Comparative Conformational Analysis of Acyclic Sugar Alcohols Ribitol, Xylitol and d-Arabitol by Solution NMR and Molecular Dynamics Simulations.

Ribitol (C5H12O5) is an acyclic sugar alcohol that was recently identified in O-mannose glycan on mammalian α-dystroglycan. The conformation and dynamics of acyclic sugar alcohols such as ribitol are dependent on the stereochemistry of the hydroxyl groups; however, the dynamics are not fully understood. To gain insights into the conformation and dynamics of sugar alcohols, we carried out comparative analyses of ribitol, d-arabitol and xylitol by a crystal structure database search, solution NMR analysis and molecular dynamics (MD) simulations. The crystal structures of the sugar alcohols showed a limited number of conformations, suggesting that only certain stable conformations are prevalent among all possible conformations. The three-bond scholar coupling constants and exchange rates of hydroxyl protons were measured to obtain information on the backbone torsion angle and possible hydrogen bonding of each hydroxyl group. The 100 ns MD simulations indicate that the ribitol backbone has frequent conformational transitions with torsion angles between 180∘ and ±60∘, while d-arabitol and xylitol showed fewer conformational transitions. Taking our experimental and computational data together, it can be concluded that ribitol is more flexible than d-arabitol or xylitol, and the flexibility is at least in part defined by the configuration of the OH groups, which may form intramolecular hydrogen bonds.

Ribitol in Solution Is an Equilibrium of Asymmetric Conformations.

Ribitol (C5H12O5), an acyclic sugar alcohol, is present on mammalian α-dystroglycan as a component of O-mannose glycan. In this study, we examine the conformation and dynamics of ribitol by database analysis, experiments, and computational methods. Database analysis reveals that the anti-conformation (180°) is populated at the C3-C4 dihedral angle, while the gauche conformation (±60°) is seen at the C2-C3 dihedral angle. Such conformational asymmetry was born out in a solid-state 13C-NMR spectrum of crystalline ribitol, where C1 and C5 signals are unequal. On the other hand, solution 13C-NMR has identical chemical shifts for C1 and C5. NMR 3J coupling constants and OH exchange rates suggest that ribitol is an equilibrium of conformations, under the influence of hydrogen bonds and/or steric hinderance. Molecular dynamics (MD) simulations allowed us to discuss such a chemically symmetric molecule, pinpointing the presence of asymmetric conformations evidenced by the presence of correlations between C2-C3 and C3-C4 dihedral angles. These findings provide a basis for understanding the dynamic structure of ribitol and the function of ribitol-binding enzymes.

Synthesis and Glycan-Protein Interaction Studies of Se-Sialosides by 77Se NMR.

To expand the potential of Se-carbohydrates for multifunctional mimicry of sugars, herein we addressed the synthesis of the highly challenging and biologically significant Se-glycosides of sialic acid (Se-sialosides). An α-sialyl selenolate anion generated in situ smoothly reacted with electrophiles to give α-Se-sialosides as single stereoisomers. A Se-sialoside was sequentially incorporated with selenium, producing a triseleno-sialoside. This molecule was used as a 77Se NMR-active handle for studying glycan-protein interaction, revealing different binding profiles of sialic acid binding proteins.

Structural analysis of a novel lipooligosaccharide (LOS) from Rhodobacter azotoformans.

Lipopolysaccharides (LPS) are components of the Gram-negative bacterial cell surface that stimulate the host innate immune system through the Toll-like receptor (TLR) 4-MD-2 complex. Rhodobacter sp. have been reported to produce LPS that lack endotoxic activity, and instead act as antagonists of other endotoxins. In this report, we focused on LPS, especially the lipooligosaccharide (LOS) fraction produced by Rhodobacter azotoformans that shows production of IL-8, but has an inverse correlation with IL-6 production. We analyzed their molecular structure by using mass spectrometry and nuclear magnetic resonance spectroscopy and report a novel LOS consisting of a shorter glycan structure containing glucuronic acid but not heptoses. A novel glycan structure, Glcα(1 → 4)GlcAα(1 → 4)KDOα(2 → 4)[Glcα(1 → 5)]KDOα(2 → 6)[4-phosphate]GlcNß(1 → 6) GlcNα1-phosphate, was proposed using NMR methods. The structure was consistent with one obtained based on MS. The MS analysis further revealed the existence of structural variation caused by extension with hexoses. The acyl composition in lipid A was suggested to contain three C14 fatty acyl chains (3-OH-14:0 or 3-oxo-14:0 at N2 of GlcN-1, 3-OH-14:0 at N2 of GlcN-2, that carried another 14:1 Δ7 on its ß-hydroxyl group) and two C10 fatty acyl chains (3-OH-10:0 at O3 of both GlcN), which are same as those found in lipid A from Rhodobacter sphaeroides.

J(77 Se,1 H) and J(77 Se,13 C) couplings of seleno-carbohydrates obtained by 77 Se satellite 1D 13 C spectroscopy and 77 Se selective HR-HMBC spectroscopy.

Seleno-carbohydrates are those in which the oxygen of the glycosidic bond or the hydroxyl group is artificially replaced with selenium. This substitution changes 1 H and 13 C chemical shifts and produces spin coupling constants involving 77 Se. Coupling constants, such as 2-3 J(77 Se, 1 H), are likely to be useful for conformational analyses of glycans because such couplings are never observed in natural glycans. Several papers have discussed the relationship between 2-3 J(77 Se, 1 H) and conformation; however, only few reports describe 1-3 J(77 Se, 13 C), which could also be useful. Here, we obtain 77 Se coupling constants of seleno-carbohydrates from 77 Se-selective HR-HMBC and 77 Se satellites in 1D 13 C spectra and examine their conformations using the Newman projection scheme.

Synthesis of a biotinylated keratan sulfate tetrasaccharide composed of dimeric Galß1-4GlcNAc6Sß.

We successfully synthesized the biotinylated keratan sulfate tetrasaccharide, Galß1-4GlcNAc6Sß1-3Galß1-4GlcNAc6Sß in a stereocontrolled manner. The suitably protected Galß1-4GlcNPhth unit was converted to the corresponding donor and acceptor. Optimization in 2 + 2 coupling using AgOTf, CuBr2, and n-Bu4NBr in CH3NO2 at a low temperature afforded the desired tetrasaccharide that suppressed glycal formation. The subsequent chemoselective removal of the protecting group at O-6 of two GlcNAcs, sulfation, and deprotection procedures as well as biotinylation gave the target compound.

Structural elucidation of a novel transglycosylated compound α-glucosyl rhoifolin and of α-glucosyl rutin by NMR spectroscopy.

We report the full assignment of 1H and 13C NMR signals belonging to α-glucosyl rhoifolin (Rhf-G), a novel transglycosylated compound synthesized from a flavone glycoside, rhoifolin, as well as its chemical structure. Furthermore, we report the complete NMR signal assignment for another transglycosylated compound, α-glucosyl rutin (Rutin-G), as the signals corresponding to its sugar moieties had not been identified. Electrospray ionization-mass spectrometry along with multiple NMR methods revealed that Rhf-G possesses three sugar moieties in its chemical structure. The additional glucose was bound directly via a transglycosylation to rhoifolin at position 3a of the sugar moiety. Interestingly, intramolecular hydrogen bonds in the basic Rhf-G and Rutin-G skeletons were confirmed by HMBC experiments. These findings will be helpful for comprehensive NMR studies on transglycosylated compounds in food, cosmetic, and pharmaceutical fields.

The α-Glycosidation of Partially Unprotected N-Acetyl and N-Glycolyl Sialyl Donors in the Absence of a Nitrile Solvent Effect.

The synthesis of α-sialosides is one of the most difficult reactions in carbohydrate chemistry and is considered to be both a thermodynamically and kinetically disfavored process. The use of acetonitrile as a solvent is an effective solution for the α-selective glycosidation of N-acetyl sialic acids. In this report, we report on the α-glycosidation of partially unprotected N-acetyl and N-glycolyl donors in the absence of a nitrile solvent effect. The 9-O-benzyl-N-acetylthiosialoside underwent glycosidation in CH2 Cl2 with a good α-selectivity. On the other hand, the 4,7,8-O-triacetyl-9-O-benzyl-N-acetylthiosialoside was converted to ß-sialoside as a major product under the same reaction conditions. The results indicate that the O-acetyl protection of the sialyl donor was a major factor in reducing the α-selectivity of sialylation. After tuning of the protecting groups of the hydroxy groups at the 4,7,8 position on the sialyl donor, we found that the 9-O-benzyl-4-O-chloroacetyl-N-acetylthiosialoside underwent sialylation with excellent α-selectivity in CH2 Cl2 . To demonstrate the utility of the method, straightforward synthesis of α(2,9) disialosides containing N-acetyl and/or N-glycolyl groups was achieved by using the two N-acetyl and N-glycolyl sialyl donors.

Structural analyses of mannose pentasaccharide of high mannose type oligosaccharides by 1D and 2D NMR spectroscopy.

NMR spectroscopy is a very important and useful method for the structural analysis of oligosaccharides, despite its low sensitivity. We first applied conventional measuring methods, 2D DQF COSY, (1)H-(13)C HSQC, and (1)H-(13)C HMBC, and also the Double Pulsed Field Gradient Spin Echo (DPFGSE)-TOCSY and DPFGSE-NOESY/ROESY techniques to analyze a branched mannose pentasaccharide as a model of high mannose type N-glycans in natural abundance. The NMR spectra of the model compound are very complex and difficult to analyze owing to overlapping signals. The superior selective irradiation capability of the DPFGSE technique is useful for fine structural and conformational analyses of such complex oligosaccharides. We here introduce a novel technique called DPFGSE-Double-Selective Population Transfer (SPT)-Difference and DPFGSE-NOE/ROE-SPT-Difference spectroscopy. The DPFGSE-Double-SPT-Difference method involves irradiation of two peaks from one proton and the subtraction of higher and lower peaks from each spectrum. The DPFGSE-NOE/ROE-SPT-Difference method involves the transfer of the magnetization polarized by NOE/ROE from the nuclei to the spin-coupled nuclei through scalar spin-spin interaction using the SPT method. Even if the signals in the NMR spectra overlap, each signal can be accurately assigned. In particular, DPFGSE-NOE/ROE-SPT-Difference is very useful for identifying sugar connectivity.

Five new pregnane glycosides from the stems of Marsdenia tenacissima.

Activity-guided fractionation of the stems of Marsdenia tenacissima led to the isolation of five new pregnane glycosides, namely marstenacissides E (1), F (2), G (3), H (4), and I (5). Their structures were determined on the basis of (1)H and (13)C NMR, COSY, TOCSY, ROESY, and FABMS experiments.

Structural analysis of O-glycans of mucin from jellyfish (Aurelia aurita) containing 2-aminoethylphosphonate.

The structure of O-glycan in qniumucin (Q-mucin), which is a novel mucin extracted from jellyfish, was analyzed by a combination of NMR and ESI-MS/MS. A previously unidentified monosaccharide involved in the glycan chains was determined to be N-acetylgalactosamine (GalNAc) substituted by 2-aminoethylphosphonate (AEP) at the C-6. The O-glycans in Q-mucin from Aurelia aurita were proved to be mainly composed of three monosaccharides: GalNAc, AEP-(O-->6)-GalNAc, and P-6-GalNAc. To the best of our knowledge, this is the first example of an O-glycan structure of glycoproteins containing AEP. This exceptionally simple structure of Q-mucin and its potential use in material science and technology are revealed.

NMR study on a novel mucin from jellyfish in natural abundance, Qniumucin from Aurelia aurita.

A novel mucin (qniumucin), which we recently discovered in jellyfish, was investigated by several NMR techniques. Almost all the peaks in the (13)C and proton NMR spectra were satisfactorily assigned to the amino acids in the main chain and to the bridging GalNAc, the major sugar in the saccharide branches. The amino acid sequence in the tandem repeat part (-VVETTAAP-) was reconfirmed by the cross-peaks between alpha protons and carbonyl carbons in the HMBC spectrum. A connectivity analysis around the O-glycoside bond (GalNAc-Thr) was also performed, and detailed information on the local configuration was obtained by the DPFGSE-NOE-HSD technique. The strategy and the results described in this paper can be extended to the structural analysis of general O-glycan chains, which are more complex than the present mucin. NMR analyses reveal the simple structure of qniumucin extracted by the present protocol, and the homogeneity and purity of qniumucin are probably the result of it being extracted from jellyfish, a primitive animal.

Characterization of a novel polyphenol-specific oligoxyloside transfer reaction by a family 11 xylanase from Bacillus sp. KT12.

A culture filtrate of Bacillus sp. KT12 was used to prepare polyphenyl beta-oligoxylosides from xylan and polyphenols in a one-step reaction. One oligoxyloside transfer enzyme was purified from multiple xylanolytic enzymes in the culture filtrate. N-terminal amino acid sequence determination classified the enzyme as a glycosyl hydrolase family 11 (endo-xylanase). The xylanolytic enzyme activities could be markedly altered; its hydrolytic activity was almost entirely inhibited at acidic pH, whereas near constant transxylosylation activity was observed at pH 4-11. Further, metal ions activated transxylosylation and almost completely inhibited hydrolysis. The enzyme specifically induced a beta-xylosyl transfer reaction to acceptor molecules, such as divalent and trivalent phenolic hydroxyl groups, and displayed no activity toward alcoholic compounds. The Bacillus sp. KT12 xylanolytic enzyme was a suitable enzyme for the synthesis of polyphenyl beta-oligoxylosides.

Brz220 interacts with DWF4, a cytochrome P450 monooxygenase in brassinosteroid biosynthesis, and exerts biological activity.

Arabidopsis thaliana (Arabidopsis) treated with the four stereoisomers of Brz220 (2RS, 4RS-1-[4-propyl-2-(4-trifluoromethylphenyl)-1, 3-dioxane-2-ylmethyl]-1H-1, 2, 4-triazole) showed a dwarf phenotype like brassinosteroid (BR) biosynthesis mutants that were rescued by treatment of BRs. The target sites of each Brz220 stereoisomer were investigated by treatment of Arabidopsis with BRs in the dark. The results suggest that the stereoisomers block the 22-hydroxylation step in BR biosynthesis. This step is catalyzed by DWF4, an Arabidopsis cytochrome P450 identified as a steroid 22-hydroxylase. The enzyme was expressed in E. coli, and the binding affinity of the stereoisomers to recombinant DWF4 was analyzed. The results indicate that in these stereoisomers there exists a positive correlation between binding affinity to DWF4 and inhibition of Arabidopsis hypocotyl growth. In this context, we concluded that DWF4 is the target site of Brz220 in Arabidopsis.

Incorporation of selective population transfer and homo-spin decoupling into selective one-dimensional experiments.

The incorporation of selective population transfer (SPT) and homo-spin decoupling (HSD) into selective one-dimensional (1D) experiments has been shown to be very useful in obtaining information on the elucidation of the structure of organic compounds. To demonstrate this, the determination of the relative configuration of the sugar moiety of Mi-saponins has been presented.

A new selective population transfer experiment using a double pulsed field gradient spin-echo.

A new pulse sequence is proposed for the determination of scalar coupling correlation in small- and medium-sized organic compounds. The method uses a combination of the double pulsed field gradient spin-echo (DPFGSE) and the selective population transfer (SPT) techniques and is shown to be useful in the analysis of complex spectra with many overlapped signals. The usefulness of this method in the structural elucidation of natural substances is demonstrated using strychnine and digitoxin as examples.

Antibacterial diterpenes and their fatty acid conjugates from rice leaves.

Six structurally oryzalide-related compounds, oryzadione (1), 2, 3, 4, 5 and 6, were isolated from a neutral fraction of the extract of healthy leaves using a bacterial leaf blight-resistant cultivar of a rice plant, "Norin-27", as a group of antimicrobial substances. Their structures were determined by spectroscopic studies to be kaurane analogues and kaurane analogues conjugated with fatty acids, i.e., 1: ent-15,16-epoxy-kauran-2,3-dione (enol form: ent-15,16-epoxy-2-hydroxy-kauran-1-en-3-one), 2: ent-15,16-epoxy-3beta-hydroxy-kauran-2-one, 3: ent-15,16-epoxy-3-oxa-kauran-2-one, 4: ent-15,16-epoxy-3beta-myristoyloxy-kauran-2-one, 5: ent-15,16-epoxy-3alpha-palmitoyloxy-kauran-2-one, and 6: ent-15,16-epoxy-2beta-palmitoyloxy-kauran-2-one.

Pregnane glycosides from the stems of Marsdenia tenacissima.

Four new pregnane glycosides, named marstenacissides A (1), B (2), C (3), and D (4), have been isolated from the stems of Marsdenia tenacissima. Their structures were established on the basis of chemical and spectral methods.

A new triterpenoid saponin with inhibition of luteal cell from the seeds of Vaccaria segetalis.

A new triterpenoid saponin, named segetoside B, showing inhibition of luteal cell activity, has been isolated from the seeds of Vaccaria segetalis. On the basis of chemical reactions and spectral analyses, its structure has been established as 28-O-[beta-D-xylopyranosyl-(1 --> 4)-alpha-L-rhamnopyranosyl-(1 --> 2)]-[alpha-L-(5-O-acetyl)arabinofuranosyl-(1 --> 3)]-beta-D-(4-O-acetyl)fucopyranosyl-gypsogenin-3-O-beta-D-galactopyranosyl-(1 --> 2)-beta-D-(6-O-methyl ester)-glucuronopyranoside.