1
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Hever E, Santhanam V, Alberi S, Dhara A, Bols M, Nasheuer HP, Murphy PV. Synthesis of C-glycoside analogues of isopropyl β-D-1-thiogalactopyranoside (IPTG) and 1-β-D-galactopyranosyl-2-methylpropane. Conformational analysis and evaluation as inhibitors of the lac repressor in E. coli and as galactosidase inhibitors. Org Biomol Chem 2024; 22:7460-7477. [PMID: 39189157 DOI: 10.1039/d4ob01286k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Isopropyl 1-thio-β-D-galactopyranoside (IPTG, 1) is used widely as an inducer of protein expression in E. coli and 1-β-D-galactopyranosyl-2-methylpropane (2), a C-glycoside analogue of 1, has also been identified as an inducer. Here, synthesis and study of mimetics of 1 and 2, 1-β-D-galactopyranosyl-2-methylpropan-1-ols and two cyclic acetals derivatives, that constrain the presentation of the iPr group in various geometries is described. Conformational analysis of C-glycosides in protic solvent is performed using (i) Desmond metadynamics simulations (OPLS4) and (ii) use of 3JHH values obtained by 1H-NMR spectroscopy. 1-β-D-Galactopyranosyl-2-methylpropane (2) is an effective protein expression inducer when compared to the new mimetics, which were less effective or did not induce expression. 1-β-D-Galactopyranosyl-2-methylpropane (2) led to significantly reduced proteolysis during protein expression, compared to IPTG suggesting that recombinant protein purification will be easier to achieve with 2, yielding proteins with higher quality and activity. IPTG reduced bacterial growth to a greater degree than 2 compared to the control. IPTG's isopropyl group was observed by molecular dynamics (MD) simulations to be flexible in the binding pocket, deviating from its crystal structure binding mode, without impacting other interactions. The MD simulations predicted that 1-β-D-galactopyranosyl-2-methylpropane (2) was more likely than IPTG to bind the repressor with a conformation favoured in protic solvent, while maintaining interactions observed for IPTG. MD simulations predicted that isobutanol derivatives may disrupt interactions associated with IPTG's binding mode. The compounds were also evaluated as inhibitors of galactosidases, with 2 being the more potent inhibitor of the E. coli β-galactosidase. The constrained cyclic acetals showed similar inhibition constants to IPTG indicating E. coli β-galactosidase can recognize galactopyranoses with varying presentation of the iPr group.
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Affiliation(s)
- Eoin Hever
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway, Ireland, H91TK33.
| | - Venkatesan Santhanam
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway, Ireland, H91TK33.
| | - Sherivan Alberi
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway, Ireland, H91TK33.
| | - Ashis Dhara
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway, Ireland, H91TK33.
| | - Mikael Bols
- Department of Chemistry, Københavns Universitet, Universitetsparken 5, 2100 København Ø, Denmark
| | - Heinz-Peter Nasheuer
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway, Ireland, H91TK33.
| | - Paul V Murphy
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway, Ireland, H91TK33.
- SSPC - the Science Foundation Ireland Research Centre for Pharmaceuticals, University of Galway, University Road, Galway, Ireland, H91TK33
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2
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Linclau B, Ardá A, Reichardt NC, Sollogoub M, Unione L, Vincent SP, Jiménez-Barbero J. Fluorinated carbohydrates as chemical probes for molecular recognition studies. Current status and perspectives. Chem Soc Rev 2021; 49:3863-3888. [PMID: 32520059 DOI: 10.1039/c9cs00099b] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review provides an extensive summary of the effects of carbohydrate fluorination with regard to changes in physical, chemical and biological properties with respect to regular saccharides. The specific structural, conformational, stability, reactivity and interaction features of fluorinated sugars are described, as well as their applications as probes and in chemical biology.
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO171BJ, UK
| | - Ana Ardá
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain.
| | | | - Matthieu Sollogoub
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Stéphane P Vincent
- Department of Chemistry, Laboratory of Bio-organic Chemistry, University of Namur (UNamur), B-5000 Namur, Belgium
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain. and Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain and Department of Organic Chemistry II, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Spain
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3
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Tyrikos-Ergas T, Fittolani G, Seeberger PH, Delbianco M. Structural Studies Using Unnatural Oligosaccharides: Toward Sugar Foldamers. Biomacromolecules 2019; 21:18-29. [DOI: 10.1021/acs.biomac.9b01090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Peter H. Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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4
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Calloni I, Unione L, Jiménez-Osés G, Corzana F, Del Bino L, Corrado A, Pitirollo O, Colombo C, Lay L, Adamo R, Jiménez-Barbero J. The Conformation of the Mannopyranosyl Phosphate Repeating Unit of the Capsular Polysaccharide of Neisseria meningitidis Serogroup A and Its Carba-Mimetic. European J Org Chem 2018; 2018:4548-4555. [PMID: 30443159 PMCID: PMC6220853 DOI: 10.1002/ejoc.201801003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 11/07/2022]
Abstract
Neisseria meningitidis serogroup A (MenA) is an aerobic diplococcal Gram-negative bacterium responsible for epidemic meningitis disease. Its capsular polysaccharide (CPS) has been identified as the primary virulence factor of MenA. This polysaccharide suffers from chemical lability in water. Thus, the design and synthesis of novel and hydrolytically stable structural analogues of MenA CPS may provide additional tools for the development of therapies against this disease. In this context, the structural features of the natural phosphorylated monomer have been analyzed and compared to those of its carba-analogue, where the endocyclic oxygen has been replaced by a methylene moiety. The lowest energy geometries of the different molecules have been calculated using a combination of quantum mechanical techniques and molecular dynamics simulations. The predicted results have been compared and validated using NMR experiments. The results indicate that the more stable designed glycomimetics may adopt the conformation adopted by the natural monomer, although they display a wider flexibility around the torsional degrees of freedom.
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Affiliation(s)
- Ilaria Calloni
- Chemical Glycobiology Lab CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Spain.,Department of Organic Chemistry II Faculty of Science and Technology University of the Basque Country, EHU-UPV Leioa Spain
| | - Luca Unione
- Atlas Molecular Pharma Bizkaia Technology Park, Building 800 48160 Derio Spain
| | - Gonzalo Jiménez-Osés
- Departamento de Quimica Universidad de la Rioja Centro Científico Tecnológico Spain
| | - Francisco Corzana
- Departamento de Quimica Universidad de la Rioja Centro Científico Tecnológico Spain
| | | | - Alessio Corrado
- Glycobiology Lab GSK Via Fiorentina 10 Siena Italy.,Department of Chemistry and ISTM_CNR University of Milan Via Golgi 19 20133 Milan Italy
| | - Olimpia Pitirollo
- Department of Chemistry and ISTM_CNR University of Milan Via Golgi 19 20133 Milan Italy
| | - Cinzia Colombo
- Department of Chemistry and ISTM_CNR University of Milan Via Golgi 19 20133 Milan Italy
| | - Luigi Lay
- Department of Chemistry and ISTM_CNR University of Milan Via Golgi 19 20133 Milan Italy
| | | | - Jesús Jiménez-Barbero
- Chemical Glycobiology Lab CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Spain.,Department of Organic Chemistry II Faculty of Science and Technology University of the Basque Country, EHU-UPV Leioa Spain.,Basque Foundation for Science (IKERBASQUE) 48009 Bilbao Spain
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5
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Lacetera A, Berbís MÁ, Nurisso A, Jiménez-Barbero J, Martín-Santamaría S. Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions. COMPUTATIONAL TOOLS FOR CHEMICAL BIOLOGY 2017. [DOI: 10.1039/9781788010139-00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular modelling provides a major impact in the field of glycosciences, helping in the characterisation of the molecular basis of the recognition between lectins from pathogens and human glycoconjugates, and in the design of glycocompounds with anti-infectious properties. The conformational properties of oligosaccharides are complex, and therefore, the simulation of these properties is a challenging task. Indeed, the development of suitable force fields is required for the proper simulation of important problems in glycobiology, such as the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics, including O-linkages in oligo- and polysaccharides, and N- and O-linkages in glycoproteins. The computational description of representative examples is discussed, herein, related to biologically active oligosaccharides and their interaction with lectins and other proteins, and the new routes open for the design of glycocompounds with promising biological activities.
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Affiliation(s)
- Alessandra Lacetera
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - M. Álvaro Berbís
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - Alessandra Nurisso
- School of Pharmaceutical Sciences University of Geneva, University of Lausanne, Rue Michel Servet 1 CH-1211 Geneva 4 Switzerland
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6
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Synthesis of β-galactosylamides as ligands of the peanut lectin. Insights into the recognition process. Carbohydr Res 2017; 443-444:58-67. [PMID: 28355582 DOI: 10.1016/j.carres.2017.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/16/2017] [Accepted: 03/22/2017] [Indexed: 11/21/2022]
Abstract
The synthesis of mono and divalent β-galactosylamides linked to a hydroxylated chain having a C2 symmetry axis derived from l-tartaric anhydride is reported. Reference compounds devoid of hydroxyl groups in the linker were also prepared from β-galactosylamine and succinic anhydride. After functionalization with an alkynyl residue, the resulting building blocks were grafted onto different azide-equipped scaffolds through the copper catalyzed azide-alkyne cycloaddition. Thus, a family of structurally related mono and divalent β-N-galactopyranosylamides was obtained and fully characterized. The binding affinities of the ligands towards the model lectin PNA were measured by the enzyme-linked lectin assay (ELLA). The IC50 values were significantly higher than that of galactose but the presence of hydroxyl groups in the aglycone chain improved lectin recognition. Docking and molecular dynamics experiments were in accordance with the hypothesis that a hydroxyl group properly disposed in the linker could mimic the Glc O3 in the recognition process. On the other hand, divalent presentation of the ligands led to lectin affinity enhancements.
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7
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Wu Y, Wu RWK, Cheu KW, Williams ID, Krishna S, Slavic K, Gravett AM, Liu WM, Wong HN, Haynes RK. Methylene Homologues of Artemisone: An Unexpected Structure-Activity Relationship and a Possible Implication for the Design of C10-Substituted Artemisinins. ChemMedChem 2016; 11:1469-79. [PMID: 27273875 DOI: 10.1002/cmdc.201600011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/13/2016] [Indexed: 11/12/2022]
Abstract
We sought to establish if methylene homologues of artemisone are biologically more active and more stable than artemisone. The analogy is drawn with the conversion of natural O- and N-glycosides into more stable C-glycosides that may possess enhanced biological activities and stabilities. Dihydroartemisinin was converted into 10β-cyano-10-deoxyartemisinin that was hydrolyzed to the α-primary amide. Reduction of the β-cyanide and the α-amide provided the respective methylamine epimers that upon treatment with divinyl sulfone gave the β- and α-methylene homologues, respectively, of artemisone. Surprisingly, the compounds were less active in vitro than artemisone against P. falciparum and displayed no appreciable activity against A549, HCT116, and MCF7 tumor cell lines. This loss in activity may be rationalized in terms of one model for the mechanism of action of artemisinins, namely the cofactor model, wherein the presence of a leaving group at C10 assists in driving hydride transfer from reduced flavin cofactors to the peroxide during perturbation of intracellular redox homeostasis by artemisinins. It is noted that the carba analogue of artemether is less active in vitro than the O-glycoside parent toward P. falciparum, although extrapolation of such activity differences to other artemisinins at this stage is not possible. However, literature data coupled with the leaving group rationale suggest that artemisinins bearing an amino group attached directly to C10 are optimal compounds.
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Affiliation(s)
- Yuet Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China
| | - Ronald Wai Kung Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China
| | - Kwan Wing Cheu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China
| | - Ian D Williams
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China
| | - Sanjeev Krishna
- Centre for Infection, Division of Cellular and Molecular Medicine, St. George's Hospital, University of London, SW17 0RE, UK
| | - Ksenija Slavic
- Centre for Infection, Division of Cellular and Molecular Medicine, St. George's Hospital, University of London, SW17 0RE, UK
| | - Andrew M Gravett
- Department of Oncology, Division of Cellular and Molecular Medicine, St. George's Hospital, University of London, Jenner Wing, London, SW17 0RE, UK
| | - Wai M Liu
- Department of Oncology, Division of Cellular and Molecular Medicine, St. George's Hospital, University of London, Jenner Wing, London, SW17 0RE, UK
| | - Ho Ning Wong
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health Sciences, North-West University, Potchefstroom, 2520, South Africa.,Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China
| | - Richard K Haynes
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health Sciences, North-West University, Potchefstroom, 2520, South Africa. , .,Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P.R. China. ,
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8
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Calle L, Roldós V, Cañada FJ, Uhrig ML, Cagnoni AJ, Manzano VE, Varela O, Jiménez-Barbero J. Escherichia coliβ-Galactosidase Inhibitors through Modifications at the Aglyconic Moiety: Experimental Evidence of Conformational Distortion in the Molecular Recognition Process. Chemistry 2013; 19:4262-70. [DOI: 10.1002/chem.201203673] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Indexed: 11/07/2022]
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9
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Sánchez‐Fernández EM, Rísquez‐Cuadro R, Ortiz Mellet C, García Fernández JM, Nieto PM, Angulo J. sp
2
‐Iminosugar
O
‐,
S
‐, and
N
‐Glycosides as Conformational Mimics of α‐Linked Disaccharides; Implications for Glycosidase Inhibition. Chemistry 2012; 18:8527-39. [DOI: 10.1002/chem.201200279] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 02/28/2012] [Indexed: 12/29/2022]
Affiliation(s)
- Elena M. Sánchez‐Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| | - Rocío Rísquez‐Cuadro
- Departmento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/Prof. García González 1, 41012, Sevilla (Spain), Fax: (+34) 954624960
| | - Carmen Ortiz Mellet
- Departmento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/Prof. García González 1, 41012, Sevilla (Spain), Fax: (+34) 954624960
| | - José M. García Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| | - Pedro M. Nieto
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| | - Jesús Angulo
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
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10
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Zhao W, Wang WG, Li XN, Du X, Zhan R, Zou J, Li Y, Zhang HB, He F, Pu JX, Sun HD. Neoadenoloside A, a highly functionalized diterpene C-glycoside, from Isodon adenolomus. Chem Commun (Camb) 2012; 48:7723-5. [DOI: 10.1039/c2cc33656a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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11
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Martín-Santamaría S, Gabius HJ, Jiménez-Barbero J. Structural studies on the interaction of saccharides and glycomimetics with galectin-1: A 3D perspective using a combined molecular modeling and NMR approach. PURE APPL CHEM 2011. [DOI: 10.1351/pac-con-11-10-01] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The interaction of a variety of saccharides and mimetics thereof with lectin receptors has been studied using a combination of molecular modeling protocols and NMR spectroscopy techniques. It is shown that both methods complement each other in a synergistic manner to provide a detailed perspective of the conformational and structural features of the recognition process.
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Affiliation(s)
- Sonsoles Martín-Santamaría
- 1Department of Chemistry, Faculty of Pharmacy, Universidad San Pablo CEU, 28668-Boadilla del Monte, Madrid, Spain
| | - Hans-Joachim Gabius
- 2Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstrasse 13, 80539 München, Germany
| | - Jesús Jiménez-Barbero
- 3Department of Chemical and Physical Biology, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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12
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Roldós V, Cañada FJ, Jiménez-Barbero J. Carbohydrate-Protein Interactions: A 3D View by NMR. Chembiochem 2011; 12:990-1005. [DOI: 10.1002/cbic.201000705] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Indexed: 12/29/2022]
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13
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Choumane M, Banchet A, Probst N, Gérard S, Plé K, Haudrechy A. The synthesis of d-C-mannopyranosides. CR CHIM 2011. [DOI: 10.1016/j.crci.2010.05.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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León EI, Martín A, Peréz-Martín I, Quintanal LM, Suárez E. Hydrogen Atom Transfer Experiments Provide Chemical Evidence for the Conformational Differences between C- and O-Disaccharides. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000470] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Senthil Kumar R, Karthikeyan K, Phani Kumar B, Muralidharan D, Perumal P. Synthesis of densely functionalised C-glycosides by a tandem oxy Michael addition–Wittig olefination pathway. Carbohydr Res 2010; 345:457-61. [DOI: 10.1016/j.carres.2009.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 11/19/2009] [Accepted: 12/14/2009] [Indexed: 10/20/2022]
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16
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Alberti A, Macciantelli D, Naggi A, Urso E, Torri G, Vismara E. Electrochemical Characterisation of 6-Iodomaltose, 6′-Iodomaltose and 6-Iodomaltotriose on a Silver Cathode and Their One-Pot Electrochemical Dimerisation to New Mixed O/C Maltotetraose and Maltohexaose Mimics. Chemistry 2009; 15:8005-8014. [DOI: 10.1002/chem.200900825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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DeMarco ML, Woods RJ. Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces. Glycobiology 2008; 19:344-55. [PMID: 19056784 DOI: 10.1093/glycob/cwn137] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic cells depend on external surface markers, such as gangliosides, to recognize and bind various other molecules as part of normal growth and maturation. The localization of gangliosides in the outer leaflet of the plasma membrane, also make them targets for pathogens trying to invade the host cells. Since ganglioside-mediated interactions are critical to both beneficial and pathological processes, much effort has been directed at determining the 3D structures of their carbohydrate head groups; however, technical difficulties have generally prevented the characterization of the head group in intact membrane-bound gangliosides. Determining the 3D structure and presentation of gangliosides at the surface of membranes is important in understanding how cells interact with their local environment. Here, we employ all-atom explicit solvent molecular dynamics (MD) simulations, using the GLYCAM06 force field, to model the conformation and dynamics of ganglioside G(M3) (alpha-Neu5Ac-(2-3)-beta-Gal-(1-4)-beta-Glc-ceramide) in a DMPC lipid bilayer. By comparison with MD simulations of the carbohydrate head-group fragment of G(M3) alone, it was possible to quantify and characterize the extent of changes in head-group presentation and dynamics associated with membrane anchoring. The accuracy of data from the MD simulations was determined by comparison to NMR and crystallographic data for the head group in solution and for G(M3) in membrane-mimicking environments. The experimentally consistent model of G(M3), in a lipid bilayer, was then used to model the recognition of G(M3) at the cell surface by known protein receptors.
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Affiliation(s)
- Mari L DeMarco
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712, USA
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18
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Mikros E, Labrinidis G, Pérez S. Conformational Analysis of C-Disaccharides using Molecular Mechanics Calculations. J Carbohydr Chem 2008. [DOI: 10.1080/07328300008544154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Emmanuel Mikros
- a Department of Pharmacy , University of Athens , Panespistimiopoli, Zografou, GR-15771, Athens, Greece
- b Department of Pharmacy , University of Athens , Panespistimiopoli, Zografou, GR-15771, Athens, Greece
- c Centre de Recherches sur les Macromolécules Végétales,1 CNRS , BP 53X, 38041 Grenoble, cedex, France
| | - George Labrinidis
- a Department of Pharmacy , University of Athens , Panespistimiopoli, Zografou, GR-15771, Athens, Greece
- b Department of Pharmacy , University of Athens , Panespistimiopoli, Zografou, GR-15771, Athens, Greece
- c Centre de Recherches sur les Macromolécules Végétales,1 CNRS , BP 53X, 38041 Grenoble, cedex, France
| | - Serge Pérez
- a Department of Pharmacy , University of Athens , Panespistimiopoli, Zografou, GR-15771, Athens, Greece
- b Department of Pharmacy , University of Athens , Panespistimiopoli, Zografou, GR-15771, Athens, Greece
- c Centre de Recherches sur les Macromolécules Végétales,1 CNRS , BP 53X, 38041 Grenoble, cedex, France
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López-Méndez B, Jia C, Zhang Y, Zhang LH, Sinaÿ P, Jiménez-Barbero J, Sollogoub M. Hemicarbasucrose: Turning off the Exoanomeric Effect Induces Less Flexibility. Chem Asian J 2008; 3:51-8. [DOI: 10.1002/asia.200700281] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mayato C, Dorta RL, Vázquez JT. New insights into the conformational properties of α-C-glucosides. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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García-Aparicio V, Malapelle A, Abdallah Z, Doisneau G, Santos JI, Asensio JL, Cañada FJ, Beau JM, Jiménez-Barbero J. The solution conformation of C-glycosyl analogues of the sialyl-Tn antigen. Carbohydr Res 2007; 342:1974-82. [PMID: 17466287 DOI: 10.1016/j.carres.2007.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 03/09/2007] [Accepted: 03/16/2007] [Indexed: 10/23/2022]
Abstract
The conformational behavior of two C-glycosyl analogues of the sialyl-Tn antigen has been determined by a combination of NMR methods and molecular mechanics calculations. Both compounds show a major solution conformation that is drastically different from the major one of the natural compound.
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22
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Vidal P, Vauzeilles B, Blériot Y, Sollogoub M, Sinaÿ P, Jiménez-Barbero J, Espinosa JF. Conformational behaviour of glycomimetics: NMR and molecular modelling studies of the C-glycoside analogue of the disaccharide methyl β-d-galactopyranosyl-(1→3)-β-d-glucopyranoside. Carbohydr Res 2007; 342:1910-7. [PMID: 17517384 DOI: 10.1016/j.carres.2007.04.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 04/16/2007] [Accepted: 04/24/2007] [Indexed: 11/19/2022]
Abstract
The conformational behaviour of the C-glycoside beta-C-Gal-(1-->3)-beta-Glc-OMe (1) has been studied using a combination of molecular mechanics and NMR spectroscopy (proton-proton coupling constants and nuclear Overhauser effects). It is shown that the C-disaccharide populates two distinctive conformational families in solution, the normal syn-psi conformation, which is the predominating conformation of parent O-glycoside 2, and the anti-psi conformation, which has not been detected for the O-disaccharide.
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Affiliation(s)
- Paloma Vidal
- Discovery Chemistry Research and Technologies, Centro de Investigación Lilly, Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
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23
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Hydrogen atom transfer experiments provide chemical evidence for the conformational differences between C- and O-glycosides. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.05.166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Mayato C, Dorta RL, Vázquez JT. The exo-deoxoanomeric effect in the conformational preferences of C-glycosides. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Hernández-Gay JJ, Panza L, Ronchetti F, Cañada FJ, Compostella F, Jiménez-Barbero J. The conformational behaviour of the C-glycosyl analogue of sulfatide studied by NMR in SDS micelles. Carbohydr Res 2007; 342:1966-73. [PMID: 17511975 DOI: 10.1016/j.carres.2007.04.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 04/16/2007] [Accepted: 04/22/2007] [Indexed: 10/23/2022]
Abstract
The conformational behaviour of sulfatide and its C-glycosyl analogue has been studied by using a combination of J and NOE data assisted by molecular mechanics calculations. There is a major exoanomeric conformation around the phi angle of both molecules with two or three conformers contributing to the equilibrium around psi. The MM3* calculations only provide a qualitative description of the actual population distribution. Despite this geometrical similarity, the quantitative analysis of the NOE intensities at a variety of mixing times indicates that the motion around the pseudoglycosidic linkages of the C-glycosyl analogue is faster than that for the natural compound.
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Affiliation(s)
- José Juan Hernández-Gay
- Departamento de Ciencia de Proteínas, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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García-Aparicio V, Sollogoub M, Blériot Y, Colliou V, André S, Asensio JL, Cañada FJ, Gabius HJ, Sinaÿ P, Jiménez-Barbero J. The conformation of the C-glycosyl analogue of N-acetyl-lactosamine in the free state and bound to a toxic plant agglutinin and human adhesion/growth-regulatory galectin-1. Carbohydr Res 2007; 342:1918-28. [PMID: 17408600 DOI: 10.1016/j.carres.2007.02.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 02/19/2007] [Accepted: 02/21/2007] [Indexed: 11/21/2022]
Abstract
The conformational behavior of the C-glycoside analogue of N-acetyl-lactosamine, beta-C-Gal-(1-->4)-beta-GlcNAc-OMe, 1, has been studied using a combination of molecular mechanics calculations and NMR spectroscopy (J and NOE data). It is shown that the C-disaccharide populates three distinctive conformational families in solution, the major one being the anti-psi conformation. Of note, this conformation is only marginally populated for the O-disaccharide. Due to its conspicuous role in the regulation of adhesion, growth and tissue invasion of tumors and its avid binding to N-acetyl-lactosamine human, galectin-1 was tested as a receptor. This endogenous lectin recognizes a local minimum of 1, the syn-PhiPsi conformer, and thus a conformational selection process is correlated with the molecular recognition event.
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Affiliation(s)
- Víctor García-Aparicio
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS 8642, 24, rue Lhomond, 75231 Paris Cedex 05, France
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27
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Pérez-Castells J, Hernández-Gay JJ, Denton RW, Tony KA, Mootoo DR, Jiménez-Barbero J. The conformational behaviour and P-selectin inhibition of fluorine-containing sialyl LeX glycomimetics. Org Biomol Chem 2007; 5:1087-92. [PMID: 17377662 DOI: 10.1039/b615752a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of experimental J/NOE NMR data with molecular mechanics and dynamics calculations has been used to examine the conformational behaviour and assign the configuration of synthetically prepared epimeric 3-carboxymethyl-O-Gal-(1-->1)-alpha-Man-fluoro-C-glycosides. It is shown that the population distributions around the glycosidic linkages strongly depend on the configuration at the fluorinated carbon of the pseudoacetal residue. It is also shown that these compounds resemble the inhibition ability of sialyl LeX towards P-selectin.
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Affiliation(s)
- Javier Pérez-Castells
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain. .
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Mikros E, Labrinidis G, Pérez S. Conformational Analysis of C‐Trehaloses Using Molecular Mechanics Calculations. J Carbohydr Chem 2006. [DOI: 10.1081/car-120025327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Emmanuel Mikros
- a Department of Pharmacy , University of Athens , Panespistimiopolis, Zografou, GR‐15771, Athens, Greece
| | - George Labrinidis
- a Department of Pharmacy , University of Athens , Panespistimiopolis, Zografou, GR‐15771, Athens, Greece
| | - Serge Pérez
- b Centre de Recherches sur les Macromolécules Végétales , CNRS, BP 53X, 38041, Grenoble Cedex, France
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Abstract
Three regions of the conformation space that describes the relative orientations of the two glucose residues of cellobiose were analyzed with quantum mechanics. A central region, in which most crystal structures are found, was covered by a 9 × 9 grid of 20° increments of the linkage torsion angles ϕ and ψ. Besides these 81 constrained minimizations, we studied two central subregions and two regions at the edges of our maps of complete ϕ,ψ space with unconstrained minimization, for a total of 85 target geometries. HF/6-31G(d) and single-point HF/6-311+G(d) calculations were used to find the lowest energies for each geometry. B3LYP/6-31G+G(d) and single point B3LYP/6-11+G(d) calculations were also used for all unconstrained minimizations. For each target, 181 starting geometries were tried (155 for the unconstrained targets). Numerous different starting geometries resulted in the lowest energies for the various target structures. The starting geometries came from five different sets that were based on molecular mechanics energies. Although all five sets contributed to the adiabatic map, use of any single set resulted in discrepancies of 37 kcal/mol (1 cal = 4.184 J) with the final map. For most of the targets, the starting geometry that gave the lowest energy depended on the basis set and whether the HF or B3LYP method was used. However, each of the above four calculations gave the same overall lowest energy structure that was found previously by Strati et al. This global minimum, stabilized by highly cooperative hydrogen bonds, is in a region that is essentially not populated by crystal structures. HF/6-31G(d) energy contours of the mapped central region were compatible with the observed crystal structures. Observed structures that lacked O3···O5′ hydrogen bonds were about 1 kcal/mol above the map's minimum, and observed structures that have a pseudo twofold screw axis ranged from about 0.4 to 1.0 kcal/mol. The HF/6-311+G(d) map accommodated the observed structures nearly as well.Key words: cellulose, carbohydrate, conformation, energy, flexibility, folding, helix, shape.
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Abstract
A high-density coding system is essential to allow cells to communicate efficiently and swiftly through complex surface interactions. All the structural requirements for forming a wide array of signals with a system of minimal size are met by oligomers of carbohydrates. These molecules surpass amino acids and nucleotides by far in information-storing capacity and serve as ligands in biorecognition processes for the transfer of information. The results of work aiming to reveal the intricate ways in which oligosaccharide determinants of cellular glycoconjugates interact with tissue lectins and thereby trigger multifarious cellular responses (e.g. in adhesion or growth regulation) are teaching amazing lessons about the range of finely tuned activities involved. The ability of enzymes to generate an enormous diversity of biochemical signals is matched by receptor proteins (lectins), which are equally elaborate. The multiformity of lectins ensures accurate signal decoding and transmission. The exquisite refinement of both sides of the protein-carbohydrate recognition system turns the structural complexity of glycans--a demanding but essentially mastered problem for analytical chemistry--into a biochemical virtue. The emerging medical importance of protein-carbohydrate recognition, for example in combating infection and the spread of tumors or in targeting drugs, also explains why this interaction system is no longer below industrial radarscopes. Our review sketches the concept of the sugar code, with a solid description of the historical background. We also place emphasis on a distinctive feature of the code, that is, the potential of a carbohydrate ligand to adopt various defined shapes, each with its own particular ligand properties (differential conformer selection). Proper consideration of the structure and shape of the ligand enables us to envision the chemical design of potent binding partners for a target (in lectin-mediated drug delivery) or ways to block lectins of medical importance (in infection, tumor spread, or inflammation).
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Affiliation(s)
- Hans-Joachim Gabius
- Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, Veterinärstrasse 13, 80539 Munich, Germany.
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The conformational behaviour of α,β-trehalose-like disaccharides and their C-glycosyl, imino-C-glycosyl and carbagalactose analogues depends on the chemical nature of the modification: an NMR investigation. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2004.11.072] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Siebert HC, Jiménez-Barbero J, André S, Kaltner H, Gabius HJ. Describing topology of bound ligand by transferred nuclear Overhauser effect spectroscopy and molecular modeling. Methods Enzymol 2003; 362:417-34. [PMID: 12968380 DOI: 10.1016/s0076-6879(03)01029-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Hans-Christian Siebert
- Institute of Physiological Chemistry, Ludwig-Maximilians University, Veterinarstrasse 13, Munich D-80539, Germany
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Mikkelsen LM, Krintel SL, Jiménez-Barbero J, Skrydstrup T. Application of the anomeric samarium route for the convergent synthesis of the C-linked trisaccharide alpha-D-Man-(1-->3)-[alpha-D-Man-(1-->6)]-D-Man and the disaccharides alpha-D-Man-(1-->3)-D-Man and alpha-D-Man-(1-->6)-D-Man. J Org Chem 2002; 67:6297-308. [PMID: 12201747 DOI: 10.1021/jo020339z] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Studies are reported on the assembly of the branched C-trisaccharide, alpha-D-Man-(1-->3)-[alpha-D-Man-(1-->6)]-D-Man, representing the core region of the asparagine-linked oligosaccharides. The key step in this synthesis uses a SmI(2)-mediated coupling of two mannosylpyridyl sulfones to a C3,C6-diformyl branched monosaccharide unit, thereby assembling all three sugar units in one reaction and with complete stereocontrol at the two anomeric carbon centers. Subsequent tin hydride-based deoxygenation followed by a deprotection step produces the target C-trimer. In contrast to many of the other C-glycosylation methods, this approach employes intact carbohydrate units as C-glycosyl donors and acceptors, which in many instances parallels the well-studied O-glycosylation reactions. The synthesis of the C-disaccharides alpha-D-Man-(1-->3)-D-Man and alpha-D-Man-(1-->6)-D-Man is also described, they being necessary for the following conformational studies of all three carbohydrate analogues both in solution and bound to several mannose-binding proteins.
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Affiliation(s)
- Lise Munch Mikkelsen
- Department of Chemistry, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
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35
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García-Herrero A, Montero E, Muñoz JL, Espinosa JF, Vián A, García JL, Asensio JL, Cañada FJ, Jiménez-Barbero J. Conformational selection of glycomimetics at enzyme catalytic sites: experimental demonstration of the binding of distinct high-energy distorted conformations of C-, S-, and O-glycosides by E. Coli beta-galactosidases. J Am Chem Soc 2002; 124:4804-10. [PMID: 11971730 DOI: 10.1021/ja0122445] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We show that the conformational features of the molecular complexes of E. coli beta-galactosidase and O-glycosides may differ from those formed with closely related compounds in their chemical nature, such as C- and S-glycosyl analogues. In the particular case presented here, NMR and ab initio quantum mechanical results show that the 3D-shapes of the ligand/inhibitor within the enzyme binding site depend on the chemical nature of the compounds. In fact, they depend on the relative size of the stereoelectronic barriers for chair deformation or for rotation around Phi glycosidic linkage.
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Affiliation(s)
- Alicia García-Herrero
- Department Bioorganic Chemistry, Instituto Quimica Organica, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
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36
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Jiménez-Barbero J, Demange R, Schenk K, Vogel P. Synthesis and solution conformational analysis of 2,3-anhydro-3-C-[(1R)-2,6-anhydro-1-deoxy-1-fluoro-D-glycero-D-gulo-heptitol-1-C-yl]-beta-D-gulo-furanose: first example of a monofluoromethylene-linked C-disaccharide. J Org Chem 2001; 66:5132-8. [PMID: 11463266 DOI: 10.1021/jo0102462] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Condensation of 2,3,4,6-tetra-O-benzyl-beta-D-glucopyranosylcarbaldehyde with isolevoglucosenone induced by Et(2)AlI, followed by epoxidation, gave an aldol that was fluorinated into a monofluoromethylene C-glucopyranoside that was converted into the title C-disaccharide 1. Its conformational behavior in water has been studied by using a combination of NMR spectroscopy (J and NOE data) and molecular mechanics calculations.
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Affiliation(s)
- J Jiménez-Barbero
- Section de Chimie, Université de Lausanne, BCH, CH-1015 Lausanne-Dorigny, Switzerland
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37
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Bukowski R, Morris L, Woods R, Weimar T. Synthesis and Conformational Analysis of the T-Antigen Disaccharide (β-D-Gal-(1→3)-α-D-GalNAc-OMe). European J Org Chem 2001. [DOI: 10.1002/1099-0690(200107)2001:14<2697::aid-ejoc2697>3.0.co;2-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Solís D, Jiménez-Barbero J, Kaltner H, Romero A, Siebert HC, von der Lieth CW, Gabius HJ. Towards defining the role of glycans as hardware in information storage and transfer: basic principles, experimental approaches and recent progress. Cells Tissues Organs 2001; 168:5-23. [PMID: 11114583 DOI: 10.1159/000016802] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The term 'code' in biological information transfer appears to be tightly and hitherto exclusively connected with the genetic code based on nucleotides and translated into functional activities via proteins. However, the recent appreciation of the enormous coding capacity of oligosaccharide chains of natural glycoconjugates has spurred to give heed to a new concept: versatile glycan assembly by the genetically encoded glycosyltransferases endows cells with a probably not yet fully catalogued array of meaningful messages. Enciphered by sugar receptors such as endogenous lectins the information of code words established by a series of covalently linked monosaccharides as letters for example guides correct intra- and intercellular routing of glycoproteins, modulates cell proliferation or migration and mediates cell adhesion. Evidently, the elucidation of the structural frameworks and the recognition strategies within the operation of the sugar code poses a fascinating conundrum. The far-reaching impact of this recognition mode on the level of cells, tissues and organs has fueled vigorous investigations to probe the subtleties of protein-carbohydrate interactions. This review presents information on the necessarily concerted approach using X-ray crystallography, molecular modeling, nuclear magnetic resonance spectroscopy, thermodynamic analysis and engineered ligands and receptors. This part of the treatise is flanked by exemplarily chosen insights made possible by these techniques.
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Affiliation(s)
- D Solís
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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Gabius HJ. Glycohistochemistry: the why and how of detection and localization of endogenous lectins. Anat Histol Embryol 2001; 30:3-31. [PMID: 11284160 DOI: 10.1046/j.1439-0264.2001.00305.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The central dogma of molecular biology limits the downstream flow of genetic information to proteins. Progress from the last two decades of research on cellular glycoconjugates justifies adding the enzymatic production of glycan antennae with information-bearing determinants to this famous and basic pathway. An impressive variety of regulatory processes including cell growth and apoptosis, folding and routing of glycoproteins and cell adhesion/migration have been unravelled and found to be mediated or modulated by specific protein (lectin)-carbohydrate interactions. The conclusion has emerged that it would have meant missing manifold opportunities not to recruit the sugar code to cellular information transfer. Currently, the potential for medical applications in anti-adhesion therapy or drug targeting is one of the major driving forces fuelling progress in glycosciences. In histochemistry, this concept has prompted the introduction of carrier-immobilized carbohydrate ligands (neoglycoconjugates) to visualize the cells' capacity to be engaged in oligosaccharide recognition. After their isolation these tissue lectins will be tested for ligand analysis. Since fine specificities of different lectins can differ despite identical monosaccharide binding, the tissue lectins will eventually replace plant agglutinins to move from glycan profiling and localization to functional considerations. Namely, these two marker types, i.e. neoglycoconjugates and tissue lectins, track down accessible binding sites with relevance for involvement in interactions in situ. The documented interplay of synthetic organic chemistry and biochemistry with cyto- and histochemistry nourishes the optimism that the application of this set of innovative custom-prepared tools will provide important insights into the ways in which glycans can act as hardware in transmitting information during normal tissue development and pathological situations.
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Affiliation(s)
- H J Gabius
- Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität München, Veterinärstr. 13, D-80539 München, Germany.
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40
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Carpintero M, Fernández-Mayoralas A, Jiménez-Barbero J. The Conformational Behaviour of Fucosyl and Carbafucosyl Mimetics in the Free and in the Protein-Bound States. European J Org Chem 2001. [DOI: 10.1002/1099-0690(200102)2001:4<681::aid-ejoc681>3.0.co;2-e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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41
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Yang G, Franck RW, Bittman R, Samadder P, Arthur G. Synthesis and growth inhibitory properties of glucosamine-derived glycerolipids. Org Lett 2001; 3:197-200. [PMID: 11430033 DOI: 10.1021/ol006783a] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[figure: see text] 2-Amino C-glycerolipid 1b was synthesized by using the Ramberg-Bäcklund rearrangement as the key step. beta-C-Glycerolipid 1b exhibits in vitro antiproliferative effects strikingly similar to those of O-glycoside analogue 1a.
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Affiliation(s)
- G Yang
- Department of Chemistry, Hunter College/CUNY, 695 Park Avenue, New York, New York 10021, USA
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42
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Imberty A, Pérez S. Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations. Chem Rev 2000; 100:4567-88. [PMID: 11749358 DOI: 10.1021/cr990343j] [Citation(s) in RCA: 212] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A Imberty
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS, affiliated with Joseph Fourier Université), 601 rue de la Chimie, BP 53, F-38041 Grenoble Cedex 9
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43
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Postema MH, Calimente D, Liu L, Behrmann TL. An olefin metathesis route for the preparation of (1-->6)-linked C-disaccharide glycals. A convergent and flexible approach to C-saccharide synthesis. J Org Chem 2000; 65:6061-8. [PMID: 10987940 DOI: 10.1021/jo0005159] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A convergent route to a variety of C-1-disaccharide glycals based on the olefin metathesis reaction of enol ethers and alkenes is described. The DCC-mediated coupling reaction of a variety of pentose enitols (1a-c) with a number of C-5- and C-6-monosaccharide carboxylic acids (2a-e) gave the corresponding esters 3a-l in good yield. Methylenation of these compounds was followed by ring-closing metathesis, mediated by the Schrock molybdenum catalyst 8 in warm toluene, to provide the target C-disaccharide glycals 5a-l. The formed enol ether double bond in 5a was then transformed, via standard manipulations, into a variety of C-disaccharide derivatives 21-25.
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Affiliation(s)
- M H Postema
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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44
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Picard C, Gruza J, Derouet C, Renard CM, Mazeau K, Koca J, Imberty A, Hervé Du Penhoat C. A conformational study of the xyloglucan oligomer, XXXG, by NMR spectroscopy and molecular modeling. Biopolymers 2000; 54:11-26. [PMID: 10799977 DOI: 10.1002/(sici)1097-0282(200007)54:1<11::aid-bip20>3.0.co;2-d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A structural study of the XXXG xyloglucan heptasaccharide (X = alpha-D-Xylp(1 --> 6)-beta-D-Glcp and G = beta-D-Glcp) isolated from apple fruit has been undertaken with nmr and molecular mechanics methods. Quantitative 400 MHz nmr data including nuclear Overhauser effect spectroscopy (NOESY) volumes were recorded at both 6 and 20 degrees C. In spite of severe overlapping of resonances, it was possible to estimate summed NOEs for the majority of the anomeric and glucosyl methylene protons. An ensemble-average population of preferred geometries has been established with the CICADA conformational searching algorithm associated with the MM3 force field. Comparison of the theoretical data obtained by back-calculation of the NOESY volumes from the ensemble-average distance matrix program and motional models based on the Stokes-Einstein-Debye relation satisfactorily reproduce the experimental data. Conformational averaging about the mainchain glycosidic linkages includes both the syn and anti conformers and a minor gauche-gauche population is highly probable. The theoretical data overestimate the syn preference of the Glc(c) --> Glc(b) linkage as well as the Glc(c) GT rotamer population. Finally, both the motional models and the conformational search indicate a fairly rigid backbone and greater flexiblity for the xylose side chains.
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Affiliation(s)
- C Picard
- Département de Chimie, URA 1679, Ecole Normale Supérieure, 24 Rue Lhomond, 75231 Paris Cedex 05, France
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Poveda A, Asensio J, Polat T, Bazin H, Linhardt R, Jiménez-Barbero J. Conformational Behavior ofC-Glycosyl Analogues of Sialyl-α-(2→3)-Galactose. European J Org Chem 2000. [DOI: 10.1002/(sici)1099-0690(200005)2000:9<1805::aid-ejoc1805>3.0.co;2-a] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Montero E, García-Herrero A, Asensio J, Hirai K, Ogawa S, Santoyo-González F, Cañada F, Jiménez-Barbero J. The Conformational Behaviour of Non-Hydrolizable Lactose Analogues: The Thioglycoside, Carbaglycoside, and Carba-Iminoglycoside Cases. European J Org Chem 2000. [DOI: 10.1002/(sici)1099-0690(200005)2000:10<1945::aid-ejoc1945>3.0.co;2-g] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Rodríguez-Carvajal MA, Bernabe M, Espartero JL, Tejero-Mateo P, Gil-Serrano A, Jiménez-Barbero J. Studies on the solution conformation and dynamics of a polysaccharide from Sinorhizobium fredii HH103 and its monosaccharide repeating unit. J Mol Graph Model 2000; 18:135-42, 166. [PMID: 10994517 DOI: 10.1016/s1093-3263(00)00045-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The conformational behavior of the homopolysaccharide isolated from Sinorhizobium fredii HH103 and its monosaccharide repeating unit (5-acetamido-3,5,7,9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero- L- manno-nonulosonic acid) was analyzed by nuclear magnetic resonance (NMR) spectroscopy and extensive molecular dynamics simulations (MD). The results indicate that the glycosidic linkages and lateral chains may adopt a variety of conformations. MD simulations using the generalized Born solvent-accessible surface area (GB/SA) continuum solvent model for water and the MM3* force field provide a population distribution of conformers that satisfactorily agrees with the experimental NMR data for the torsional degrees of freedom of the molecule.
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Csonka GI, Sosa CP, Csizmadia IG. Ab Initio Study of Lowest-Energy Conformers of Lewis X (Lex) Trisaccharide. J Phys Chem A 2000. [DOI: 10.1021/jp9935034] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gábor I. Csonka
- Department of Inorganic Chemistry, Budapest University of Technology, H-1521 Budapest, Hungary
| | - Carlos P. Sosa
- Silicon Graphics Inc., 655 E. Lone Oak Drive Eagan, Minnesota 55123
| | - Imre G. Csizmadia
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
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Krintel SL, Jiménez-Barbero J, Skrydstrup T. A convergent synthesis of α-C-1,3-mannobioside via SmI2-promoted C-glycosylation. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)01604-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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