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Pharande SG. The Merger of Isocyanide‐Based Multicomponent Reaction and Ring‐Closing Metathesis (IMCR/RCM). ChemistrySelect 2021. [DOI: 10.1002/slct.202004131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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2
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Liu W, Jia X, Wang M, Li P, Wang X, Hu W, Zheng J, Mei Y. Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-l-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels. RSC Adv 2017. [DOI: 10.1039/c7ra06215j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, both a molecular mechanical (MM) method and a hybrid quantum mechanical/molecular mechanical (QM/MM) method have been applied in the study of the binding affinities of methyl-α-l-fucoside to Ralstonia solanacearum lectins.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Xiangyu Jia
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Meiting Wang
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Pengfei Li
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
| | - Wenxin Hu
- The Computer Center
- School of Computer Science and Software Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Jun Zheng
- The Computer Center
- School of Computer Science and Software Engineering
- East China Normal University
- Shanghai 200062
- China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy
- School of Physics and Materials Science
- East China Normal University
- Shanghai 200062
- China
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3
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Multivalent Carbohydrate-Lectin Interactions: How Synthetic Chemistry Enables Insights into Nanometric Recognition. Molecules 2016; 21:molecules21050629. [PMID: 27187342 PMCID: PMC6274006 DOI: 10.3390/molecules21050629] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 12/15/2022] Open
Abstract
Glycan recognition by sugar receptors (lectins) is intimately involved in many aspects of cell physiology. However, the factors explaining the exquisite selectivity of their functional pairing are not yet fully understood. Studies toward this aim will also help appraise the potential for lectin-directed drug design. With the network of adhesion/growth-regulatory galectins as therapeutic targets, the strategy to recruit synthetic chemistry to systematically elucidate structure-activity relationships is outlined, from monovalent compounds to glyco-clusters and glycodendrimers to biomimetic surfaces. The versatility of the synthetic procedures enables to take examining structural and spatial parameters, alone and in combination, to its limits, for example with the aim to produce inhibitors for distinct galectin(s) that exhibit minimal reactivity to other members of this group. Shaping spatial architectures similar to glycoconjugate aggregates, microdomains or vesicles provides attractive tools to disclose the often still hidden significance of nanometric aspects of the different modes of lectin design (sequence divergence at the lectin site, differences of spatial type of lectin-site presentation). Of note, testing the effectors alone or in combination simulating (patho)physiological conditions, is sure to bring about new insights into the cooperation between lectins and the regulation of their activity.
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4
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Sweeney SM, Bullen GA, Gillis RB, Adams GG, Rowe AJ, Harding SE, Tucker JH, Peacock AF, Murphy PV. Coiled coil type neoglycoproteins presenting three lactose residues. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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5
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Müller C, Despras G, Lindhorst TK. Organizing multivalency in carbohydrate recognition. Chem Soc Rev 2016; 45:3275-302. [DOI: 10.1039/c6cs00165c] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Merging carbohydrate chemistry with lectin histochemistry to study inhibition of lectin binding by glycoclusters in the natural tissue context. Histochem Cell Biol 2015; 145:185-99. [PMID: 26553286 DOI: 10.1007/s00418-015-1383-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2015] [Indexed: 01/22/2023]
Abstract
Recognition of glycans by lectins leads to cell adhesion and growth regulation. The specificity and selectivity of this process are determined by carbohydrate structure (sequence and shape) and topology of its presentation. The synthesis of (neo)glycoconjugates with bi- to oligo-valency (glycoclusters) affords tools to delineate structure-activity relationships by blocking lectin binding to an artificial matrix, often a glycoprotein, or cultured cell lines. The drawback of these assays is that glycan presentation is different from that in tissues. In order to approach the natural context, we here introduce lectin histochemistry on fixed tissue sections to determine the susceptibility of binding of two plant lectins, i.e., GSA-II and WGA, to a series of 10 glycoclusters. Besides valency, this panel covers changes in the anomeric position (α/β) and the atom at the glycosidic linkage (O/S). Flanked by cell and solid-phase assays with human tumor lines and two mucins, respectively, staining (intensity and profile) was analyzed in sections of murine jejunum, stomach and epididymis as a function of glycocluster presence. The marked and differential sensitivity of signal generation to structural aspects of the glycoclusters proves the applicability of this method. This enables comparisons between data sets obtained by using (neo)glycoconjugates, cells and the tissue context as platforms. The special advantage of processing tissue sections is the monitoring of interference with lectin association at sites that are relevant for functionality. Testing glycoclusters in lectin histochemistry will especially be attractive in cases of multi-target recognition (glycans, proteins and lipids) by a tissue lectin.
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7
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Bound DJ, Murthy PS, Srinivas P. Synthesis and antibacterial properties of 2,3-dideoxyglucosides of terpene alcohols and phenols. Food Chem 2015; 185:192-9. [DOI: 10.1016/j.foodchem.2015.03.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/20/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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9
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Zhou J, Reidy M, O’Reilly C, Jarikote DV, Negi A, Samali A, Szegezdi E, Murphy PV. Decorated Macrocycles via Ring-Closing Double-Reductive Amination. Identification of an Apoptosis Inducer of Leukemic Cells That at Least Partially Antagonizes a 5-HT2 Receptor. Org Lett 2015; 17:1672-5. [DOI: 10.1021/acs.orglett.5b00404] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jian Zhou
- School of Chemistry and ‡School of Natural
Sciences, National University of Ireland, Galway, Ireland
| | - Mairead Reidy
- School of Chemistry and ‡School of Natural
Sciences, National University of Ireland, Galway, Ireland
| | - Ciaran O’Reilly
- School of Chemistry and ‡School of Natural
Sciences, National University of Ireland, Galway, Ireland
| | - Dilip V. Jarikote
- School of Chemistry and ‡School of Natural
Sciences, National University of Ireland, Galway, Ireland
| | - Arvind Negi
- School of Chemistry and ‡School of Natural
Sciences, National University of Ireland, Galway, Ireland
| | - Afshin Samali
- School of Chemistry and ‡School of Natural
Sciences, National University of Ireland, Galway, Ireland
| | - Eva Szegezdi
- School of Chemistry and ‡School of Natural
Sciences, National University of Ireland, Galway, Ireland
| | - Paul V. Murphy
- School of Chemistry and ‡School of Natural
Sciences, National University of Ireland, Galway, Ireland
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10
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Solís D, Bovin NV, Davis AP, Jiménez-Barbero J, Romero A, Roy R, Smetana K, Gabius HJ. A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. Biochim Biophys Acta Gen Subj 2014; 1850:186-235. [PMID: 24685397 DOI: 10.1016/j.bbagen.2014.03.016] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 01/17/2023]
Abstract
BACKGROUND The most demanding challenge in research on molecular aspects within the flow of biological information is posed by the complex carbohydrates (glycan part of cellular glycoconjugates). How the 'message' encoded in carbohydrate 'letters' is 'read' and 'translated' can only be unraveled by interdisciplinary efforts. SCOPE OF REVIEW This review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure-function relationships, with resources for teaching. MAJOR CONCLUSIONS The unsurpassed coding capacity of glycans is an ideal platform for generating a broad range of molecular 'messages'. Structural and functional analyses of complex carbohydrates have been made possible by advances in chemical synthesis, rendering production of oligosaccharides, glycoclusters and neoglycoconjugates possible. This availability facilitates to test the glycans as ligands for natural sugar receptors (lectins). Their interaction is a means to turn sugar-encoded information into cellular effects. Glycan/lectin structures and their spatial modes of presentation underlie the exquisite specificity of the endogenous lectins in counterreceptor selection, that is, to home in on certain cellular glycoproteins or glycolipids. GENERAL SIGNIFICANCE Understanding how sugar-encoded 'messages' are 'read' and 'translated' by lectins provides insights into fundamental mechanisms of life, with potential for medical applications.
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Affiliation(s)
- Dolores Solís
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 07110 Bunyola, Mallorca, Illes Baleares, Spain.
| | - Nicolai V Bovin
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho-Maklaya 16/10, 117871 GSP-7, V-437, Moscow, Russian Federation.
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - Antonio Romero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - René Roy
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
| | - Karel Smetana
- Charles University, 1st Faculty of Medicine, Institute of Anatomy, U nemocnice 3, 128 00 Prague 2, Czech Republic.
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 München, Germany.
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11
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André S, Wang GN, Gabius HJ, Murphy PV. Combining glycocluster synthesis with protein engineering: an approach to probe into the significance of linker length in a tandem-repeat-type lectin (galectin-4). Carbohydr Res 2014; 389:25-38. [PMID: 24698724 DOI: 10.1016/j.carres.2013.12.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 12/23/2013] [Accepted: 12/27/2013] [Indexed: 11/24/2022]
Abstract
Complementarity in lectin-glycan interactions in situ is assumed to involve spatial features in both the lectin and the glycan, giving a functional meaning to structural aspects of the lectin beyond its carbohydrate-binding site. In combining protein engineering with glycocluster synthesis, it is shown that the natural linker length of a tandem-repeat-type human lectin (galectin-4) determines binding properties in two binding assays (using surface-presented glycoprotein and cell surface assays). The types of glycocluster tested included bivalent lactosides based on tertiary amides of terephthalic, isophthalic, 2,6-naphthalic and oxalic acids as well as bivalent H(type 2) trisaccharides grafted on secondary/tertiary terephthalamides and two triazole-linker-containing cores. The presented data reveal a marked change in susceptibility to the test compounds when turning the tandem-repeat-type to a proto-type-like display. The testing of glycoclusters is suggested as a general strategy to help to delineate the significance of distinct structural features of lectins beyond their contact sites to the glycan.
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Affiliation(s)
- Sabine André
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Guan-Nan Wang
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Paul V Murphy
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.
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12
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Yao W, Xia MJ, Meng XB, Li Q, Li ZJ. Adaptable synthesis of C-lactosyl glycoclusters and their binding properties with galectin-3. Org Biomol Chem 2014; 12:8180-95. [DOI: 10.1039/c4ob01374c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The synthesis of mono- to tetravalent C-β-lactosyl glycoclusters has been achieved in good yield. The KD values of glycoclusters against galectin-3 were tested by SPR assay, and the structure–activity relationship has been summarized in detail.
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Affiliation(s)
- Wang Yao
- The State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Science
- Peking University
- Beijing 100191, P R China
| | - Meng-jie Xia
- The State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Science
- Peking University
- Beijing 100191, P R China
| | - Xiang-bao Meng
- The State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Science
- Peking University
- Beijing 100191, P R China
| | - Qing Li
- The State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Science
- Peking University
- Beijing 100191, P R China
| | - Zhong-jun Li
- The State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Science
- Peking University
- Beijing 100191, P R China
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Abstract
Nitrogen-containing macrocyclic compounds (amines, amides, and N-heterocyclic derivatives) are important targets in supramolecular chemistry. This chapter discusses the importance of aza-macrocycles in general and, in particular, those receptors containing sugar unit(s). The combination of a carbohydrate scaffold bearing nitrogen-containing functional groups in macrocyclic molecules opens a convenient route to chiral receptors having potentially useful properties. The carbohydrate-based macrocycles discussed are classified into several general groups: (1) aza-crown ethers containing a carbohydrate subunit, (2) cyclic homooligomers from amino sugars, (3) sugar-based cryptands, (4) cyclic peptides containing amino sugar units (including C2- and C3-symmetrical macrocyclic glycopeptides), (5) nitrogen- containing glycophanes, and (6) 1,2,3-triazoles containing synthetic cyclodextrin analogues. The general strategies employed, as well as specific ones leading to such complex derivatives, are surveyed. Applications of such carbohydrate receptors, pointing to their importance as hosts in supramolecular chemistry, are discussed.
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14
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Farrell M, Zhou J, Murphy PV. Regiospecific Anomerisation of Acylated Glycosyl Azides and Benzoylated Disaccharides by Using TiCl4. Chemistry 2013; 19:14836-51. [DOI: 10.1002/chem.201302572] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Indexed: 01/28/2023]
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15
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The third dimension of reading the sugar code by lectins: design of glycoclusters with cyclic scaffolds as tools with the aim to define correlations between spatial presentation and activity. Molecules 2013; 18:4026-53. [PMID: 23558543 PMCID: PMC6269965 DOI: 10.3390/molecules18044026] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 03/22/2013] [Accepted: 04/01/2013] [Indexed: 01/21/2023] Open
Abstract
Coding of biological information is not confined to nucleic acids and proteins. Endowed with the highest level of structural versatility among biomolecules, the glycan chains of cellular glycoconjugates are well-suited to generate molecular messages/signals in a minimum of space. The sequence and shape of oligosaccharides as well as spatial aspects of multivalent presentation are assumed to underlie the natural specificity/selectivity that cellular glycans have for endogenous lectins. In order to eventually unravel structure-activity profiles cyclic scaffolds have been used as platforms to produce glycoclusters and afford valuable tools. Using adhesion/growth-regulatory galectins and the pan-galectin ligand lactose as a model, emerging insights into the potential of cyclodextrins, cyclic peptides, calixarenes and glycophanes for this purpose are presented herein. The systematic testing of lectin panels with spatially defined ligand presentations can be considered as a biomimetic means to help clarify the mechanisms, which lead to the exquisite accuracy at which endogenous lectins select their physiological counterreceptors from the complexity of the cellular glycome.
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Chabre YM, Roy R. Multivalent glycoconjugate syntheses and applications using aromatic scaffolds. Chem Soc Rev 2013; 42:4657-708. [PMID: 23400414 DOI: 10.1039/c3cs35483k] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Glycan-protein interactions are of utmost importance in several biological phenomena. Although the variety of carbohydrate residues in mammalian cells is limited to less than a dozen different sugars, their spatial topographical presentation in what is now associated as the "glycocodes" provides the fundamental keys for specific and high affinity "lock-in" recognition events associated with a wide range of pathologies. Toward deciphering our understanding of these glycocodes, chemists have developed new creative tools that included dendrimer chemistry in order to provide monodisperse multivalent glycoconjugates. This review provides a survey of the numerous aromatic architectures generated for the multivalent presentation of relevant carbohydrates using covalent attachment or supramolecular self-assemblies. The basic concepts toward their controlled syntheses will be described using modern synthetic procedures with a particular emphasis on powerful organometallic methodologies. The large variety of dendritic aromatic scaffolds, together with a brief survey of their unique biophysical and biological properties will be critically reviewed. The distinctiveness of the resulting multivalent glycoarchitectures, encompassing glycoclusters, glycodendrimers and molecularly defined self-assemblies, in forming well organized cross-linked lattices with multivalent carbohydrate binding proteins (lectins) together with their photophysical, medical, and imaging properties will also be briefly highlighted. The topic will be presented in increasing order of aromatic backbone complexities and will end with fullerenes together with self-assembled nanostructures, thus complementing the various scaffolds described in this special thematic issue dedicated to multivalent glycoscience.
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Affiliation(s)
- Yoann M Chabre
- Pharmaqam - Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-ville, Montréal, Québec, Canada H3C 3P8
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Wang GN, André S, Gabius HJ, Murphy PV. Bi- to tetravalent glycoclusters: synthesis, structure-activity profiles as lectin inhibitors and impact of combining both valency and headgroup tailoring on selectivity. Org Biomol Chem 2012; 10:6893-907. [PMID: 22842468 DOI: 10.1039/c2ob25870f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The emerging functional versatility of cellular glycans makes research on the design of synthetic inhibitors a timely topic. In detail, the combination of ligand (or headgroup or contact site) structure with spatial parameters that depend on topological and geometrical factors underlies the physiological selectivity of glycan-protein (lectin) recognition. We herein tested a panel of bi-, tri- and tetravalent compounds against two plant agglutinins and adhesion/growth-regulatory lectins (galectins). In addition, we examined the impact of headgroup tailoring (converting lactose to 2'-fucosyllactose) in combination with valency increase in two assay types of increasing biorelevance (from solid-phase binding to cell binding). Compounds were prepared using copper-catalysed azide alkyne cycloaddition from peracetylated lactosyl or 2'-fucosyllactosyl azides. Significant inhibition was achieved for the plant toxin with a tetravalent compound. Different levels of sensitivity were noted for the three groups of the galectin family. The headgroup extension to 2'-fucosyllactose led to a selectivity gain, especially for the chimera-type galectin-3. Valency increase established discrimination against the homodimeric proteins, whereas the combination of valency with the headgroup extension led to discrimination against the tandem-repeat-type galectin-8 for chicken galectins but not human galectins-3 and -4. Thus, detailed structure-activity profiling of glycoclusters combined with suitably modifying the contact site for the targeted lectin will help minimize cross-reactivity among this class of closely related proteins.
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Affiliation(s)
- Guan-Nan Wang
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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18
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Synthesis of bivalent glycoclusters containing GlcNAc as hexasaccharide mimetics. Bactericidal activity against Helicobacter pylori. Carbohydr Res 2012; 360:1-7. [PMID: 22975273 DOI: 10.1016/j.carres.2012.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 11/23/2022]
Abstract
The Cu(I) catalysed cycloaddition reaction of azides and alkynes has been used to generate a series of divalent GlcNAc clusters with both α and β configurations. These glycoclusters can be considered as potential mimetics of an anti Helicobacter pylori hexasaccharide as they present two GlcNAc residues grafted onto a core scaffold. Two bivalent compounds based on α-O-GlcNAc were identified that selectively reduced the viability of H. pylori. These compounds showed activity towards different strains of H. pylori (Pu4 vs P12). The activity of the oligosaccharide mimetics is speculated to be due to the GlcNAc residues being able to adopt spatial arrangements accessible to the anti H. pylori hexasaccharide which may be important for activity.
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Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
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Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
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20
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André S, Cañada FJ, Shiao TC, Largartera L, Diercks T, Bergeron-Brlek M, el Biari K, Papadopoulos A, Ribeiro JP, Touaibia M, Solís D, Menéndez M, Jiménez-Barbero J, Roy R, Gabius HJ. Fluorinated Carbohydrates as Lectin Ligands: Biorelevant Sensors with Capacity to Monitor Anomer Affinity in 19F-NMR-Based Inhibitor Screening. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200397] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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André S, Jarikote DV, Yan D, Vincenz L, Wang GN, Kaltner H, Murphy PV, Gabius HJ. Synthesis of bivalent lactosides and their activity as sensors for differences between lectins in inter- and intrafamily comparisons. Bioorg Med Chem Lett 2012; 22:313-8. [DOI: 10.1016/j.bmcl.2011.11.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 02/02/2023]
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22
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André S, Renaudet O, Bossu I, Dumy P, Gabius HJ. Cyclic neoglycodecapeptides: how to increase their inhibitory activity and selectivity on lectin/toxin binding to a glycoprotein and cells. J Pept Sci 2011; 17:427-37. [DOI: 10.1002/psc.1338] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 09/03/2010] [Accepted: 11/02/2010] [Indexed: 11/10/2022]
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23
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Deniaud D, Julienne K, Gouin SG. Insights in the rational design of synthetic multivalent glycoconjugates as lectin ligands. Org Biomol Chem 2011; 9:966-79. [DOI: 10.1039/c0ob00389a] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Herndon JW. The chemistry of the carbon–transition metal double and triple bond: Annual survey covering the year 2009. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Jarikote DV, Li W, Jiang T, Eriksson LA, Murphy PV. Towards echinomycin mimetics by grafting quinoxaline residues on glycophane scaffolds. Bioorg Med Chem 2010; 19:826-35. [PMID: 21195622 DOI: 10.1016/j.bmc.2010.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 11/23/2010] [Accepted: 12/03/2010] [Indexed: 11/25/2022]
Abstract
Echinomycin is a natural depsipeptide, which is a bisintercalator, inserting quinoxaline units preferentially adjacent to CG base pairs of DNA. Herein the design and synthesis of echinomycin mimetics based on grafting of two quinoxaline residues onto a macrocyclic scaffold (glycophane) is addressed. Binding of the compounds to calf-thymus DNA was studied using UV-vis and steady state fluorescence spectroscopy, as well as thermal denaturation. An interesting observation was enhancement of fluorescence emission for the peptidomimetics on binding to DNA, which contrasted with observations for echinomycin. Molecular dynamics simulations were exploited to explore in more detail if bis-intercalation to DNA was possible for one of the glycophanes. Bis-intercalating echinomycin complexes with DNA were found to be stable during 20ns simulations at 298K. However, the MD simulations of a glycophane complexed with a DNA octamer displayed very different behaviour to echinomycin and its quinoxaline units were found to rapidly migrate out from the intercalation site. Release of bis-intercalation strain occurred with only one of the quinoxaline chromophores remaining intercalated throughout the simulation. The distance between the quinoxaline residues in the glycophane at the end of the MD simulation was 7.3-7.5Å, whereas in echinomycin, the distance between the residues was ∼11Å, suggesting that longer glycophane scaffolds would be required to generate bis-intercalating echinomycin mimetics.
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Pilgrim W, Murphy PV. SnCl4- and TiCl4-Catalyzed Anomerization of Acylated O- and S-Glycosides: Analysis of Factors That Lead to Higher α:β Anomer Ratios and Reaction Rates. J Org Chem 2010; 75:6747-55. [DOI: 10.1021/jo101090f] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wayne Pilgrim
- School of Chemistry, National University of Ireland, Galway, Ireland
- Centre for Synthesis and Chemical Biology, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul V. Murphy
- School of Chemistry, National University of Ireland, Galway, Ireland
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Affiliation(s)
| | - Paul V. Murphy
- School of Chemistry, National University of Ireland, Galway, Ireland, Fax: +353‐91‐525700
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Gouin SG, García Fernández JM, Vanquelef E, Dupradeau FY, Salomonsson E, Leffler H, Ortega-Muñoz M, Nilsson UJ, Kovensky J. Multimeric Lactoside “Click Clusters” as Tools to Investigate the Effect of Linker Length in Specific Interactions with Peanut Lectin, Galectin-1, and -3. Chembiochem 2010; 11:1430-42. [DOI: 10.1002/cbic.201000167] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Leyden R, Velasco-Torrijos T, André S, Gouin S, Gabius HJ, Murphy PV. Synthesis of Bivalent Lactosides Based on Terephthalamide, N,N′-Diglucosylterephthalamide, and Glycophane Scaffolds and Assessment of Their Inhibitory Capacity on Medically Relevant Lectins. J Org Chem 2009; 74:9010-26. [DOI: 10.1021/jo901667r] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rosaria Leyden
- School of Chemistry and Chemical Biology, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Trinidad Velasco-Torrijos
- School of Chemistry and Chemical Biology, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sabine André
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstrasse 13, 80539 Munich, Germany
| | - Sebastien Gouin
- School of Chemistry and Chemical Biology, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstrasse 13, 80539 Munich, Germany
| | - Paul V. Murphy
- School of Chemistry and Chemical Biology, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
- School of Chemistry, National University of Ireland, Galway
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