues within the three-amino acid motif (D)(S/T)(A/I/L/M/T/V) on either S-layer protein. This S-layer glycan obviously impacts the life style of T. forsythia because increased biofilm formation of an UDP-N-acetylmannosaminuronic acid dehydrogenase mutant can be correlated with the presence of truncated S-layer glycans. We found that several other proteins of T. forsythia are modified with that specific oligosaccharide. Proteomics identified two of them as being among previously classified antigenic outer membrane proteins that are up-regulated under biofilm conditions, in addition to two predicted antigenic lipoproteins. Theoretical analysis of the S-layer O-glycosylation of T. forsythia indicates the involvement of a 6.8-kb gene locus that is conserved among different bacteria from the Bacteroidetes phylum. Together, these findings reveal the presence of a protein O-glycosylation system in T. forsythia that is essential for creating a rich glycoproteome pinpointing a possible relevance for the virulence of this bacterium.
virulence factor, S-layer, O-glycosylation, Proteomics, Tannerella forsythia
NCBI PubMed ID: 21911490Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: christina.schaeffer@boku.ac.at
Institutions: Department of NanoBiotechnology, NanoGlycobiology, Vienna Institute of BioTechnology, Universitat fur Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, sugar analysis, GLC, b-elimination, NMR-1D, CID-MS, ESI-TOF-MS, LC-ESI-MS/MS
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3. Compound ID: 9777
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a-D-Xylp-(1-3)-+ b-Digp-(1-2)-+
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a-D-Galp4Me-(1-2)-a-D-Fucp-(1-4)-b-D-GlcpA-(1-3)-a-D-Galp-(1--/(1->3)Ser/Thr of S-layer protein/ |
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Structure type: oligomer
Aglycon: (1->3)Ser/Thr of S-layer protein
Compound class: S-layer glycan
Contained glycoepitopes: IEDB_114701,IEDB_115015,IEDB_115136,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142489,IEDB_149135,IEDB_151528,IEDB_190606,IEDB_423153,SB_7,SB_86
The structure is contained in the following publication(s):
- Article ID: 4098
Posch G, Pabst M, Brecker L, Altmann F, Messner P, Schäffer C "Characterization and scope of S-layer protein O-glycosylation in Tannerella forsythia" -
Journal of Biological Chemistry 286(44) (2011) 38714-38724
Cell surface glycosylation is an important element in defining the life of pathogenic bacteria. Tannerella forsythia is a Gram-negative, anaerobic periodontal pathogen inhabiting the subgingival plaque biofilms. It is completely covered by a two-dimensional crystalline surface layer (S-layer) composed of two glycoproteins. Although the S-layer has previously been shown to delay the bacterium's recognition by the innate immune system, we characterize here the S-layer protein O-glycosylation as a potential virulence factor. The T. forsythia S-layer glycan was elucidated by a combination of electrospray ionization-tandem mass spectrometry and nuclear magnetic resonance spectroscopy as an oligosaccharide with the structure 4-Me-β-ManpNAcCONH(2)-(1→3)-[Pse5Am7Gc-(2→4)-]-β-ManpNAcA-(1→4)-[4-Me-α-Galp-(1→2)-]-α-Fucp-(1→4)-[-α-Xylp-(1→3)-]-β-GlcpA-(1→3)-[-β-Digp-(1→2)-]-α-Galp, which is O-glycosidically linked to distinct serine and threonine residues within the three-amino acid motif (D)(S/T)(A/I/L/M/T/V) on either S-layer protein. This S-layer glycan obviously impacts the life style of T. forsythia because increased biofilm formation of an UDP-N-acetylmannosaminuronic acid dehydrogenase mutant can be correlated with the presence of truncated S-layer glycans. We found that several other proteins of T. forsythia are modified with that specific oligosaccharide. Proteomics identified two of them as being among previously classified antigenic outer membrane proteins that are up-regulated under biofilm conditions, in addition to two predicted antigenic lipoproteins. Theoretical analysis of the S-layer O-glycosylation of T. forsythia indicates the involvement of a 6.8-kb gene locus that is conserved among different bacteria from the Bacteroidetes phylum. Together, these findings reveal the presence of a protein O-glycosylation system in T. forsythia that is essential for creating a rich glycoproteome pinpointing a possible relevance for the virulence of this bacterium.
virulence factor, S-layer, O-glycosylation, Proteomics, Tannerella forsythia
NCBI PubMed ID: 21911490Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: christina.schaeffer@boku.ac.at
Institutions: Department of NanoBiotechnology, NanoGlycobiology, Vienna Institute of BioTechnology, Universitat fur Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, sugar analysis, GLC, b-elimination, NMR-1D, CID-MS, ESI-TOF-MS, LC-ESI-MS/MS
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4. Compound ID: 11256
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a-D-Xylp-(1-3)-+
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a-D-Galp4Me-(1-2)-+ |
| |
b-D-ManpNAcA4Me6NH2-(1-3)-+ | | b-Digp-(1-2)-+
| | | |
Gc-(1-7)-Psep5Am-(2-4)-b-D-ManpNAcA-(1-4)-a-D-Fucp-(1-4)-b-D-GlcpA-(1-3)-a-D-Galp-(1--/S-layer protein/ |
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Structure type: oligomer
Aglycon: S-layer protein
Compound class: O-glycoprotein
Contained glycoepitopes: IEDB_114701,IEDB_115015,IEDB_115136,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142489,IEDB_149135,IEDB_151528,IEDB_190606,IEDB_423153,SB_7,SB_86
The structure is contained in the following publication(s):
- Article ID: 4537
Iwashkiw JA, Vozza NF, Kinsella RL, Feldman MF "Pour some sugar on it: the expanding world of bacterial protein O-linked glycosylation" -
Molecular Microbiology 89(1) (2013) 14-28
Protein glycosylation was once considered as an eccentricity of a few bacteria. However in the recent years multiple O-glycosylation mechanisms have been identified in bacterial species from the most diverse genera, including various important human pathogens. This review focuses on summarizing the structural diversity, the various pathways and the physiological roles of this post-translational protein modification. We propose a classification of O-glycosylation based on the requirement of an oligosaccharyltransferase (OTase). OTase-dependent glycosylation utilizes an oligosaccharide synthesized on a lipid carrier that is transferred to proteins en bloc by an OTase. Multiple proteins, including the pilins, are glycosylated using this mechanism. OTase-independent glycosylation refers to the pathway in which glycosyltransferases sequentially add monosaccharides onto the target proteins. This pathway is employed for glycosylation of flagella and autotransporters. Both systems play key roles in pathogenesis. Exploiting glycosylation machineries it is now possible to generate glycoconjugates made of different proteins attached to polysaccharides derived from LPS or capsule biosynthesis. These recombinant glycoproteins can be exploited for vaccines and diagnostics of bacterial infections. Furthermore, O-glycosylation systems are promising targets for antibiotic development. Technological advances in MS and NMR will facilitate the discovery of novel glycosylation systems. Likely, the O-glycosylation pathways we currently know constitute just the tip of the iceberg of a still largely uncharacterized bacterial glycosylation world.
biosynthesis, glycoconjugates, bacteria, glycosyltransferases, capsule, glycoproteins, flagella, Glycomics, O-glycosylation
NCBI PubMed ID: 23679002Publication DOI: 10.1111/mmi.12265Journal NLM ID: 8712028Publisher: Blackwell Publishing
Correspondence: mfeldman@ualberta.ca
Institutions: Alberta Glycomics Centre, Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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5. Compound ID: 12556
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a-D-Xylp-(1-3)-+
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L-Fucp-(1-?)-a-D-Galp4Me-(1-2)-+ |
| |
b-D-ManpNAcA4Me6NH2-(1-3)-+ | | b-Digp-(1-2)-+
| | | |
GroA-(1-7)-Psep5Am-(2-4)-b-D-ManpNAcA-(1-4)-a-L-Fucp-(1-4)-b-D-GlcpA-(1-3)-a-D-Galp-(1--/(->3) Ser/Thr-protein/ |
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Structure type: oligomer
Aglycon: (->3) Ser/Thr-protein
Compound class: S-layer glycan
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_151528,IEDB_152214,IEDB_153553,IEDB_174333,IEDB_190606,IEDB_423153,SB_154,SB_7,SB_86
The structure is contained in the following publication(s):
- Article ID: 4994
Friedrich V, Janesch B, Windwarder M, Maresch D, Braun ML, Megson ZA, Vinogradov E, Goneau MF, Sharma A, Altmann F, Messner P, Schoenhofen IC, Schäffer C "Tannerella forsythia strains display different cell-surface nonulosonic acids: biosynthetic pathway characterization and first insight into biological implications" -
Glycobiology 7(4) (2017) 342-357
Tannerella forsythia is an anaerobic, Gram-negative periodontal pathogen. A unique O-linked oligosaccharide decorates the bacterium's cell surface proteins and was shown to modulate the host immune response. In our study, we investigated the biosynthesis of the nonulosonic acid (NulO) present at the terminal position of this glycan. A bioinformatic analysis of T. forsythia genomes revealed a gene locus for the synthesis of pseudaminic acid (Pse) in the type strain ATCC 43037 while strains FDC 92A2 and UB4 possess a locus for the synthesis of legionaminic acid (Leg) instead. In contrast to the NulO in ATCC 43037, which has been previously identified as a Pse derivative (5-N-acetimidoyl-7-N-glyceroyl-3,5,7,9-tetradeoxy-l-glycero-l-manno-NulO), glycan analysis of strain UB4 performed in this study indicated a 350-Da, possibly N-glycolyl Leg (3,5,7,9-tetradeoxy-d-glycero-d-galacto-NulO) derivative with unknown C5,7 N-acyl moieties. We have expressed, purified and characterized enzymes of both NulO pathways to confirm these genes' functions. Using capillary electrophoresis (CE), CE-mass spectrometry and NMR spectroscopy, our studies revealed that Pse biosynthesis in ATCC 43037 essentially follows the UDP-sugar route described in Helicobacter pylori, while the pathway in strain FDC 92A2 corresponds to Leg biosynthesis in Campylobacter jejuni involving GDP-sugar intermediates. To demonstrate that the NulO biosynthesis enzymes are functional in vivo, we created knockout mutants resulting in glycans lacking the respective NulO. Compared to the wild-type strains, the mutants exhibited significantly reduced biofilm formation on mucin-coated surfaces, suggestive of their involvement in host-pathogen interactions or host survival. This study contributes to understanding possible biological roles of bacterial NulOs.
Campylobacter jejuni, Helicobacter, Biofilm, biosynthesis pathway, bacterium, pseudaminic and legionaminic acid
NCBI PubMed ID: 27986835Publication DOI: 10.1093/glycob/cww129Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: christina.schaeffer@boku.ac.at; Ian.Schoenhofen@nrc-cnrc.gc.ca
Institutions: Department of Oral Biology, School of Dental Medicine, University at Buffalo, 311 Foster Hall, 3435 Main St. Buffalo, New York 14214, USA, Department of Chemistry, Universitat fur Bodenkultur Wien, Muthgasse 18, A-1190 Vienna, Austria, National Research Council, Human Health Therapeutics Portfolio, 100 Sussex Drive, Ottawa, ON, Canada K1A 0R6, Department of NanoBiotechnology, NanoGlycobiology Unit, Universitat fur Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
Methods: 13C NMR, 1H NMR, PCR, SDS-PAGE, DNA techniques, b-elimination, genetic methods, biochemical methods, CE-MS, bioinformatic analysis, CE, LC-ESI-MS/MS, biofilm assays
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6. Compound ID: 14310
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Subst2-(1-4)-b-D-Sugp-(1-17)-+
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b-L-Digp4Me-(1-4)-a-L-Digp-(1-3)-a-L-Digp-(1-9)-Subst
Sug = 3C-methyl-3-nitro-4-amino-2,3,4,6-tetradeoxy-xylo-hexose = SMILES C[C@H]1O{1}[C@@H](O)C[C@](C)(N(=O)=O){4}[C@H]1N;
Subst = 3-hydroxy-26-oxo-kijanolide = SMILES C/C2=C/C{17}[C@H](O)/C(C)=C\[C@H]1\C=C(CO)/[C@H](C)CC15OC(=O)/C(=C(O)\[C@]4(C)[C@H]2/C=C\[C@@H]3{9}[C@@H](O)[C@@H](C)C[C@H](C)[C@H]34)C5=O;
Subst2 = carbamic acid methyl ester = SMILES CO{1}C(N)=O |
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Structure type: oligomer
; 1209.5958 [M+Na]+
C61H90N2O21
Trivial name: lobophorin C
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 5650
Wei RB, Xi T, Li J, Wang P, Li FC, Lin YC, Qin S "Lobophorin C and D, new kijanimicin derivatives from a marine sponge-associated actinomycetal strain AZS17" -
Marine Drugs 9(3) (2011) 359-368
Marine sponge Hymeniacidon sp. was collected from coastal waters of the East China Sea to isolate symbiotic microorganisms. The resulting sponge-associated actinomycete, Streptomyces carnosus strain AZS17, was cultivated in a 20 L volume of medium for production of bioactive secondary metabolites. Bioassay-guided isolation and purification by varied chromatographic methods yielded two new compounds of kijanimicin derivatives, AS7-2 and AS9-12. Their structures were elucidated by spectroscopy and comparison with literatures. Results showed these two compounds were structurally similar to the previously reported compounds lobophorin A and B, yet differed in specific bond forms, stereochemistry and optical activities. The two novel compounds were named lobophorin C and D. In vitro cytotoxicity investigation by MTT assay indicated their selective activities. Lobophorin C displayed potent cytotoxic activity against the human liver cancer cell line 7402, while lobophorin D showed significant inhibitory effect on human breast cancer cells MDA-MB 435
actinomycete, marine sponge, cytotoxic activity, lobophorin C and D
NCBI PubMed ID: 21556165Publication DOI: 10.3390/md9030359Journal NLM ID: 101213729Publisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: Wei RB
; Wang P ; Xi T ; Li FC ; Li J ; Qin S
Institutions: College of Marine Science, Zhejiang Ocean University, Zhoushan, China, Marine Drugs Research Centre, China Pharmaceutical University, Nanjing, China, Open Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, China
Methods: 13C NMR, 1H NMR, NMR-2D, IR, TLC, ESI-MS, UV, extraction, microscopy, optical rotation measurement, elemental analysis, CC, cell growth, HR-ESI-MS, cytotoxicity assay, sonication, MTT
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7. Compound ID: 14311
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Subst2-(1-4)-b-D-Sugp-(1-17)-+
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b-L-Digp4Me-(1-4)-a-L-Digp-(1-3)-a-L-Digp-(1-9)-Subst
Sug = 3C-methyl-3,4-diamino-2,3,4,6-tetradeoxy-xylo-hexose = SMILES C[C@H]1O{1}[C@@H](O)C[C@](C)(N){4}[C@H]1N;
Subst = 3-hydroxy-26-oxo-kijanolide = SMILES C/C2=C/C{17}[C@H](O)/C(C)=C\[C@H]1\C=C(CO)/[C@H](C)CC15OC(=O)/C(=C(O)\[C@]4(C)[C@H]2/C=C\[C@@H]3{9}[C@@H](O)[C@@H](C)C[C@H](C)[C@H]34)C5=O;
Subst2 = carbamic acid methyl ester = SMILES CO{1}C(N)=O |
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Structure type: oligomer
Trivial name: lobophorin D
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 5650
Wei RB, Xi T, Li J, Wang P, Li FC, Lin YC, Qin S "Lobophorin C and D, new kijanimicin derivatives from a marine sponge-associated actinomycetal strain AZS17" -
Marine Drugs 9(3) (2011) 359-368
Marine sponge Hymeniacidon sp. was collected from coastal waters of the East China Sea to isolate symbiotic microorganisms. The resulting sponge-associated actinomycete, Streptomyces carnosus strain AZS17, was cultivated in a 20 L volume of medium for production of bioactive secondary metabolites. Bioassay-guided isolation and purification by varied chromatographic methods yielded two new compounds of kijanimicin derivatives, AS7-2 and AS9-12. Their structures were elucidated by spectroscopy and comparison with literatures. Results showed these two compounds were structurally similar to the previously reported compounds lobophorin A and B, yet differed in specific bond forms, stereochemistry and optical activities. The two novel compounds were named lobophorin C and D. In vitro cytotoxicity investigation by MTT assay indicated their selective activities. Lobophorin C displayed potent cytotoxic activity against the human liver cancer cell line 7402, while lobophorin D showed significant inhibitory effect on human breast cancer cells MDA-MB 435
actinomycete, marine sponge, cytotoxic activity, lobophorin C and D
NCBI PubMed ID: 21556165Publication DOI: 10.3390/md9030359Journal NLM ID: 101213729Publisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: Wei RB
; Wang P ; Xi T ; Li FC ; Li J ; Qin S
Institutions: College of Marine Science, Zhejiang Ocean University, Zhoushan, China, Marine Drugs Research Centre, China Pharmaceutical University, Nanjing, China, Open Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, China
Methods: 13C NMR, 1H NMR, NMR-2D, IR, TLC, ESI-MS, UV, extraction, microscopy, optical rotation measurement, elemental analysis, CC, cell growth, HR-ESI-MS, cytotoxicity assay, sonication, MTT
- Article ID: 5654
Gomes NGM, Buttachon S, Kijjoa A "Meroterpenoids from marine microorganisms: potential scaffolds for new chemotherapy leads" -
Book: Handbook of Anticancer Drugs from Marine Origin (2015) Chapter 16, 323-366
Meroterpenoids, including several biologically active metabolites from marine microorganisms mainly fungi and actinomycete bacteria, represent promising structural scaffolds with not only diverse biological activities such as antimicrotubule, cytotoxic and antiproliferative but also different mechanisms of action. In this chapter, an overview on structural diversity and anticancer activity of mixed biogenesis terpenoid derivatives (meroterpenoids) from marine microorganisms is presented with highlight on individual examples of the most promising candidates in cancer chemotherapy and prevention
cytotoxicity, Marine bacteria, marine microorganisms, anticancer activities, marine-derived fungi, marine-derived actinomycetes, meroterpenoids, terpenyl alkaloids, terpenyl glycosides, terpenyl polyketides
Publication DOI: 10.1007/978-3-319-07145-9_16Publisher: Cham: Springer
Correspondence: ankijjoa@icbas.up.pt
Editors: Kim S-K
Institutions: ICBAS—Instituto de Ciências Biomédicas Abel Salazar and Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Porto, Portugal
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8. Compound ID: 14312
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Subst2-(1-4)-b-D-Sugp-(1-17)-+
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a-L-Digp-(1-3)-+ |
| |
b-L-Digp4Me-(1-4)-a-L-Digp-(1-3)-a-L-Digp-(1-9)-Subst
Sug = 3C-methyl-3-nitro-4-amino-2,3,4,6-tetradeoxy-xylo-hexose = SMILES C[C@H]1O{1}[C@@H](O)C[C@](C)(N(=O)=O){4}[C@H]1N;
Subst = kijanolide = SMILES C/C3=C/C{17}[C@H](O)/C(C)=C\[C@H]1\C=C(CO)/[C@H](C)C[C@]12OC(=O)/C(=C2/O)C(=O)[C@]5(C)[C@H]3/C=C\[C@@H]4{9}[C@@H](O)[C@@H](C)C[C@H](C)[C@H]45;
Subst2 = carbamic acid methyl ester = SMILES CO{1}C(N)=O |
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Structure type: oligomer
C67H100N2O24
Trivial name: kijanimicin
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 5651
Mallams AK, Puar MS, Rossman RR, McPhail AT, Macfarlane RD "Kijanimicin. 2. Structure and absolute stereochemistry of kijanimicin" -
Journal of the American Chemical Society 103(13) (1981) 3940-3943
Kijanimicin, the major component of a complex of antibiotics produced by Actinomadura kijaniata nov. sp., has been shown to have the novel tetronic acid structure. Kijanimicin has antitumor activity and is active against P.acnes and is a member of a new class of tetronic acid containing antibiotics of which the tetrocarcins and antlermicins are the only other known members. The latter differ in the structure of the aglycon as well as in the structures of some of the glycosidic components, and full structures for these antiobiotics have not yet been published.
antibiotic, kijanimicin, Actinomadura kijaniata
Publication DOI: 10.1021/ja00403a063Journal NLM ID: 7503056Publisher: American Chemical Society
Institutions: Research Division, Schering-Plough Corporation, Bloomfield, USA, Paul M. Gross Chemical Laboratory, Duke University, Durham, USA, Department of Chemistry, Texas A&M University College Station, Texas, USA
Methods: 13C NMR, 1H NMR, EI-MS, IR, X-ray, acid hydrolysis, PD-MS, HPLC, UV, optical rotation measurement, CI-MS, FD-MS, derivatization
- Article ID: 5652
Mallams AK, Puar MS, Rossman RR "Kijanimicin. 1. Structures of the individual sugar components" -
Journal of the American Chemical Society 103(13) (1981) 3938-3940
Kijanimicin, the major component of a complex of antibiotics produced by Actinomadura kijaniata nov. sp., has been shown to have the novel tetronic acid structure. Kijanimicin has antitumor activity and is active against P.acnes and is a member of a new class of tetronic acid containing antibiotics of which the tetrocarcins and antlermicins are the only other known members. The latter differ in the structure of the aglycon as well as in the structures of some of the glycosidic components, and full structures for these antiobiotics have not yet been published.
antibiotic, kijanimicin, Actinomadura kijaniata
Publication DOI: 10.1021/ja00403a062Journal NLM ID: 7503056Publisher: American Chemical Society
Institutions: Research Division, Schering-Plough Corporation, Bloomfield, USA
Methods: 13C NMR, 1H NMR, EI-MS, IR, acid hydrolysis, UV, optical rotation measurement, CI-MS, CD, reduction, melting point determination, derivatization
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9. Compound ID: 14313
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Subst2-(1-4)-b-D-Sugp-(1-17)-+
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b-L-Digp4Me-(1-4)-a-L-Digp-(1-3)-a-L-Digp-(1-9)-Subst
Sug = 3C-methyl-3,4-diamino-2,3,4,6-tetradeoxy-xylo-hexose = SMILES C[C@H]1O{1}[C@@H](O)C[C@](C)(N){4}[C@H]1N;
Subst = kijanolide = SMILES C/C3=C/C{17}[C@H](O)/C(C)=C\[C@H]1\C=C(CO)/[C@H](C)C[C@]12OC(=O)/C(=C2/O)C(=O)[C@]5(C)[C@H]3/C=C\[C@@H]4{9}[C@@H](O)[C@@H](C)C[C@H](C)[C@H]45;
Subst2 = carbamic acid methyl ester = SMILES CO{1}C(N)=O |
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Structure type: oligomer
Trivial name: lobophorin A
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 5653
Jiang ZD, Jensen PR, Fenical W "Lobophorins A and B, new antiinflammatory macrolides produced by a tropical marine bacterium" -
Bioorganic and Medicinal Chemistry Letters 9(14) (1999) 2003-2006
Two new antiinflammatory macrolides, lobophorins A and B (1 and 2), have been isolated from fermentation broths of a marine bacterium isolated from the surface the Caribbean brown alga Lobophora variegata (Dictyotales). The new compounds, distantly related to antibiotics of the kijanimicin class, are potent inhibitors of topical PMA-induced edema in the mouse ear assay when administered either topically or IP
lobophorins, antiinflammatory activity, Lobophora variegata
NCBI PubMed ID: 10450970Publication DOI: 10.1016/s0960-894x(99)00337-6Journal NLM ID: 9107377Publisher: Elsevier
Institutions: Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
Methods: 13C NMR, 1H NMR, methylation, NMR-2D, acid hydrolysis, biological assays, HPLC, extraction, acetylation, CC, cell growth, DEPT, HR-FAB-MS
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10. Compound ID: 14314
|
Subst2-(1-4)-b-D-Sugp-(1-17)-+
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b-L-Digp4Me-(1-4)-a-L-Digp-(1-3)-a-L-Digp-(1-9)-Subst
Sug = 3C-methyl-3-nitro-4-amino-2,3,4,6-tetradeoxy-xylo-hexose = SMILES C[C@H]1O{1}[C@@H](O)C[C@](C)(N(=O)=O){4}[C@H]1N;
Subst = kijanolide = SMILES C/C3=C/C{17}[C@H](O)/C(C)=C\[C@H]1\C=C(CO)/[C@H](C)C[C@]12OC(=O)/C(=C2/O)C(=O)[C@]5(C)[C@H]3/C=C\[C@@H]4{9}[C@@H](O)[C@@H](C)C[C@H](C)[C@H]45;
Subst2 = carbamic acid methyl ester = SMILES CO{1}C(N)=O |
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Structure type: oligomer
Trivial name: lobophorin B
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 5653
Jiang ZD, Jensen PR, Fenical W "Lobophorins A and B, new antiinflammatory macrolides produced by a tropical marine bacterium" -
Bioorganic and Medicinal Chemistry Letters 9(14) (1999) 2003-2006
Two new antiinflammatory macrolides, lobophorins A and B (1 and 2), have been isolated from fermentation broths of a marine bacterium isolated from the surface the Caribbean brown alga Lobophora variegata (Dictyotales). The new compounds, distantly related to antibiotics of the kijanimicin class, are potent inhibitors of topical PMA-induced edema in the mouse ear assay when administered either topically or IP
lobophorins, antiinflammatory activity, Lobophora variegata
NCBI PubMed ID: 10450970Publication DOI: 10.1016/s0960-894x(99)00337-6Journal NLM ID: 9107377Publisher: Elsevier
Institutions: Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
Methods: 13C NMR, 1H NMR, methylation, NMR-2D, acid hydrolysis, biological assays, HPLC, extraction, acetylation, CC, cell growth, DEPT, HR-FAB-MS
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11. Compound ID: 14315
|
Subst2-(1-4)-b-D-Sugp-(1-17)-+
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b-L-Digp4Me-(1-4)-a-L-Digp-(1-3)-a-L-Digp-(1-9)-Subst
Sug = 3C-methyl-3-nitro-4-amino-2,3,4,6-tetradeoxy-xylo-hexose = SMILES C[C@H]1O{1}[C@@H](O)C[C@](C)(N(=O)=O){4}[C@H]1N;
Subst = 3-hydroxy-26-oxo-kijanolide = SMILES C/C2=C/C{17}[C@H](O)/C(C)=C\[C@H]1\C=C(CO)/[C@H](C)CC15OC(=O)/C(=C(O)\[C@]4(C)[C@H]2/C=C\[C@@H]3{9}[C@@H](O)[C@@H](C)C[C@H](C)[C@H]34)C5=O;
Subst2 = carbamic acid methyl ester = SMILES CO{1}C(N)=O |
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Structure type: oligomer
Trivial name: lobophorin C
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 5654
Gomes NGM, Buttachon S, Kijjoa A "Meroterpenoids from marine microorganisms: potential scaffolds for new chemotherapy leads" -
Book: Handbook of Anticancer Drugs from Marine Origin (2015) Chapter 16, 323-366
Meroterpenoids, including several biologically active metabolites from marine microorganisms mainly fungi and actinomycete bacteria, represent promising structural scaffolds with not only diverse biological activities such as antimicrotubule, cytotoxic and antiproliferative but also different mechanisms of action. In this chapter, an overview on structural diversity and anticancer activity of mixed biogenesis terpenoid derivatives (meroterpenoids) from marine microorganisms is presented with highlight on individual examples of the most promising candidates in cancer chemotherapy and prevention
cytotoxicity, Marine bacteria, marine microorganisms, anticancer activities, marine-derived fungi, marine-derived actinomycetes, meroterpenoids, terpenyl alkaloids, terpenyl glycosides, terpenyl polyketides
Publication DOI: 10.1007/978-3-319-07145-9_16Publisher: Cham: Springer
Correspondence: ankijjoa@icbas.up.pt
Editors: Kim S-K
Institutions: ICBAS—Instituto de Ciências Biomédicas Abel Salazar and Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Porto, Portugal
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12. Compound ID: 16415
|
a-D-Xylp-(1-3)-+
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a-D-Galp4Me-(1-2)-+ |
| |
b-D-ManpNAcA4Me6NH2-(1-3)-+ | | b-Digp-(1-2)-+
| | | |
GroA-(1-7)-Psep5Am-(2-4)-b-D-ManpNAcA-(1-4)-a-L-Fucp-(1-4)-b-D-GlcpA-(1-3)-a-D-Galp-(1--/(1->3) Ser/Thr of S-layer protein/
|
L-Fucp-(1-?)-+ |
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Structure type: oligomer
Aglycon: (1->3) Ser/Thr of S-layer protein
Trivial name: O-glycan
Compound class: S-layer glycan
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_151528,IEDB_152214,IEDB_174333,IEDB_190606,IEDB_423153,SB_7,SB_86
The structure is contained in the following publication(s):
- Article ID: 6383
Fontana C, Widmalm G "Primary Structure of Glycans by NMR Spectroscopy" -
Chemical Reviews 123(3) (2023) 1040-1102
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
NMR, glycan
NCBI PubMed ID: 36622423Publication DOI: 10.1021/acs.chemrev.2c00580Journal NLM ID: 2985134RPublisher: Chem Rev
Correspondence: G. Widmalm
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, Departamento de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
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13. Compound ID: 16541
|
a-D-Xylp-(1-3)-+
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L-Fucp-(1-?)-a-D-Galp4Me-(1-2)-+ |
| |
b-D-ManpNAcA4Me6NH2-(1-3)-+ | | b-Digp-(1-2)-+
| | | |
GroA-(1-7)-Psep5Am-(2-4)-b-D-ManpNAcA-(1-4)-a-L-Fucp-(1-4)-b-D-GlcpA-(1-3)-a-D-Galp-(1--/Ser/Thr/ |
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Structure type: oligomer
Aglycon: Ser/Thr
Compound class: S-layer glycan
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_136045,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142489,IEDB_144562,IEDB_151528,IEDB_152214,IEDB_153553,IEDB_174333,IEDB_190606,IEDB_423153,SB_154,SB_7,SB_86
The structure is contained in the following publication(s):
- Article ID: 6423
Lewis AL, Toukach P, Bolton E, Chen X, Frank M, Lütteke T, Knirel Y, Schoenhofen I, Varki A, Vinogradov E, Woods RJ, Zachra N, Zhang J, Kamerling JP, Neelamegham S "Cataloging natural sialic acids and other nonulosonic acids (NulOs), and their representation using the Symbol Nomenclature for Glycans" -
Glycobiology 33(2) (2023) 99-103
Nonulosonic acids or non-2-ulosonic acids (NulOs) are an ancient family of 2-ketoaldonic acids (alpha-ketoaldonic acids) with a 9-carbon backbone. In nature, these monosaccharides occur either in a 3-deoxy form (referred to as 'sialic acids') or in a 3,9-dideoxy 'sialic-acid-like' form. The former sialic acids are most common in the deuterostome lineage, including vertebrates, and mimicked by some of their pathogens. The latter sialic-acid-like molecules are found in bacteria and archaea. NulOs are often prominently positioned at the outermost tips of cell surface glycans, and have many key roles in evolution, biology and disease. The diversity of stereochemistry and structural modifications among the NulOs contributes to more than 90 sialic acid forms and 50 sialic-acid-like variants described thus far in nature. This paper reports the curation of these diverse naturally occurring NulOs at the NCBI sialic acid page (https://www.ncbi.nlm.nih.gov/glycans/sialic.html) as part of the NCBI-Glycans initiative. This includes external links to relevant Carbohydrate Structure Databases. As the amino and hydroxyl groups of these monosaccharides are extensively derivatized by various substituents in nature, the Symbol Nomenclature For Glycans (SNFG) rules have been expanded to represent this natural diversity. These developments help illustrate the natural diversity of sialic acids and related NulOs, and enable their systematic representation in publications and online resources.
glycan, evolution, glycobiology
NCBI PubMed ID: 36648443Publication DOI: 10.1093/glycob/cwac072Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: S. Neelamegham
; J.P. Kamerling ; A.L. Lewis
Institutions: Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA, Department of Chemistry, University of California, Davis, CA 95616, USA, Department of Obstetrics, Gynecology, and Reproductive Sciences, Glycobiology Research and Training Center, University of California, San Diego, CA 92093, USA, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA, Biognos AB, Generatorsgatan 1/Box 8963, 402 74 Goteborg, Sweden, Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Str. 100, 35392 Giessen, Germany, Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, ON K1A OR6, Canada, Department of Medicine and Cellular & Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, CA 92093, USA, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA, Bijvoet Center, Utrecht University, 3584 CH Utrecht, The Netherlands, Department of Chemical & Biological Engineering, Biomedical Engineering and Medicine, State University of New York, Buffalo, NY 14260, USA
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14. Compound ID: 16651
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Subst2-(1-4)-b-D-Sugp-(1-17)-+
|
b-L-Digp4Me-(1-4)-a-L-Digp-(1-3)-a-L-Digp-(1-9)-Subst
Sug = 3C-methyl-3,4-diamino-2,3,4,6-tetradeoxy-xylo-hexose = SMILES C[C@H]1O{1}[C@@H](O)C[C@](C)(N){4}[C@H]1N;
Subst = kijanolide = SMILES C/C3=C/C{17}[C@H](O)/C(C)=C\[C@H]1\C=C(CO)/[C@H](C)C[C@]12OC(=O)/C(=C2/O)C(=O)[C@]5(C)[C@H]3/C=C\[C@@H]4{9}[C@@H](O)[C@@H](C)C[C@H](C)[C@H]45;
Subst2 = carbamic acid methyl ester = SMILES CO{1}C(N)=O |
Show graphically |
Structure type: oligomer
; 1157.6359 [M+H]+
C61H92N2O19
Trivial name: lobophorin A
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 6462
Shi J, Peng D, Peng FF, Zhang QB, Duan YW, Huang Y "The Isolation and Structure Elucidation of Spirotetronate Lobophorins A, B, and H8 from Streptomyces sp. CB09030 and Their Biosynthetic Gene Cluster" -
Molecules 28(8) (2023) 3597
Lobophorins (LOBs) are a growing family of spirotetronate natural products with significant cytotoxicity, anti-inflammatory, and antibacterial activities. Herein, we report the transwell-based discovery of Streptomyces sp. CB09030 from a panel of 16 in-house Streptomyces strains, which has significant anti-mycobacterial activity and produces LOB A (1), LOB B (2), and LOB H8 (3). Genome sequencing and bioinformatic analyses revealed the potential biosynthetic gene cluster (BGC) for 1-3, which is highly homologous with the reported BGCs for LOBs. However, the glycosyltransferase LobG1 in S. sp. CB09030 has certain point mutations compared to the reported LobG1. Finally, LOB analogue 4 (O-β-D-kijanosyl-(1→17)-kijanolide) was obtained through an acid-catalyzed hydrolysis of 2. Compounds 1-4 showed different antibacterial activities against Mycobacterium smegmatis and Bacillus subtilis, which revealed the varying roles of different sugars in their antibacterial activities.
Streptomyces, lobophorins, anti-mycobacterial activity, spirotetronate, transwell
NCBI PubMed ID: 37110828Publication DOI: 10.3390/molecules28083597Journal NLM ID: 100964009Publisher: Basel, Switzerland: MDPI
Correspondence: Y.W. Duan
; Y. Huang ;
Institutions: Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China, School of Pharmaceutical Sciences, Changsha Health Vocational College, Changsha 410100, China, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China, Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha 410011, China, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha 410011, China, Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei 230093, China
Methods: 13C NMR, 1H NMR, NMR-2D, acid hydrolysis, bioinformatic analysis, CC, RP-HPLC, fermentation, phylogenetic analysis, HR-ESI-MS, antibacterial assay, cytotoxicity assay, genome sequencing, HR-ESI-MS/MS
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15. Compound ID: 16652
|
Subst2-(1-4)-b-D-Sugp-(1-17)-+
|
b-L-Digp4Me-(1-4)-a-L-Digp-(1-3)-a-L-Digp-(1-9)-Subst
Sug = 3C-methyl-3-nitro-4-amino-2,3,4,6-tetradeoxy-xylo-hexose = SMILES C[C@H]1O{1}[C@@H](O)C[C@](C)(N(=O)=O){4}[C@H]1N;
Subst = kijanolide = SMILES C/C3=C/C{17}[C@H](O)/C(C)=C\[C@H]1\C=C(CO)/[C@H](C)C[C@]12OC(=O)/C(=C2/O)C(=O)[C@]5(C)[C@H]3/C=C\[C@@H]4{9}[C@@H](O)[C@@H](C)C[C@H](C)[C@H]45;
Subst2 = carbamic acid methyl ester = SMILES CO{1}C(N)=O |
Show graphically |
Structure type: oligomer
; 1209.5921 [M+H]+
C61H90N2O21
Trivial name: lobophorin B
Compound class: glycoside
The structure is contained in the following publication(s):
- Article ID: 6462
Shi J, Peng D, Peng FF, Zhang QB, Duan YW, Huang Y "The Isolation and Structure Elucidation of Spirotetronate Lobophorins A, B, and H8 from Streptomyces sp. CB09030 and Their Biosynthetic Gene Cluster" -
Molecules 28(8) (2023) 3597
Lobophorins (LOBs) are a growing family of spirotetronate natural products with significant cytotoxicity, anti-inflammatory, and antibacterial activities. Herein, we report the transwell-based discovery of Streptomyces sp. CB09030 from a panel of 16 in-house Streptomyces strains, which has significant anti-mycobacterial activity and produces LOB A (1), LOB B (2), and LOB H8 (3). Genome sequencing and bioinformatic analyses revealed the potential biosynthetic gene cluster (BGC) for 1-3, which is highly homologous with the reported BGCs for LOBs. However, the glycosyltransferase LobG1 in S. sp. CB09030 has certain point mutations compared to the reported LobG1. Finally, LOB analogue 4 (O-β-D-kijanosyl-(1→17)-kijanolide) was obtained through an acid-catalyzed hydrolysis of 2. Compounds 1-4 showed different antibacterial activities against Mycobacterium smegmatis and Bacillus subtilis, which revealed the varying roles of different sugars in their antibacterial activities.
Streptomyces, lobophorins, anti-mycobacterial activity, spirotetronate, transwell
NCBI PubMed ID: 37110828Publication DOI: 10.3390/molecules28083597Journal NLM ID: 100964009Publisher: Basel, Switzerland: MDPI
Correspondence: Y.W. Duan
; Y. Huang ;
Institutions: Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China, School of Pharmaceutical Sciences, Changsha Health Vocational College, Changsha 410100, China, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China, Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha 410011, China, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha 410011, China, Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei 230093, China
Methods: 13C NMR, 1H NMR, NMR-2D, acid hydrolysis, bioinformatic analysis, CC, RP-HPLC, fermentation, phylogenetic analysis, HR-ESI-MS, antibacterial assay, cytotoxicity assay, genome sequencing, HR-ESI-MS/MS
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