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Identification of New L-Fucosyl and L-Galactosyl Amides as Glycomimetic Ligands of TNF Lectin Domain of BC2L-C from Burkholderia cenocepacia. Molecules 2023; 28:molecules28031494. [PMID: 36771163 PMCID: PMC9919437 DOI: 10.3390/molecules28031494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
The inhibition of carbohydrate-lectin interactions is being explored as an efficient approach to anti adhesion therapy and biofilm destabilization, two alternative antimicrobial strategies that are being explored against resistant pathogens. BC2L-C is a new type of lectin from Burkholderia cenocepacia that binds (mammalian) fucosides at the N-terminal domain and (bacterial) mannosides at the C-terminal domain. This double carbohydrate specificity allows the lectin to crosslink host cells and bacterial cells. We have recently reported the design and generation of the first glycomimetic antagonists of BC2L-C, β-C- or β-N-fucosides that target the fucose-specific N-terminal domain (BC2L-C-Nt). The low water solubility of the designed N-fucosides prevented a full examination of this promising series of ligands. In this work, we describe the synthesis and biophysical evaluation of new L-fucosyl and L-galactosyl amides, designed to be water soluble and to interact with BC2L-C-Nt. The protein-ligand interaction was investigated by Saturation Transfer Difference NMR, Isothermal Titration Calorimetry and crystallographic studies. STD-NMR experiments showed that both fucosyl and galactosyl amides compete with α-methyl fucoside for lectin binding. A new hit compound was identified with good water solubility and an affinity for BC2L-C-Nt of 159 μM (ITC), which represents a one order of magnitude gain over α-methyl fucoside. The x-ray structure of its complex with BC2L-C-Nt was solved at 1.55 Å resolution.
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Goyard D, Ortiz AMS, Boturyn D, Renaudet O. Multivalent glycocyclopeptides: conjugation methods and biological applications. Chem Soc Rev 2022; 51:8756-8783. [PMID: 36193815 PMCID: PMC9575389 DOI: 10.1039/d2cs00640e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Indexed: 11/21/2022]
Abstract
Click chemistry was extensively used to decorate synthetic multivalent scaffolds with glycans to mimic the cell surface glycocalyx and to develop applications in glycosciences. Conjugation methods such as oxime ligation, copper(I)-catalyzed alkyne-azide cycloaddition, thiol-ene coupling, squaramide coupling or Lansbury aspartylation proved particularly suitable to achieve this purpose. This review summarizes the synthetic strategies that can be used either in a stepwise manner or in an orthogonal one-pot approach, to conjugate multiple copies of identical or different glycans to cyclopeptide scaffolds (namely multivalent glycocyclopeptides) having different size, valency, geometry and molecular composition. The second part of this review will describe the potential of these structures to interact with various carbohydrate binding proteins or to stimulate immunity against tumor cells.
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Affiliation(s)
- David Goyard
- Univ. Grenoble Alpes, CNRS, DCM UMR 5250, F-38000 Grenoble, France.
| | | | - Didier Boturyn
- Univ. Grenoble Alpes, CNRS, DCM UMR 5250, F-38000 Grenoble, France.
| | - Olivier Renaudet
- Univ. Grenoble Alpes, CNRS, DCM UMR 5250, F-38000 Grenoble, France.
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3
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Coyle T, Wu L, Debowski AW, Davies GJ, Stubbs KA. Synthetic and Crystallographic Insight into Exploiting sp 2 Hybridization in the Development of α-l-Fucosidase Inhibitors. Chembiochem 2019; 20:1365-1368. [PMID: 30663832 PMCID: PMC6589914 DOI: 10.1002/cbic.201800710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/20/2019] [Indexed: 11/25/2022]
Abstract
The sugar fucose plays a myriad of roles in biological recognition. Enzymes hydrolyzing fucose from glycoconjugates, α‐l‐fucosidases, are important targets for inhibitor and probe development. Here we describe the synthesis and evaluation of novel α‐l‐fucosidase inhibitors, with X‐ray crystallographic analysis using an α‐l‐fucosidase from Bacteroides thetaiotamicron helping to lay a foundation for future development of inhibitors for this important enzyme class.
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Affiliation(s)
- Travis Coyle
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Present address: School of Chemistry, University College Dublin, Stillorgan Road, Belfield, Dublin, 4, Ireland
| | - Liang Wu
- Department of Chemistry, York Structural Laboratory, University of York, Heslington, York, YO10 5DD, UK
| | - Aleksandra W Debowski
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Gideon J Davies
- Department of Chemistry, York Structural Laboratory, University of York, Heslington, York, YO10 5DD, UK
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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4
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Goyard D, Baldoneschi V, Varrot A, Fiore M, Imberty A, Richichi B, Renaudet O, Nativi C. Multivalent Glycomimetics with Affinity and Selectivity toward Fucose-Binding Receptors from Emerging Pathogens. Bioconjug Chem 2017; 29:83-88. [DOI: 10.1021/acs.bioconjchem.7b00616] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Veronica Baldoneschi
- Department
of Chemistry Ugo Schiff, University of Florence, via della Lastruccia, 13−50019 Sesto F.no (FI) Italy
| | | | - Michele Fiore
- ICBMS, University of Lyon, 43 Blvd. du 11 novembre 1918, 69622, Villeubanne Cedex, France
| | | | - Barbara Richichi
- Department
of Chemistry Ugo Schiff, University of Florence, via della Lastruccia, 13−50019 Sesto F.no (FI) Italy
| | | | - Cristina Nativi
- Department
of Chemistry Ugo Schiff, University of Florence, via della Lastruccia, 13−50019 Sesto F.no (FI) Italy
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Pifferi C, Daskhan GC, Fiore M, Shiao TC, Roy R, Renaudet O. Aminooxylated Carbohydrates: Synthesis and Applications. Chem Rev 2017; 117:9839-9873. [PMID: 28682060 DOI: 10.1021/acs.chemrev.6b00733] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Among other classes of biomolecules, carbohydrates and glycoconjugates are widely involved in numerous biological functions. In addition to addressing the related synthetic challenges, glycochemists have invested intense efforts in providing access to structures that can be used to study, activate, or inhibit these biological processes. Over the past few decades, aminooxylated carbohydrates have been found to be key building blocks for achieving these goals. This review provides the first in-depth overview covering several aspects related to the syntheses and applications of aminooxylated carbohydrates. After a brief introduction to oxime bonds and their relative stabilities compared to related C═N functions, synthetic aspects of oxime ligation and methodologies for introducing the aminooxy functionality onto both glycofuranosyls and glycopyranosyls are described. The subsequent section focuses on biological applications involving aminooxylated carbohydrates as components for the construcion of diverse architectures. Mimetics of natural structures represent useful tools for better understanding the features that drive carbohydrate-receptor interaction, their biological output and they also represent interesting structures with improved stability and tunable properties. In the next section, multivalent structures such as glycoclusters and glycodendrimers obtained through oxime ligation are described in terms of synthetic design and their biological applications such as immunomodulators. The second-to-last section discusses miscellaneous applications of oxime-based glycoconjugates, such as enantioselective catalysis and glycosylated oligonucleotides, and conclusions and perspectives are provided in the last section.
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Affiliation(s)
- Carlo Pifferi
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Gour Chand Daskhan
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Michele Fiore
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Tze Chieh Shiao
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - René Roy
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - Olivier Renaudet
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France.,Institut Universitaire de France , 103 Boulevard Saint-Michel, 75005 Paris, France
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6
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Abstract
The synthesis and chemical and physicochemical properties as well as biological and medical applications of various hydroxylamine-functionalized carbohydrate derivatives are summarized.
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Affiliation(s)
- N. Chen
- PPSM
- ENS Cachan
- CNRS
- Alembert Institute
- Université Paris-Saclay
| | - J. Xie
- PPSM
- ENS Cachan
- CNRS
- Alembert Institute
- Université Paris-Saclay
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7
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Daskhan GC, Berthet N, Thomas B, Fiore M, Renaudet O. Multivalent glycocyclopeptides: toward nano-sized glycostructures. Carbohydr Res 2015; 405:13-22. [DOI: 10.1016/j.carres.2014.07.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 10/25/2022]
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Bini D, Nicotra F, Cipolla L. Bifunctional dendrons for multiple carbohydrate presentation via carbonyl chemistry. Beilstein J Org Chem 2014; 10:1686-91. [PMID: 25161728 PMCID: PMC4143090 DOI: 10.3762/bjoc.10.177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/27/2014] [Indexed: 01/01/2023] Open
Abstract
The synthesis of new dendrons of the generations 0, 1 and 2 with a double bond at the focal point and a carbonyl group at the termini has been carried out. The carbonyl group has been exploited for the multivalent conjugation to a sample saccharide by reductive amination and alkoxyamine conjugation.
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Affiliation(s)
- Davide Bini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Francesco Nicotra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Laura Cipolla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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Kancharla PK, Kato T, Crich D. Probing the influence of protecting groups on the anomeric equilibrium in sialic acid glycosides with the persistent radical effect. J Am Chem Soc 2014; 136:5472-80. [PMID: 24606062 PMCID: PMC4004215 DOI: 10.1021/ja501276r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/11/2022]
Abstract
A method for the investigation of the influence of protecting groups on the anomeric equilibrium in the sialic acid glycosides has been developed on the basis of the equilibration of O-sialyl hydroxylamines by reversible homolytic scission of the glycosidic bond following the dictates of the Fischer-Ingold persistent radical effect. It is found that a trans-fused 4O,5N-oxazolidinone group stabilizes the equatorial glycoside, i.e., reduces the anomeric effect, when compared to the 4O,5N-diacetyl protected systems. This effect is discussed in terms of the powerful electron-withdrawing nature of the oxazolidinone system, which in turn is a function of its strong dipole moment in the mean plane of the pyranose ring system. The new equilibration method displays a small solvent effect and is most pronounced in less polar media consistent with the anomeric effect in general. The unusual (for anomeric radicals) poor kinetic selectivity of anomeric sialyl radicals is discussed in terms of the planar π-type structure of these radicals and of competing 1,3-diaxial interactions in the diastereomeric transition states for trapping on the α- and β-faces of the radical.
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Affiliation(s)
- Pavan K Kancharla
- Department of Chemistry, Wayne State University , 5101 Cass Avenue, Detroit, Michigan 48202, United States
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Berthet N, Thomas B, Bossu I, Dufour E, Gillon E, Garcia J, Spinelli N, Imberty A, Dumy P, Renaudet O. High affinity glycodendrimers for the lectin LecB from Pseudomonas aeruginosa. Bioconjug Chem 2013; 24:1598-611. [PMID: 23888914 DOI: 10.1021/bc400239m] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Following an iterative oxime ligation procedure, cyclopeptide (R) and lysine-based dendron (D) were combined in all possible arrangements and successively functionalized with α-fucose and β-fucose to provide a new series of hexadecavalent glycosylated scaffolds (i.e., scaffolds RD16, RR16, DR16, and DD16). These compounds and smaller analogs (tetra- and hexavalent scaffolds R4 and R6) were used to evaluate the influence of the ligand valency and architecture, and of the anomer configuration in the binding to the αFuc-specific lectin LecB from Pseudomonas aeruginosa . Competitive enzyme-linked lectin assays (ELLA) revealed that only the RD16 architecture displaying αFuc (9A) reaches strong binding improvement (IC50 of 0.6 nM) over αMeFuc, and increases the α-selectivity of LecB. Dissociation constant of 28 nM was measured by isothermal titration micorcalorimetry (ITC) for 9A, which represents the highest affinity ligand ever reported for LecB. ITC and molecular modeling suggested that the high affinity observed might be due to an aggregative chelate binding involving four sugar head groups and two lectins. Interestingly, unprecedented binding effects were observed with β-fucosylated conjugates, albeit being less active than the corresponding ligands of the αFuc series. In particular, the more flexible lysine-based dendritic structures (15B and 18B) showed a slight inhibitory enhancement in comparison with those having cyclopeptide core.
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Affiliation(s)
- Nathalie Berthet
- Département de Chimie Moléculaire, UMR-CNRS 5250 & ICMG FR 2607 , Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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Thomas B, Berthet N, Garcia J, Dumy P, Renaudet O. Expanding the scope of oxime ligation: facile synthesis of large cyclopeptide-based glycodendrimers. Chem Commun (Camb) 2013; 49:10796-8. [DOI: 10.1039/c3cc45368e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
Because of the importance of carbohydrate-protein interactions in biological processes, the development of glycoclusters and glycodendrimers capable of mimicking the multivalent display of carbohydrates at the cell surface has become a major field of research over the last decade. Among the large variety of scaffolds that are now available, peptides and cyclopeptides are widely used for the multivalent presentation of glycans. This review will provide an overview of the most recent advances in the preparation and utilization of linear glycopeptides and glycocyclopeptides in glycobiology.
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Affiliation(s)
- M Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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13
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Thomas B, Fiore M, Bossu I, Dumy P, Renaudet O. Synthesis of heteroglycoclusters by using orthogonal chemoselective ligations. Beilstein J Org Chem 2012; 8:421-7. [PMID: 22509212 PMCID: PMC3326620 DOI: 10.3762/bjoc.8.47] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 02/29/2012] [Indexed: 12/20/2022] Open
Abstract
Synthetic heteroglycoclusters are being subjected to increasing interest due to their potential to serve as selective ligands for carbohydrate-binding proteins. In this paper, we describe an expedient strategy to prepare cyclopeptides displaying well-defined distributions and combinations of carbohydrates. By using both oxime ligation and copper(I)-catalyzed alkyne–azide cycloaddition, two series of compounds bearing binary combinations of αMan, αFuc or βLac in an overall tetravalent presentation, and either 2:2 or 3:1 relative proportions, have been prepared.
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Affiliation(s)
- Baptiste Thomas
- Département de Chimie Moléculaire, UMR-CNRS 5250 & ICMG FR 2607, Université Joseph Fourier, PB 53, 38041 Grenoble Cedex 9, France
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Bossu I, Berthet N, Dumy P, Renaudet O. Synthesis of Glycocyclopeptides by Click Chemistry and Inhibition Assays with Lectins. J Carbohydr Chem 2011. [DOI: 10.1080/07328303.2011.590260] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Isabelle Bossu
- a Département de Chimie Moléculaire, UMR-CNRS 5250 & ICMG FR 2607 , Université Joseph Fourier , 570 rue de la chimie, BP 53, 38041 , Grenoble Cedex 9 , France
| | - Nathalie Berthet
- a Département de Chimie Moléculaire, UMR-CNRS 5250 & ICMG FR 2607 , Université Joseph Fourier , 570 rue de la chimie, BP 53, 38041 , Grenoble Cedex 9 , France
| | - Pascal Dumy
- a Département de Chimie Moléculaire, UMR-CNRS 5250 & ICMG FR 2607 , Université Joseph Fourier , 570 rue de la chimie, BP 53, 38041 , Grenoble Cedex 9 , France
| | - Olivier Renaudet
- a Département de Chimie Moléculaire, UMR-CNRS 5250 & ICMG FR 2607 , Université Joseph Fourier , 570 rue de la chimie, BP 53, 38041 , Grenoble Cedex 9 , France
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Renaudet O, Boturyn D, Dumy P. Biomolecular assembly by iterative oxime ligations. Bioorg Med Chem Lett 2009; 19:3880-3. [DOI: 10.1016/j.bmcl.2009.03.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 03/24/2009] [Accepted: 03/25/2009] [Indexed: 10/21/2022]
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16
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Renaudet O, Dumy P. Oxime-Based Synthesis of New Chromogenic and Fluorogenic Oligosaccharides. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Duléry V, Renaudet O, Wilczewski M, Van der Heyden A, Labbé P, Dumy P. Randomized Combinatorial Library of Heteroglycoclusters (hGC). ACTA ACUST UNITED AC 2008; 10:368-71. [DOI: 10.1021/cc800029v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vincent Duléry
- Département de Chimie Moléculaire, UMR CNRS 5250 & ICMG FR-2607, Université Joseph Fourier, 38041 Grenoble Cedex 9, France
| | - Olivier Renaudet
- Département de Chimie Moléculaire, UMR CNRS 5250 & ICMG FR-2607, Université Joseph Fourier, 38041 Grenoble Cedex 9, France
| | - Marie Wilczewski
- Département de Chimie Moléculaire, UMR CNRS 5250 & ICMG FR-2607, Université Joseph Fourier, 38041 Grenoble Cedex 9, France
| | - Angéline Van der Heyden
- Département de Chimie Moléculaire, UMR CNRS 5250 & ICMG FR-2607, Université Joseph Fourier, 38041 Grenoble Cedex 9, France
| | - Pierre Labbé
- Département de Chimie Moléculaire, UMR CNRS 5250 & ICMG FR-2607, Université Joseph Fourier, 38041 Grenoble Cedex 9, France
| | - Pascal Dumy
- Département de Chimie Moléculaire, UMR CNRS 5250 & ICMG FR-2607, Université Joseph Fourier, 38041 Grenoble Cedex 9, France
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