1
|
Homayonia S, Ling CC. Epoxide-Mediated Trans-Thioglycosylation and Application to the Synthesis of Oligosaccharides Related to the Capsular Polysaccharides of C. jejuni HS:4. Chemistry 2024; 30:e202303753. [PMID: 38215247 DOI: 10.1002/chem.202303753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 01/14/2024]
Abstract
The enzyme-resistant thioglycosides are highly valuable immunogens because of their enhanced metabolic stability. We report the first synthesis of a family of thiooligosaccharides related to the capsular polysaccharides (CPS) of Campylobacter jejuni HS:4 for potential use in conjugate vaccines. The native CPS structures of the pathogen consist of a challenging repeating disaccharide formed with β(1→4)-linked 6-deoxy-β-D-ido-heptopyranoside and N-acetyl-D-glucosamine; the rare 6-deoxy-ido-heptopyranosyl backbone and β-anomeric configuration of the former monosaccharide makes the synthesis of this family of antigens very challenging. So far, no synthesis of the thioanalogs of the CPS antigens have been reported. The unprecedented synthesis presented in this work is built on an elegant approach by using β-glycosylthiolate as a glycosyl donor to open the 2,3-epoxide functionality of pre-designed 6-deoxy-β-D-talo-heptopyranosides. Our results illustrated that this key trans-thioglycosylation can be designed in a modular and regio and stereo-selective manner. Built on the success of this novel approach, we succeeded the synthesis of a family of thiooligosaccharides including a thiohexasaccharide which is considered to be the desired antigen length and complexity for immunizations. We also report the first direct conversion of base-stable but acid-labile 2-trimethylsilylethyl glycosides to glycosyl-1-thioacetates in a one-pot manner.
Collapse
Affiliation(s)
- Saba Homayonia
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Chang-Chun Ling
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| |
Collapse
|
2
|
Feng G, Wang S, Lv J, Luo T, Wu Y, Dong H. Improved Synthesis of 1‐Glycosyl Thioacetates and Its Application in the Synthesis of Thioglucoside Gliflozin Analogues. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Guang‐Jing Feng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, School of Chemistry & Chemical Engineering Huazhong University of Science & Technology Luoyu Road 1037 Wuhan 430074 PR China
| | - Shuang‐Shuang Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, School of Chemistry & Chemical Engineering Huazhong University of Science & Technology Luoyu Road 1037 Wuhan 430074 PR China
| | - Jian Lv
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, School of Chemistry & Chemical Engineering Huazhong University of Science & Technology Luoyu Road 1037 Wuhan 430074 PR China
| | - Tao Luo
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, School of Chemistry & Chemical Engineering Huazhong University of Science & Technology Luoyu Road 1037 Wuhan 430074 PR China
| | - Yuzhou Wu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, School of Chemistry & Chemical Engineering Huazhong University of Science & Technology Luoyu Road 1037 Wuhan 430074 PR China
| | - Hai Dong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education, School of Chemistry & Chemical Engineering Huazhong University of Science & Technology Luoyu Road 1037 Wuhan 430074 PR China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Huazhong University of Science & Technology Luoyu Road 1037 Wuhan 430074 PR China
| |
Collapse
|
3
|
Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
Collapse
Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
| |
Collapse
|
4
|
Norberg O, Wu B, Thota N, Ge JT, Fauquet G, Saur AK, Aastrup T, Dong H, Yan M, Ramström O. Synthesis and binding affinity analysis of α1-2- and α1-6- O / S -linked dimannosides for the elucidation of sulfur in glycosidic bonds using quartz crystal microbalance sensors. Carbohydr Res 2017; 452:35-42. [DOI: 10.1016/j.carres.2017.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/26/2017] [Accepted: 09/30/2017] [Indexed: 01/05/2023]
|
5
|
Labonte JW, Adolf-Bryfogle J, Schief WR, Gray JJ. Residue-centric modeling and design of saccharide and glycoconjugate structures. J Comput Chem 2016; 38:276-287. [PMID: 27900782 DOI: 10.1002/jcc.24679] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/23/2016] [Accepted: 11/06/2016] [Indexed: 01/18/2023]
Abstract
The RosettaCarbohydrate framework is a new tool for modeling a wide variety of saccharide and glycoconjugate structures. This report describes the development of the framework and highlights its applications. The framework integrates with established protocols within the Rosetta modeling and design suite, and it handles the vast complexity and variety of carbohydrate molecules, including branching and sugar modifications. To address challenges of sampling and scoring, RosettaCarbohydrate can sample glycosidic bonds, side-chain conformations, and ring forms, and it utilizes a glycan-specific term within its scoring function. Rosetta can work with standard PDB, GLYCAM, and GlycoWorkbench (.gws) file formats. Saccharide residue-specific chemical information is stored internally, permitting glycoengineering and design. Carbohydrate-specific applications described herein include virtual glycosylation, loop-modeling of carbohydrates, and docking of glyco-ligands to antibodies. Benchmarking data are presented and compared to other studies, demonstrating Rosetta's ability to predict glyco-ligand binding. The framework expands the tools available to glycoscientists and engineers. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Jason W Labonte
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland, 21218
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, 92037
| | - William R Schief
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, 92037.,The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, 02139
| | - Jeffrey J Gray
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland, 21218
| |
Collapse
|
6
|
Vidal P, Jiménez-Barbero J, Espinosa JF. Conformational flexibility around the Gal-β-(1 → 3)-Glc linkage: Experimental evidence for the existence of the anti-ψ conformation in aqueous solution. Carbohydr Res 2016; 433:36-40. [PMID: 27434833 DOI: 10.1016/j.carres.2016.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/24/2016] [Accepted: 06/26/2016] [Indexed: 10/21/2022]
Abstract
NOE-based analysis of the disaccharide β-Gal-(1 → 3)-β-Glc-OMe (1), especially a diagnostic Gal1-Glc4 NOE detected in a HSQC-NOESY spectrum, reveals the existence of the anti-ψ conformer in aqueous solution in addition to the major syn conformer. This result provides experimental proof of conformational flexibility around the aglyconic bond of β-(1 → 3) disaccharides, in contrast to previous studies that suggested that the flexibility around this linkage was restricted to the syn conformational region.
Collapse
Affiliation(s)
- Paloma Vidal
- Discovery Chemistry Research and Technologies, Centro de Investigación Lilly, Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | | | - Juan F Espinosa
- Discovery Chemistry Research and Technologies, Centro de Investigación Lilly, Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain.
| |
Collapse
|
7
|
Synthesis and binding affinity analysis of positional thiol analogs of mannopyranose for the elucidation of sulfur in different position. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.04.060] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
8
|
|
9
|
Sánchez‐Fernández EM, Rísquez‐Cuadro R, Ortiz Mellet C, García Fernández JM, Nieto PM, Angulo J. sp
2
‐Iminosugar
O
‐,
S
‐, and
N
‐Glycosides as Conformational Mimics of α‐Linked Disaccharides; Implications for Glycosidase Inhibition. Chemistry 2012; 18:8527-39. [DOI: 10.1002/chem.201200279] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 02/28/2012] [Indexed: 12/29/2022]
Affiliation(s)
- Elena M. Sánchez‐Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| | - Rocío Rísquez‐Cuadro
- Departmento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/Prof. García González 1, 41012, Sevilla (Spain), Fax: (+34) 954624960
| | - Carmen Ortiz Mellet
- Departmento de Química Orgánica, Facultad de Química, Universidad de Sevilla, C/Prof. García González 1, 41012, Sevilla (Spain), Fax: (+34) 954624960
| | - José M. García Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| | - Pedro M. Nieto
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| | - Jesús Angulo
- Instituto de Investigaciones Químicas (IIQ), CSIC–Universidad de Sevilla, Avda. Americo Vespucio 49, 41092, Sevilla (Spain), Fax: (+34) 954460565
| |
Collapse
|
10
|
Fettke A, Kramer M, Kleinpeter E. Lectin-bound conformations and non-covalent interactions of glycomimetic analogs of thiochitobiose. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
11
|
Fettke A, Peikow D, Peter MG, Kleinpeter E. Synthesis and conformational analysis of glycomimetic analogs of thiochitobiose. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.03.067] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
DeMatteo MP, Mei S, Fenton R, Morton M, Baldisseri DM, Hadad CM, Peczuh MW. Conformational analysis of methyl 5-O-methyl septanosides: effect of glycosylation on conformer populations. Carbohydr Res 2006; 341:2927-45. [PMID: 17056019 DOI: 10.1016/j.carres.2006.09.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 09/15/2006] [Accepted: 09/28/2006] [Indexed: 11/26/2022]
Abstract
Methyl 5-O-methyl-alpha-d-glycero-d-idoseptanoside (3) and methyl 5-O-methyl-beta-d-glycero-d-guloseptanoside (4) were investigated as (1-->5)-linked di-/oligoseptanoside mimetics. Here we report the synthesis of 3 and 4 and describe their preferred solution conformations through a combination of ab initio/DFT calculations and (1)H (3)J(H,H) NMR coupling constant analysis. The conformations of 3 and 4 observed in this study are discussed in comparison to those of the parent (C5 hydroxy) compounds 1 and 2. The results indicate that methyl 5-O-methyl-alpha-septanoside 3 is relatively rigid and adopts the same (3,4)TC(5,6) conformation as 1. Methyl 5-O-methyl-beta-septanoside 4 is somewhat less rigid than its parent septanoside (2). In addition to the (6,O)TC(4,5) conformation adopted by 2, beta-septanoside 4 also populates the adjacent (3,4)TC(5,6) conformation. Glycosylation at C5 on beta-septanoside 4 therefore increases its overall flexibility and allows access to alternative ring conformations.
Collapse
Affiliation(s)
- Matthew P DeMatteo
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | | | | | | | | | | | | |
Collapse
|
13
|
Rich JR, Wakarchuk WW, Bundle DR. Chemical and Chemoenzymatic Synthesis of S-Linked Ganglioside Analogues and Their Protein Conjugates for Use as Immunogens. Chemistry 2006; 12:845-58. [PMID: 16196067 DOI: 10.1002/chem.200500518] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Analogues of the tumor-associated gangliosides GM(3) and GM(2) containing terminal S-linked neuraminic acid residues and an amino terminated, truncated ceramide homologue have been synthesized and conjugated to a protein. The synthesis involved coupling of a S-linked sialyl alpha(2-->3) galactose disaccharide with a glucosyl sphingosine analogue, followed by elaboration and deprotection to give amino-terminated glycosyl ceramide 1. Glycosyltransferase-catalyzed extension of the trisaccharide 1 provided access to the modified GM(2) tetrasaccharide 2 or sulphur-containing GD(3) analogue 30. Owing to their potentially enhanced resistance to endogenous exo-glycoside hydrolases and their inherent non-self character, carbohydrate antigens containing non-reducing terminal thioglycosidic linkages may be more immunogenic than O-linked antigens and may stimulate the production of antibodies capable of recognizing naturally occurring oligosaccharides. Our initial results suggest that in fact these antigens are viable immunogens and furthermore, that immune sera cross reacts with O-gangliosides in the context of a heterologous glycoprotein conjugate.
Collapse
Affiliation(s)
- Jamie R Rich
- Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Canada
| | | | | |
Collapse
|
14
|
Nitz M, Ling CC, Otter A, Cutler JE, Bundle DR. The unique solution structure and immunochemistry of the Candida albicans beta -1,2-mannopyranan cell wall antigens. J Biol Chem 2002; 277:3440-6. [PMID: 11700318 DOI: 10.1074/jbc.m109274200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Synthetic oligomers of the antigenic Candida albicans (1-->2)-beta-mannopyranans adopt a compact solution conformation that leads to numerous inter-residue nuclear Overhauser effects, including unprecedented nuclear Overhauser effects between n and n + 3 residues. In excellent agreement with experimentally determined distances, unrestrained molecular dynamics point to a single family of conformations that approximate a compact helical motif with a three-residue repeat for this unique homopolymer. When the synthetic di- to hexasaccharides were employed as inhibitors of monoclonal antibodies, which protect mice against a lethal dose of the yeast pathogen, a novel pattern of inhibitor activity was observed. Instead of the paradigm first reported by Kabat (Kabat, E. A. (1962) Fed. Proc. 21, 694-701; Kabat, E. A. (1966) J. Immunol. 97, 1-11), wherein homo-oligosaccharides exhibit increasing inhibitory activity with increasing size, here the maximum activity is reached for di- and trisaccharides and diminishes significantly for tetra-, penta-, and hexasaccharides. These immunochemical data correlate with the ordered conformation of the beta-1,2-linked mannopyranan and imply that a uniquely small antigenic determinant has potential as a component of synthetic conjugate vaccines against Candida albicans.
Collapse
Affiliation(s)
- Mark Nitz
- Department of Chemistry, the University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | | | | | | | | |
Collapse
|
15
|
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.
Collapse
Affiliation(s)
- C Höög
- Department of Organic Chemistry, Arrhenius Laboratory Stockholm University, Sweden
| | | | | |
Collapse
|
16
|
Wacowich-Sgarbi SA, Ling CC, Otter A, Bundle DR. A tethered disaccharide trapped as its anti conformer calibrates the Karplus relationship for 3J(C,H) coupling constants. J Am Chem Soc 2001; 123:4362-3. [PMID: 11457214 DOI: 10.1021/ja005901m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S A Wacowich-Sgarbi
- Department of Chemistry, The University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | | | | | | |
Collapse
|
17
|
Montero E, García-Herrero A, Asensio J, Hirai K, Ogawa S, Santoyo-González F, Cañada F, Jiménez-Barbero J. The Conformational Behaviour of Non-Hydrolizable Lactose Analogues: The Thioglycoside, Carbaglycoside, and Carba-Iminoglycoside Cases. European J Org Chem 2000. [DOI: 10.1002/(sici)1099-0690(200005)2000:10<1945::aid-ejoc1945>3.0.co;2-g] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
18
|
Weimar T, Stoffer B, Svensson B, Pinto BM. Complexes of glucoamylase with maltoside heteroanalogues: bound ligand conformations by use of transferred NOE experiments and molecular modeling. Biochemistry 2000; 39:300-6. [PMID: 10630989 DOI: 10.1021/bi991645i] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transferred nuclear Overhauser effect (trNOE) experiments have been performed to investigate the conformations of the competitive inhibitors, methyl 5'-thio-4-N-alpha-maltoside 3a and methyl 5'-thio-4-S-alpha-maltoside 4 when bound to the catalytic subunit of the enzyme glucoamylase. These NMR data suggest that, although each of the free ligands populates two conformational families, both heteroanalogues are bound by the enzyme in conformations in the area of the global energy minimum. These conformations have been used as initial points for docking into the active site of the enzyme taken from a X-ray crystal structure of the related glucoamylase-D-gluco-dihydroacarbose 2 complex. Minimization of the resulting complexes has yielded structures for the bound complexes. Corroboration of the structures is provided by fast T(1)(rho)-relaxation effects for certain ligand protons as a result of close contacts with protons in the enzyme active site. The results auger well for the combined use of transferred NOE spectroscopy and molecular modeling based on X-ray crystal structures of complexes of suitable congeners for the rapid analysis of ligand-receptor interactions.
Collapse
Affiliation(s)
- T Weimar
- Institut für Chemie, Medizinische Universität zu Lübeck, Ratzeburger Allee 160, Lübeck 23538, Germany.
| | | | | | | |
Collapse
|
19
|
Geyer A, Müller M, Schmidt RR. A Glycosidic Linkage Constrained to the “Anti” Conformation. J Am Chem Soc 1999. [DOI: 10.1021/ja990294s] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Armin Geyer
- Fakultät für Chemie, Universität Konstanz D-78457 Konstanz, Germany
| | - Matthias Müller
- Fakultät für Chemie, Universität Konstanz D-78457 Konstanz, Germany
| | | |
Collapse
|
20
|
Conformational analysis of maltoside heteroanalogues using high-quality NOE data and molecular mechanics calculations. Flexibility as a function of the interglycosidic chalcogen atom. Carbohydr Res 1999. [DOI: 10.1016/s0008-6215(99)00011-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
21
|
Milton MJ, Bundle DR. Observation of the Anti Conformation of a Glycosidic Linkage in an Antibody-Bound Oligosaccharide. J Am Chem Soc 1998. [DOI: 10.1021/ja982263n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark J. Milton
- Department of Chemistry, University of Alberta Edmonton, Alberta T6G 2G2 Canada
| | - David R. Bundle
- Department of Chemistry, University of Alberta Edmonton, Alberta T6G 2G2 Canada
| |
Collapse
|
22
|
Schmidt AK, Cottaz S, Driguez H, Schulz GE. Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin. Biochemistry 1998; 37:5909-15. [PMID: 9558324 DOI: 10.1021/bi9729918] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Crystals of the inactive mutant Glu257-->Ala of cyclodextrin glycosyltransferase were soaked with the cyclodextrin (CD) derivative S-(alpha-D-glucopyranosyl)-6-thio-beta-CD. The structural analysis showed its beta-CD moiety with no density indication for the exocyclic glucosyl unit. For steric reasons, however, the position of this unit is restricted to be at only two of the seven glucosyl groups of beta-CD. The analysis indicated that the enzyme can cyclize branched alpha-glucans. The ligated beta-CD moiety revealed how the enzyme binds its predominant cyclic product. The conformation of the ligated beta-CD was intermediate between the more symmetrical conformation in beta-CD dodecahydrate crystals and the conformation of a bound linear alpha-glucan chain. Its scissile bond was displaced by 2.8 A from the position in linear alpha-glucans. Accordingly, the complex represents the situation after the cyclization reaction but before diffusion into the solvent, where a more symmetrical conformation is assumed, or the equivalent state in the reverse reaction. Furthermore, a unifying nomenclature for oligosaccharide-binding subsites in proteins is proposed.
Collapse
Affiliation(s)
- A K Schmidt
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany
| | | | | | | |
Collapse
|
23
|
Aguilera B, Jiménez-Barbero J, Fernández-Mayoralas A. Conformational differences between Fuc(alpha 1-3) GlcNAc and its thioglycoside analogue. Carbohydr Res 1998; 308:19-27. [PMID: 9675354 DOI: 10.1016/s0008-6215(98)00066-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
NOE measurements and molecular mechanics calculations have been performed to study the conformational behaviour of Fuc(alpha 1-3)GlcNAc and its thioglycoside analogue in solution. Experimental data show that, in contrast with the natural O-disaccharide, which is basically monoconformational, the S-analogue shows two conformational families, namely syn and anti.
Collapse
Affiliation(s)
- B Aguilera
- Departmento de Química Orgánica Biológica, Instituto de Química Orgánica, CSIC, Madrid, Spain
| | | | | |
Collapse
|
24
|
Milton MJ, Harris R, Probert MA, Field RA, Homans SW. New conformational constraints in isotopically (13C) enriched oligosaccharides. Glycobiology 1998; 8:147-53. [PMID: 9451024 DOI: 10.1093/glycob/8.2.147] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Multidimensional heteronuclear NMR studies have been applied to the resonance assignment and conformational analysis of 13C-enriched Neu5Acalpha2-3Galbeta1-4Glc. It is demonstrated that three-dimensional ROESY-HSQC experiments provide through-space distance restraints which cannot be observed with conventional homonuclear 1H techniques due to resonance overlap. In particular, connectivities demonstrating the existence of the "anti" conformation about the Galbeta1-4Glc glycosidic linkage are unambiguously observed. It is shown that 13C isotopic enrichment of the trisaccharide at a level >95% enables straightforward measurement of trans-glycosidic 1H-13C and 13C-13C coupling constants and a Karplus-type relation is derived for the latter. In total 15 conformational restraints were obtained for the trisaccharide in aqueous solution, all of which were in excellent agreement with theoretical parameters computed from a 5 ns molecular dynamics simulation of the glycan.
Collapse
Affiliation(s)
- M J Milton
- Centre for Biomolecular Sciences, University of St. Andrews, Fife, United Kingdom
| | | | | | | | | |
Collapse
|
25
|
Montero E, Vallmitjana M, Pérez-Pons JA, Querol E, Jiménez-Barbero J, Cañada FJ. NMR studies of the conformation of thiocellobiose bound to a beta-glucosidase from Streptomyces sp. FEBS Lett 1998; 421:243-8. [PMID: 9468315 DOI: 10.1016/s0014-5793(97)01571-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The conformation of 4-thiocellobiose bound to beta-glucosidase from Streptomyces sp. has been studied by 1H-NMR transferred nuclear Overhauser effect spectroscopy (TR-NOE). Thiocellobiose behaves as an inhibitor of this glucosidase when cellobiose is used as substrate. NOE measurements and molecular mechanics calculations have also been performed to estimate the probability distribution of conformers of thiocellobiose when free in solution. Experimental data show that, in contrast with the natural O-analogue, thiocellobiose presents three conformational families in the free state, namely syn, anti-psi and anti-phi, whilst only one of them (syn) is recognized by the enzyme.
Collapse
Affiliation(s)
- E Montero
- Instituto de Química Orgánica, CSIC, Madrid, Spain
| | | | | | | | | | | |
Collapse
|
26
|
Qian M, Spinelli S, Driguez H, Payan F. Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution. Protein Sci 1997; 6:2285-96. [PMID: 9385631 PMCID: PMC2143580 DOI: 10.1002/pro.5560061102] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The structure of pig pancreatic alpha-amylase in complex with carbohydrate inhibitor and proteinaceous inhibitors is known but the successive events occurring at the catalytic center still remain to be elucidated. The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC 3.2.1.1.) soaked with an enzyme-resistant substrate analogue, methyl 4,4'-dithio-alpha-maltotrioside, showed electron density corresponding to the binding of substrate analogue molecules at the active site and at the "second binding site." The electron density observed at the active site was interpreted in terms of overlapping networks of oligosaccharides, which show binding of substrate analogue molecules at subsites prior to and subsequent to the cleavage site. A weaker patch of density observed at subsite -1 (using a nomenclature where the site of hydrolysis is taken to be between subsites -1 and +1) was modeled with water molecules. Conformational changes take place upon substrate analogue binding and the "flexible loop" that constitutes the surface edge of the active site is observed in a specific conformation. This confirms that this loop plays an important role in the recognition and binding of the ligand. The crystal structure was refined at 2.03 A resolution, to an R-factor of 16.0 (Rfree, 18.5).
Collapse
Affiliation(s)
- M Qian
- AFMB-IBSM-CNRS, Marseille, France
| | | | | | | |
Collapse
|
27
|
Thiooligosaccharides in glycobiology. GLYCOSCIENCE SYNTHESIS OF SUBSTRATE ANALOGS AND MIMETICS 1997. [DOI: 10.1007/bfb0119254] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
28
|
Jezowska-Bojczuk M, Bal W, Kasprzak KS. Copper(II) interactions with an experimental antiviral agent, I-deoxynojirimycin, and oxygen activation by resulting complexes. J Inorg Biochem 1996; 64:231-46. [PMID: 8916412 DOI: 10.1016/s0162-0134(96)00051-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
1-deoxynojirimycin (DNJ), a 5-imino analog of 1-deoxyglucose, is a potent inhibitor of alpha-glucosidase 1. DNJ and its derivatives have been considered as experimental drugs against human HIV-1 and hepatitis B viruses. Since amino and imino ligands have a high affinity for copper, it seems possible that biological activity of DNJ may be, at least in part, modulated by tissue copper. To test this possibility, potentiometric and spectroscopic studies of the complexation of DNJ by cupric ions were performed in order to obtain thermodynamic and structural background for further pharmacologic investigations. The effect of histidine, a major tissue copper carrier, on coordination equilibria was also studied. Results indicate that DNJ and Cu(II) form two stable complexes at physiological pH, CuH-1(DNJ)2+ and CuH-2(DNJ)2, involving Cu(II) chelation by the N-5 and O-6 donor atoms. In the presence of histidine, ternary complexes are also formed, of which the CuDNJHis+ species is stable in the physiological pH range. Binary Cu(II)-DNJ complexes are extremely effective mediators of in vitro oxidation of the guanine moiety in both 2'-deoxyguanosine (dG) and DNA to 8-oxoguanine (8-oxo-dG) and of DNA double strand scission by ambient O2 or H2O2. This mediation is suppressed by histidine in dG, but not in DNA. The results suggest that tissue Cu(II) may greatly enhance nonspecific cytotoxic effects of systemically administered DNJ through oxidative damage mechanisms, and therefore the prospective use of DNJ for therapeutic purposes must be developed with caution. On the other hand, however, the expected high genotoxic potential of synthetic Cu(II)-DNJ complexes may be used against viruses by means of targeted delivery of these complexes to the infected cells.
Collapse
Affiliation(s)
- M Jezowska-Bojczuk
- Laboratory of Comparative Carcinogenesis, National Cancer Institute, Frederick Cancer Research and Development Center, Maryland, USA
| | | | | |
Collapse
|
29
|
Espinosa JF, Cañada FJ, Asensio JL, Martín-Pastor M, Dietrich H, Martín-Lomas M, Schmidt RR, Jiménez-Barbero J. Experimental Evidence of Conformational Differences between C-Glycosides and O-Glycosides in Solution and in the Protein-Bound State: The C-Lactose/O-Lactose Case. J Am Chem Soc 1996. [DOI: 10.1021/ja9603463] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan-Félix Espinosa
- Contribution from the Grupo de Carbohidratos, Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain, and Fakultät für Chemie der Universität Konstanz, Postfach 5560 M 725, D-78434 Konstanz, Germany
| | - F. Javier Cañada
- Contribution from the Grupo de Carbohidratos, Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain, and Fakultät für Chemie der Universität Konstanz, Postfach 5560 M 725, D-78434 Konstanz, Germany
| | - Juan Luis Asensio
- Contribution from the Grupo de Carbohidratos, Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain, and Fakultät für Chemie der Universität Konstanz, Postfach 5560 M 725, D-78434 Konstanz, Germany
| | - Manuel Martín-Pastor
- Contribution from the Grupo de Carbohidratos, Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain, and Fakultät für Chemie der Universität Konstanz, Postfach 5560 M 725, D-78434 Konstanz, Germany
| | - Hansjörg Dietrich
- Contribution from the Grupo de Carbohidratos, Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain, and Fakultät für Chemie der Universität Konstanz, Postfach 5560 M 725, D-78434 Konstanz, Germany
| | - Manuel Martín-Lomas
- Contribution from the Grupo de Carbohidratos, Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain, and Fakultät für Chemie der Universität Konstanz, Postfach 5560 M 725, D-78434 Konstanz, Germany
| | - Richard R. Schmidt
- Contribution from the Grupo de Carbohidratos, Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain, and Fakultät für Chemie der Universität Konstanz, Postfach 5560 M 725, D-78434 Konstanz, Germany
| | - Jesús Jiménez-Barbero
- Contribution from the Grupo de Carbohidratos, Instituto de Química Orgánica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain, and Fakultät für Chemie der Universität Konstanz, Postfach 5560 M 725, D-78434 Konstanz, Germany
| |
Collapse
|
30
|
Geyer A, Hummel G, Eisele T, Reinhardt S, Schmidt RR. Structural Motifs of the Dimeric Lewis Glycolipids as Determined by NMR Spectroscopy and Molecular Dynamics Simulations. Chemistry 1996. [DOI: 10.1002/chem.19960020813] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
31
|
Conformational flexibility of C-glycosides: Experimental evidence of the existence of a gauche-gauche confirmation around the glycosidic linkage for a lactose analogue. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(95)02397-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
32
|
Thiooligosaccharides: toys or tools for the studies of Glycanases. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s0921-0423(06)80098-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
33
|
Sigurskjold BW, Berland CR, Svensson B. Thermodynamics of inhibitor binding to the catalytic site of glucoamylase from Aspergillus niger determined by displacement titration calorimetry. Biochemistry 1994; 33:10191-9. [PMID: 8060985 DOI: 10.1021/bi00199a048] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The binding of different inhibitors to glucoamylase G2 from Aspergillus niger and its temperature and pH dependencies have been studied by titration calorimetry. The enzyme binds the inhibitors 1-deoxynojirimycin and the pseudo-tetrasaccharide acarbose with association constants of 3 x 10(4) and 9 x 10(11) M-1, respectively, at 27 degrees C. The binding free energy for both ligands is remarkably temperature-invariant in the interval from 9 to 54 degrees C as the result of large compensating changes in enthalpy and entropy. Acarbose and 1-deoxynojirimycin bound with slightly different free energy-pH profiles, with optima at 5.5 and 5.5-7.0, respectively. Variations in delta H degrees and T delta S degrees as a function of pH were substantially larger than variations in delta G degrees in a partly compensatory manner. Two titratable groups at or near subsite 1 of the catalytic site were found to change their pKa slightly upon binding. The hydrogenated forms of acarbose, D-gluco- and L-ido-dihydroacarbose, bind with greatly reduced association constants of 3 x 10(7) and 2 x 10(5) M-1, respectively, and the pseudo-disaccharide methyl acarviosinide, lacking the two glucose units at the reducing end compared to acarbose, has a binding constant of 8 x 10(6) M-1; these values all result from losses in both enthalpy and entropy compared to acarbose. Three thio analogues of the substrate maltose, methyl alpha- and beta-4-thiomaltoside and methyl alpha-4,5'-dithiomaltoside, bind with affinities from 3 x 10(3) to 6 x 10(4) M-1.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- B W Sigurskjold
- Department of Chemistry, Carlsberg Laboratory, Copenhagen Valby, Denmark
| | | | | |
Collapse
|