| 1. |
- Angles d'Ortoli, Thibault, 1987-
(author)
-
Assembling and Unraveling Carbohydrates Structures : Conformational analysis of synthesized branched oligosaccharides
- 2016
-
Doctoral thesis (other academic/artistic)abstract
- Advances in the elaboration of vaccines and enzyme inhibitors rely on acquiring more knowledge about protein-carbohydrate binding events. Furthermore, the relationships between biological function and the three-dimensional properties of large glycans can be studied by focusing on the structural components they contained, namely, by scaling down the system under analysis. Chemical methods are useful assets as they allow the isolation and determination of epitopes; these small and recognizable fragments that lead to very specific interactions. In this thesis, biologically relevant saccharides were obtained using recently developed concepts in carbohydrate synthesis and NMR spectroscopy was used to unravel their conformational preferences.In paper I, the convergent synthesis of the tetrasaccharide found in the natural product solaradixine is described. Reactivity enhanced disaccharide glycosyl donors were coupled to a disaccharide acceptor in a 2 + 2 fashion. The computer program CASPER was subsequently used to verify the synthesized structure.The conformation arming concept employed in paper I was further investigated in paper II. An NMR-based methodology enabled the determination of the ring conformations of a set of donors. Subsequently, glycosylation reactions were performed and yields were correlated to donors ring shapes. Perturbations in the rings shape caused by bulky silyl ether protective groups were sufficient to boost the potency of several donors. As a matter of fact, complex branched oligosaccharides could be obtained in good to excellent yields.In paper III, NMR spectroscopy observables were measured to elucidate the ring shape, the mutual orientation of the rings across the glycosidic bond and the positions of the side chains of 5 trisaccharides found in larger structures. With the aid of molecular dynamics simulations, their overall conformational propensities were revealed.Finally, the software CASPER prediction skills were improved by adding, inter alia, NMR information of synthesized mono- and disaccharides to its database. Unassigned chemical shifts from polysaccharides served as input to challenge its ability to solve large carbohydrate structures.
|
|
| 2. |
- Angles d'Ortoli, Thibault, et al.
(author)
-
Structure-Reactivity Relationships of Conformationally Armed Disaccharide Donors and Their Use in the Synthesis of a Hexasaccharide Related to the Capsular Polysaccharide from Streptococcus pneumoniae Type 37
- 2017
-
In: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 82:15, s. 8123-8140
-
Journal article (peer-reviewed)abstract
- To advance the field of glycobiology, efficient synthesis methods of oligosaccharides and glycoconjugates are a requisite. In glycosylation reactions using superarmed donors, both selectivity and reactivity issues must be considered, and we herein investigate these aspects for differently protected beta-linked 2-O-glycosylated glucosyl donors carrying bulky tert-butyldimethylsilyl groups to different extents. The acceptors in reactions being secondary alcohols presents a challenging situation with respect to steric crowding. Conformational pyranose ring equilibria of the superarmed disaccharide donors with axial-rich substituents contained skew and boat conformations, and three-state models were generally assumed. With NIS/TfOH as the promotor, 2,6-di-tert-butyl-4-methylpyridine as the base, and a dichloromethane/toluene solvent mixture, ethyl 1-thio-beta-d-glucosyl disaccharide donors having 6-O-benzyl group(s) besides tert-butyldimethylsilyl groups were efficiently coupled at -40 degrees C to the hydroxyl group at position 3 of glucopyranosyl acceptors to form beta-(1 -> 2),beta-(1 -> 3)-linked trisaccharides, isolated in excellent 95% yield. The more axial-rich donors in skew and boat conformations are thus preorganized closer to the assumed transition state in these glycosylation reactions. The developed methodology was subsequently applied in the synthesis of a multibranched hexasaccharide related to the capsular polysaccharide from Streptococcus pneumoniae type 37, which consists of a beta-(1 -> 3)-linked backbone and a beta-(1 -> 2)-linked side chain of D-glucosyl residues in disaccharide repeating units.
|
|
| 3. |
- Angles d'Ortoli, Thibault, et al.
(author)
-
Synthesis of the tetrasaccharide glycoside moiety of Solaradixine and rapid NMR-based structure verification using the program CASPER
- 2016
-
In: Tetrahedron. - : Elsevier. - 0040-4020 .- 1464-5416. ; 72:7, s. 912-927
-
Journal article (peer-reviewed)abstract
- The major glycoalkaloid in the roots of Solanum laciniatum is Solaradixine having the branched tetrasaccharide beta-D-Glcp-(1 -> 2)-beta-D-Glcp-(1 -> 3)[alpha-L-Rhap-(1 -> 2)]-beta-D-Galp linked to O3 of the steroidal alkaloid Solasodine. We herein describe the synthesis of the methyl glycoside of the tetrasaccharide using a super-armed disaccharide as a donor molecule. A 2-(naphthyl)methyl protecting group was used in the synthesis of the donor since it was tolerant to a wide range of reaction conditions. The 6-O-benzylated-hexa-O-tert-butyldimethylsilyi-protected beta-D-Glcp-(1 -> 2)-beta-D-Glcp-SEt donor, which avoided 1,6-anydro formation, was successfully glycosylated at O3 of a galactoside acceptor molecule. However, subsequent glycosylation at O2 by a rhamnosyl donor was unsuccessful and instead a suitably protected alpha-L-Rhap(1 -> 2)-beta-D-Galp-OMe disaccharide was used as the acceptor molecule together with a super-armed beta-D-Glcp-(1 -> 2)-beta-D-Glcp-SEt donor in the glycosylation reaction, to give a tetrasaccharide in a yield of 55%, which after deprotection resulted in the target molecule, the structure of which was verified by the NMR chemical shift prediction program CASPER.
|
|
| 4. |
- Angles d'Ortoli, Thibault, et al.
(author)
-
Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers
- 2015
-
In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:30, s. 9559-9570
-
Journal article (peer-reviewed)abstract
- Empirical force fields for computer simulations of carbohydrates are often implicitly assumed to be valid also at temperatures different from room temperature for which they were optimited: Herein, the temperature dependence of the hydroxymethyl group rotamer populations in short oligogaccharides is invegtigated using Molecular dynamics simulations and NMR spectroscopy. Two oligosaccharides, methyl beta-cellobioside and beta-cellotetraose were simulated using three different carbohydrate force fields (CHARMM C35, GLYCAM06, and GROMOS 56A(carbo)) in combination with different water models (SPC, SPC/E, and TIP3P) using replica exchange molecular dynamics simulations. For comparison, hydroxymethyl group rotamer populations were investigated for methyl beta-cellobioside and cellopentaose based- on measured NMR (3)J(H5,H6) coupling constants, in the latter case by using a chemical shift selective NMR-filter. Molecular dynamics simulations in combination with NMR spectroscopy show that the temperature dependence of the hydroxymethyl rotamer population in these short cellooligomers, in the range 263-344 K, generally becomes exaggerated in simulations when compared to experimental data, but also that it is dependent on simulation conditions, and most notably properties of the water model.
|
|
| 5. |
- Bergenstrahle-Wohlert, Malin, et al.
(author)
-
On the anomalous temperature dependence of cellulose aqueous solubility
- 2016
-
In: Cellulose. - : Springer. - 0969-0239 .- 1572-882X. ; 23:4, s. 2375-2387
-
Journal article (peer-reviewed)abstract
- The solubility of cellulose in water-based media is promoted by low temperature, which may appear counter-intuitive. An explanation to this phenomenon has been proposed that is based on a temperature-dependent orientation of the hydroxymethyl group. In this paper, this hypothesis is investigated using molecular dynamics computer simulations and NMR spectroscopy, and is discussed in conjunction with alternative explanations based on solvent–solute and solvent–solvent hydrogen bond formation respectively. It is shown that neither simulations nor experiments lend support to the proposed mechanism based on the hydroxymethyl orientation, whereas the two alternative explanations give rise to two distinct contributions to the hydration free energy of cellooligomers.
|
|
| 6. |
- Berglund, Jennie, et al.
(author)
-
A molecular dynamics study of the effect of glycosidic linkage type in the hemicellulose backbone on the molecular chain flexibility
- 2016
-
In: The Plant Journal. - : John Wiley & Sons Ltd.. - 0960-7412 .- 1365-313X. ; 88:1, s. 56-70
-
Journal article (peer-reviewed)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 NMR 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 hemicelluloses’ function both in the cell wall and in technical products.
|
|
| 7. |
|
|
| 8. |
- Dorst, Kevin M., et al.
(author)
-
On the Influence of Solvent on the Stereoselectivity of Glycosylation Reactions
-
Other publication (other academic/artistic)abstract
- Methodology development in carbohydrate chemistry entails the stereoselective formation of C–O bonds as a key step in the synthesis of oligo- and polysaccharides. The anomeric selectivity of aglycosylation reaction is affected by a multitude of parameters, such as the nature of the donor andacceptor, activator/promotor system, temperature and solvent. The influence of different solvents onthe stereoselective outcome of glycosylation reactions employing thioglucopyranosides as glycosyldonors with a non-participating protecting group at position 2 has been studied. A large change inselectivity as a function of solvent was observed and a correlation between selectivity and the Kamlet-Taft solvent parameter π* was found. Furthermore, molecular modeling using density functionaltheory methodology was conducted to decipher the role of the solvent and possible reaction pathwayswere investigated.
|
|
| 9. |
- Dorst, Kevin, 1992-, et al.
(author)
-
On the influence of solvent on the stereoselectivity of glycosylation reactions
- 2024
-
In: Carbohydrate Research. - 0008-6215 .- 1873-426X. ; 535
-
Journal article (peer-reviewed)abstract
- Methodology development in carbohydrate chemistry entails the stereoselective formation of C-O bonds as a key step in the synthesis of oligo- and polysaccharides. The anomeric selectivity of a glycosylation reaction is affected by a multitude of parameters, such as the nature of the donor and acceptor, activator/promotor system, temperature and solvent. The influence of different solvents on the stereoselective outcome of glycosylation reactions employing thioglucopyranosides as glycosyl donors with a non-participating protecting group at position 2 has been studied. A large change in selectivity as a function of solvent was observed and a correlation between selectivity and the Kamlet-Taft solvent parameter pi* was found. Furthermore, molecular modeling using density functional theory methodology was conducted to decipher the role of the solvent and possible reaction pathways were investigated.
|
|
| 10. |
- Furevi, Axel, 1992-, et al.
(author)
-
Complete 1H and 13C NMR chemical shift assignments of mono-to tetrasaccharides as basis for NMR chemical shift predictions of oligo- and polysaccharides using the computer program CASPER
- 2022
-
In: Carbohydrate Research. - : Elsevier BV. - 0008-6215 .- 1873-426X. ; 513
-
Journal article (peer-reviewed)abstract
- Carbohydrate structure can be elucidated or confirmed by using NMR spectroscopy as the prime technique. Prediction of 1H and 13C NMR chemical shifts by computational approaches makes this assignment process more efficient and the program CASPER can perform this task rapidly. It does so by relying on chemical shift data of mono-, di-, and trisaccharides. In order to improve accuracy and quality of these predictions we have assigned 1H and 13C NMR chemical shifts of 30 monosaccharides, 17 disaccharides, 10 trisaccharides and one tetrasaccharide; in total 58 compounds. Due to different rotamers, ring forms, α- and β-anomeric forms and pD conditions this resulted in 74 1H and 13C NMR chemical shift data sets, all of which were refined using total line-shape analysis for the 1H resonances in order to obtain accurate chemical shifts. Subsequent NMR chemical shift predictions for three sialic acid-containing oligosaccharides, viz., GD1a, a disialyl-LNnT hexasaccharide and a polysialic acid-lactose decasaccharide, and NMR-based structural elucidations of two O-antigen polysaccharides from E. coli O174 were performed by the CASPER program (http://www.casper.organ.su.se/casper/) resulting in very good to excellent agreement between experimental and predicted data thereby demonstrating its utility for carbohydrate compounds that have been chemically or enzymatically synthesized, structurally modified or isolated from nature.
|
|
