Pyranoside Ring Research Articles

Influence of Configuration at the 4- and 6-Positions on the Conformation and Anomeric Reactivity and Selectivity of 7-Deoxyheptopyranosyl Donors: Discovery of a Highly Equatorially Selective l-glycero-d-gluco-Heptopyranosyl Donor.

The preparation of four per-O-benzyl-d- or l-glycero-d-galacto and d- or l-glycero-d-gluco heptopyranosyl sulfoxides and the influence of their side-chain conformations on reactivity and stereoselectivity in glycosylation reactions are described. The side-chain conformation in these donors is determined by the relative configuration of its point of attachment to the pyranoside ring and the two flanking centers in agreement with a recent model. In the d- and l-glycero-d-galacto glycosyl donors, the d-glycero-d-galacto isomer with the more electron-withdrawing trans,gauche conformation of its side chain was the more equatorially selective isomer. In the d- and l-glycero-d-gluco glycosyl donors, the l-glycero-d-gluco isomer with the least disarming gauche,gauche side-chain conformation was the most equatorially selective donor. Variable temperature NMR studies, while supporting the formation of intermediate glycosyl triflates at -80 °C in all cases, were inconclusive owing to a change in the decomposition mechanism with the change in configuration. It is suggested that the equatorial selectivity of the l-glycero-d-gluco isomer arises from H-bonding between the glycosyl acceptor and O6 of the donor, which is poised to deliver the acceptor antiperiplanar to the glycosyl triflate, resulting in a high degree of SN2 character in the displacement reaction.

Predictive Analysis of the Side Chain Conformation of the Higher Carbon Sugars: Application to the Preorganization of the Aminoglycoside Ring 1 Side Chain for Binding to the Bacterial Ribosomal Decoding A Site.

With a view to facilitating prediction of the exocyclic bond to the pyranoside ring in higher carbon sugars, a model is advanced that relates the relative configuration of the three stereogenic centers comprised of the branchpoint and of the two flanking centers (C4-C5-C6 in aldoheptoses and higher and C5-C6-C7 in sialic and ulosonic acids) to that of the simple ring-opened pentoses. Assignment of a given stereotriad as arabino, lxyo, ribo, or xylo by inspection of the Fischer projection formulas permits prediction of conformation of the exocyclic bond by comparison with the known solution (= crystal in all cases) conformations of the simple pentitols. More remote stereogenic centers in the side chain, as in the 8-position of N-acetylneuraminic acid, have little impact on the conformation of the exocyclic bond. On the basis of this model the conformation of the exocyclic bond in ring I of 6'-homologated 4,5-disubstituted 2-deoxystreptamine class aminoglycoside antibiotics was predicted and was borne out by NMR analysis of newly synthesized derivatives in D2O at pD5. The antiribosomal and antibacterial activity of these derivatives is briefly presented and discussed in terms of preorganization of the side chain for binding to the ribosomal decoding A site. It is anticipated that this predictive analysis will also find use in the prediction of the conformation of the exocyclic bonds in other 2-(1-hydroxyalkyl)-3-hydroxytetrahydropyrans and tetrahydrofurans.

Conformationally Switchable Glycosyl Donors.

Glycosyl donors functionalized with 2,2'-bipyridine moieties on the 3-OH and 6-OH or the 2-OH and 4-OH undergo a conformational change when forming 1:1 complexes with Zn2+ ions. The pyranoside ring of the zinc complexes adopted axial-rich skew boat conformations. The reactivities of the two glycosyl donors were investigated by performing a series of glycosylations in the presence or absence of Zn2+ ions. These glycosylations suggested a decrease in reactivity when binding Zn2+. The conformational effect of binding Zn2+ was therefore studied using a third glycosyl donor, unable to undergo conformational changes when binding Zn2+. From competition experiments, it was observed that the binding-induced conformational change increased the reactivity slightly compared to the glycosyl donor unable to undergo a conformational change.

How the configurational changes influence on molecular characteristics. The alkyl 3-azido-2,3-dideoxy-D-hexopyranosides - Theoretical approach

In this paper we present two currents of our research. The first goal was the geometry optimization of the structures of derivatives of the alkyl 3-azido-2,3-dideoxy-D-hexopyranosides. Then, we examine the influence of the applied quantum methods on the values of molecular features describing these structures. We use two methods for geometry optimization: the semi-empirical PM7 method and DFT B3LYP/6–31++G* method. The results of comparison parameters of descriptors indicate that there are no statistical differences obtained from both methods. Thus, we recommend the PM7 method for geometry optimization of the derivatives of the alkyl 3-azido-2,3-dideoxy-D-hexopyranosides due to its time and computer resources requirements.Another part of the research was the examination, which groups of descriptors are the most suitable for identifying the similarities in the configuration, the substituents pattern and the molecular mass of 232 examined structures.To explore relation between configuration changes of the 3-azidosaccharides and influence of these changes on the molecular characteristic, we use hierarchical cluster analysis (HCA), where WHIM, 3D-MORSE, RDF and GETAWAY descriptors were selected.Depending on the group of descriptors, molecules are divided in various ways. In general, saccharide’ structures are divided into groups based on the configuration of substituents (combination of epimers) or length of the O-glycoside chain. Never before, these saccharides derivatives, were investigated by chemometric analysis. The most problematic issue in experimental and theoretical research is the configuration of substituents in pyranoside ring. Due to vast number of configurations, it is possible to obtain massive amount of diverse structures. This problem concerns us and opens opportunity in investigation the effect of configuration on the parameter of molecules.

Synthesis and Evaluation of 1,5-Dithia-d-laminaribiose, Triose, and Tetraose as Truncated β-(1→3)-Glucan Mimetics.

The preparation and characterization of a series of di-, tri-, and tetrasaccharide analogues of β-(1→3)-glucans is described in which each pyranoside ring is replaced by a 5-thiopyranosyl ring and each glycosidic oxygen by a thioether. These oligomeric 1,5-dithio-d-glucopyranose derivatives were shown to inhibit the staining of human neutrophils and of mouse macrophages by fluorescent anti-CR3 and anti-Dectin-1 antibodies, respectively. The compounds were also demonstrated to stimulate phagocytosis and pinocytosis indicative of binding to the carbohydrate binding domains of complement receptor 3 (CR3) and Dectin-1. Activity in all three assays was optimum at the level of the trisaccharide mimic, suggesting that, while the replacement of ethereal oxygens by thioethers results in a greater affinity for the aromatic lined hydrophobic binding pockets, the presence of multiple longer C-S bonds eventually results in a mismatch and a loss of affinity.

Selenized polysaccharides – Biosynthesis and structural analysis

The main objective of our research was to analyze the structure of the Se-containing polysaccharides and to examine how the selenium is bound to the polysaccharide molecule. During investigation of the biosynthesis of new immunomodulators, we isolated a selenium (Se)-containing polysaccharide-protein fraction containing proteoglycans of molecular weights of 3.9 × 106 Da and 2.6 × 105 Da, composed of glucose or mannose, nearly 8% of protein and 190 μg Se/g dry weight. X-ray absorption spectroscopy (XAS) data analysis in the near edge region (XANES) confirmed that selenium in the Se-polysaccharides structure is present at the –II oxidation state and that Se is organically bound. The simulation analysis in the EXAFS (extended X-ray absorption fine structure) region suggested that selenium is most likely bound by a glycosidic-link in a β-1,3 or α-1,4-glycosidic bond or substituted for oxygen in a pyranosidic ring. Calculations performed with Gaussian 03 software predicted deformations in the polysaccharide structure caused by the incorporation of the selenium atom including change in bond lengths and torsion angles and, as a result, disappearance of hydrogen bonds in the vicinity of the selenium atoms.

Сonformational study of persulfated propyl glucuronide

Glucuronic acid is an important constituting block of biologically active glycosaminoglycans where it can be present in non-sulfated, mono-sulfated and di-sulfated forms. Despite that some investigators reported previously that the exhaustively sulfated glucuronic acid moiety was characterized with unusual 1H-1H coupling constants and some times chemical shifts, these were just qualitative studies in which their authors suggested that the mentioned deviations in NMR spectra might mean complete inversion of the normal D-pyranoside chair conformation 4C1 to 1C4. Herein we outline a detailed conformational investigation showing that the distortion in the pyranoside ring of the persulfated glucuronic acid cannot be described simply with 4C1↔1C4 inversion. Instead, the experimental NOE data clearly indicate that two skew-boat conformers, OS2 and 3S1, provide significant contribution to the conformational equilibrium.

Oxidative Deamination of N-Acetyl Neuraminic Acid: Substituent Effects and Mechanism.

A study of the mechanism of the oxidative deamination of the N-nitroso-N-acetyl sialyl glycosides leading with overall retention of configuration to the corresponding 2-keto-3-deoxy-D-glycero-D-galacto-nonulopyranosidonic acid (KDN) glycosides is described, making use of a series of differentially O-protected N-nitroso-N-acetyl sialyl glycosides and of isotopic labeling studies. No evidence is found for stereodirecting participation by ester groups at the 4- and 7-positions. Comparisons are drawn with oxidative deamination reactions of 4-amino-4-deoxy and 2-amino-2-deoxy hexopyranosides and a common mechanism is formulated involving the intermediacy of 1-oxabicyclo[3.1.0]hexyl oxonium ions following participation by the pyranoside ring oxygen. A minor reaction pathway has been uncovered by labeling studies in the β-thiosialosides that results in the exchange of the 4-O-acetyl group by the glacial acetic acid that serves as external nucleophile in the general oxidative deamination process. A mechanism is proposed for this exchange involving participation by the thioglycoside at the level of an intermediate diazoalkane.

A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides

Hydrolysis of β-d-mannosides by β-mannosidases typically proceeds via a B2,5 transition state conformation for the pyranoside ring, while that of β-d-glucosides by β-glucosidases proceeds through a distinct 4H3 transition state conformation. However, rice Os7BGlu26 β-glycosidase hydrolyzes 4-nitrophenyl β-d-glucoside and β-d-mannoside with similar efficiencies. The origin of this dual substrate specificity was investigated by kinetic, structural, and computational approaches. The glycosidase inhibitors glucoimidazole and mannoimidazole inhibited Os7BGlu26 with Ki values of 2.7 nM and 10.4 μM, respectively. In X-ray crystal structures of complexes with Os7BGlu26, glucoimidazole bound to the active site in a 4E conformation, while mannoimidazole bound in a B2,5 conformation, suggesting different transition state conformations. Moreover, calculation of quantum mechanics/molecular mechanics (QM/MM) free energy landscapes showed that 4-nitrophenyl β-d-glucoside adopts a 1S3/4E conformation in the Michaelis com...

Pyranoside-into-furanoside rearrangement: new reaction in carbohydrate chemistry and its application in oligosaccharide synthesis.

Great interest in natural furanoside-containing compounds has challenged the development of preparative methods for their synthesis. Herein a novel reaction in carbohydrate chemistry, namely a pyranoside-into-furanoside (PIF) rearrangement permitting the transformation of selectively O-substituted pyranosides into the corresponding furanosides is reported. The discovered process includes acid-promoted sulfation accompanied by rearrangement of the pyranoside ring into a furanoside ring followed by solvolytic O-desulfation. This process, which has no analogy in organic chemistry, was shown to be a very useful tool for the synthesis of furanoside-containing complex oligosaccharides, which was demonstrated by synthesizing disaccharide derivatives α-D-Galp-(1→3)-β-D-Galf-OPr, 3-O-s-lactyl-β-D-Galf-(1→3)-β-D-Glcp-OPr, and α-L-Fucf-(1→4)-β-D-GlcpA-OPr related to polysaccharides from the bacteria Klebsiella pneumoniae and Enterococcus faecalis and the brown seaweed Chordaria flagelliformis.

Does the “C3 effect” offset the Δ2 effect, as regards the solution flexibility of aldoses?

The solution flexibility of carbohydrates influences a variety of molecular recognition and regulatory processes. For aldoses and other monosaccharides, this flexibility is dictated by the orientations of the various hydroxyl (OH) groups present, which influences conformer and anomer ratios, interactions among these OH groups, and interactions between them and the surrounding solvent. Depending on the number and position of axial OH groups, a variety of structures can coexist in solutions at equilibrium. In 1950, as part of his pioneering studies on the shape of pyranoside rings, Reeves described the Δ2 effect, the greater destabilization of the pyranose ring conformation when the OH group on carbon 2 (C2 ) is in the axial position. It was later proposed by Angyal that the Δ2 effect could be cancelled by the presence of an axial OH on C3 , termed here the "C3 effect." Employing size-exclusion chromatography, an entropically-controlled separation technique, we have investigated whether or not the C3 and Δ2 effects indeed do compensate for one another with respect to their influence on the solution flexibility of select aldohexoses and aldopentoses. As will be seen, while qualitatively and semiquantitatively this mutual cancellation of effects does occur in aldohexoses, it does not appear to do so in aldopentoses. An explanation for the latter appears to lie in the variety of anomers and conformers present in equilibrium solutions of those aldopentoses studied and in the relative entropic contribution of individual conformers or anomers to the total solution flexibility.

Bisubstrate UDP–peptide conjugates as human O-GlcNAc transferase inhibitors

Inhibitors of OGT (O-GlcNAc transferase) are valuable tools to study the cell biology of protein O-GlcNAcylation. We report OGT bisubstrate-linked inhibitors (goblins) in which the acceptor serine in the peptide VTPVSTA is covalently linked to UDP, eliminating the GlcNAc pyranoside ring. Goblin1 co-crystallizes with OGT, revealing an ordered C3 linker and retained substrate-binding modes, and binds the enzyme with micromolar affinity, inhibiting glycosyltransfer on to protein and peptide substrates.

Glycosyl rotation and distortion by key residues in Endocellulase Cel6A from Theromobifida fusca

Endocellulases are one kind of the important biodegrading cellulose enzymes. Experimental results show that a rotated and distorted preactivated structure exists before the substrate entering the transition state. The molecular dynamic simulation of endocellulase Cel6A models revealed a correlation between the rotation and distortion of pyranoside ring in -1 glycosyl unit of the substrate. The two key residues, Tyr73 and Ser189, in Cal6A cooperate to rotate and distort the pyranoside ring in the cellulose hydrolysis.

Stereoelectronic control of cleavage of dioxolane five-membered ring on carbohydrates

A mechanism about the origin of the selectivities for the cleavage of dioxolane five-membered rings on pyranoside rings was suggested. Quantum chemical studies were performed to testify the rationality of the mechanism. It is thus suggested that the selectivities should be dependent on the differences of the free energy at the transition states when the five-membered ring cleaves. Natural bond orbital(NBO) analysis was further made to assess the influence of stereoelectronic effects on the selectivities.

Analysis of the Mildiomycin Biosynthesis Gene Cluster in Streptoverticillum remofaciens ZJU5119 and Characterization of MilC, a Hydroxymethyl cytosyl‐glucuronic Acid Synthase

Mildiomycin (MIL) is a peptidyl-nucleoside antibiotic produced by Streptoverticillum remofaciens ZJU5119 that exhibits strong inhibitory activity against powdery mildew. The entire MIL biosynthesis gene cluster was cloned and expressed in Streptomyces lividans 1326. Systematic gene disruptions narrowed down the cluster to 16 functional ORFs and identified the boundaries of the gene cluster. A putative cytosylglucuronic acid (CGA) synthase gene, milC, was disrupted in Sv. remofaciens and heterologously expressed in E. coli. An in vitro assay revealed that purified MilC could utilize either cytosine or hydroxymethylcytosine as substrate to yield CGA or hydroxymethyl-CGA (HM-CGA), respectively. MilG is believed to be a key enzyme in the MIL biosynthesis pathway and contains the C(XXX)C(XX)C motif characteristic of members of the radical S-adenosyl methionine (SAM) superfamily. Disruption of milG leads to accumulation of HM-CGA. Labeling experiments with (13)C(6)-L-arginine indicated that decarboxylation at C5 of the pyranoside ring was coupled with the attachment of 5-guanidino-2,4-dihydroxyvalerate side chain through C-C bond formation. In contrast, exogenous (13)C(6)-labeled 4-hydroxy-L-arginine was not incorporated into the MIL structure. Comparative analysis of the 16 MIL ORFs with counterparts involved in the biosynthesis of the structurally similar compound blasticidin S, along with the results above, provide insight into the complete MIL biosynthetic pathway.

Stereoelectronic Control in Regioselective Carbohydrate Protection

Organotin-mediated regioselective protection has been extensively used in organic synthesis for many years. However, the mechanistic origin of the resulting regioselectivity is still not clear. By the comparison of the steric and stereoelectronic effects controlling the geometry of five-membered rings formed from neighboring group participation, from intramolecular acyl group migration, or from orthoester transesterification on pyranoside rings, a theory on the pattern resulting from the reaction with dibutyltin oxide is presented. It is thus suggested that the regioselectivity of organotin-mediated protection is controlled by analogous steric and stereoelectronic effects as in neighboring group participation and acyl group migration, mainly dependent on the stereoelectronic effects of the pyranoside itself, and not related to complex stannylene structures. An organotin protection mechanism is also suggested, emanating from steric and stereoelectronic effects, nucleophilicity, and organotin acyl migration.

Structural Basis for Norovirus Inhibition and Fucose Mimicry by Citrate

Human noroviruses bind with their capsid-protruding domains to histo-blood-group antigens (HBGAs), an interaction thought to direct their entry into cells. Although human noroviruses are the major cause of gastroenteritis outbreaks, development of antivirals has been lacking, mainly because human noroviruses cannot be cultivated. Here we use X-ray crystallography and saturation transfer difference nuclear magnetic resonance (STD NMR) to analyze the interaction of citrate with genogroup II (GII) noroviruses. Crystals of citrate in complex with the protruding domain from norovirus GII.10 Vietnam026 diffracted to 1.4 Å and showed a single citrate bound at the site of HBGA interaction. The citrate interaction was coordinated with a set of capsid interactions almost identical to that involved in recognizing the terminal HBGA fucose, the saccharide which forms the primary conserved interaction between HBGAs and GII noroviruses. Citrate and a water molecule formed a ring-like structure that mimicked the pyranoside ring of fucose. STD NMR showed the protruding domain to have weak affinity for citrate (460 μM). This affinity, however, was similar to the affinities of the protruding domain for fucose (460 μM) and H type 2 trisaccharide (390 μM), an HBGA shown previously to be specifically recognized by human noroviruses. Importantly, competition STD NMR showed that citrate could compete with HBGA for norovirus binding. Together, the results suggest that citrate and other glycomimetics have the potential to block human noroviruses from binding to HBGAs.

Endocyclic Cleavage in Glycosides with 2,3-transCyclic Protecting Groups

An endocyclic pathway is proposed as a reaction mechanism for the anomerization from the β (1,2-trans) to the α (1,2-cis) configuration observed in glycosides carrying 2,3-trans cyclic protecting groups. This reaction occurs in the presence of a weak Lewis or Brønsted acid, while endocyclic cleavage (endocleavage) in typical glycosides was observed only when mediated by protic media or strong Lewis acids. To rationalize the behavior of this class of compounds, the reaction mechanism and the promoting factors of the endocleavage are investigated using quantum-mechanical (QM) calculations and experimental studies. We examine anomerization reactions of thioglycosides carrying 2,3-trans cyclic protecting groups, employing boron trifluoride etherate (BF(3)·OEt(2)) as a Lewis acid. The estimated theoretical reactivity, based on a simple model to predict transition state (TS) energies from the strain caused by the fused rings, is very close to the TS energies calculated by the TS search along the C1-C2 bond rotation after the endo C-O bond breaking. Excellent agreement is found between the predicted TS energies and the experimental reactivity ranking. The series of calculations and experiments strongly supports the predominance of the endocyclic rather than the exocyclic mechanism. Furthermore, these investigations suggest that the inner strain is the primary factor enhancing the endocleavage reaction. The effect of the cyclic protecting group in restricting the pyranoside ring to a (4)C(1) conformation, extensively discussed in conjunction with the stereoelectronic effect theory, is shown to be a secondary factor.

4-Formylphenyl 2,3,4,6-tetra-O-acetyl-β-D-galactopyranoside

The galactose ring in the title compound, C21H24O11, has a chair conformation with the substituted benzene ring occupying an equatorial position. The crystal packing features C—H⋯O inter­actions that lead to the formation of supra­molecular layers in the ab plane.

1,2,3,3′,4′,6′-Hexaacetyl-4,6-O-benzylidenesucrose

In the title compound, C31H38O17, the 1,3-dioxane and pyran­oside rings both show 4 C 1 chair conformations while for the d-fructofuran­oside moiety an envelop 3E conformation is observed. The phenyl ring is oriented almost perpendicular to the 1,3-dioxane ring [dihedral angle = 79.3 (2)°], and the acetate groups are equatorial for the pyran­oside ring and axial for the furan­oside ring. The analysis of potential hydrogen bonds shows both intra- and inter­molecular C—H⋯O contacts to be present.