Conformational analysis of maltoside heteroanalogues using high-quality NOE data and molecular mechanics calculations. Flexibility as a function of the interglycosidic chalcogen atom

Epoxide-Mediated Trans-Thioglycosylation and Application to the Synthesis of Oligosaccharides Related to the Capsular Polysaccharides of C. jejuni HS:4

The enzyme-resistant thioglycosides are highly valuable immunogens because of their enhanced metabolic stability. We report the first synthesis of a family of thiooligosaccharides related to the capsular polysaccharides (CPS) of Campylobacter jejuni HS:4 for potential use in conjugate vaccines. The native CPS structures of the pathogen consist of a challenging repeating disaccharide formed with β(1→4)-linked 6-deoxy-β-D-ido-heptopyranoside and N-acetyl-D-glucosamine; the rare 6-deoxy-ido-heptopyranosyl backbone and β-anomeric configuration of the former monosaccharide makes the synthesis of this family of antigens very challenging. So far, no synthesis of the thioanalogs of the CPS antigens have been reported. The unprecedented synthesis presented in this work is built on an elegant approach by using β-glycosylthiolate as a glycosyl donor to open the 2,3-epoxide functionality of pre-designed 6-deoxy-β-D-talo-heptopyranosides. Our results illustrated that this key trans-thioglycosylation can be designed in a modular and regio and stereo-selective manner. Built on the success of this novel approach, we succeeded the synthesis of a family of thiooligosaccharides including a thiohexasaccharide which is considered to be the desired antigen length and complexity for immunizations. We also report the first direct conversion of base-stable but acid-labile 2-trimethylsilylethyl glycosides to glycosyl-1-thioacetates in a one-pot manner.

Synthesis of 4-thiol-furanosidic uronate via hydrothiolation reaction

Uronic acids are not only important building blocks of polysaccharides and oligosaccharides but also are widely used in the food and pharmaceutical industries. Inspired by the structure of natural products, here, we disclosed base-mediated and radical-mediated hydrothiolation reactions for the preparation of thiol-contained uronates. In comparison with base-mediated reaction, radical-mediated hydrothiolation is inefficient due to the electron-withdrawing group on the ethylene group; nevertheless, the adduct had excellent stereoselectivity at both C-4 and C-5 positions. For the alkaline approach, thiols as nucleophiles can regioselectively and stereoselectively attach to the C-4 position of Δ-^4,5-unsaturated uronate with moderate to good yields. However, poor stereoselectivity at the C-5 position was observed due to retro thiol-Michael addition. After removing the protecting group of the thiol, the thiol adduct was isomerized to the furanosidic form and the 4-thiol-furanosidic uronate derivative was synthesized for the first time.

Uronic acids are not only important building blocks of bioactive molecules but also are widely used in the food and pharmaceutical industries. Its derivative, 4-thiol-furanosidic uronate was successfully synthesized and firstly reported here.

Synthetic Nucleosomes Reveal that GlcNAcylation Modulates Direct Interaction with the FACT Complex

Transcriptional regulation can be established by various post-translational modifications (PTMs) on histone proteins in the nucleosome and by nucleobase modifications on chromosomal DNA. Functional consequences of histone O-GlcNAcylation (O-GlcNAc=O-linked β-N-acetylglucosamine) are largely unexplored. Herein, we generate homogeneously GlcNAcylated histones and nucleosomes by chemical post-translational modification. Mass-spectrometry-based quantitative interaction proteomics reveals a direct interaction between GlcNAcylated nucleosomes and the "facilitates chromatin transcription" (FACT) complex. Preferential binding of FACT to GlcNAcylated nucleosomes may point towards O-GlcNAcylation as one of the triggers for FACT-driven transcriptional control.

Mechanistic Study on Electronic Excitation Dissociation of the Cellobiose-Na(+) Complex

The recent development of electron activated dissociation (ExD) techniques has opened the door for high-throughput, detailed glycan structural elucidation. Among them, ExD methods employing higher-energy electrons offer several advantages over low-energy electron capture dissociation (ECD), owing to their applicability towards chromophore-labeled glycans and singly charged ions, and ability to provide more extensive structural information. However, a lack of understanding of these processes has hindered rational optimization of the experimental conditions for more efficient fragmentation as well as the development of informatics tools for interpretation of the complex glycan ExD spectra. Here, cellobiose-Na(+) was used as the model system to investigate the fragmentation behavior of metal-adducted glycans under irradiation of electrons with energy exceeding their ionization potential, and served as the basis on which a novel electronic excitation dissociation (EED) mechanism was proposed. It was found that ionization of the glycan produces a mixture of radical cations and ring-opened distonic ions. These distonic ions then capture a low-energy electron to produce diradicals with trivial singlet-triplet splitting, and subsequently undergo radical-induced dissociation to produce a variety of fragment ions, the abundances of which are influenced by the stability of the distonic ions from which they originate. Graphical Abstract ᅟ.

Mechanistic study on electron capture dissociation of the oligosaccharide-Mg²⁺ complex

Electron capture dissociation (ECD) has shown great potential in structural characterization of glycans. However, our current understanding of the glycan ECD process is inadequate for accurate interpretation of the complex glycan ECD spectra. Here, we present the first comprehensive theoretical investigation on the ECD fragmentation behavior of metal-adducted glycans, using the cellobiose-Mg²⁺ complex as the model system. Molecular dynamics simulation was carried out to determine the typical glycan-Mg²⁺ binding patterns and the lowest-energy conformer identified was used as the initial geometry for density functional theory-based theoretical modeling. It was found that the electron is preferentially captured by Mg²⁺ and the resultant Mg⁺• can abstract a hydroxyl group from the glycan moiety to form a carbon radical. Subsequent radical migration and α-cleavage(s) result in the formation of a variety of product ions. The proposed hydroxyl abstraction mechanism correlates well with the major features in the ECD spectrum of the Mg²⁺-adducted cellohexaose. The mechanism presented here also predicts the presence of secondary, radical-induced fragmentation pathways. These secondary fragment ions could be misinterpreted, leading to erroneous structural determination. The present study highlights an urgent need for continuing investigation of the glycan ECD mechanism, which is imperative for successful development of bioinformatics tools that can take advantage of the rich structural information provided by ECD of metal-adducted glycans.

Synthesis and conformational analysis of neoglycoconjugates derived from O- and S-glucose

Using olefin metathesis as a key step, four neoglycoconjugates incorporating α-O-glucose, α-S-glucose or β-S-glucose as a carbohydrate unit and L-serine or L-cysteine as an amino acid moiety have been synthesized. The four-atom carbon spacer allows the carbohydrate to explore a wide-ranging conformational space, which may have important implications for the molecular recognition of these molecules.

Recent advances in developing synthetic carbohydrate-based vaccines for cancer immunotherapies

Cancer cells can often be distinguished from healthy cells by the expression of unique carbohydrate sequences decorating the cell surface as a result of aberrant glycosyltransferase activity occurring within the cell; these unusual carbohydrates can be used as valuable immunological targets in modern vaccine designs to raise carbohydrate-specific antibodies. Many tumor antigens (e.g., GM2, Ley, globo H, sialyl Tn and TF) have been identified to date in a variety of cancers. Unfortunately, carbohydrates alone evoke poor immunogenicity, owing to their lack of ability in inducing T-cell-dependent immune responses. In order to enhance their immunogenicity and promote long-lasting immune responses, carbohydrates are often chemically modified to link to an immunogenic protein or peptide fragment for eliciting T-cell-dependent responses. This review will present a summary of efforts and advancements made to date on creating carbohydrate-based anticancer vaccines, and will include novel approaches to overcoming the poor immunogenicity of carbohydrate-based vaccines.

Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters

This paper deals with the development and validation of new potential parameter sets, based on the CHARMM36 and GLYCAM06 force fields, to simulate micelles of the two anomeric forms (α and β) of N-dodecyl-β-maltoside (C(12)G(2)), a surfactant widely used in the extraction and purification of membrane proteins. In this context, properties such as size, shape, internal structure, and hydration of the C(12)G(2) anomer micelles were thoroughly investigated by molecular dynamics simulations and the results compared with experiments. Additional simulations were also performed with the older CHARMM22 force field for carbohydrates (Kuttel, M.; et al. J. Comput. Chem. 2002, 23, 1236-1243). We find that our CHARMM and GLYCAM parameter sets yield similar results in the case of properties related to the micelle structure but differ for other properties such as the headgroup conformation or the micelle hydration. In agreement with experiments, our results show that for all model potentials the β-C(12)G(2) micelles have a more pronounced ellipsoidal shape than those containing α anomers. The computed radius of gyration is 20.2 and 25.4 Å for the α- and β-anomer micelles, respectively. Finally, we show that depending on the potential the water translational diffusion of the interfacial water is 7-11.5 times slower than that of bulk water due to the entrapment of the water in the micelle crevices. This retardation is independent of the headgroup in α- or β-anomers.

Alpha-S-GalCer: synthesis and evaluation for iNKT cell stimulation

The synthesis and evaluation for iNKT stimulation of alpha-S-galactosylceramide is reported. Prepared by alkylation of a galactosylthiol, this analog of the potent immunostimulatory agent, KRN7000, did not stimulate iNKT cells either in vitro or in vivo.

Thio-isoglobotrihexosylceramide, an agonist for activating invariant natural killer T cells

Thio-isoglobotrihexosylceramide (S-iGb3) might be resistant to alpha-galactosidases in antigen-presenting cells and have a longer retaining time in the lysosome before being loaded to CD1d. The biological assay showed that S-iGb3 demonstrates a much higher increase as a stimulatory ligand toward invariant natural killer T (iNKT) cells as compared to iGb3. [structure: see text].

Exploring reaction pathways with transition path and umbrella sampling: Application to methyl maltoside

The transition path sampling (TPS) method is a powerful approach to study chemical reactions or transitional properties on complex potential energy landscapes. One of the main advantages of the method over potential of mean force methods is that reaction rates can be directly accessed without knowledge of the exact reaction coordinate. We have investigated the complementary nature of these two differing approaches, comparing transition path sampling with the weighted histogram analysis method to study a conformational change in a small model system. In this case study, the transition paths for a transition between two rotational conformers of a model disaccharide molecule, methyl beta-D-maltoside, were compared with a free energy surface constrained by the two commonly used glycosidic (phi,psi) torsional angles. The TPS method revealed a reaction channel that was not apparent from the potential of mean force method, and the suitability of phi and psi as reaction coordinates to describe the isomerization in vacuo was confirmed by examination of the transition path ensemble. Using both transition state theory and transition path sampling methods, the transition rate was estimated. We have estimated a characteristic time between transitions of approximately 160 ns for this rare isomerization event between the two conformations of the carbohydrate. We conclude that transition path sampling can extract subtle information about the dynamics not apparent from the potential of mean force method. However, in calculating the reaction rate, the transition path sampling method required 27.5 times the computational effort than was needed by the potential of mean force method.

Chemical and Chemoenzymatic Synthesis of S-Linked Ganglioside Analogues and Their Protein Conjugates for Use as Immunogens

Analogues of the tumor-associated gangliosides GM(3) and GM(2) containing terminal S-linked neuraminic acid residues and an amino terminated, truncated ceramide homologue have been synthesized and conjugated to a protein. The synthesis involved coupling of a S-linked sialyl alpha(2-->3) galactose disaccharide with a glucosyl sphingosine analogue, followed by elaboration and deprotection to give amino-terminated glycosyl ceramide 1. Glycosyltransferase-catalyzed extension of the trisaccharide 1 provided access to the modified GM(2) tetrasaccharide 2 or sulphur-containing GD(3) analogue 30. Owing to their potentially enhanced resistance to endogenous exo-glycoside hydrolases and their inherent non-self character, carbohydrate antigens containing non-reducing terminal thioglycosidic linkages may be more immunogenic than O-linked antigens and may stimulate the production of antibodies capable of recognizing naturally occurring oligosaccharides. Our initial results suggest that in fact these antigens are viable immunogens and furthermore, that immune sera cross reacts with O-gangliosides in the context of a heterologous glycoprotein conjugate.

Synthesis and conformational analysis of disaccharide analogues containing disulfide and selenosulfide functionalities in the interglycosidic linkages

The synthesis of novel disaccharides containing disulfide (methyl-4-S-(β-D-galactopyranosyl-1'-thio)-4-thio-α-D-glucopyranoside (1)) and selenosulfide (methyl-4-Se-(β-D-galactopyranosyl-1'-thio)-4-seleno-α-D-glucopyranoside (2)) functionalities in the interglycosidic linkages is described. The synthetic strategy relied on the reaction of a β-glycosylthiosulfonate with a carbohydrate thiol or selenol nucleophile. The resulting protected β-dihetero-linked disaccharides were deprotected to give the target compounds. The conformational preferences of these dihetero analogues were inferred from NOESY experiments and line-broadening effects in variable-temperature NMR spectra, and are rationalized in terms of molecular orbital theory. Low-energy conformations of these compounds can populate regions of conformational space not usually occupied by β-linked disaccharides, and offer the possibility for presentation of novel ligand topographies.Key words: disaccharides, disulfides, selenosulfides, interglycosidic linkages, conformations, MO explanation.

Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides

Recent atomic force microscopy stretching measurements of single polysaccharide molecules suggest that their elasticity is governed by force-induced conformational transitions of the pyranose ring. However, the mechanism of these transitions and the mechanics of the pyranose ring are not fully understood. Here we use steered molecular dynamics simulations of the stretching process to unravel the mechanism of forced conformational transitions in 1,6 linked polysaccharides. In contrast to most sugars, 1,6 linked polysaccharides have an extra bond in their inter-residue linkage, C5-C6, around which restricted rotations occur and this additional degree of freedom increases the mechanical complexity of these polymers. By comparing the computational results with the atomic force microscopy data we determine that forced rotations around the C5-C6 bond have a significant and different impact on the elasticity of alpha- and beta-linked polysaccharides. Beta-linkages of a polysaccharide pustulan force the rotation around the C5-C6 bonds and produce a Hookean-like elasticity but do not affect the conformation of the pyranose rings. However, alpha-linkages of dextran induce compound conformational transitions that include simultaneous rotations around the C5-C6 bonds and chair-boat transitions of the pyranose rings. These previously not-recognized transitions are responsible for the characteristic plateau in the force-extension relationship of dextran.

Synthesis and Evaluation of 5-Thio-L-Fucose-Containing Oligosaccharide

5-Thio-L-fucose-containing trisaccharide H-type II was synthesized. The 3',4'-O-isopropylidene-2-azido-2-deoxylactoside derivative, which was prepared from lactose by azidonitration of lactal, was used as a starting material. By regio- and stereoselective 5-thio-L-fucosylation of the 6,6'-dibenzoate 5 with 5-thiofucosyl trichloroacetimidate 6 and subsequent deprotection gave the 5-thio-L-fucose-containing H-type II 1. Conformational analysis of the 5-thio-L-fucose-containing H-type II and the native H-type II was carried out through NOESY experiments. The observed NOE values between N-acetylglucosamine and galactose, and galactose and fucose were same for these two trisaccharides. However, NOE values between fucose and N-acetylglucosamine were significantly different. Binding of the 5-thio-L-fucose-containing H-type II to lectins and antibodies were in some case stronger and in some case weaker than those of the native trisaccharide.

S-Linked Ganglioside Analogues for Use in Conjugate Vaccines

[structure: see text] Glycosidase resistant thioglycoside precursors of the melanoma-associated ganglioside GM(2) have been synthesized starting from lactose. Syntheses of several analogues of ganglioside GM(3) and a positional isomer have been developed. These compounds contain thio-linked sialic acid residues and a modified ceramide aglycon functionalized for coupling to proteins, surfaces, or matrices. The hydrolytic stability of these oligosaccharides enhances the immunogenicity of the corresponding conjugate vaccines by ensuring their integrity in the acidic compartments of antigen processing cells.

Computational studies on carbohydrates: solvation studies on maltose and cyclomaltooligosaccharides (cyclodextrins) using a DFT/ab initio-derived empirical force field, AMB99C

An empirical force field, denoted AMB99C, has been used to study molecular properties of alpha-(1-->4)-linked carbohydrates in solution. AMB99C was parameterized using structural and energetic parameters from density functional ab initio methodology. In this work we examine the solution behavior of the beta anomer of maltose and cyclohexa-, cyclohepta-, and cyclooctaamyloses (alpha-, beta-, and gamma-cyclodextrins or alpha-, beta-, and gamma-CDs, respectively), as well as of two larger (DP 10, epsilon-CD; DP 21) cyclomaltooligosaccharides, CA10 and CA21. Experimental data used for comparison purposes include X-ray structures, small-angle scattering radius of gyration values, NMR nuclear Overhauser enhancements (NOEs), and proton coupling constants. Molecular dynamics simulations were carried out using explicit water molecules (TIP3P) to establish equilibrium populations of conformations in solution, and these results are compared with other calculated values and a variety of experimental parameters, such as average H-1-H-4' distances between the rings in beta-maltose, and the primary hydroxyl groups' conformational populations. Medium-to-large cyclomaltooligosaccharide molecules were studied to test for glucose ring puckering and stability of kinked and 'flipped' conformations. The results of the solvation studies are in excellent agreement with experimental structural parameters.