Enzymatic synthesis of complex glycosaminotrioses and study of their molecular recognition by hevein domains

Hevein, a protein found in Hevea brasiliensis, has a CRD domain, which is known to bind chitin and GlcNAc-containing oligosaccharides. By using NMR and molecular modeling as major tools we have demonstrated that trisaccharides containing GalNAc and ManNAc residues are also recognized by hevein domains. Thus far unknown trisaccharides GlcNAcbeta(1-->4)GlcNAcbeta(1-->4)ManNAc (1) and GalNAcbeta(1-->4)GlcNAcbeta(1-->4)ManNAc (2) were synthesized with the use of beta-N-acetylhexosaminidase from Aspergillus oryzae. This method is based on the rather unique phenomenon that some fungal beta-N-acetylhexosaminidases cannot hydrolyze disaccharide GlcNAcbeta(1-->4)ManNAc (5) contrary to chitobiose GlcNAcbeta(1-->4)GlcNAc (4) that is cleaved and, therefore, cannot be used as an acceptor for further transglycosylation. Both trisaccharides 1 and 2 were prepared by transglycosylation from disaccharidic acceptor in good yields ranging from 35% to 40%. Our observations strongly indicate that the present nature of the modifications of chitotriose (GlcNAcbeta(1-->lcNAcbeta(1-->4)GlcNAc, 3) at either the non-reducing end (GalNAc instead of GlcNAc) or at the reducing end (ManNAc instead of GlcNAc) do not modify the mode of binding of the trisaccharide to hevein. The association constant values indicate that chitotriose (3) binding is better than that of 1 and 2, and that the binding of (with ManNAc at the reducing end) is favored with respect to that of 2 (with ManNAc at the reducing end with a non-reducing GalNAc moiety).     

1,1'-Binaphthyl-substituted macrocycles as receptors for saccharide recognition

The preparation of receptors for saccharide recognition in a natural environment has been an unmet goal for a long time. We present herein the synthesis and binding properties of (R,S)-1,1'-binaphthyl-substituted macrocycles as receptors for saccharide recognition in water/acetonitrile (1:1) and in DMSO. Porphyrin and metalloporphyrin macrocycles with two to four 1,1'-binaphthyl substituents and multiple hydroxy groups generate a binding site for saccharides that incorporates hydrogen-bonding hydroxy groups together with the aromatic hydrophobic pocket. The specificity for di- and trisaccharides is governed by the cavity size. The mechanism of binding has been studied by 1H NMR spectroscopy and the role of H-bonding and CH-pi interactions has been evaluated; the ability to bind saccharides has been demonstrated by the surface plasmon resonance (SPR) technique. The application of these macrocyclic receptors to sensor development is also presented.     

Docking, synthesis, and NMR studies of mannosyl trisaccharide ligands for DC-SIGN lectin

DC-SIGN, a lectin, which presents at the surface of immature dendritic cells, constitutes nowadays a promising target for the design of new antiviral drugs. This lectin recognizes highly glycosylated proteins present at the surface of several pathogens such as HIV, Ebola virus, Candida albicans, Mycobacterium tuberculosis, etc. Understanding the binding mode of this lectin is a topic of tremendous interest and will permit a rational design of new and more selective ligands. Here, we present computational and experimental tools to study the interaction of di- and trisaccharides with DC-SIGN. Docking analysis of complexes involving mannosyl di- and trisaccharides and the carbohydrate recognition domain (CRD) of DC-SIGN have been performed. Trisaccharides Manalpha1,2[Manalpha1,6]Man 1 and Manalpha1,3[Manalpha1,6]Man 2 were synthesized from an orthogonally protected mannose as a common intermediate. Using these ligands and the soluble extracellular domain (ECD) of DC-SIGN, NMR experiments based on STD and transfer-NOE were performed providing additional information. Conformational analysis of the mannosyl ligands in the free and bound states was done. These studies have demonstrated that terminal mannoses at positions 2 or 3 in the trisaccharides are the most important moiety and present the strongest contact with the binding site of the lectin. Multiple binding modes could be proposed and therefore should be considered in the design of new ligands.     

Synthesis of the putative minimal FGF binding motif heparan sulfate trisaccharides by an orthogonal protecting group strategy

The synthesis of two trisaccharides, the putative minimal heparan sulfate sequences responsible for binding to acidic and basic fibroblast growth factors, respectively, is described from a common protected intermediate using an orthogonal protecting group strategy.     

Characterization of O-trimethylsilyl oximes of trisaccharides by gas chromatography–mass spectrometry

Gas chromatography (GC) data (linear retention indices and relative areas) and mass spectra (most representative m/z fragments) of 12 reducing trisaccharides as trimethylsilyl oximes (TMSO) and four non-reducing as trimethylsilyl (TMS) ethers have been described for the first time and related to their structural features. Some trends have been observed: earlier elution of non-reducing compounds and fructotrioses; aldotrioses bearing the reducing end with link in position 6 showing the highest retention. Abundance of several fragment ions and their ratios were useful for trisaccharide characterization; some of these features seem to be useful for the characterization of new trisaccharides.     

Effect of the Substituents of the Neighboring Ring in the Conformational Equilibrium of Iduronate in Heparin‐like Trisaccharides

Based on the structure of the regular heparin, we have prepared a smart library of heparin‐like trisaccharides by incorporating some sulfate groups in the sequence α‐D ‐GlcNS‐ (1‐4)‐α‐L ‐Ido2S‐(1‐4)‐α‐D ‐GlcN. According to the 3D structure of heparin, which features one helix turn every four residues, this fragment corresponds to the minimum binding motif. We have performed a complete NMR study and found that the trisaccharides have a similar 3D structure to regular heparin itself, but their spectral properties are such that allow to extract very detailed information about distances and coupling constants as they are isotropic molecules. The characteristic conformational equilibrium of the central iduronate ring has been analyzed combining NMR and molecular dynamics and the populations of the conformers of the central iduronate ring have been calculated. We have found that in those compounds lacking the sulfate group at position 6 of the reducing end glucosamine, the population of ²S₀ of the central iduronate residue is sensitive to the temperature decreasing to 19 % at 278 K. On the contrary, the trisaccharides with 6‐O‐sulfate in the reducing end glucosamine keep the level of population constant with temperature circa 40 % of ²S₀ similar to that observed at room temperature. Another structural feature that has been revealed through this analysis is the larger flexibility of the L ‐IdoAS‐ D ‐GlcN glycosidic linkage, compared with the D ‐GlcNS‐L ‐IdoA. We propose that this is the point where the heparin chain is bended to form structures far from the regular helix known as kink that have been proposed to play an important role in the specificity of the heparin–protein interaction.     

An Ion Mobility/Ion Trap/Photodissociation Instrument for Characterization of Ion Structure

A new instrument that combines ion mobility spectrometry (IMS) separations with tandem mass spectrometry (MS(n)) is described. Ion fragmentation is achieved with vacuum ultraviolet photodissociation (VUV PD) and/or collision-induced dissociation (CID). The instrument is comprised of an approximately 1 m long drift tube connected to a linear trap that has been interfaced to a pulsed F(2) laser (157 nm). Ion gates positioned in the front and the back of the primary drift region allow for mobility selection of specific ions prior to their storage in the ion trap, mass analysis, and fragmentation. The ion characterization advantages of the new instrument are demonstrated with the analysis of the isomeric trisaccharides, melezitose and raffinose. Mobility separation of precursor ions provides a means of separating the isomers and subsequent VUV PD generates unique fragments allowing them to be distinguished.     

一种木葡聚糖类寡糖的化学合成及生物活性

天然木葡聚糖类寡糖是一类对植物生长具有调节作用的寡糖, 本文以3个单糖组分为原料, 经5步合成了一种木葡聚糖三糖(1)(总产率15%), 以及该三糖的糖苷缀合物1a及其异构体1b. 利用糖基化立体选择性原则, 一步偶联反应同时得到所需的α,β连接产物, 整个合成路线高效简捷. 活性测试结果表明, 3种目标寡糖在1 mg/L浓度下, 对烟草的生长均显示出一定的促进作用, 表明所合成的3种寡糖有望发展成为植物生长促进剂.     

Optimization of the capillary gas chromatographic analysis of mono- and oligosaccharides in honeys

Summary A capillary gas chromatographic method has been developed for simultaneous determination of at least 18 sugars (2 monosaccharides, 11 disaccharides and 5 trisaccharides) in honey, as their oxime-trimethylsilyl ethers. The chromatographic conditions have been systematically and thoroughly optimized, to eliminate the peak overlap commonly reported for this and other methods, especially for disaccharides. Complete analytical details are reported.     

One‐Pot Synthesis of N‐Acetyl‐ and N‐Glycolylneuraminic Acid Capped Trisaccharides and Evaluation of Their Influenza A(H1 N1) Inhibition

Human lung epithelial cells natively offer terminal N‐acetylneuraminic acid (Neu5Ac) α(2→6)‐linked to galactose (Gal) as binding sites for influenza virus hemagglutinin. N‐Glycolylneuraminic acid (Neu5Gc) in place of Neu5Ac is known to affect hemagglutinin binding in other species. Not normally generated by humans, Neu5Gc may find its way to human cells from dietary sources. To compare their influence in influenza virus infection, six trisaccharides with Neu5Ac or Neu5Gc α(2→6) linked to Gal and with different reducing end sugar units were prepared using one‐pot assembly and divergent transformation. The sugar assembly made use of an N‐phthaloyl‐protected sialyl imidate for chemoselective activation and α‐stereoselective coupling with a thiogalactoside. Assessment of cytopathic effect showed that the Neu5Gc‐capped trisaccharides inhibited the viral infection better than their Neu5Ac counterparts.     

Convergent synthesis of a beta-(1-->3)-mannohexaose

An as yet unknown beta-(1-->3)-mannohexaose has been synthesized by a block route involving the coupling of two trisaccharides. Comparison of three closely related attempted mannohexaose syntheses reinforces the influence of subtle matching and/or mismatching interactions on the outcome of convergent oligosaccharide synthesis.     

Sequential one-pot glycosylations using 1-hydroxyl and 1-thiodonors

[reaction: see text] A novel sequential glycosylation procedure is described that combines the use of 1-hydroxyl and thiodonors. The Ph(2)SO/Tf(2)O-mediated dehydrative condensation of 1-hydroxyl donors with thioglycosides affords in good yield the thiodisaccharides, which in turn can be activated by the same activator system to furnish trisaccharides. The alpha-Gal epitope and a hyaluronan trisaccharide were efficiently assembled in a one-pot procedure.     

Synthesis of mono-, di- and trisulfated Lewis x trisaccharides

3′-Sulfated and 3′,6′-disulfated Lewis x trisaccharides have been prepared through selective sulfation of methyl 2-acetamido-6-O-benzyl-2-deoxy-4-O-β-D-galactopyranosyl-3-O-(2,3,4-tri-O-benzyl-α-L-fucopyranosyl)-β-D-glucopyranoside, followed by catalytic hydrogenolysis. In a similar manner, 3′,6-disulfated and 3′,6,6′-trisulfated Lewis x trisaccharides have been selectively obtained from methyl 2-acetamido-2-deoxy-4-O-β-D-galactopyranosyl-3-O-(2,3,4-tri-O-benzyl-α-L-fucopyranosyl)-β-D-glucopyranoside.     

Linear and nonlinear 3D-QSAR approaches in tandem with ligand-based homology modeling as a computational strategy to depict the pyrazolo-triazolo-pyrimidine antagonists binding site of the human adenosine A2A receptor

The integration of ligand- and structure-based strategies might sensitively increase the success of drug discovery process. We have recently described the application of Molecular Electrostatic Potential autocorrelated vectors (autoMEPs) in generating both linear (Partial Least-Square, PLS) and nonlinear (Response Surface Analysis, RSA) 3D-QSAR models to quantitatively predict the binding affinity of human adenosine A3 receptor antagonists. Moreover, we have also reported a novel GPCR modeling approach, called Ligand-Based Homology Modeling (LBHM), as a tool to simulate the conformational changes of the receptor induced by ligand binding. In the present study, the application of both linear and nonlinear 3D-QSAR methods and LBHM computational techniques has been used to depict the hypothetical antagonist binding site of the human adenosine A2A receptor. In particular, a collection of 127 known human A2A antagonists has been utilized to derive two 3D-QSAR models (autoMEPs/PLS&RSA). In parallel, using a rhodopsin-driven homology modeling approach, we have built a model of the human adenosine A2A receptor. Finally, 3D-QSAR and LBHM strategies have been utilized to predict the binding affinity of five new human A2A pyrazolo-triazolo-pyrimidine antagonists finding a good agreement between the theoretical and the experimental predictions.     

Synthesis of mono- and di-α-l-fucosylated 2-acetamido-2-deoxy-N-glycyl-β-d-glucopyranosylamines modeling N-glycoprotein carbohydrate-peptide bond region based on 2-acetamido-N-(N-tert-butyloxycarbonylglycyl)-2-deoxy-β-d-glucopyranosylamine

Russian Chemical Bulletin - A synthesis of glycyl-spacered N-β-glycosides of diand trisaccharides such as α-l-Fucp-(1→3)-β-d-GlcNAcp-NHCOCH2NH2 (1),...     

1D 13C-NMR data as molecular descriptors in spectra--structure relationship analysis of oligosaccharides

Spectra-structure relationships were investigated for estimating the anomeric configuration, residues and type of linkages of linear and branched trisaccharides using 13C-NMR chemical shifts. For this study, 119 pyranosyl trisaccharides were used that are trimers of the α or β anomers of D-glucose, D-galactose, D-mannose, L-fucose or L-rhamnose residues bonded through a or b glycosidic linkages of types 1→2, 1→3, 1→4, or 1→6, as well as methoxylated and/or N-acetylated amino trisaccharides. Machine learning experiments were performed for: (1) classification of the anomeric configuration of the first unit, second unit and reducing end; (2) classification of the type of first and second linkages; (3) classification of the three residues: reducing end, middle and first residue; and (4) classification of the chain type. Our previously model for predicting the structure of disaccharides was incorporated in this new model with an improvement of the predictive power. The best results were achieved using Random Forests with 204 di- and trisaccharides for the training set-it could correctly classify 83%, 90%, 88%, 85%, 85%, 75%, 79%, 68% and 94% of the test set (69 compounds) for the nine tasks, respectively, on the basis of unassigned chemical shifts.     

Gas chromatographic-mass spectrometric method for the qualitative and quantitative determination of disaccharides and trisaccharides in honey

An improved method has been developed to identify and quantify honey disaccharides and trisaccharides by gas chromatography and mass spectrometry. The procedure, based on mass spectral and retention data ("retention time windows") determined on two capillary columns with different stationary phases allowed the identification and quantitation in honey of 16 disaccharides and 9 trisaccharides, some of which were not previously identified by GC. The reliability of the analytical results was considerably improved by the use of this procedure: several unidentified disaccharides and trisaccharides were detected, and their presence was taken into account in the quantification.     

A Monte Carlo pharmacophore generation procedure: Application to the human PAF receptor

Summary A novel pharmacophore definition procedure is described, which uses a Monte Carlo method to superimpose molecules. Pharmacophore space is searched by a technique similar to high temperature annealing. Subsequent refinement of candidate pharmacophores by energy minimization produces low-energy conformations that may be involved in receptor binding. The method has been applied to compounds that bind to the human platelet-activating factor (PAF) receptor. Alternative binding site models for the PAF receptor are presented and discussed.A preliminary account of this work has been published elsewhere [1].     

Comparative performance of MM3(92) and two TINKER MM3 versions for the modeling of carbohydrates

The 1992 version of MM3 was largely used for modeling mono-, di-, and trisaccharides. In later versions of MM3 improvements were made in some parameters that may be important for carbohydrates. This corrected MM3 force field is part of the Tinker package, freely available (as its 4.1 version), and included in the Chem 3D Ultra 8.0 package (as the 3.7 version). The latter version lacks the corrections to the standard bond lengths produced by electronegativity and anomeric effects, whereas the Tinker 4.1 version only lacks the latter correction. The present work compares the performance of the three MM3 versions (and in some cases, DFT and/or HF/ab initio procedures) on several carbohydrate model problems as the chair and rotamer equilibria in 2-hydroxy- and 2-methoxytetrahydropyran, hydrogen bonding in cis-2,3-dihydroxytetrahydropyran, and the potential energy surfaces around the glycosidic bonds of two sulfated disaccharides and two trisaccharides. Tinker MM3 can be used accurately to estimate carbohydrate energies and geometries, and-with the help of some programming-to pursue studies on the potential energy surfaces of di- and trisaccharides. In most cases results obtained using the three MM3 versions are similar, although large energy differences are obtained when comparing a rotameric distribution around a O-C-O-H dihedral, which is almost forced to the exo-anomeric position by the Tinker versions. In other systems smaller energy differences are found, but they can nevertheless lead to a different global minimum when comparing conformers of similar energy. MM3(92) establishes better the differences between the bond lengths in both anomers, as an expected expression of the anomeric correction.     

Extended RCM-ROM sequences: a novel approach to polyunsaturated trisaccharides

The first examples of RCM-ROM-RCM-ROM-RCM sequences involving non-strained heterocyclic relays are described. The method can be used for the preparation of polyunsaturated trisaccharides.