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Choutka J, Parkan K, Pohl R, Kaminský J. On the origin of the electronic and magnetic circular dichroism of naphthyl C-glycosides: Anomeric configuration. Carbohydr Res 2024; 535:109021. [PMID: 38171193 DOI: 10.1016/j.carres.2023.109021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
Aryl C-glycosides, in which the glycosidic bond is changed to a carbon-carbon bond, are an important family of biologically-active compounds. They often serve as secondary metabolites or exhibit antibiotic and cytostatic activities. Their stability to hydrolysis has made them attractive targets for new drugs. Their conformational behavior often strongly influences the resulting function. Their detailed structural and conformational description is thus highly desirable. This work studies the structure of three different naphthyl C-glycosides using UV-vis absorption as well as electronic and magnetic circular dichroism. It also describes their conformational preferences using a combination of molecular dynamics and DFT calculations. The reliability of these preferences has been verified by simulations of spectral properties and a comparison with their measured spectra. In particular, ECD spectroscopy has been shown to distinguish easily between α- and β-pseudoanomers of aryl C-glycosides. Computer simulations and spectral decomposition have revealed how the resulting ECD patterns of the naphthyl glycosides studied are influenced by different conformer populations. In conclusion, reliable ECD patterns cannot be calculated by separating the naphthyl rotation from other conformational motions. MCD patterns have been similar for all the naphthyl C-glycosides studied. No clear diagnostic features have been found for either the pseudoanomeric configuration or the preferred hydroxymethyl rotamer. Nevertheless, the work has demonstrated the potential of MCD for the study of aryl glycosides interacting with proteins.
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Affiliation(s)
- Jan Choutka
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic
| | - Kamil Parkan
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic; Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo nám. 2, 160 00, Prague, Czech Republic.
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2
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Ruda A, Aytenfisu AH, Angles d’Ortoli T, MacKerell AD, Widmalm G. Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields. Phys Chem Chem Phys 2023; 25:3042-3060. [PMID: 36607620 PMCID: PMC9890503 DOI: 10.1039/d2cp05203b] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
D-Mannose is a structural component in N-linked glycoproteins from viruses and mammals as well as in polysaccharides from fungi and bacteria. Structural components often consist of D-Manp residues joined via α-(1→2)-, α-(1→3)-, α-(1→4)- or α-(1→6)-linkages. As models for these oligo- and polysaccharides, a series of mannose-containing disaccharides have been investigated with respect to conformation and dynamics. Translational diffusion NMR experiments were performed to deduce rotational correlation times for the molecules, 1D 1H,1H-NOESY and 1D 1H,1H-T-ROESY NMR experiments were carried out to obtain inter-residue proton-proton distances and one-dimensional long-range and 2D J-HMBC experiments were acquired to gain information about conformationally dependent heteronuclear coupling constants across glycosidic linkages. To attain further spectroscopic data, the doubly 13C-isotope labeled α-D-[1,2-13C2]Manp-(1→4)-α-D-Manp-OMe was synthesized thereby facilitating conformational analysis based on 13C,13C coupling constants as interpreted by Karplus-type relationships. Molecular dynamics simulations were carried out for the disaccharides with explicit water as solvent using the additive CHARMM36 and Drude polarizable force fields for carbohydrates, where the latter showed broader population distributions. Both simulations sampled conformational space in such a way that inter-glycosidic proton-proton distances were very well described whereas in some cases deviations were observed between calculated conformationally dependent NMR scalar coupling constants and those determined from experiment, with closely similar root-mean-square differences for the two force fields. However, analyses of dipole moments and radial distribution functions with water of the hydroxyl groups indicate differences in the underlying physical forces dictating the wider conformational sampling with the Drude polarizable versus additive C36 force field and indicate the improved utility of the Drude polarizable model in investigating complex carbohydrates.
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Affiliation(s)
- Alessandro Ruda
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
| | - Asaminew H. Aytenfisu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of MarylandBaltimoreMaryland 21201USA
| | - Thibault Angles d’Ortoli
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of MarylandBaltimoreMaryland 21201USA
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
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3
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Palivec V, Pohl R, Kaminský J, Martinez-Seara H. Efficiently Computing NMR 1H and 13C Chemical Shifts of Saccharides in Aqueous Environment. J Chem Theory Comput 2022; 18:4373-4386. [PMID: 35687789 DOI: 10.1021/acs.jctc.2c00127] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Determining the structure of saccharides in their native environment is crucial to understanding their function and more accurately targeting their utilization. Nuclear magnetic resonance observables such as the nuclear Overhauser effect or spin-spin coupling constants are routinely utilized to study saccharides in their native water environment. However, while highly sensitive to the local environment, chemical shifts are mostly overlooked, despite being commonly measured for compounds identification. Although chemical shifts carry considerable structural information, their direct association with structure is notoriously difficult. This is mostly due to the similarity in the chemical nature of most saccharides causing similar physicochemical environments close to sugar C and H atoms, resulting in comparable chemical shifts. The rise of computational power allows one to compute reliable chemical shifts and use them to determine atomistic details of these sugars in solution. However, any prediction is severely limited by the computational protocol used and its accuracy. In this work, we studied a set of 31 saccharides on which we evaluated various computational protocols to calculate the total number of 375 1H and 327 13C chemical shifts of sugars in an aqueous environment. Our study proposes two cost-effective protocols for simulating 1H and 13C chemical shifts that we recommend for further use. These protocols can help with the interpretation of experimental spectra, but we also show that they are also capable of structure prediction independently. This is possible because of the low mean absolute deviations of calculated shifts from the experiment (0.06 ppm for 1H and 1.09 ppm for 13C). We explore different solvation methods, basis sets, and optimization schemes to reach such accuracy. A correct sampling of the conformation phase space of flexible sugar molecules is also key to obtaining accurately converged theoretical chemical shifts. The linear regression method was applied to convert the calculated isotropic nuclear magnetic shielding constants to simulated chemical shifts comparable with the experiment. The achieved level of accuracy can help in utilizing chemical shifts for elucidating the 3D atomistic structure of saccharides in aqueous solutions. All linear regression parameters obtained on our extensive set of sugars for all the tested protocols can be reutilized in future works.
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Affiliation(s)
- Vladimír Palivec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, Prague 6 CZ166 10, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, Prague 6 CZ166 10, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, Prague 6 CZ166 10, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo námĕstí 542/2, Prague 6 CZ166 10, Czech Republic
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4
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Hussain N, Hussain A. Advances in Pd-catalyzed C-C bond formation in carbohydrates and their applications in the synthesis of natural products and medicinally relevant molecules. RSC Adv 2021; 11:34369-34391. [PMID: 35497292 PMCID: PMC9042403 DOI: 10.1039/d1ra06351k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
Advances in the Pd-catalyzed synthesis of C-glycosides and branched sugars are summarized herein and the strategies are categorized based on named reactions or types of sugar moieties involved in the reactions. These include cross-coupling reactions, C-H activations, and carbonylative cross-coupling reactions. Applications of Pd-catalyzed C-glycosylation reactions are discussed in the synthesis of natural products and biologically active molecules such as bergenin, papulacandin D, and SGLT2-inhibitors. Important mechanistic cycles are drawn and the mechanisms for how Pd-activates the sugar moieties for various coupling partners are discussed. The directing group-assisted C-glycosylation and some intramolecular C-H activation reactions are also included.
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Affiliation(s)
- Nazar Hussain
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, BHU Varanasi-221005 India
| | - Altaf Hussain
- Department of Chemistry, Govt. Degree College Poonch J&K India 185101
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5
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Walia V, Chaudhary SK, Kumar Sethiya N. Therapeutic potential of mangiferin in the treatment of various neuropsychiatric and neurodegenerative disorders. Neurochem Int 2021; 143:104939. [PMID: 33346032 DOI: 10.1016/j.neuint.2020.104939] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/02/2020] [Accepted: 12/12/2020] [Indexed: 12/19/2022]
Abstract
Xanthones are important chemical class of bioactive products that confers therapeutic benefits. Of several xanthones, mangiferin is known to be distributed widely across several fruits, vegetables and medicinal plants. Mangiferin has been shown to exert neuroprotective effects in both in-vitro and in-vivo models. Mangiferin attenuates cerebral infarction, cerebral edema, lipid peroxidation (MDA), neuronal damage, etc. Mangiferin further potentiate levels of endogenous antioxidants to confer protection against the oxidative stress inside the neurons. Mangiferin is involved in the regulation of various signaling pathways that influences the production and levels of proinflammatory cytokines in brain. Mangiferin cosunteracted the neurotoxic effect of amyloid-beta, MPTP, rotenone, 6-OHDA etc and confer protection to neurons. These evidence suggested that the mangiferin may be a potential therapeutic strategy for the treatment of various neurological disorders. The present review demonstrated the pharmacodynamics-pharmacokinetics of mangiferin and neurotherapeutic potential in several neurological disorders with underlying mechanisms.
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6
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Jonker HRA, Saxena K, Shcherbakova A, Tiemann B, Bakker H, Schwalbe H. NMR Spectroscopic Characterization of the C‐Mannose Conformation in a Thrombospondin Repeat Using a Selective Labeling Approach. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
| | - Aleksandra Shcherbakova
- Institute of Clinical Biochemistry Hannover Medical School Carl-Neuberg-Strasse 1 30625 Hannover Germany
| | - Birgit Tiemann
- Institute of Clinical Biochemistry Hannover Medical School Carl-Neuberg-Strasse 1 30625 Hannover Germany
| | - Hans Bakker
- Institute of Clinical Biochemistry Hannover Medical School Carl-Neuberg-Strasse 1 30625 Hannover Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ) Goethe University Frankfurt Max-von-Laue Strasse 7 60438 Frankfurt am Main Germany
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7
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Jonker HRA, Saxena K, Shcherbakova A, Tiemann B, Bakker H, Schwalbe H. NMR Spectroscopic Characterization of the C-Mannose Conformation in a Thrombospondin Repeat Using a Selective Labeling Approach. Angew Chem Int Ed Engl 2020; 59:20659-20665. [PMID: 32745319 PMCID: PMC7692951 DOI: 10.1002/anie.202009489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Indexed: 12/24/2022]
Abstract
Despite the great interest in glycoproteins, structural information reporting on conformation and dynamics of the sugar moieties are limited. We present a new biochemical method to express proteins with glycans that are selectively labeled with NMR-active nuclei. We report on the incorporation of 13 C-labeled mannose in the C-mannosylated UNC-5 thrombospondin repeat. The conformational landscape of the C-mannose sugar puckers attached to tryptophan residues of UNC-5 is characterized by interconversion between the canonical 1 C4 state and the B03 / 1 S3 state. This flexibility may be essential for protein folding and stabilization. We foresee that this versatile tool to produce proteins with selectively labeled C-mannose can be applied and adjusted to other systems and modifications and potentially paves a way to advance glycoprotein research by unravelling the dynamical and conformational properties of glycan structures and their interactions.
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Affiliation(s)
- Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
| | - Aleksandra Shcherbakova
- Institute of Clinical BiochemistryHannover Medical SchoolCarl-Neuberg-Strasse 130625HannoverGermany
| | - Birgit Tiemann
- Institute of Clinical BiochemistryHannover Medical SchoolCarl-Neuberg-Strasse 130625HannoverGermany
| | - Hans Bakker
- Institute of Clinical BiochemistryHannover Medical SchoolCarl-Neuberg-Strasse 130625HannoverGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 760438Frankfurt am MainGermany
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8
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Abstract
Carbonic anhydrases (CAs) are metalloenzymes responsible for the reversible hydration of carbon dioxide to bicarbonate, a fundamental reaction involved in various physiological and pathological processes. In the last decades, CAs have been considered as important drug targets for different pathologies such as glaucoma, epilepsy and cancer. The design of potent and selective inhibitors has been an outstanding goal leading to the discovery of new drugs. Among the different strategies developed to date, the design of carbohydrate-based CA inhibitors (CAIs) has emerged as a versatile tool in order to selectively target CAs. The insertion of a glycosyl moiety as a hydrophilic tail in sulfonamide, sulfenamide, sulfamate or coumarin scaffolds allowed the discovery of many different series of sugar-based CAIs, with relevant inhibitory results. This review will focus on carbohydrate-based CAIs developed so far, classifying them in glycosidic and glycoconjugated inhibitors based on the conjugation chemistry adopted.
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Affiliation(s)
| | - Elisa Nuti
- Department of Pharmacy, University of Pisa, Pisa, Italy
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9
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Hevey R. Bioisosteres of Carbohydrate Functional Groups in Glycomimetic Design. Biomimetics (Basel) 2019; 4:E53. [PMID: 31357673 DOI: 10.3390/biomimetics4030053] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 02/07/2023] Open
Abstract
The aberrant presentation of carbohydrates has been linked to a number of diseases, such as cancer metastasis and immune dysregulation. These altered glycan structures represent a target for novel therapies by modulating their associated interactions with neighboring cells and molecules. Although these interactions are highly specific, native carbohydrates are characterized by very low affinities and inherently poor pharmacokinetic properties. Glycomimetic compounds, which mimic the structure and function of native glycans, have been successful in producing molecules with improved pharmacokinetic (PK) and pharmacodynamic (PD) features. Several strategies have been developed for glycomimetic design such as ligand pre-organization or reducing polar surface area. A related approach to developing glycomimetics relies on the bioisosteric replacement of carbohydrate functional groups. These changes can offer improvements to both binding affinity (e.g., reduced desolvation costs, enhanced metal chelation) and pharmacokinetic parameters (e.g., improved oral bioavailability). Several examples of bioisosteric modifications to carbohydrates have been reported; this review aims to consolidate them and presents different possibilities for enhancing core interactions in glycomimetics.
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Hevey R. Strategies for the Development of Glycomimetic Drug Candidates. Pharmaceuticals (Basel) 2019; 12:E55. [PMID: 30978966 DOI: 10.3390/ph12020055] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/03/2019] [Accepted: 04/09/2019] [Indexed: 02/06/2023] Open
Abstract
Carbohydrates are a structurally-diverse group of natural products which play an important role in numerous biological processes, including immune regulation, infection, and cancer metastasis. Many diseases have been correlated with changes in the composition of cell-surface glycans, highlighting their potential as a therapeutic target. Unfortunately, native carbohydrates suffer from inherently weak binding affinities and poor pharmacokinetic properties. To enhance their usefulness as drug candidates, 'glycomimetics' have been developed: more drug-like compounds which mimic the structure and function of native carbohydrates. Approaches to improve binding affinities (e.g., deoxygenation, pre-organization) and pharmacokinetic properties (e.g., limiting metabolic degradation, improving permeability) have been highlighted in this review, accompanied by relevant examples. By utilizing these strategies, high-affinity ligands with optimized properties can be rationally designed and used to address therapies for novel carbohydrate-binding targets.
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Calloni I, Unione L, Jiménez-Osés G, Corzana F, Del Bino L, Corrado A, Pitirollo O, Colombo C, Lay L, Adamo R, Jiménez-Barbero J. The Conformation of the Mannopyranosyl Phosphate Repeating Unit of the Capsular Polysaccharide of Neisseria meningitidis Serogroup A and Its Carba-Mimetic. European J Org Chem 2018; 2018:4548-4555. [PMID: 30443159 PMCID: PMC6220853 DOI: 10.1002/ejoc.201801003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 11/07/2022]
Abstract
Neisseria meningitidis serogroup A (MenA) is an aerobic diplococcal Gram-negative bacterium responsible for epidemic meningitis disease. Its capsular polysaccharide (CPS) has been identified as the primary virulence factor of MenA. This polysaccharide suffers from chemical lability in water. Thus, the design and synthesis of novel and hydrolytically stable structural analogues of MenA CPS may provide additional tools for the development of therapies against this disease. In this context, the structural features of the natural phosphorylated monomer have been analyzed and compared to those of its carba-analogue, where the endocyclic oxygen has been replaced by a methylene moiety. The lowest energy geometries of the different molecules have been calculated using a combination of quantum mechanical techniques and molecular dynamics simulations. The predicted results have been compared and validated using NMR experiments. The results indicate that the more stable designed glycomimetics may adopt the conformation adopted by the natural monomer, although they display a wider flexibility around the torsional degrees of freedom.
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Affiliation(s)
- Ilaria Calloni
- Chemical Glycobiology Lab CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Spain.,Department of Organic Chemistry II Faculty of Science and Technology University of the Basque Country, EHU-UPV Leioa Spain
| | - Luca Unione
- Atlas Molecular Pharma Bizkaia Technology Park, Building 800 48160 Derio Spain
| | - Gonzalo Jiménez-Osés
- Departamento de Quimica Universidad de la Rioja Centro Científico Tecnológico Spain
| | - Francisco Corzana
- Departamento de Quimica Universidad de la Rioja Centro Científico Tecnológico Spain
| | | | - Alessio Corrado
- Glycobiology Lab GSK Via Fiorentina 10 Siena Italy.,Department of Chemistry and ISTM_CNR University of Milan Via Golgi 19 20133 Milan Italy
| | - Olimpia Pitirollo
- Department of Chemistry and ISTM_CNR University of Milan Via Golgi 19 20133 Milan Italy
| | - Cinzia Colombo
- Department of Chemistry and ISTM_CNR University of Milan Via Golgi 19 20133 Milan Italy
| | - Luigi Lay
- Department of Chemistry and ISTM_CNR University of Milan Via Golgi 19 20133 Milan Italy
| | | | - Jesús Jiménez-Barbero
- Chemical Glycobiology Lab CIC bioGUNE Bizkaia Technology Park, Building 800 48160 Derio Spain.,Department of Organic Chemistry II Faculty of Science and Technology University of the Basque Country, EHU-UPV Leioa Spain.,Basque Foundation for Science (IKERBASQUE) 48009 Bilbao Spain
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12
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Marchetti R, Bedini E, Gully D, Lanzetta R, Giraud E, Molinaro A, Silipo A. Rhodopseudomonas palustris Strain CGA009 Produces an O-Antigen Built up by a C-4-Branched Monosaccharide: Structural and Conformational Studies. Org Lett 2018; 20:3656-3660. [PMID: 29874087 DOI: 10.1021/acs.orglett.8b01439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, the analysis of the peculiar homopolymeric O-chain, isolated from the lipopolysaccharide (LPS) of Rhodopseudomonas palustris strain CGA009, is reported. The O-chain is built up of a novel 4-C-branched sugar (12-deoxy-4- C-(d- altro-5,7,8,9-tetrahydroxyhexyl))-3- O-methyl-d-galactopyranose)) whose structure, absolute configuration, and conformational features were deduced by 2D NMR spectroscopy, optical rotation measurements, and molecular dynamics simulations.
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Affiliation(s)
- Roberta Marchetti
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
| | - Emiliano Bedini
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) , UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J - Campus de Baillarguet , Montpellier 34398 Cedex 5 , France
| | - Rosa Lanzetta
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) , UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J - Campus de Baillarguet , Montpellier 34398 Cedex 5 , France
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
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13
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Raich I, Lövyová Z, Trnka L, Parkan K, Kessler J, Pohl R, Kaminský J. Limitations in the description of conformational preferences of C-disaccharides: The (1 → 3)-C-mannobiose case. Carbohydr Res 2017; 451:42-50. [PMID: 28950209 DOI: 10.1016/j.carres.2017.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/07/2017] [Accepted: 09/11/2017] [Indexed: 11/19/2022]
Abstract
Conformational preferences of two C-glycosyl analogues of Manp-(1 → 3)-Manp, were studied using a combined method of theoretical and experimental chemistry. Molecular dynamics was utilized to provide conformational behavior along C-glycosidic bonds of methyl 3-deoxy-3-C-[(α-d-mannopyranosyl)methyl]-α-d- and l-mannopyranosides. The OPLS2005 and Glycam06 force fields were used. Simulations were performed with explicit water (TIP3P) and methanol. Results were compared with a complete conformational scan at the MM4 level with the dielectric constant corresponding to methanol. In order to verify predicted conformational preferences, vicinal 3JHH NMR coupling constants were calculated by the Karplus equation on simulated potential energy surfaces (PES). A set of new parameters for the Karplus equation was also designed. Predicted 3JHH were compared with experimental data. We also used reverse methodology, in which the 3JHH coupling constants were calculated at the DFT level for each family of (ϕ, ψ)-conformers separately and then experimental values were decomposed onto calculated 3JHH couplings in order to obtain experimentally derived populations of conformers. As an alternative method of evaluation of preferred conformers, analysis of sensitive 13C chemical shifts was introduced. We were able to thoroughly discuss several fundamental issues in predictions of preferred conformers of C-saccharides, such as the solvent effect, reliability of the force field, character of empirical Karplus equation or applicability of NMR parameters in predictions of conformational preferences in general.
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Affiliation(s)
- Ivan Raich
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Zuzana Lövyová
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Ladislav Trnka
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Kamil Parkan
- University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic; Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry AS CR, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
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14
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Imran M, Arshad MS, Butt MS, Kwon JH, Arshad MU, Sultan MT. Mangiferin: a natural miracle bioactive compound against lifestyle related disorders. Lipids Health Dis 2017; 16:84. [PMID: 28464819 PMCID: PMC5414237 DOI: 10.1186/s12944-017-0449-y] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/09/2017] [Indexed: 12/17/2022] Open
Abstract
The current review article is an attempt to explain the therapeutic potential of mangiferin, a bioactive compound of the mango, against lifestyle-related disorders. Mangiferin (2-β-D-glucopyranosyl-1,3,6,7-tetrahydroxy-9H-xanthen-9-one) can be isolated from higher plants as well as the mango fruit and their byproducts (i.e. peel, seed, and kernel). It possesses several health endorsing properties such as antioxidant, antimicrobial, antidiabetic, antiallergic, anticancer, hypocholesterolemic, and immunomodulatory. It suppresses the activation of peroxisome proliferator activated receptor isoforms by changing the transcription process. Mangiferin protects against different human cancers, including lung, colon, breast, and neuronal cancers, through the suppression of tumor necrosis factor α expression, inducible nitric oxide synthase potential, and proliferation and induction of apoptosis. It also protects against neural and breast cancers by suppressing the expression of matrix metalloproteinase (MMP)-9 and MMP-7 and inhibiting enzymatic activity, metastatic potential, and activation of the β-catenin pathway. It has the capacity to block lipid peroxidation, in order to provide a shielding effect against physiological threats. Additionally, mangiferin enhances the capacity of the monocyte-macrophage system and possesses antibacterial activity against gram-positive and gram-negative bacteria. This review summarizes the literature pertaining to mangiferin and its associated health claims.
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Affiliation(s)
- Muhammad Imran
- Department of Diet and Nutritional Sciences, Imperial College of Business Studies, Lahore, Pakistan.,National institute of Food Science and Technology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Sajid Arshad
- Institute of Home and Food Sciences, Government College University, Faisalabad, 36000, Pakistan. .,School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, Republic of South Korea.
| | - Masood Sadiq Butt
- National institute of Food Science and Technology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Joong-Ho Kwon
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, Republic of South Korea
| | - Muhammad Umair Arshad
- Institute of Home and Food Sciences, Government College University, Faisalabad, 36000, Pakistan
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Llantén H, Barata-Vallejo S, Postigo A, Colinas PA. Synthesis of C -glycosylmethyl isoxazoles via aerobic oxidation of ketoximes catalyzed by TEMPO. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Small MC, Aytenfisu AH, Lin FY, He X, MacKerell AD. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J Comput Aided Mol Des 2017; 31:349-363. [PMID: 28190218 PMCID: PMC5392138 DOI: 10.1007/s10822-017-0010-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/17/2017] [Indexed: 10/20/2022]
Abstract
The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (D-allose and D-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars D-allose and D-psicose, thereby extending the available biomolecules in the Drude polarizable FF.
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Affiliation(s)
- Meagan C Small
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA
| | - Asaminew H Aytenfisu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA
| | - Fang-Yu Lin
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA
| | - Xibing He
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD, 21201, USA.
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Berglund J, Angles d'Ortoli T, Vilaplana F, Widmalm G, Bergenstråhle-Wohlert M, Lawoko M, Henriksson G, Lindström M, Wohlert J. A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility. Plant J 2016; 88:56-70. [PMID: 27385537 DOI: 10.1111/tpj.13259] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/16/2016] [Accepted: 06/28/2016] [Indexed: 06/06/2023]
Abstract
The macromolecular conformation of the constituent polysaccharides in lignocellulosic biomass influences their supramolecular interactions, and therefore their function in plants and their performance in technical products. The flexibility of glycosidic linkages from the backbone of hemicelluloses was studied by evaluating the conformational freedom of the φ and ψ dihedral angles using molecular dynamic simulations, additionally selected molecules were correlated with experimental data by nuclear magnetic resonance spectroscopy. Three types of β-(1→4) glycosidic linkages involving the monosaccharides (Glcp, Xylp and Manp) present in the backbone of hemicelluloses were defined. Different di- and tetrasaccharides with combinations of such sugar monomers from hemicelluloses were simulated, and free energy maps of the φ - ψ space and hydrogen-bonding patterns were obtained. The glycosidic linkage between Glc-Glc or Glc-Man (C-type) was the stiffest with mainly one probable conformation; the linkage from Man-Man or Man-Glc (M-type) was similar but with an increased probability for an alternative conformation making it more flexible, and the linkage between two Xyl-units (X-type) was the most flexible with two almost equally populated conformations. Glycosidic linkages of the same type showed essentially the same conformational space in both disaccharides and in the central region of tetrasaccharides. Different probabilities of glycosidic linkage conformations in the backbone of hemicelluloses can be directly estimated from the free energy maps, which to a large degree affect the overall macromolecular conformations of these polymers. The information gained contributes to an increased understanding of the function of hemicelluloses both in the cell wall and in technical products.
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Affiliation(s)
- Jennie Berglund
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Thibault Angles d'Ortoli
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Francisco Vilaplana
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Centre, SE-106 91, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Malin Bergenstråhle-Wohlert
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Martin Lawoko
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Gunnar Henriksson
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Mikael Lindström
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden
| | - Jakob Wohlert
- Wallenberg Wood Science Centre (WWSC), Department of Fiber and Polymer Technology, School of Chemical Engineering, Royal Institute of Technology KTH, SE-100 44, Stockholm, Sweden.
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Zaro MJ, Bortolotti A, Riafrecha LE, Concellón A, Morbidoni HR, Colinas PA. Anti-tubercular and antioxidant activities of C-glycosyl carbonic anhydrase inhibitors: towards the development of novel chemotherapeutic agents against Mycobacterium tuberculosis. J Enzyme Inhib Med Chem 2016; 31:1726-30. [DOI: 10.3109/14756366.2016.1172577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- María J. Zaro
- CIDCA (Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata-CONICET, UNLP), La Plata, Argentina,
| | - Ana Bortolotti
- Laboratorio de Microbiologia Molecular, Cátedra de Microbiología, Virología y Parasitología; Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina, and
| | - Leonardo E. Riafrecha
- LADECOR CONICET, Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Analía Concellón
- CIDCA (Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata-CONICET, UNLP), La Plata, Argentina,
| | - Héctor R. Morbidoni
- Laboratorio de Microbiologia Molecular, Cátedra de Microbiología, Virología y Parasitología; Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina, and
| | - Pedro A. Colinas
- LADECOR CONICET, Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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Silipo A, Di Lorenzo F, De Felice A, Vanacore A, De Castro C, Gully D, Lanzetta R, Parrilli M, Giraud E, Molinaro A. Structural and conformational study of the O-polysaccharide produced by the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris strain BisA53. Carbohydr Polym 2014; 114:384-91. [DOI: 10.1016/j.carbpol.2014.08.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 11/20/2022]
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Garate JA, Stöckl J, Fernández-Alonso MDC, Artner D, Haegman M, Oostenbrink C, Jiménez-Barbero J, Beyaert R, Heine H, Kosma P, Zamyatina A. Anti-endotoxic activity and structural basis for human MD-2·TLR4 antagonism of tetraacylated lipid A mimetics based on βGlcN(1↔1)αGlcN scaffold. Innate Immun 2014; 21:490-503. [PMID: 25394365 PMCID: PMC4452626 DOI: 10.1177/1753425914550426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/11/2014] [Indexed: 01/25/2023] Open
Abstract
Interfering with LPS binding by the co-receptor protein myeloid differentiation factor 2 (MD-2) represents a useful approach for down-regulation of MD-2·TLR4-mediated innate immune signaling, which is implicated in the pathogenesis of a variety of human diseases, including sepsis syndrome. The antagonistic activity of a series of novel synthetic tetraacylated bis-phosphorylated glycolipids based on the βGlcN(1↔1)αGlcN scaffold was assessed in human monocytic macrophage-like cell line THP-1, dendritic cells and human epithelial cells. Two compounds were shown to inhibit efficiently the LPS-induced inflammatory signaling by down-regulation of the expression of TNF-α, IL-6, IL-8, IL-10 and IL-12 to background levels. The binding of the tetraacylated by (R)-3-hydroxy-fatty acids (2 × C12, 2 × C14), 4,4′-bisphosphorylated βGlcN(1↔1)αGlcN-based lipid A mimetic DA193 to human MD-2 was calculated to be 20-fold stronger than that of Escherichia coli lipid A. Potent antagonistic activity was related to a specific molecular shape induced by the β,α(1↔1)-diglucosamine backbone. ‘Co-planar’ relative arrangement of the GlcN rings was inflicted by the double exo-anomeric conformation around both glycosidic torsions in the rigid β,α(1↔1) linkage, which was ascertained using NOESY NMR experiments and confirmed by molecular dynamics simulation. In contrast to the native lipid A ligands, the binding affinity of βGlcN(1↔1)αGlcN-based lipid A mimetics to human MD-2 was independent on the orientation of the diglucosamine backbone of the synthetic antagonist within the binding pocket of hMD-2 (rotation by 180°) allowing for two equally efficient binding modes as shown by molecular dynamics simulation.
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Affiliation(s)
- Jose Antonio Garate
- Institute of Molecular Modelling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johannes Stöckl
- Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Daniel Artner
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Mira Haegman
- Department for Biomedical Molecular Biology, Unit of Molecular Signal Transduction in Inflammation, Ghent University, Inflammation Research Center, VIB, Ghent, Belgium
| | - Chris Oostenbrink
- Institute of Molecular Modelling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Rudi Beyaert
- Department for Biomedical Molecular Biology, Unit of Molecular Signal Transduction in Inflammation, Ghent University, Inflammation Research Center, VIB, Ghent, Belgium
| | - Holger Heine
- Research Group Innate Immunity, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
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Riafrecha LE, Rodríguez OM, Vullo D, Supuran CT, Colinas PA. Synthesis of C-cinnamoyl glycosides and their inhibitory activity against mammalian carbonic anhydrases. Bioorg Med Chem 2013; 21:1489-94. [DOI: 10.1016/j.bmc.2012.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 08/27/2012] [Accepted: 09/01/2012] [Indexed: 01/03/2023]
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Koester DC, Kriemen E, Werz DB. Flexible Synthesis of 2-Deoxy-C-Glycosides and (1→2)-, (1→3)-, and (1→4)-LinkedC-Glycosides. Angew Chem Int Ed Engl 2013; 52:2985-9. [DOI: 10.1002/anie.201209697] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Indexed: 11/07/2022]
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Koester DC, Kriemen E, Werz DB. Flexible Synthese von 2-Desoxy-C-Glycosiden sowie (1→2)-, (1→3)- und (1→4)-verknüpftenC-Glycosiden. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Zaccheus M, Pendrill R, Jackson TA, Wang A, Auzanneau FI, Widmalm G. Conformational Dynamics of a Central Trisaccharide Fragment of the LeaLex Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Bachan S, Fantini J, Joshi A, Garg H, Mootoo DR. Synthesis, gp120 binding and anti-HIV activity of fatty acid esters of 1,1-linked disaccharides. Bioorg Med Chem 2011; 19:4803-11. [PMID: 21783371 DOI: 10.1016/j.bmc.2011.06.078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 06/22/2011] [Accepted: 06/27/2011] [Indexed: 11/19/2022]
Abstract
Inspired by the anti-human immunodeficiency virus (HIV) activity of analogues of β-galactosylceramide (GalCer), a set of mono- and di-saccharide fatty acid esters were designed as GalCer mimetics and their binding to the V3 loop peptide of HIV-1 and anti-HIV activity evaluated. 1,1-linked Gal-Man and Glu-Man disaccharides with an ester on the Man subunit bound the V3 loop peptide and inhibited HIV infectivity in single round infection assays with the TZM-bl cell line. IC(50)'s were in the 50 μM range with no toxicity to the cells at concentrations up to 200 μM. These compounds appear to inhibit virus entry at early steps in viral infection since they were inactive if added post viral entry. Although these compounds were found to bind to the V3 loop peptide of gp120, it is not clear that this interaction is responsible for their anti-HIV activity because the relative binding affinity of closely related analogues did not correlate with their antiviral behavior. The low cytotoxicity of these 1,1-linked disaccharide fatty acid esters, combined with the easy accessibility to structurally diverse analogues make these molecules attractive leads for new topical anti-viral agents.
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Affiliation(s)
- Stewart Bachan
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10021, USA
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Silipo A, Molinaro A, Molteni M, Rossetti C, Parrilli M, Lanzetta R. Full Structural Characterization of an Extracellular Polysaccharide Produced by the Freshwater Cyanobacterium Oscillatoria planktothrix FP1. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000749] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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León EI, Martín A, Peréz-Martín I, Quintanal LM, Suárez E. Hydrogen Atom Transfer Experiments Provide Chemical Evidence for the Conformational Differences between C- and O-Disaccharides. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000470] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Affiliation(s)
- Dennis C. Koester
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstr. 2, D-37077 Göttingen, Germany
| | - Markus Leibeling
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstr. 2, D-37077 Göttingen, Germany
| | - Roman Neufeld
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstr. 2, D-37077 Göttingen, Germany
| | - Daniel B. Werz
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstr. 2, D-37077 Göttingen, Germany
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Säwén E, Massad T, Landersjö C, Damberg P, Widmalm G. Population distribution of flexible molecules from maximum entropy analysis using different priors as background information: application to the Φ, Ψ-conformational space of the α-(1-->2)-linked mannose disaccharide present in N- and O-linked glycoproteins. Org Biomol Chem 2010; 8:3684-95. [PMID: 20574564 DOI: 10.1039/c003958f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational space available to the flexible molecule α-D-Manp-(1-->2)-α-D-Manp-OMe, a model for the α-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that leads to a converged population distribution utilizing different input information. A database survey of the Protein Data Bank where structures having the constituent disaccharide were retrieved resulted in an ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave the database (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linked structures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealed a two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. These two different conformation ensembles of the disaccharide were compared to measured experimental spectroscopic data for the molecule in water solution. However, neither of the two populations were compatible with experimental data from optical rotation, NMR (1)H,(1)H cross-relaxation rates as well as homo- and heteronuclear (3)J couplings. The conformational distributions were subsequently used as background information to generate priors that were used in a maximum entropy analysis. The resulting posteriors, i.e., the population distributions after the application of the maximum entropy analysis, still showed notable deviations that were not anticipated based on the prior information. Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidic torsion angles Φ and Ψ were carried out in which the importance of electronegative substituents on the coupling pathway was deemed essential resulting in four derived equations, two (3)J(COCC) and two (3)J(COCH) being different for the Φ and Ψ torsions, respectively. These Karplus relationships are denoted JCX/SU09. Reapplication of the maximum entropy analysis gave excellent agreement between the MD- and DB-posteriors. The information entropies show that the current reparametrization of the Karplus relationships constitutes a significant improvement. The Φ(H) torsion angle of the disaccharide is governed by the exo-anomeric effect and for the dominating conformation Φ(H) = -40 degrees and Ψ(H) = 33 degrees. The minor conformational state has a negative Ψ(H) torsion angle; the relative populations of the major and the minor states are approximately 3 : 1. It is anticipated that application of the methodology will be useful to flexible molecules ranging from small organic molecules to large biomolecules.
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Affiliation(s)
- Elin Säwén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
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Kövér KE, Szilágyi L, Batta G, Uhrín D, Jiménez-Barbero J. Biomolecular Recognition by Oligosaccharides and Glycopeptides: The NMR Point of View. Comprehensive Natural Products II 2010:197-246. [DOI: 10.1016/b978-008045382-8.00193-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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Ieranò T, Silipo A, Cescutti P, Leone MR, Rizzo R, Lanzetta R, Parrilli M, Molinaro A. Structural Study and Conformational Behavior of the Two Different Lipopolysaccharide O-Antigens Produced by the Cystic Fibrosis PathogenBurkholderia multivorans. Chemistry 2009; 15:7156-66. [DOI: 10.1002/chem.200900647] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Arsequell G, Salvatella M, Valencia G, Fernández-Mayoralas A, Fontanella M, Venturi C, Jiménez-Barbero J, Marrón E, Rodríguez RE. Synthesis, conformation, and biological characterization of a sugar derivative of morphine that is a potent, long-lasting, and nontolerant antinociceptive. J Med Chem 2009; 52:2656-66. [PMID: 19351163 DOI: 10.1021/jm8011245] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A synthetic mannoside derivative, namely, 6-morphinyl-alpha-D-mannopyranoside, shows a naloxone-reversible antinociception that is 100-fold more potent and twice as long lasting compared to morphine when administered intraperitoneally to rats in paw pressure and tail flick tests. The compound does not produce tolerance and binds to rat mu opioid receptors with twice the affinity of morphine. NMR studies suggest that differences of activity between the derivative and its parent compound M6G might be related to their differing molecular dynamic behavior.
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Affiliation(s)
- Gemma Arsequell
- Unit of Glycoconjugate Chemistry, Instituto de Química Avanzada de Cataluña (IQAC-CSIC), Barcelona, Jordi Girona 18-26, E08034-Barcelona, Spain
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Kolympadi M, Fontanella M, Venturi C, André S, Gabius HJ, Jiménez-Barbero J, Vogel P. Synthesis and Conformational Analysis of (α-D-Galactosyl)phenylmethane and α-,β-Difluoromethane Analogues: Interactions with the Plant Lectin Viscumin. Chemistry 2009; 15:2861-73. [DOI: 10.1002/chem.200801394] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Muñoz FJ, Pérez J, Rumbero Á, Santos JI, Cañada FJ, André S, Gabius HJ, Jiménez-Barbero J, Sinisterra JV, Hernáiz MJ. Glycan Tagging to Produce Bioactive Ligands for a Surface Plasmon Resonance (SPR) Study via Immobilization on Different Surfaces. Bioconjug Chem 2009; 20:673-82. [DOI: 10.1021/bc800350q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F. Javier Muñoz
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - José Pérez
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - Ángel Rumbero
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - J. Ignacio Santos
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - F. Javier Cañada
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - Sabine André
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - Hans-Joachim Gabius
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - Jesús Jiménez-Barbero
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - José V. Sinisterra
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
| | - María J. Hernáiz
- Departamento de Química Orgánica y Farmacéutica, Universidad Complutense de Madrid, Pz/ Ramón y Cajal s/n. 28040 Madrid, Spain, Departamento de Química Orgánica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain, Departamento de Ciencia de Proteínas, CIB-CSIC, c/Ramiro de Maeztu 9, 28040 Madrid, Spain, Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstr 13, 80539 München, Germany, Servicio de Biotransformaciones
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Muñoz FJ, Rumbero Á, Sinisterra JV, Santos JI, André S, Gabius H, Jiménez-barbero J, Hernáiz MJ. Versatile strategy for the synthesis of biotin-labelled glycans, their immobilization to establish a bioactive surface and interaction studies with a lectin on a biochip. Glycoconj J 2008; 25:633-46. [DOI: 10.1007/s10719-008-9115-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2007] [Revised: 01/25/2008] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
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Silipo A, Zhang Z, Cañada FJ, Molinaro A, Linhardt RJ, Jiménez-Barbero J. Conformational analysis of a dermatan sulfate-derived tetrasaccharide by NMR, molecular modeling, and residual dipolar couplings. Chembiochem 2008; 9:240-52. [PMID: 18072186 PMCID: PMC4135520 DOI: 10.1002/cbic.200700400] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Indexed: 11/08/2022]
Abstract
The solution conformation behavior of a dermatan-derived tetrasaccharide--Delta HexA-(1-->3)-GalNAc4S-beta-(1-->4)-IdoA-alpha-(1-->3)-red-GalNAc4S (S is a sulfate group)--has been explored by means of NMR spectroscopy, especially by NOE-based conformational analysis. The tetrasaccharide was present as four species, two of which are chemically different in the anomeric orientation of the reducing 2-deoxy-2-acetamido-galactose (red-GalNAc) residue, while the other two are the result of different conformations of the iduronic acid (IdoA) unit. The two alpha-beta-interconverting anomers were present in a 0.6:1 ratio. Ring conformations have been defined by analysis of (3)J(H,H) coupling constants and interresidual NOE contacts. Both 2-deoxy-2-acetamido-galactose (GalNAc) residues were found in the (4)C(1) chair conformation, the unsaturated uronic acid (Delta-Hex A) adopts a strongly predominant half-chair (1)H(2) conformation, while the IdoA residue exists either in the (1)C(4) chair or in the (2)S(0) skewed boat geometries, in a 4:1 ratio. There is a moderate flexibility of Phi and Psi torsions as suggested by nuclear Overhauser effects (NOEs), molecular modeling (MM), and molecular dynamics (MD) studies. This was further investigated by residual dipolar couplings (RDCs). One-bond C--H RDCs ((1)D(C,H)) and long-range H-H ((3)D(H,H)) RDCs were measured for the tetrasaccharide in a phage solution and interpreted in combination with restrained MD simulation. The RDC-derived data substantially confirmed the validity of the conformer distribution resulting from the NOE-derived simulations, but allowed an improved definition of the conformational behavior of the oligosaccharides in solution. In summary, the data show a moderate flexibility of the four tetrasaccharide species at the central glycosidic linkage. Differences in the shapes of species with the IdoA in skew and in chair conformations and in the distribution of the sulfate groups have also been highlighted.
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Affiliation(s)
- Alba Silipo
- Centro de Investigaciones Biològicas, CSIC, Ramiro de Maeztu 9,28040 Madrid (Spain)
- Dipartimento di Chimica Organica e Biochimica Università di Napoli “Federico II” Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli (Italy)
| | - Zhenqing Zhang
- Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 (USA)
| | - F. Javier Cañada
- Centro de Investigaciones Biològicas, CSIC, Ramiro de Maeztu 9,28040 Madrid (Spain)
| | - Antonio Molinaro
- Dipartimento di Chimica Organica e Biochimica Università di Napoli “Federico II” Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Napoli (Italy)
| | - Robert J. Linhardt
- Departments of Chemistry and Chemical Biology, Biology, and Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180 (USA)
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López-Méndez B, Jia C, Zhang Y, Zhang LH, Sinaÿ P, Jiménez-Barbero J, Sollogoub M. Hemicarbasucrose: Turning off the Exoanomeric Effect Induces Less Flexibility. Chem Asian J 2008; 3:51-8. [DOI: 10.1002/asia.200700281] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Norsikian S, Zeitouni J, Rat S, Gérard S, Lubineau A. New and general synthesis of β-C-glycosylformaldehydes from easily available β-C-glycosylpropanones. Carbohydr Res 2007; 342:2716-28. [PMID: 17892865 DOI: 10.1016/j.carres.2007.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 09/02/2007] [Accepted: 09/04/2007] [Indexed: 10/22/2022]
Abstract
A highly effective method for the introduction of a formyl group at the anomeric position of pyranosides was developed via enolisation of beta-C-D-glycopyranosylpropan-2-one using thermodynamic conditions then oxidative cleavage of the more substituted double bond. This sequence affords the desired aldehydes that are conveniently protected as aminals for purification and storage and easily regenerated using Dowex resin H+. In this paper, the syntheses of nine differently protected aldehydes derived from d-glucose, d-galactose, lactose and N-acetyl-d-glucosamine are presented. Our strategy proved to be very efficient in most cases excepted in the D-mannose series.
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Affiliation(s)
- Stéphanie Norsikian
- Laboratoire de Chimie Organique Multifonctionnelle, UMR CNRS-UPS 8614 Glycochimie Moléculaire, Bât. 420, Université Paris Sud, F-91405 Orsay, France.
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García-Aparicio V, Malapelle A, Abdallah Z, Doisneau G, Santos JI, Asensio JL, Cañada FJ, Beau JM, Jiménez-Barbero J. The solution conformation of C-glycosyl analogues of the sialyl-Tn antigen. Carbohydr Res 2007; 342:1974-82. [PMID: 17466287 DOI: 10.1016/j.carres.2007.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 03/09/2007] [Accepted: 03/16/2007] [Indexed: 10/23/2022]
Abstract
The conformational behavior of two C-glycosyl analogues of the sialyl-Tn antigen has been determined by a combination of NMR methods and molecular mechanics calculations. Both compounds show a major solution conformation that is drastically different from the major one of the natural compound.
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Denton RW, Tony KA, Hernández-Gay JJ, Cañada FJ, Jiménez-Barbero J, Mootoo DR. Synthesis and conformational behavior of the difluoromethylene linked C-glycoside analog of beta-galactopyranosyl-(1<-->1)-alpha-mannopyranoside. Carbohydr Res 2007; 342:1624-35. [PMID: 17601514 PMCID: PMC2084073 DOI: 10.1016/j.carres.2007.06.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 10/23/2022]
Abstract
C-Glycosides in which the pseudoglycosidic substituent is a methylene group have been advertised as hydrolytically stable mimetics of their parent O-glycosides. While this substitution assures greater stability, the lower polarity and increased conformational flexibility in the intersaccharide linker brought about by this change may compromise biological mimicry. In this regard, C-glycosides, in which the pseudoanomeric methylene is replaced with a difluoromethylene group, are interesting because the CF2 group is more of an isopolar replacement for oxygen than CH2. In addition, the CF2 residue is expected to instill conformational bias into the intersaccharide torsions. Herein is described the synthesis and conformational behavior of the difluoromethylene linked C-glycoside of beta-D-galactopyranosyl-(1<-->1)-alpha-D-mannopyranoside. The synthesis centers on the formation of the galactose residue via an oxocarbenium ion-enol ether cyclization. Conformational analysis, using a combination of molecular mechanics, dynamics, and NMR spectroscopy, suggests that the difluoro-C-glycoside populates the non-exo-Gal/exo-Man conformer to a major extent (ca 50%), with a minor contribution ( approximately 15%) from the exo-Gal/exo-Man conformer that corresponds to the ground sate of the parent O-glycoside.
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Affiliation(s)
- Richard W Denton
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10021, USA
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Eklund R, Lycknert K, Söderman P, Widmalm G. A conformational dynamics study of alpha-l-Rhap-(1-->2)[alpha-l-Rhap-(1-->3)]-alpha-l-Rhap-OMe in solution by NMR experiments and molecular simulations. J Phys Chem B 2007; 109:19936-45. [PMID: 16853578 DOI: 10.1021/jp053198o] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational preference of alpha-l-Rhap-(1-->2)[alpha-l-Rhap-(1-->3)]-alpha-l-Rhap-OMe in solution has been studied by NMR spectroscopy using one-dimensional (1)H,(1)H T-ROESY experiments and measurement of trans-glycosidic (3)J(C,H) coupling constants. Molecular dynamics (MD) simulations with a CHARMM22 type of force field modified for carbohydrates were performed with water as the explicit solvent. The homonuclear cross-relaxation rates, interpreted as effective proton-proton distances, were compared to those obtained from simulation. Via a Karplus torsional relationship, (3)J(C,H) values were calculated from simulation and compared to experimental data. Good agreement was observed between experimental data and the MD simulation, except for one inter-residue T-ROE between protons in the terminal sugar residues. The results show that the trisaccharide exhibits substantial conformational flexibility, in particular along the psi glycosidic torsion angles. Notably, for these torsions, a high degree of correlation (77%) was observed in the MD simulation revealing either psi(2)(+) psi(3)(+) or psi(2)(-)psi(3)(-) states. The simulations also showed that non-exoanomeric conformations were present at the phi torsion angles, but to a limited extent, with the phi(3) state populated to a larger extent than the phi(2) state. Further NMR analysis of the trisaccharide by translational diffusion measurements and (13)C T(1) relaxation experiments quantified global reorientation using an anisotropic model together with interpretation of the internal dynamics via the "model-free" approach. Fitting of the dynamically averaged states to experimental data showed that the psi(2)(+)psi(3)(+) state is present to approximately 49%, psi(2)(-) psi(3)(-) to approximately 39%, and phi(3) (non-exo) to approximately 12%. Finally, using a dynamic and population-averaged model, (1)H,(1)H T-ROE buildup curves were calculated using a full relaxation matrix approach and were found to be in excellent agreement with experimental data, in particular for the above inter-residue proton-proton interaction between the terminal residues.
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Affiliation(s)
- Robert Eklund
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
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Martín A, Quintanal LM, Suárez E. Hydrogen atom transfer experiments provide chemical evidence for the conformational differences between C- and O-glycosides. Tetrahedron Lett 2007; 48:5507-11. [DOI: 10.1016/j.tetlet.2007.05.166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Clavel C, Canales A, Gupta G, Santos JI, Cañada FJ, Penadés S, Surolia A, Jiménez-Barbero J. NMR studies on the conformation of oligomannosides and their interaction with banana lectin. Glycoconj J 2007; 24:449-64. [PMID: 17492504 DOI: 10.1007/s10719-007-9037-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 02/22/2007] [Accepted: 04/04/2007] [Indexed: 10/23/2022]
Abstract
The conformational and dynamic behaviour of three mannose containing oligosaccharides, a tetrasaccharide with alpha1-->2, and alpha1-->3, and a penta and a heptasaccharide with alpha1-->2, alpha1-->3, and alpha1-->6 linkages has been evaluated by molecular mechanics and dynamics simulations and NMR spectroscopical methods. It is found that they display a fair amount of conformational freedom, with one major and one minor conformation per glycosidic linkage. The evaluation of their recognition by banana lectin has also been performed by STD NMR methods and a preliminary view of their putative interaction mode has been carried out by means of docking procedures.
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Affiliation(s)
- Caroline Clavel
- Laboratory of Glyconanotechnology, CIC biomaGUNE, Paseo Miramón 182, 20009 San Sebastián, Spain
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Affiliation(s)
- Odón Arjona
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
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Hernández-Gay JJ, Panza L, Ronchetti F, Cañada FJ, Compostella F, Jiménez-Barbero J. The conformational behaviour of the C-glycosyl analogue of sulfatide studied by NMR in SDS micelles. Carbohydr Res 2007; 342:1966-73. [PMID: 17511975 DOI: 10.1016/j.carres.2007.04.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 04/16/2007] [Accepted: 04/22/2007] [Indexed: 10/23/2022]
Abstract
The conformational behaviour of sulfatide and its C-glycosyl analogue has been studied by using a combination of J and NOE data assisted by molecular mechanics calculations. There is a major exoanomeric conformation around the phi angle of both molecules with two or three conformers contributing to the equilibrium around psi. The MM3* calculations only provide a qualitative description of the actual population distribution. Despite this geometrical similarity, the quantitative analysis of the NOE intensities at a variety of mixing times indicates that the motion around the pseudoglycosidic linkages of the C-glycosyl analogue is faster than that for the natural compound.
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Affiliation(s)
- José Juan Hernández-Gay
- Departamento de Ciencia de Proteínas, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Clavel C, Canales A, Gupta G, Cañada FJ, Penadés S, Surolia A, Jiménez-Barbero J. NMR Investigation of the Bound Conformation of Natural and Synthetic Oligomannosides to Banana Lectin. European J Org Chem 2007. [DOI: 10.1002/ejoc.200600897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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