Sugar Ring Research Articles

Synthesis of Triazole-Linked Fluorescent Saccharides and Glycosyl Amino Esters

Synthesis of fluorescent carbohydrates and glycopeptides has been emerging as an attractive research field because of various biological roles of carbohydrates and glycoproteins. Fluorescent glycosides and C-glycosides were synthesized by copper(I)-catalyzed Huisgen reaction between 6- O -(2-azidoacetyl) glycopyranosides and alkyne-functionalized fluorophores. For the fluorescent disaccharides as well as glycosyl amino acids derivatives, glycosylation of azido-functionalized thioglycosides, followed by click reaction with corresponding fluorophores is preferred than the inversed procedure (click reaction before the glycosylation). Fluorophores like dansyl, NBD, or rhodamine have been successfully introduced on the sugar ring. All the newly synthesized fluorescent glycosides and glycoconjugates showed similar photophysical properties to the native fluorophores, with a higher quantum yield for the dansyl derivatives.

MiR‐TRAP: A Benchtop Chemical Biology Strategy to Identify microRNA Targets

miR‐TRAP: A Benchtop Chemical Biology Strategy to Identify microRNA Targets

The Two Faces of Iminoalditols: Powerful Inhibitors Trigger Glycosidase Activation

Understanding and controlling carbohydrate processing enzymes (CPE) have been major issues and challenges for chemists, biochemists and clinical practitioners alike. One of the most powerful families of substances for probing active sites as well as allosteric interactions with CPEs are basic sugar analogues, in particular iminoalditols. This compound class presents a basic trivalent nitrogen instead of oxygen in the sugar ring as the common feature. Depending on the task, such molecules may show two faces, acting as powerful competitive inhibitors or as folding templates for the same CPE protein. When applied at sub-inhibitory concentration iminoalditols and derivatives thereof have become attractive as pharmacological chaperones for the treatment of lysosomal storage diseases. As such these structures can restore protein activity by assisting correct folding of mutant enzymes thus facilitating transportation to the lysosome and consequently substrate hydrolysis. This review surveys iminoalditol structures which have recently been investigated as potential pharmacological chaperones for the treatment of lysosomal storage diseases.

Theoretical study on the deglycosylation mechanism of rice BGlu1 β‐glucosidase

AbstractIt is proposed that the catalysis of GH1 enzymes follows a double‐displacement mechanism involving a glycosylation and a deglycosylation steps. In this article, the deglycosylation step was studied using quantum mechanical/molecular mechanical (QM/MM) approach. The calculation results reveal that the nucleophilic water (Wat1) attacks to the anomeric C1, and the deglycosylation step experiences a barrier of 21.4 kcal/mol from the glycosyl‐enzyme intermediate to the hydrolysis product, in which an oxocarbenium cation‐like transition state (TS) is formed. At the TS, the covalent glycosyl‐enzyme bond is almost broken (distance of 2.45 Å), and the new covalent bond between the attacking oxygen of the water molecule and C1 is basically established (length of 2.14 Å). In addition, a short hydrogen bridge is observed between the nucleophilic E386 and the C2OH of sugar ring (distance of 1.94 Å) at the TS, which facilitates the ring changing from a chair form to half‐chair form, and stabilizes the oxocarbenium cation‐like TS. © 2013 Wiley Periodicals, Inc.

Evaluation of ion activation strategies and mechanisms for the gas-phase fragmentation of sulfoquinovosyldiacylglycerol lipids from Rhodobacter sphaeroides

Sulfoquinovosyldiacylglycerol (SQDG) lipids, found in plants and photosynthetic bacteria, can substitute for phospholipids under phosphate limiting conditions. Here, various low-energy ion activation strategies have been evaluated for the identification and characterization of deprotonated SQDG lipids from a crude membrane lipid extract of Rhodobacter sphaeroides, using collision-induced dissociation-tandem mass spectrometry (CID-MS/MS) in either a triple quadrupole mass spectrometer or in a hybrid quadrupole ion trap-multipole mass spectrometer coupled with high resolution/accurate mass analysis capabilities. In the triple quadrupole instrument, using energy resolved CID-MS/MS experiments, the SQDG head group specific product ion at m/z 225 (C6H9O7S−), rather than m/z 81 (SO3H−), was determined to provide the greatest sensitivity for SQDG lipid detection, and is therefore the preferred ‘fingerprint’ ion for the identification of this lipid class from within complex lipid mixtures when using precursor ion scan mode MS/MS experiments. A comparison of conventional ion trap CID-MS/MS and -MSn, with ‘low Q’ CID-MS/MS, pulsed Q dissociation (PQD)-MS/MS and higher energy collision induced dissociation (HCD)-MS/MS performed in an LTQ Orbitrap Velos mass spectrometer, revealed that HCD-MS/MS coupled with high resolution/accurate mass analysis represents the most sensitive, and perhaps most importantly the most specific strategy, for ion trap based identification and characterization of SQDG lipids, due to the ability to readily distinguish the SQDG head group specific product ion at m/z 225.0069 from other products that may be present at the same nominal m/z value. Finally, the mechanisms responsible for formation of each of the major product ions observed by low-energy CID-MS/MS of deprotonated SQDG lipids were elucidated using uniform H/D exchange, HCD-MS/MS and high resolution mass analysis. Formation of the m/z 225 ‘fingerprint’ ion occurs via a charge-remote cis-elimination reaction, likely involving transfer of a hydrogen from the hydroxyl group located on the C2 position of the sugar ring.

Conformational Study of the Hydroxyproline–O–Glycosidic Linkage: Sugar–Peptide Orientation and Prolyl Amide Isomerization in (α/β)–Galactosylated 4(R/S)–Hydroxyproline

Glycosylation is a frequent post-translational modification of proteins that has been shown to influence protein structure and function. Glycosylation of hydroxyproline occurs widely in plants, but is absent in humans and animals. Previous experimental studies on model amides have indicated that α/β-galactosylation of 4R-hydroxyproline (Hyp) has no measurable effect on prolyl amide isomerization, while a 7% increase in the trans isomer population, as well as a 25-50% increase in the isomerization rate, was observed for the 4S stereoisomer (hyp). In this work, molecular dynamics simulations in explicit water and implicit solvent DFT optimizations are used to examine the structure of the hydroxyproline-O-galactosyl linkage and the effect of glycosylation on the structure and cis/trans isomerization of the peptide backbone. The calculations show two major minima with respect to the glycosidic linkage in all compounds. The C(γ)-exo puckering observed in 4R compounds projects the sugar away from the peptide backbone, while a twisted C(γ)-endo/C(β)-exo pucker in the 4S compounds brings the peptide and sugar rings together and leads to an intramolecular hydrogen-bonding interaction that is sometimes bridged by a water molecule. This hydrogen bond changes the conformation of the peptide backbone, inducing a favorable n → π* interaction between the oxygen lone pair from the prolyl N-terminal amide and the C═O, which explains the observed increase in trans isomer population in α/β-galactosylated 4S-hydroxyproline. Our results provide the first molecular level information about this important glycosidic linkage, as well as provide an explanation for the previously observed increase in trans isomer population in 4S-hyp compounds. Moreover, this study provides evidence that sugar-mediated long-range hydrogen bonding between hydroxyl groups and the carbonyl peptide backbone can modify the properties of N-terminal prolyl cis/trans isomerization in peptides.

Nanodiamonds in sugar rings: an experimental and theoretical investigation of cyclodextrin–nanodiamond inclusion complexes

We report on the noncovalent interactions of nanodiamond carboxylic acids derived from adamantane, diamantane, and triamantane with β- and γ-cyclodextrins. The water solubility of the nanodiamonds was increased by attaching an aromatic dicarboxylic acid via peptide coupling. Isothermal titration calorimetry experiments were performed to determine the thermodynamic parameters (K(a), ΔH, ΔG and ΔS) for the host-guest inclusion. The stoichiometry of the complexes is invariably 1:1. It was found that K(a), ΔG and ΔH of inclusion increase for larger nanodiamonds. ΔS is generally positive, in particular for the largest nanodiamonds. β-Cyclodextrin binds all nanodiamonds, γ-cyclodextrin clearly prefers the most bulky nanodiamonds. The interaction of 9-triamantane carboxylic acid shows one of the strongest complexation constants towards γ-cyclodextrin ever reported, K(a) = 5.0 × 10(5) M(-1). In order to gain some insight into the possible structural basis of these inclusion complexes we performed density functional calculations at the B97-D3/def2-TZVPP level of theory.

Assigning kinetic 3D-signatures to glycocodes

Reconciling glycocodes and their associated bioactivities, via 3D-structure, will rationalise burgeoning high-throughput functional glycomics data and underpin a new era of opportunity in chemical biology. A major impasse to achieving this goal is a detailed understanding of pyranose sugar ring 3D-conformation (or pucker) and the affiliated microsecond-timescale exchange kinetics. Here, we perform hardware-accelerated kinetically-rigorous equilibrium simulations of fundamental monosaccharides to produce the hypothesis that pyranoses have microsecond-timescale kinetic puckering signatures in water, classified as unstable (rare in the glycome), metastable (infrequently observed) and stable (prevalent). The predicted μs-metastability of β-d-glucose explained hitherto irreconcilable experimental measurements. Twisted puckers seen in carbohydrate enzymes were present in the aqueous 3D-ensemble (suggesting preorganization) and pyranose-water interactions accounted for the relative stability of β-d-galactose. Characteristic 3D-shapes for biologically- and commercially-important carbohydrates and new rules linking chemical modifications with pyranose μs-puckering kinetics are proposed. The observations advance structural-glycomics towards dynamic 3D-templates suitable for structure-based design.

Theoretical investigation of interaction between psoralen and altretamine with stacked DNA base pairs

The present study is an attempt to have a better understanding of physicochemical interaction between anticancer drugs psoralen and altretamine with stacked DNA base pairs. The isolated structural parameters of the stacked base pairs were taken from the Protein Data Bank (PDB) of A-DNA file. The influence of the intercalators on the stability of stacked base pairs was studied based on the results of the interaction energies, which were calculated by the structures of intercalation complexes of psoralen and altretamine with stacked DNA base pairs. The higher dipole moment and polarizability which account for the dispersion forces play an important role during the intercalation of psoralen and altretamine molecules with the base pairs. The stability of the stacking base pairs and their interaction with the intercalator molecules due to the formation of hydrogen bond have been analyzed by Natural Bond Orbital analysis. It has also been noted that intercalator molecules produce significant changes in the values of the phase angle P of pseudorotation conformation of the sugar ring. The physicochemical properties of the psoralen and altretamine as well as the mechanism by which the drug interacts with DNA base pairs allow the rational design of novel anticancer drugs.

Effects of sugar ring puckering, anti-syn interconversion and intramolecular interactions on N-glycosidic bond cleavage in 3-methyl-2′-deoxyadenosine and 2′-deoxyadenosine

The effects of structural parameters and intramolecular interactions on N-glycosidic bond length in 3-methyl-2′- deoxyadenosine (3MDA) and 2′-deoxyadenosine (DA) were investigated employing quantum mechanical methods. All calculations were performed at B3LYP/6-311++G** level in the gas phase. The N-glycosidic bond length strongly depends on sugar configuration; it is shorter in syn conformation relative to anti in many cases where they have the same sugar ring configuration. The sugar conformation can influence the N-glycosidic bond through interaction with the O4′ atom. The impact of intramolecular improper hydrogen bonds and H-H bonding interactions on N-glycosidic bond length was investigated in DA and 3MDA and their modeled structures. Improper hydrogen bonds decrease N-glycosidic bond length while H-H bonding interactions increase it.

Activation of human RNase L by 2′- and 5′-O-methylphosphonate-modified oligoadenylates

To determine the influence of internucleotide linkage and sugar ring conformation, and the role of 5'-terminal phosphate, on the activation of human RNase L, a series of 2'- and 5'-O-methylphosphonate-modified tetramers were synthesized from appropriate monomeric units and evaluated for their ability to activate human RNase L. Tetramers pAAAp(c)X modified by ribo, arabino or xylo 5'-phosphonate unit p(c)X activated RNase L with efficiency comparable to that of natural activator. Moreover, incorporation of phosphonate linkages ensured the stability against cleavage by nucleases. The substitution of 5'-terminal phosphate for 5'-terminal phosphonate in tetramer p(c)XAAA afforded tetramers with excellent activation efficiency and with complete stability against cleavage by phosphomonoesterases.

Comparison of the α and β isomeric forms of the detergent n-dodecyl-D-maltoside for solubilizing photosynthetic complexes from pea thylakoid membranes

Mild non-ionic detergents are indispensable in the isolation of intact integral membrane proteins and protein-complexes from biological membranes. Dodecylmaltoside (DM) belongs to this class of detergents being a glucoside-based surfactant with a bulky hydrophilic head group composed of two sugar rings and a non-charged alkyl glycoside chain. Two isomers of this molecule exist, differing only in the configuration of the alkyl chain around the anomeric center of the carbohydrate head group, axial in α-DM and equatorial in β-DM. In this paper, we have investigated the solubilizing properties of α-DM and β-DM on the isolation of photosynthetic complexes from pea thylakoids membranes maintaining their native architecture of stacked grana and stroma lamellae. Exposure of these stacked thylakoids to a single step treatment with increasing concentrations (5–100mM) of α-DM or β-DM resulted in a quick partial or complete solubilization of the membranes. Regardless of the isomeric form used: 1) at the lowest DM concentrations only a partial solubilization of thylakoids was achieved, giving rise to the release of mainly small protein complexes mixed with membrane fragments enriched in PSI from stroma lamellae; 2) at concentrations above 30mM a complete solubilization occurred with the further release of high molecular weight protein complexes identified as dimeric PSII, PSI-LHCI and PSII–LHCII supercomplexes. However, at concentrations of detergent which fully solubilized the thylakoids, the α and β isomeric forms of DM exerted a somewhat different solubilizing effect on the membranes: higher abundance of larger sized PSII–LHCII supercomplexes retaining a higher proportion of LHCII and lower amounts of PSI–LHCI intermediates were observed in α-DM treated membranes, reflecting the mildness of α-DM compared with its isomer. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.

Influence of Sugar Ring Conformation on the Transportability of Nucleosides by Human Nucleoside Transporters

The conformational preference of human nucleoside transporters (hNTs) with respect to sugar ring was examined using conformationally fixed purine and pyrimidine nucleosides built on a bicyclo[3.1.0]hexane template. These fixed-conformation nucleosides, methanocarba-deoxyadenosine or methanocarba-deoxycytidine in North (C3'-endo, N-MCdA and N-MCdC) or South (C2'-endo, S-MCdA and S-MCdC) conformations, were used to study inhibition of equilibrative (hENT1-4) and concentrative (hCNT1-3) nucleoside transport by individual recombinant hNTs produced in Saccharomyces cerevisiae cells or Xenopus laevis oocytes. Our results indicated that nucleosides in the North conformation were potent inhibitors of transport mediated by hCNTs whereas South nucleosides were inhibitors of hENTs, thus showing differences in the interaction with the hNTs. In summary, hCNTs exhibited strong preferences for North nucleosides whereas hENTs exhibited slight preferences for South nucleosides, demonstrating for the first time different conformational preferences among members of the two families of hNTs.

Regioselective Synthesis of Novel 3‐Thiazolidine Acetic Acid Derivatives from Glycosido Ureides

A series of 3-thiazolidine acetic acid-2-(per-O-acetylglycosyl)-1'-imino-α-(substituted)-4-oxo ethyl ester derivatives (3a-t) were prepared via the reaction of substituted amino acid-N-[(per-O-acetylglycosylamino)thioxomethyl]-ethyl ester with ethyl bromoacetate. The crystal structure of 3-thiazolidine acetic acid-2-(2',3',4',6'-tetra-O-acetyl-β-D-galactoyranosyl)-1'-imino-α-methyl-4-oxo ethyl ester 3g and ¹H-¹³C HMBC (2D NMR experiments) measurements of 3-thiazolidine acetic acid-2-(2',3',4',6'-tetra-O-acetyl-β-D-galactopyranosyl)-1'-imino-α-(1-methylthio)ethyl-4-oxo ethyl ester 3j revealed the exclusive regioselectivity during the closure of these rings toward the N-2 position of the thiourea moiety. Furthermore, the crystal structure of compound 3g showed that the attack of N-1 was blocked by sugar ring owing to the steric effect. The bioactivity data suggested that compound 2e has mild anticancer activity.

Do Intermolecular Interactions Control Crystallization Abilities of Glass-Forming Liquids?

Broadband dielectric spectroscopy was used to investigate molecular dynamics of three very similar systems: D-glucose, α-pentaacetylglucose, and β-pentaacetylglucose in a wide range of temperatures. We found out that two latter systems (differing only in location of the acetyl group attached to the first carbon in the sugar ring) reveal completely opposite tendencies to crystallization. Therefore, the aim of this Article was to investigate in detail molecular dynamics of both pentaacetylglucoses to assess what are the underlying of different crystallization abilities of so closely related carbohydrates. To analyze the kinetics of crystallization, we used Avrami and Avramov approaches. Interestingly, we found out that both α-and β-pentaacetylglucose exhibit completely different crystallization mechanisms. In the first case, the value of Avrami exponent was estimated to be n = 2, whereas for the second carbohydrate this exponent was equaled to n = 5.5. Additionally, we have carried out isothermal time-dependent dielectric measurements on D-glucose to demonstrate that this saccharide is more stable than its acetyl derivatives. Results presented in this Article indicate that besides molecular mobility, the character of the intermolecular interactions might also be another important factor governing crystallization process. Surprisingly, this issue is not often addressed during studies on crystallization abilities of different glass-formers. Finally, additional optical measurements were carried out to get more detailed information about nucleation density, activation barrier for a crystal growth, and morphology of crystallization structures.

Facilitating high-force single-polysaccharide stretching using covalent attachment of one end of the chain.

Single polysaccharide force spectroscopy has yielded particularly interesting data, the interpretation of which requires the marriage of statistical-mechanical theories of polymer physics to the complexities afforded by possible force-induced conformational transitions of the constituent sugar rings. However, the difficulty of designing handles for the specific attachment of the different ends of polysaccharide chains to substrates, such as piezoelectric scanners, cantilevers or microbeads has meant that the majority of studies to date have been carried out with the polymer physisorbed to the substrates between which it is stretched, or at best chemically attached via bonds formed at uncontrolled locations along the length of the molecule. This means that the lengths of obtained polysaccharide stretches, as well as the forces that can be placed on the molecule without generating detachment, are generally smaller than those obtainable for polymers that offer the ability to be covalently attached to substrates specifically at their ends. As a consequence it is troublesome and tedious to record a statistically significant number of force curves that extend chains to high enough forces to investigate certain conformational transitions, such as the boat-to-inverted chair, exhibited by polysaccharides such as pectin. Herein, single molecule force-extension curves have been measured for the several pectin samples using AFM. The results are compared when either (1) the polymers have been physisorbed between the cantilever and the surface of the piezo-electric scanner, under several different solvent conditions of pH and ionic strength, or (2) the polymer molecule has been chemically attached at one end to the piezo surface using a recently reported coupling procedure. In fact, using such a chemical attachment to tether the end of the polysaccharide, reduced the frequency of successful stretching events obtained in a particular location, confirming the role of surface diffusion in the physisorbed experiments. Nevertheless, when polymer stretches were successfully recorded, the force that could be applied before detachment was significantly increased, indicating that this methodology has great potential for improving the acquisition of data reporting on force-induced conformational transitions of the sugar ring that require the application of significant stresses.

ChemInform Abstract: Synthesis of Trifluoromethylated and gem‐Difluoromethylenated Biologically Interesting Compounds from Fluorine‐Containing Synthons

AbstractReview: ca. 100 refs.

Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance

Pretreatment for deconstructing the multifaceted interaction network in crystalline cellulose is a limiting step in making fuels from lignocellulosic biomass. Not soluble in water and most organic solvents, cellulose was found to dissolve in certain classes of ionic liquids (ILs). To elucidate the underlying mechanisms, we simulated cellulose deconstruction by peeling off an 11-residue glucan chain from a cellulose microfibril and computed the free-energy profile in water and in 1-butyl-3-methylimidazolium chloride (BmimCl) IL. For this deconstruction process, the calculated free-energy cost/reduction in water/BmimCl is ∼2 kcal/mol per glucose residue, respectively. To unravel the molecular origin of solvent-induced differences, we devised a coarse graining scheme to dissect force interactions in simulation models by a force-matching method. The results establish that solvent-glucan interactions are dependent on the deconstruction state of cellulose. Water couples to the hydroxyl and side-chain groups of glucose residues more strongly in the peeled-off state but lacks driving forces to interact with sugar rings and linker oxygens. Conversely, BmimCl demonstrates versatility in targeting glucose residues in cellulose. Anions strongly interact with hydroxyl groups, and the coupling of cations to side chains and linker oxygens is stronger in the peeled-off state. Other than enhancing anion-hydroxyl group coupling, coarse-grain analysis of force interactions identifies configuring cations to target side chains and linker oxygens as a useful design strategy for pretreatment ILs. Furthermore, the state dependence of solvent-glucan interactions highlights specific stabilization and/or frustration of the different structure states of cellulose as important design parameters for pretreatment solvents.

Solid-state NMR spectroscopy provides atomic-level insights into the dehydration of cartilage.

An atomic-level insight into the functioning of articular cartilage would be useful to develop prevention strategies and therapies for joint diseases such as osteoarthritis. However, the composition and structure of cartilage and their relationship to its unique mechanical properties are quite complex and pose tremendous challenges to most biophysical techniques. In this study, we present an investigation of the structure and dynamics of polymeric molecules of articular cartilage using time-resolved solid-state NMR spectroscopy during dehydration. Full-thickness cartilage explants were used in magic-angle spinning experiments to monitor the structural changes of rigid and mobile carbons. Our results reveal that the dehydration reduced the mobility of collagen amino acid residues and carbon sugar ring structures in glycosaminoglycans but had no effect on the trans-Xaa-Pro conformation. Equally interestingly, our results demonstrate that the dehydration effects are reversible, and the molecular structure and mobility are restored upon rehydration.

Crystal Structure of the E2 Domain of Amyloid Precursor Protein-like Protein 1 in Complex with Sucrose Octasulfate

Missense mutations in the amyloid precursor protein (APP) gene can cause familial Alzheimer disease. It is thought that APP and APP-like proteins (APLPs) may play a role in adhesion and signal transduction because their ectodomains interact with components of the extracellular matrix. Heparin binding induces dimerization of APP and APLPs. To help explain how these proteins interact with heparin, we have determined the crystal structure of the E2 domain of APLP1 in complex with sucrose octasulfate (SOS). A total of three SOS molecules are bound to the E2 dimer. Two SOSs are bound inside a narrow intersubdomain groove, and the third SOS is bound near the two-fold axis of the protein. Mutational analyses show that most residues interacting with SOS also contribute to heparin binding, although in varying degrees; a deep pocket, defined by His-376, Lys-422, and Arg-429, and an interfacial site between Lys-314 and its symmetry mate are most important in the binding of the negatively charged polysaccharide. Comparison with a lower resolution APP structure shows that all key heparin binding residues are conserved and identically positioned, suggesting that APLP1 and APP may bind heparin similarly. In transfected HEK-293 cells, mutating residues responsible for heparin binding causes little change in the proteolysis of APP by the secretases. However, mutating a pair of conserved basic residues (equivalent to Arg-414 and Arg-415 of APLP1) immediately adjacent to the heparin binding site affects both the maturation and the processing of APP.