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Hayes JA, Eccles KS, Coles SJ, Lawrence SE, Moynihan HA. Supramolecular stacking motifs in the solid state of amide and triazole derivatives of cellobiose. Carbohydr Res 2014; 388:67-72. [PMID: 24631669 DOI: 10.1016/j.carres.2014.02.011] [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: 12/12/2013] [Revised: 01/29/2014] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
Abstract
1-Acetamido-1-deoxy-(4-O-β-d-glucopyranosyl-β-d-glucopyranose) (5) and 1-deoxy-1-(4-phenyl-1,2,3-triazolyl)-(4-O-β-d-glucopyranosyl-β-d-glucopyranose) (7) were synthesised from 1-azido-1-deoxy-(4-O-β-d-glucopyranosyl-β-d-glucopyranose) (2) and crystallised as dihydrates. Crystal structural analysis of 5·2H2O displayed an acetamide C(4) chain and stacked cellobiose residues. The structure of 7·2H2O featured π-π stacking and stacking of the cellobiose residues.
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Affiliation(s)
- John A Hayes
- Department of Chemistry / Analytical and Biological Chemistry Research Facility / Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, Cork, Ireland
| | - Kevin S Eccles
- Department of Chemistry / Analytical and Biological Chemistry Research Facility / Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, Cork, Ireland
| | - Simon J Coles
- UK National Crystallographic Service, Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Simon E Lawrence
- Department of Chemistry / Analytical and Biological Chemistry Research Facility / Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, Cork, Ireland
| | - Humphrey A Moynihan
- Department of Chemistry / Analytical and Biological Chemistry Research Facility / Synthesis and Solid State Pharmaceutical Centre, University College Cork, College Road, Cork, Ireland.
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2
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Examination of the influence of C5-hydroxymethyl group and configurations of hydroxyl groups at C2, C3, and C4 stereocentres on the N-glycosidic torsion: synthesis and X-ray crystallographic investigation of N-(d-ribopyranosyl)alkanamides as N-glycoprotein linkage region analogs. Carbohydr Res 2014; 384:37-45. [DOI: 10.1016/j.carres.2013.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/03/2013] [Accepted: 11/11/2013] [Indexed: 11/23/2022]
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3
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Srivastava A, Varghese B, Loganathan D. Exploring the Effect of Bioisosteric Replacement of Carboxamide by a Sulfonamide Moiety on N-Glycosidic Torsions and Molecular Assembly: Synthesis and X-ray Crystallographic Investigation of N-(β-D-Glycosyl)sulfonamides as N-Glycoprotein Linkage Region An. Chemistry 2013; 19:17720-32. [DOI: 10.1002/chem.201302018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Indexed: 11/09/2022]
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4
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Mathiselvam M, Ramkumar V, Loganathan D, Pérez S. Effect of distal sugars and interglycosidic linkage on the N-glycoprotein linkage region conformation: synthesis and X-ray crystallographic investigation of β-1-N-alkanamide derivatives of cellobiose and maltose as disaccharide analogs of the conserved chitobiosylasparagine linkage. Glycoconj J 2013; 31:71-87. [PMID: 24150739 DOI: 10.1007/s10719-013-9504-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 10/07/2013] [Accepted: 10/07/2013] [Indexed: 11/27/2022]
Abstract
The linkage region constituents, 2-deoxy-2-acetamido-β-D-glucopyranose (GlcNAc) and L-asparagine (Asn) are conserved in the N-glycoproteins of all eukaryotes. Elucidation of the structure and conformation of the linkage region of glycoproteins is important to understand the presentation and dynamics of the carbohydrate chain at the protein/cell surface. Earlier crystallographic studies using monosaccharide models and analogs of N-glycoprotein linkage region have shown that the N-glycosidic torsion, ϕN, is more influenced by the structural variation in the sugar part than that of the aglycon moiety. To access the influence of distal sugar as well as interglycosidic linkage (α or β) on the N-glycosidic torsion angles, cellobiosyl and maltosyl alkanamides have been synthesized and structural features of seven of these analogs have been characterized by X-ray crystallography. Comparative analysis of the seven disaccharide analogs with the reported monosaccharide analogs showed that the ϕN value of cellobiosyl analogs deviate ~9° with respect to GlcβNHAc. In the case of maltosyl analogs, deviation is more than 18°. These deviations indicate that the N-glycosidic torsion is influenced by addition of distal sugar as well as with respect to inter glycosidic linkage (α or β); it is less influenced by changes occurring at the aglycon. The χ₂ value of alkanamide derived from glucose, cellobiose and maltose exhibit a large range of variations (from 1.6° to -109.9°). This large span of χ₂ value suggests the greater degree of rotational freedom around C1'-C2' bond which is restricted in GlcNAc alkanamides. The present finding explicitly proved the importance of molecular architecture in the N-glycoproteins linkage region to maintain the linearity, planarity and rigidity. These factors are necessary for N-glycan to serve role in inter- as well as intramolecular carbohydrate-protein interactions.
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Affiliation(s)
- Manoharan Mathiselvam
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India,
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5
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Srivastava A, Varghese B, Loganathan D. Synthesis and X-ray crystallographic investigation of N-(α-D-arabinopyranosyl)alkanamides as N-glycoprotein linkage region analogs. Carbohydr Res 2013; 380:92-100. [PMID: 23981855 DOI: 10.1016/j.carres.2013.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/28/2013] [Accepted: 07/29/2013] [Indexed: 01/10/2023]
Abstract
N-Glycoprotein linkage region constituents namely 2-deoxy-2-acetamido-β-D-glucopyranose (GlcNAc) and asparagine (Asn) are conserved among all eukaryotes. Earlier crystallographic studies on the linkage region conformation revealed that among all the models and analogs of the N-glycoprotein linkage region, XylβNHAc showed maximum deviation in the ϕN value as compared to the value reported for the model compound, GlcNAcβNHAc. In order to understand the effect of another pentopyranose, viz., arabinose, on the N-glycosidic torsion angles and molecular assembly, three arabinopyranosyl alkanamides were synthesized and their X-ray crystal structures elucidated. A comparative analysis of the N-glycosidic torsion, ϕN of the three analogs revealed the greater rotational freedom around the C1-N1 bond as compared to the GlcNAc derivatives. Molecular assembly of propionamido and chloroacetamido derivatives is characterized by the presence of anti-parallel bilayers of the molecules. This unique molecular assembly is hitherto unknown in all other models and analogs of N-glycoprotein linkage region. This study reveals that N-glycosidic torsions are influenced by the glycan as well as molecular packing.
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Affiliation(s)
- Amrita Srivastava
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
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6
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Mathiselvam M, Loganathan D, Varghese B. Synthesis of N-(β-D-glycuronopyranosyl)alkanamides and 1-(β-D-glycuronopyranosyl)-4-phenyl-[1,2,3]-triazoles as N-glycoprotein linkage region analogs: examination of the effect of C5 substituent on the N-glycosidic torsion (ΦN) based on X-ray crystallography. Carbohydr Res 2013; 380:1-8. [PMID: 23896157 DOI: 10.1016/j.carres.2013.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/20/2013] [Accepted: 06/26/2013] [Indexed: 11/30/2022]
Abstract
The torsion angle around the N-glycoprotein linkage region (GlcNAc-Asn) is an important factor for presenting sugar on the cell surface which is crucial for many biological processes. Earlier studies using model and analogs showed that this important torsion angle is greatly influenced by substitutions in the sugar part. In the present work, uronic acid alkanamides and triazole derivatives have been designed and synthesized as newer analogs of N-glycoprotein linkage region to understand the influence of the carboxylic group on linkage region torsion as well as on molecular packing. Crystal structure of N-(β-D-galacturonopyranosyl)acetamide is solved with the space group of P22121. Comparison of the torsion angle and molecular packing of this compound with N-(β-D-galactopyranosyl)acetamide showed that changing the C6-hydoxymethyl group to the carboxylic acid group has minimum influence on the N-glycosidic torsion angle, ΦN and significant influence on the molecular packing.
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Affiliation(s)
- Manoharan Mathiselvam
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
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Topin J, Arnaud J, Sarkar A, Audfray A, Gillon E, Perez S, Jamet H, Varrot A, Imberty A, Thomas A. Deciphering the glycan preference of bacterial lectins by glycan array and molecular docking with validation by microcalorimetry and crystallography. PLoS One 2013; 8:e71149. [PMID: 23976992 PMCID: PMC3747263 DOI: 10.1371/journal.pone.0071149] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/26/2013] [Indexed: 11/18/2022] Open
Abstract
Recent advances in glycobiology revealed the essential role of lectins for deciphering the glycocode by specific recognition of carbohydrates. Integrated multiscale approaches are needed for characterizing lectin specificity: combining on one hand high-throughput analysis by glycan array experiments and systematic molecular docking of oligosaccharide libraries and on the other hand detailed analysis of the lectin/oligosaccharide interaction by x-ray crystallography, microcalorimetry and free energy calculations. The lectins LecB from Pseudomonas aeruginosa and BambL from Burkholderia ambifaria are part of the virulence factors used by the pathogenic bacteria to invade the targeted host. These two lectins are not related but both recognize fucosylated oligosaccharides such as the histo-blood group oligosaccharides of the ABH(O) and Lewis epitopes. The specificities were characterized using semi-quantitative data from glycan array and analyzed by molecular docking with the Glide software. Reliable prediction of protein/oligosaccharide structures could be obtained as validated by existing crystal structures of complexes. Additionally, the crystal structure of BambL/Lewis x was determined at 1.6 Å resolution, which confirms that Lewis x has to adopt a high-energy conformation so as to bind to this lectin. Free energies of binding were calculated using a procedure combining the Glide docking protocol followed by free energy rescoring with the Prime/Molecular Mechanics Generalized Born Surface Area (MM-GBSA) method. The calculated data were in reasonable agreement with experimental free energies of binding obtained by titration microcalorimetry. The established predictive protocol is proposed to rationalize large sets of data such as glycan arrays and to help in lead discovery projects based on such high throughput technology.
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Affiliation(s)
- Jeremie Topin
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
- Département de Chimie Moléculaire, UMR- Centre national de la recherche scientifique 5250 & ICMG FR 2607, Université Joseph Fourier, BP 53, 38041 Grenoble, France
| | - Julie Arnaud
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Anita Sarkar
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Aymeric Audfray
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Emilie Gillon
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Serge Perez
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Helene Jamet
- Département de Chimie Moléculaire, UMR- Centre national de la recherche scientifique 5250 & ICMG FR 2607, Université Joseph Fourier, BP 53, 38041 Grenoble, France
| | - Annabelle Varrot
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
| | - Anne Imberty
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
- * E-mail:
| | - Aline Thomas
- CERMAV- Centre national de la recherche scientifique UPR5301 (affiliated to Université Joseph Fourier and ICMG), BP53, 38041 Grenoble, France
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Cioci G, Srivastava A, Loganathan D, Mason SA, Pérez S, Imberty A. Low-Temperature Neutron Diffraction Structures of N-Glycoprotein Linkage Models and Analogues: Structure Refinement and Trifurcated Hydrogen Bonds. J Am Chem Soc 2011; 133:10042-5. [DOI: 10.1021/ja203239j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gianluca Cioci
- European Synchrotron Radiation Facility, BP220 Grenoble, France
| | | | | | | | - Serge Pérez
- European Synchrotron Radiation Facility, BP220 Grenoble, France
| | - Anne Imberty
- CERMAV-CNRS (affiliated with Université Joseph Fourier and ICMG), BP53 Grenoble, France
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