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Arend LB, Verli H. Revisiting the structural basis for biological activity of GMI-1070, a sialyl Lewis x mimetic. Carbohydr Res 2023; 529:108829. [PMID: 37182470 DOI: 10.1016/j.carres.2023.108829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/16/2023]
Abstract
When it comes to the treatment of pathologies in which aberrant cell adhesion and extravasation from the bloodstream have been implicated, the selectins represent a central therapeutic target. In this context, the present work investigates the conformational landscape of two prototypes for the design of new antineoplasic and anti-inflammatory agents: the natural selectin ligand sialyl Lewisx and its mimetic GMI-1070. Accordingly, a series of unbiased molecular dynamics simulations at the microsecond scale using GROMOS 53A6 (GLYC), CHARMM36m and GLYCAM06 force fields were employed, together with ConfID, an analytical method for the characterization of conformational populations of small molecules. Our results for sialyl Lewisx are in agreement with and expand upon prior work. As for the mimetic, our results indicate that, in spite of its conformational restriction, GMI-1070's behavior in solution deviates from what had been proposed, highlighting thus some features that could be optimized, as the development of sialyl Lewisx mimetics continues, and new candidates emerge.
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Affiliation(s)
- Laís B Arend
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves, 9500, CP 15005, Porto Alegre, 91500-970, RS, Brazil
| | - Hugo Verli
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves, 9500, CP 15005, Porto Alegre, 91500-970, RS, Brazil.
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2
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Peesapati S, Sajeevan KA, Patel SK, Roy D. Relation between glycosidic linkage, structure and dynamics of α- and β-glucans in water. Biopolymers 2021; 112:e23423. [PMID: 33572006 DOI: 10.1002/bip.23423] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/16/2021] [Accepted: 01/21/2021] [Indexed: 11/09/2022]
Abstract
In a molecular dynamics simulation study of several oligosaccharides comprising of the very basic building block of carbohydrate, the α- or β-d glucopyranose units, linked by any one of the 1-3/1-4 or 1-6 glycosidic linkages, we compare and contrast their structural and dynamical properties. Results indicate that the litheness of the oligosaccharide chain is noticeably controlled by the composition, anomeric nature and glycosidic linkage type of the units. In mixed β 1-4/1-3 d-glucopyranosides, as those found in oats and barley, the ratio of the β 1-4 and β 1-3 linked residues is crucial in determining the structural and dynamical attributes. Principal component analysis (PCA) using the internal coordinates of torsion angles subtended by glycosidic oxygen atoms and subsequent K-means clustering of the dynamical space spanned by PC1 to PC2 point to the dynamical and structural disparity in the various types of oligosaccharides studied. The properties simulated in this work are meant to provide a systematic yet comparative understanding of the importance of linkage and anomericity on the oligosaccharide chain properties and are in line with some experimental structural attributes.
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Affiliation(s)
- Sruthi Peesapati
- Department of Chemistry, Birla Institute of Technology and Science- Pilani, Hyderabad, Telangana, India
| | - Karuna Anna Sajeevan
- Department of Chemistry, Birla Institute of Technology and Science- Pilani, Hyderabad, Telangana, India
| | - Siddhant Kumar Patel
- Department of Chemistry, Birla Institute of Technology and Science- Pilani, Hyderabad, Telangana, India
| | - Durba Roy
- Department of Chemistry, Birla Institute of Technology and Science- Pilani, Hyderabad, Telangana, India
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3
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Nestor G, Anderson T, Oscarson S, Gronenborn AM. Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy. J Am Chem Soc 2017; 139:6210-6216. [PMID: 28406013 DOI: 10.1021/jacs.7b01929] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
NMR of a uniformly 13C-labeled carbohydrate was used to elucidate the atomic details of a sugar-protein complex. The structure of the 13C-labeled Manα(1-2)Manα(1-2)ManαOMe trisaccharide ligand, when bound to cyanovirin-N (CV-N), was characterized and revealed that in the complex the glycosidic linkage torsion angles between the two reducing-end mannoses are different from the free trisaccharide. Distances within the carbohydrate were employed for conformational analysis, and NOE-based distance mapping between sugar and protein revealed that Manα(1-2)Manα(1-2)ManαOMe is bound more intimately with its two reducing-end mannoses into the domain A binding site of CV-N than with the nonreducing end unit. Taking advantage of the 13C spectral dispersion of 13C-labeled carbohydrates in isotope-filtered experiments is a versatile means for a simultaneous mapping of the binding interactions on both, the carbohydrate and the protein.
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Affiliation(s)
- Gustav Nestor
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
| | - Taigh Anderson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
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4
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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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Zierke M, Smieško M, Rabbani S, Aeschbacher T, Cutting B, Allain FHT, Schubert M, Ernst B. Stabilization of branched oligosaccharides: Lewis(x) benefits from a nonconventional C-H···O hydrogen bond. J Am Chem Soc 2013; 135:13464-72. [PMID: 24001318 DOI: 10.1021/ja4054702] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although animal lectins usually show a high degree of specificity for glycan structures, their single-site binding affinities are typically weak, a drawback which is often compensated in biological systems by an oligovalent presentation of carbohydrate epitopes. For the design of monovalent glycomimetics, structural information regarding solution and bound conformation of the carbohydrate lead represents a valuable starting point. In this paper, we focus on the conformation of the trisaccharide Le(x) (Gal[Fucα(1-3)]β(1-4)GlcNAc). Mainly because of the unfavorable tumbling regime, the elucidation of the solution conformation of Le(x) by NMR has only been partially successful so far. Le(x) was therefore attached to a (13)C,(15)N-labeled protein. (13)C,(15)N-filtered NOESY NMR techniques at ultrahigh field allowed increasing the maximal NOE enhancement, resulting in a high number of distance restraints per glycosidic bond and, consequently, a well-defined structure. In addition to the known contributors to the conformational restriction of the Le(x) structure (exoanomeric effect, steric compression induced by the NHAc group adjacent to the linking position of L-fucose, and the hydrophobic interaction of L-fucose with the β-face of D-galactose), a nonconventional C-H···O hydrogen bond between H-C(5) of L-fucose and O(5) of D-galactose was identified. According to quantum mechanical calculations, this C-H···O hydrogen bond is the most prominent factor in stabilization, contributing 40% of the total stabilization energy. We therefore propose that the nonconventional hydrogen bond contributing to a reduction of the conformational flexibility of the Le(x) core represents a novel element of the glycocode. Its relevance to the stabilization of related branched oligosaccharides is currently being studied.
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Affiliation(s)
- Mirko Zierke
- University of Basel , Klingelbergstraße 50, CH-4056 Basel, Basel-City, Switzerland
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6
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Peters T. A matter of order: how E-selectin makes sweet contacts. Chembiochem 2012; 13:2325-6. [PMID: 23011897 DOI: 10.1002/cbic.201200551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Indexed: 11/09/2022]
Abstract
An entropy exclusive: Sialyl Lewis(x) can be thought of as a "preorganized water oligomer". Recent research in the Ernst laboratory shows that the recognition of sialyl Lewis(x) by E-selectin is exclusively entropy driven. This finding has implications for the design of carbohydrate-based drugs in general.
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Affiliation(s)
- Thomas Peters
- Institute of Chemistry, Center for Structural and Cell Biology in Medicine (CSCM), University of Luebeck, Ratzeburger Alle 160, 23562 Luebeck, Germany.
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7
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Re S, Nishima W, Miyashita N, Sugita Y. Conformational flexibility of N-glycans in solution studied by REMD simulations. Biophys Rev 2012; 4:179-187. [PMID: 28510079 DOI: 10.1007/s12551-012-0090-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 06/21/2012] [Indexed: 01/09/2023] Open
Abstract
Protein-glycan recognition regulates a wide range of biological and pathogenic processes. Conformational diversity of glycans in solution is apparently incompatible with specific binding to their receptor proteins. One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein. However, the labile nature of glycans makes characterizing their conformational states a challenging issue. All-atom molecular dynamics (MD) simulations provide the atomic details of glycan structures in solution, but fairly extensive sampling is required for simulating the transitions between rotameric states. This difficulty limits application of conventional MD simulations to small fragments like di- and tri-saccharides. Replica-exchange molecular dynamics (REMD) simulation, with extensive sampling of structures in solution, provides a valuable way to identify a family of glycan conformers. This article reviews recent REMD simulations of glycans carried out by us or other research groups and provides new insights into the conformational equilibria of N-glycans and their alteration by chemical modification. We also emphasize the importance of statistical averaging over the multiple conformers of glycans for comparing simulation results with experimental observables. The results support the concept of "conformer selection" in protein-glycan recognition.
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Affiliation(s)
- Suyong Re
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Wataru Nishima
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoyuki Miyashita
- RIKEN Quantitative Biology Center, IMDA 6F, 1-6-5 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Yuji Sugita
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,RIKEN Quantitative Biology Center, IMDA 6F, 1-6-5 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. .,RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
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8
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Binder FPC, Lemme K, Preston RC, Ernst B. Sialyl-Lewisx - ein “präorganisiertes Wasseroligomer”? Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202555] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Binder FPC, Lemme K, Preston RC, Ernst B. Sialyl Lewis(x): a "pre-organized water oligomer"? Angew Chem Int Ed Engl 2012; 51:7327-31. [PMID: 22782926 DOI: 10.1002/anie.201202555] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Indexed: 01/18/2023]
Abstract
Organized and released: Sialyl Lewis(x) (sLe(x)) represents a "pre-organized water oligomer", that is, a surrogate for clustered water molecules attached to a scaffold. The impetus for sLe(x) binding to E-selectin is shown to be the high degree of pre-organization allowing an array of directed hydrogen bonds, and the entropic benefit of the release of water molecules from the large binding interface to bulk water (see picture).
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Affiliation(s)
- Florian P C Binder
- Institute of Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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10
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An expedient enzymatic route to isomeric 2-, 3- and 6-monodeoxy-monofluoro-maltose derivatives. Carbohydr Res 2012; 358:12-8. [PMID: 22795862 DOI: 10.1016/j.carres.2012.05.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/23/2012] [Accepted: 05/25/2012] [Indexed: 11/22/2022]
Abstract
2-Deoxy-2-fluoro-d-glucose, 3-deoxy-3-fluoro-D-glucose and 6-deoxy-6-fluoro-D-glucose were converted into the corresponding maltose derivatives using Arabidopsis thaliana DPE2-mediated trans-glycosylation reaction with glycogen acting as a glucosyl donor. (19)F NMR spectroscopy proved to be a valuable tool for monitoring the progress of these reactions and to assess the nature of resulting oligomeric products.
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11
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Fiege B, Rademacher C, Cartmell J, Kitov PI, Parra F, Peters T. Molecular Details of the Recognition of Blood Group Antigens by a Human Norovirus as Determined by STD NMR Spectroscopy. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105719] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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Field RA, Andrade P, Campo VL, Carvalho I, Collet BYM, Crocker PR, Fais M, Karamanska R, Mukhopadhayay B, Nepogodiev SA, Rashid A, Rejzek M, Russell DA, Schofield CL, van Well RM. Synthetic Glycans, Glycoarrays, and Glyconanoparticles To Investigate Host Infection by Trypanosoma cruzi. ACTA ACUST UNITED AC 2011. [DOI: 10.1021/bk-2011-1091.ch009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Affiliation(s)
- Robert A. Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Peterson Andrade
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Vanessa L. Campo
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Ivone Carvalho
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Beatrice Y. M. Collet
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Paul R. Crocker
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Margherita Fais
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Rositsa Karamanska
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Balaram Mukhopadhayay
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Sergey A. Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Abdul Rashid
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - David A. Russell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Claire L. Schofield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Renate M. van Well
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
- Division of Cell Biology and Immunology, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
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13
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Fiege B, Rademacher C, Cartmell J, Kitov PI, Parra F, Peters T. Molecular details of the recognition of blood group antigens by a human norovirus as determined by STD NMR spectroscopy. Angew Chem Int Ed Engl 2011; 51:928-32. [PMID: 22170811 DOI: 10.1002/anie.201105719] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Indexed: 01/26/2023]
Affiliation(s)
- Brigitte Fiege
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
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14
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Harrison JA, Kartha KPR, Fournier EJL, Lowary TL, Malet C, Nilsson UJ, Hindsgaul O, Schenkman S, Naismith JH, Field RA. Probing the acceptor substrate binding site of Trypanosoma cruzi trans-sialidase with systematically modified substrates and glycoside libraries. Org Biomol Chem 2011; 9:1653-60. [PMID: 21253654 PMCID: PMC3315775 DOI: 10.1039/c0ob00826e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 11/22/2010] [Indexed: 01/31/2023]
Abstract
Systematically modified octyl galactosides and octyl N-acetyllactosamines were assessed as inhibitors of, and substrates for, T. cruzi trans-sialidase (TcTS) in the context of exploring its acceptor substrate binding site. These studies show that TcTS, which catalyses the α-(2→3)-sialylation of non-reducing terminal β-galactose residues, is largely intolerant of substitution of the galactose 2 and 4 positions whereas substitution of the galactose 6 position is well tolerated. Further studies show that even the addition of a bulky sugar residue (glucose, galactose) does not impact negatively on TcTS binding and turnover, which highlights the potential of 'internal' 6-substituted galactose residues to serve as TcTS acceptor substrates. Results from screening a 93-membered thiogalactoside library highlight a number of structural features (notably imidazoles and indoles) that are worthy of further investigation in the context of TcTS inhibitor development.
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Affiliation(s)
- Jennifer A. Harrison
- Centre for Biomolecular Sciences , University of St Andrews , St Andrews , UK KY16 9ST
| | - K. P. Ravindranathan Kartha
- Department of Medicinal Chemistry , National Institute of Pharmaceutical Education and Research , Sector 67 , SAS Nagar , Punjab 160 062 , India
| | - Eric J. L. Fournier
- Department of Chemistry , University of Alberta , Edmonton , Alberta T6G2G2 , Canada
| | - Todd L. Lowary
- Department of Chemistry , University of Alberta , Edmonton , Alberta T6G2G2 , Canada
| | - Carles Malet
- Department of Chemistry , University of Alberta , Edmonton , Alberta T6G2G2 , Canada
| | - Ulf J. Nilsson
- Department of Organic Chemistry , Lund University , Box 124 , SE-22100 , Lund , Sweden
| | - Ole Hindsgaul
- Department of Chemistry , University of Alberta , Edmonton , Alberta T6G2G2 , Canada
- Carlsberg Laboratory , Gamle Carlsberg Vej 10 , Valby-Copenhagen , DK-2500 , Denmark
| | - Sergio Schenkman
- Department of Microbiology , Immunology and Parasitology , Universidade Federal de São Paulo , Rua Botucatu 862 8 andar , 04023-062 , São Paulo , SP , Brazil
| | - James H. Naismith
- Centre for Biomolecular Sciences , University of St Andrews , St Andrews , UK KY16 9ST
| | - Robert A. Field
- Department of Biological Chemistry , John Innes Centre , Norwich , UK NR4 7TJ .
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15
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Ishida T. Computational modeling of carbohydrate-recognition process in E-selectin complex: structural mapping of sialyl Lewis X onto ab initio QM/MM free energy surface. J Phys Chem B 2010; 114:3950-64. [PMID: 20078087 DOI: 10.1021/jp905872t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To advance our knowledge of carbohydrate recognition by lectins, we propose a systematic computational modeling strategy to identify complex sugar-chain conformations on the reduced free energy surface (FES). We selected the complex of E-selectin with sialyl Lewis X (denoted E-selectin/SLe(x) complex) as a first target molecule. First, we introduced the reduced 2D-FES that characterizes conformational changes in carbohydrate structure as well as the degree of solvation stability of the carbohydrate ligand, and evaluated the overall free energy profile by classical molecular dynamics simulation combined with ab initio QM/MM energy corrections. Second, we mapped flexible carbohydrate structures onto the reduced QM/MM 2D-FES, and identified the details of molecular interactions between each monosaccharide component and the amino acid residues at the carbohydrate-recognition domain. Finally, we confirmed the validity of our modeling strategy by evaluating the chemical shielding tensor by ab initio QM/MM-GIAO computations for several QM/MM-refined geometries sampled from the minimum free energy region in the 2D-FES, and compared this theoretical averaging data with the experimental 1D-NMR profile. The model clearly shows that the binding geometries of the E-selectin/SLe(x) complex are determined not by one single, rigid carbohydrate structure but rather by the sum of averaged conformations fluctuating around the minimum free energy region. For the E-selectin/SLe(x) complex, the major molecular interactions are hydrogen bonds between Fuc and the Ca(2+) binding site in the carbohydrate-recognition domain, and Gal is important in determining the ligand specificity.
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Affiliation(s)
- Toyokazu Ishida
- Research Institute for Computational Sciences, 1-1-1 Umezono, Tsukuba, 305-8568, Japan.
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16
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Carvalho I, Andrade P, Campo VL, Guedes PMM, Sesti-Costa R, Silva JS, Schenkman S, Dedola S, Hill L, Rejzek M, Nepogodiev SA, Field RA. 'Click chemistry' synthesis of a library of 1,2,3-triazole-substituted galactose derivatives and their evaluation against Trypanosoma cruzi and its cell surface trans-sialidase. Bioorg Med Chem 2010; 18:2412-27. [PMID: 20335038 DOI: 10.1016/j.bmc.2010.02.053] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 02/23/2010] [Accepted: 02/25/2010] [Indexed: 10/19/2022]
Abstract
Trypanosoma cruzi trans-sialidase (TcTS) plays a key role in the recognition and invasion of host cells and in enabling the parasite to escape the human immune response. To explore this potential drug target, we have synthesized a small library of substrate analogues based on 1,4-disubstituted 1,2,3-triazole derivatives of galactose modified at either the C-1 or C-6 positions. This was achieved by coupling the appropriate azido-sugars with a panel of 23 structurally diverse terminal alkynes by using the copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction, giving a library of 46 derivatives in good to excellent yield and with complete regioselectivity. The sugar triazoles showed weak inhibition towards TcTS-catalyzed hydrolysis of 2'-(4-methylumbelliferyl)-alpha-d-N-acetylneuraminic acid in vitro (<40% inhibition at 1mM concentration); many of the compounds assessed proved to be acceptor substrates for the enzyme. Despite this modest inhibitory activity, in vitro trypanocidal activity assays against the trypomastigote form of T. cruzi Y strain revealed several compounds active in the low 100s of muM range. Further assessment of these compounds against cultured mouse spleen cells suggests a specific mode of anti-parasite action rather than a generic cytotoxic effect.
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Affiliation(s)
- Ivone Carvalho
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP, Av. Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil.
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17
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Campo VL, Carvalho I, Da Silva CHTP, Schenkman S, Hill L, Nepogodiev SA, Field RA. Cyclooligomerisation of azido-alkyne-functionalised sugars: synthesis of 1,6-linked cyclic pseudo-galactooligosaccharides and assessment of their sialylation by Trypanosoma cruzi trans-sialidase. Chem Sci 2010. [DOI: 10.1039/c0sc00301h] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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18
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Skrisovska L, Schubert M, Allain FHT. Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins. JOURNAL OF BIOMOLECULAR NMR 2010; 46:51-65. [PMID: 19690964 DOI: 10.1007/s10858-009-9362-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 07/17/2009] [Indexed: 05/19/2023]
Abstract
In the last 15 years substantial advances have been made to place isotope labels in native and glycosylated proteins for NMR studies and structure determination. Key developments include segmental isotope labeling using Native Chemical Ligation, Expressed Protein Ligation and Protein Trans-Splicing. These advances are pushing the size limit of NMR spectroscopy further making larger proteins accessible for this technique. It is just emerging that segmental isotope labeling can be used to define inter-domain interactions in NMR structure determination. Labeling of post-translational modified proteins like glycoproteins remains difficult but some promising developments were recently achieved. Key achievements are segmental and site-specific labeling schemes that improve resonance assignment and structure determination of the glycan moiety. We adjusted the focus of this perspective article to concentrate on the NMR applications based on recent developments rather than on labeling methods themselves to illustrate the considerable potential for biomolecular NMR.
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Affiliation(s)
- Lenka Skrisovska
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zurich, Switzerland
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19
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Abstract
Carbohydrates are the most abundant natural products. Besides their role in metabolism and as structural building blocks, they are fundamental constituents of every cell surface, where they are involved in vital cellular recognition processes. Carbohydrates are a relatively untapped source of new drugs and therefore offer exciting new therapeutic opportunities. Advances in the functional understanding of carbohydrate-protein interactions have enabled the development of a new class of small-molecule drugs, known as glycomimetics. These compounds mimic the bioactive function of carbohydrates and address the drawbacks of carbohydrate leads, namely their low activity and insufficient drug-like properties. Here, we examine examples of approved carbohydrate-derived drugs, discuss the potential of carbohydrate-binding proteins as new drug targets (focusing on the lectin families) and consider ways to overcome the challenges of developing this unique class of novel therapeutics.
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Affiliation(s)
- Beat Ernst
- Institute of Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, Basel, Switzerland.
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20
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Salisburg AM, Deline AL, Lexa KW, Shields GC, Kirschner KN. Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field. J Comput Chem 2009; 30:910-21. [DOI: 10.1002/jcc.21099] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Bhunia A, Schwardt O, Gäthje H, Gao GP, Kelm S, Benie AJ, Hricovini M, Peters T, Ernst B. Consistent bioactive conformation of the Neu5Acalpha(2-->3)Gal epitope upon lectin binding. Chembiochem 2009; 9:2941-5. [PMID: 18850605 DOI: 10.1002/cbic.200800458] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Anirban Bhunia
- Institute of Chemistry, University of Luebeck, Luebeck, Germany
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22
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Patel RY, Balaji PV. Characterization of the conformational and orientational dynamics of ganglioside GM1 in a dipalmitoylphosphatidylcholine bilayer by molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:1628-40. [PMID: 17408589 DOI: 10.1016/j.bbamem.2007.02.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 02/10/2007] [Accepted: 02/23/2007] [Indexed: 01/18/2023]
Abstract
The structure and dynamics of a single GM1 (Gal5-beta1,3-GalNAc4-beta1,4-(NeuAc3-alpha2,3)-Gal2-beta1,4-Glc1-beta1,1-Cer) embedded in a DPPC bilayer have been studied by MD simulations. Eleven simulations, each of 10 ns productive run, were performed with different initial conformations of GM1. Simulations of GM1-Os in water and of a DPPC bilayer were also performed to delineate the effects of the bilayer and GM1 on the conformational and orientational dynamics of each other. The conformation of the GM1 headgroup observed in the simulations is in agreement with those reported in literature; but the headgroup is restricted when embedded in the bilayer. NeuAc3 is the outermost saccharide towards the water phase. Glc1 and Gal2 prefer a parallel, and NeuAc3, GalNac4 and Gal5 prefer a perpendicular, orientation with respect to the bilayer normal. The overall characteristics of the bilayer are not affected by the presence of GM1; however, GM1 does influence the DPPC molecules in its immediate vicinity. The implications of these observations on the specific recognition and binding of GM1 embedded in a lipid bilayer by exogenous proteins as well as proteins embedded in lipids have been discussed.
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Affiliation(s)
- Ronak Y Patel
- School of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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23
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Kaltner H, Gabius HJ. Animal lectins: from initial description to elaborated structural and functional classification. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2003; 491:79-94. [PMID: 14533791 DOI: 10.1007/978-1-4615-1267-7_6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The genetic code connects the two biochemical dimensions of nucleic acids and proteins. Theoretical calculations on coding capacity reveal that oligosaccharides as hardware surpass peptides by more than seven orders of magnitude based on hexamer synthesis. Thus, the sugar code establishes the third dimension of biological information transfer. Using carbohydrate-binding proteins (lectins, enzymes and antibodies) the information content of such epitopes is decoded. Currently, five families of animal lectins are defined in structural terms. i.e. the C-type, I-type and P-type groups, the galectins and the pentraxins. They are involved in intra- and intercellular glycan routing using oligosaccharides as postal-code equivalents and acting as defense molecules homing in on foreign or aberrant glycosignatures, as crosslinking agent in biosignaling and as coordinator of transient or firm cell-cell/cell-matrix contacts. By delineating the driving forces toward complex formation, knowledge about the causes for specificity can be turned into design of custom-made high-affinity ligands for clinical application, e.g. in anti-adhesion therapy, drug targeting or diagnostic histopathology.
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Affiliation(s)
- H Kaltner
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Veterinärstr. 13, D-80539 München, Germany
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24
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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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25
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Sato KI, Akai S, Sakuma M, Kojima M, Suzuki KJ. Practical synthesis of [1-13C]- and [6-13C]-d-galactose. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)01098-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Watts J, Jiménez-Barbero J, Poveda A, Grindley TB. Control of disaccharide conformation by π-stacking. CAN J CHEM 2003. [DOI: 10.1139/v03-062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The conformations of a series of derivatives of the disaccharide α-L-fucopyranosyl-(1[Formula: see text]3)-2-acetamido-2-deoxy-D-glucopyranoside, part of the Lex determinant, were studied by molecular modelling using the MM3* forcefield and by 1H NMR spectroscopy. Unusually shielded O-benzyl protons were observed in the 1H NMR spectrum of phenyl 2,3,4-tri-O-benzyl-α-L-fucopyranosyl-(1[Formula: see text]3)-2-deoxy-2-phthalimido-1-thio-α-D-glucopyranoside and assigned to the 2-O-benzyl group. This observation was explained by a shift in the population of the conformational mixture present about the glycosidic linkage from the positive Ψ region in the unsubstituted disaccharide to the negative Ψ region induced by π-stacking between the phthalimide and the 2-O-benzyl phenyl ring. The experimental nuclear Overhauser enhancements confirm the accuracy of the calculations.Key words: disaccharide, conformation, π-stacking, Lex determinant, NOE measurements, MM3 calculations.
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27
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Sato KI, Akai S, Hiroshima T, Aoki H, Sakuma M, Suzuki KJ. Chemoenzymatic synthesis of [3,9-13C]-labeled NeuAc and KDN. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)00690-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Kaila N, Thomas BE. Design and synthesis of sialyl Lewis(x) mimics as E- and P-selectin inhibitors. Med Res Rev 2002; 22:566-601. [PMID: 12369089 DOI: 10.1002/med.10018] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The selectins are a family of cell-adhesion proteins that mediate the rolling of leukocytes on activated endothelial cells through the recognition of the carbohydrate epitope sialyl Lewis(x) (sLe(x)). Control of the leukocyte-endothelial cell adhesion process may prove useful in cases where excess recruitment of leukocytes can contribute to acute diseases such as stroke and reperfusion injury and chronic diseases such as psoriasis and rheumatoid arthritis. The development of molecules that block the interactions between sLe(x) and the selectins has become an active area of research. In this review, we will highlight the various approaches taken toward the development of sLe(x) mimetics as antagonists of E- and P-selectin, including the use of structural information about the selectins and their interactions with sLe(x) that have been revealed through the use of NMR, protein crystallography and molecular modeling.
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Affiliation(s)
- Neelu Kaila
- Department of Chemical Sciences and Biological Chemistry, WYETH, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, USA.
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29
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Live D, Silks LA, Schmidt J. 13C isotopic enrichment for nuclear magnetic resonance studies of carbohydrates and glycoconjugates. Methods Enzymol 2002; 338:305-19. [PMID: 11460555 DOI: 10.1016/s0076-6879(02)38226-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- D Live
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School and College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota 55455, USA
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30
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Haselhorst T, Weimar T, Peters T. Molecular recognition of sialyl Lewis(x) and related saccharides by two lectins. J Am Chem Soc 2001; 123:10705-14. [PMID: 11674003 DOI: 10.1021/ja011156h] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of sialyl Lewis(x), Lewis(x), and alpha-L-Fuc-(1-->3)-beta-D-GlcNAc with isolectin A from Lotus tetragonolobus (LTL-A), and with Aleuria aurantia agglutinin (AAA) was studied using NMR experiments and surface plasmon resonance. Both lectins are specific for fucose residues. From NMR experiments it was concluded that alpha-L-Fuc-(1-->3)-beta-D-GlcNAc and Lewis(x) bound to both lectins, whereas sialyl Lewis(x) only bound to AAA. Increased line broadening of 1H NMR signals of the carbohydrate ligands upon binding to AAA and LTL-A suggested that AAA bound to the ligands more tightly. Further comparison of line widths showed that for both lectins binding strengths decreased from alpha-L-Fuc-(1-->3)-beta-D-GlcNAc to Lewis(x) and were lowest for sialyl Lewis(x). Surface plasmon resonance measurements were then employed to yield accurate dissociation constants. TrNOESY, QUIET-trNOESY, and trROESY experiments delivered bioactive conformations of the carbohydrate ligands, and STD NMR experiments allowed a precise epitope mapping of the carbohydrates bound to the lectins. The bioactive conformation of Lewis(x) bound to LTL-A, or AAA revealed an unusual orientation of the fucose residue, with negative values for both dihedral angles, phi and psi, at the alpha(1-->3)-glycosidic linkage. A similar distortion of the fucose orientation was also observed for sialyl Lewis(x) bound to AAA. From STD NMR experiments it followed that only the L-fucose residues are in intimate contact with the protein. Presumably steric interactions are responsible for locking the sialic acid residue of sialyl Lewis(x) in one out of many orientations that are present in aqueous solution. The sialic acid residue of sialyl Lewis(x) bound to AAA adopts an orientation similar to that in the corresponding sialyl Lewis(x)/E-selectin complex.
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Affiliation(s)
- T Haselhorst
- Institut für Chemie, Medizinische Universität zu Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
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Kogelberg H, Feizi T. New structural insights into lectin-type proteins of the immune system. Curr Opin Struct Biol 2001; 11:635-43. [PMID: 11785767 DOI: 10.1016/s0959-440x(00)00259-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New structural data have emerged for the ligand-binding sites of C-type lectin domains and C-type lectin-like domains of receptors of the immune system. These include binding sites for oligosaccharide or polypeptide ligands, or both oligosaccharide and polypeptide ligands. The structural basis for the binding of a lectin domain of the beta-trefoil family to different sulfooligosaccharide sequences has been revealed. Lectin activity has been documented for a beta/alpha TIM barrel fold that does not have the chitinase activity of the prototype enzyme with this fold.
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Affiliation(s)
- H Kogelberg
- The Glycosciences Laboratory, Faculty of Medicine, Imperial College of Science, Technology and Medicine, Northwick Park Institute for Medical Research, Harrow, Middlesex, UK.
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Höög C, Landersjö C, Widmalm G. Oligosaccharides display both rigidity and high flexibility in water as determined by 13C NMR relaxation and 1H,1H NOE spectroscopy: evidence of anti-phi and anti-psi torsions in the same glycosidic linkage. Chemistry 2001; 7:3069-77. [PMID: 11495434 DOI: 10.1002/1521-3765(20010716)7:14<3069::aid-chem3069>3.0.co;2-a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The trisaccharide beta-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe has been investigated by molecular dynamics (MD) simulations and NMR experiments in water. 13C spin-lattice (T1) and spin-spin (T2) relaxation times, together with 1H,13C NOE data were measured at two magnetic field strengths (9.4 and 14.1 T) in a 277 K D2O solution. Relaxation data interpreted by means of the model-free formalism revealed a rigid (S2 approximately 0.9) oligosaccharide tumbling in solution. 1H,1H Cross-relaxation rates were determined at 600 MHz by 1D DPFGSE NOESY and T-ROESY experiments, which provided high quality data and subsequently proton-proton distances within the trisaccharide. The presence of anti conformers at both torsions of a glycosidic linkage is demonstrated for the first time. MD simulations were carried out to facilitate analysis of the NOE data. In total, 15 simulations-starting from five different conformational states--were performed, with production runs of up to 10 ns, resulting in 83 ns of oligosaccharide dynamics in water. anti Conformers were populated to different degrees in the simulations, especially at the phi2 torsion angle. By combining the results from the NOE experiments and the MD simulations, the anti conformers at the (1-->2)-linkage were quantified as 7% anti-phi2 and 2% anti-psi2, revealing a highly flexible trisaccharide in which large conformational changes occur. From the MD simulations, interresidue hydrogen bonding, from HO2" to O2 or O3, was significantly populated (approximately 40%) in both of the anti conformational states. The contentious issue over rigidity versus flexibility in oligosaccharides has thus been thoroughly examined, showing that the dynamics should be taken into account for a relevant description of the molecular system.
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Affiliation(s)
- C Höög
- Department of Organic Chemistry, Arrhenius Laboratory Stockholm University, Sweden
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Thoma G, Magnani JL, Patton JT, Ernst B, Jahnke W. Preorganization of the Bioactive Conformation of Sialyl LewisX Analogues Correlates with Their Affinity to E-Selectin. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010518)113:10<1995::aid-ange1995>3.0.co;2-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Thoma G, Magnani JL, Patton JT, Ernst B, Jahnke W. Preorganization of the Bioactive Conformation of Sialyl LewisX Analogues Correlates with Their Affinity to E-Selectin. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3773(20010518)40:10<1941::aid-anie1941>3.0.co;2-t] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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36
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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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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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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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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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Jiménez-Barbero J, Asensio JL, Cañada FJ, Poveda A. Free and protein-bound carbohydrate structures. Curr Opin Struct Biol 1999; 9:549-55. [PMID: 10508763 DOI: 10.1016/s0959-440x(99)00004-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Several areas of research in the study of the structure and dynamics of free and protein-bound carbohydrates have experienced considerable advances during the past year. These include the application of state-of-the-art NMR techniques using (13)C-labeled sugars to obtain conformational information, the full structural characterization of several saccharides that either form part of glycoproteins or form noncovalent complexes, both in solution and in the solid state, the description of several enzyme-carbohydrate complexes at the atomic level and last, but not least, the development and analysis of calculation protocols to predict the dynamical and conformational behavior of oligosaccharides.
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Affiliation(s)
- J Jiménez-Barbero
- Dept Química Orgánica Biológica, Instituto Química Orgánica, CSIC Juan de la Cierva 3, 28006, Madrid, Spain.
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