Structure-based design of UDP-GlcNAc analogs as candidate GnT-V inhibitors.

BACKGROUND: N-Glycan branching regulates various functions of glycoproteins. N-Acetylglucosaminyltransferase V (GnT-V) is a GlcNAc transferase that acts on N-glycans and the GnT-V-producing branch is highly related to cancer progression. This indicates that specific GnT-V inhibitors may be drug candidates for cancer treatment. To design novel GnT-V inhibitors, we focused on the unique and weak recognition of the donor substrate UDP-GlcNAc by GnT-V. On the basis of the catalytic pocket structure, we hypothesized that UDP-GlcNAc analogs with increasing hydrophobicity may be GnT-V inhibitors. METHODS: We chemically synthesized 10 UDP-GlcNAc analogs in which one or two phosphate groups were replaced with hydrophobic groups. To test these compounds, we set up an HPLC-based enzyme assay system for all N-glycan-branching GlcNAc transferases in which GnT-I-V activity was measured using purified truncated enzymes. Using this system, we assessed the inhibitory effects of the synthesized compounds on GnT-V and their specificity. RESULTS: Several UDP-GlcNAc analogs inhibited GnT-V activity, although the inhibition potency was modest. Compared with other GnTs, these compounds showed a preference for GnT-V, which suggested that GnT-V was relatively tolerant of hydrophobicity in the donor substrate. Docking models of the inhibitory compounds with GnT-V suggested the mechanisms of how these compounds interacted with GnT-V and inhibited its action. CONCLUSIONS: Chemical modification of the donor substrate may be a promising strategy to develop selective inhibitors of GnT-V. GENERAL SIGNIFICANCE: Our findings provide new insights into the design of GnT inhibitors and how GnTs recognize the donor substrate.

Advanced Chemical Methods for Stereoselective Sialylation and Their Applications in Sialoglycan Syntheses.

Sialic acid is an important component of cell surface glycans, which are responsible for many vital body functions and should therefore be thoroughly studied to understand their biological roles and association with disorders. The difficulty of isolating large quantities of homogenous-state sialoglycans from natural sources has inspired the development of the corresponding chemical synthesis methods affording acceptable purities, yields, and amounts. However, the related syntheses are challenging because of the difficulties in α-glycosylation of sialic acid, which arises from its certain structural features such as the absence of a stereodirecting group at the C3 position and presence of carboxyl group at the anomeric position. Moreover, the structural complexities of sialoglycans with diverse numbers and locations of sialic acid on the glycan chains pose additional barriers. Thus, efficient α-stereoselective routes to sialosides remain highly sought after, although various types of sialyl donors/acceptors have been developed for the straightforward synthesis of α-sialosides. Herein, we review the latest progress in the α-stereoselective synthesis of sialosides and their applications in the preparation of gangliosides and other sialoglycans.

Azide-Functionalized Derivatives of the Virulence-Associated Sugar Pseudaminic Acid: Chiral Pool Synthesis and Labeling of Bacteria.

Pseudaminic acid (Pse) is a significant prokaryotic monosaccharide found in important Gram-negative and Gram-positive bacteria. This unique sugar serves as a component of cell-surface-associated glycans or glycoproteins and is associated with their virulence. We report the synthesis of azidoacetamido-functionalized Pse derivatives as part of a search for Pse-derived metabolic labeling reagents. The synthesis was initiated with d-glucose (Glc), which served as a cost-effective chiral pool starting material. Key synthetic steps involve the conversion of C1 of Glc into the terminal methyl group of Pse, and inverting deoxyaminations at C3 and C5 of Glc followed by backbone elongation with a three-carbon unit using the Barbier reaction. Metabolic labeling experiments revealed that, of the four Pse derivatives, ester-protected C5 azidoacetamido-Pse successfully labeled cells of Pse-expressing Gram-positive and Gram-negative strains. No labeling was observed in cells of non-Pse-expressing strains. The ester-protected and C5 azidoacetamido-functionalized Pse is thus a useful reagent for the identification of bacteria expressing this unique virulence-associated nonulosonic acid.

Quantification of Noncovalent Interactions in Azide-Pnictogen, -Chalcogen, and -Halogen Contacts.

The noncovalent interactions between azides and oxygen-containing moieties are investigated through a computational study based on experimental findings. The targeted synthesis of organic compounds with close intramolecular azide-oxygen contacts yielded six new representatives, for which X-ray structures were determined. Two of those compounds were investigated with respect to their potential conformations in the gas phase and a possible significantly shorter azide-oxygen contact. Furthermore, a set of 44 high-quality, gas-phase computational model systems with intermolecular azide-pnictogen (N, P, As, Sb), -chalcogen (O, S, Se, Te), and -halogen (F, Cl, Br, I) contacts are compiled and investigated through semiempirical quantum mechanical methods, density functional approximations, and wave function theory. A local energy decomposition (LED) analysis is applied to study the nature of the noncovalent interaction. The special role of electrostatic and London dispersion interactions is discussed in detail. London dispersion is identified as a dominant factor of the azide-donor interaction with mean London dispersion energy-interaction energy ratios of 1.3. Electrostatic contributions enhance the azide-donor coordination motif. The association energies range from -1.00 to -5.5 kcal mol-1 .

Stereoselective Synthesis of Diglycosyl Diacylglycerols with Glycosyl Donors Bearing a ß-Stereodirecting 2,3-Naphthalenedimethyl Protecting Group.

Diglycosyl diacylglycerols (DGDGs) are major components of Gram-positive bacterial plasma membranes and are involved in the immune response systems. The chemical synthesis of DGDGs has been highly demanded, as it will allow the elucidation of their biological functions at the molecular level. In this study, we have developed a novel ß-stereodirecting 2,3-naphthalenedimethyl (NapDM) protecting group that is orthogonal to protecting groups commonly used in oligosaccharide synthesis. The NapDM group can be easily cleaved under TFA-mediated acidic conditions. Futhermore, we demonstrated the application of this protecting group to an acyl protecting-group-free strategy by utilizing the NapDM group for the synthesis of DGDGs. This strategy features the use of the ß-stereodirecting NapDM group as an acid-cleavable permanent protecting group and late-stage glycosylation of monoglycosyl diacylglycerol acceptors, enabling the stereoselective synthesis of three different bacterial DGDGs with unsaturated fatty acid chain(s).

How Far Are We in Combating Marine Oil Spills by Using Phase-Selective Organogelators?

Marine oil spills is one of the frequent natural disasters that adversely affect the economy and ecosystem. A variety of methods have been developed to combat marine oil spills. However, none of these methods is ideal and universal for tackling different kinds of oil spills. In addition, most of these methods do not offer the possibility for recovering the spilt oil. There is great interest in developing novel and better methods for combating marine oil spills that allow recovery of the spilt oil. The use of low molecular weight organogelators that can selectively congeal oil from oil-water mixtures have been proposed to be useful for oil spill recovery. From this initial proposal, the area has progressed gradually towards their practical implementation. The advancements and novel concepts in this area are reviewed.

Correction: Model molecules to classify CHO hydrogen-bonds.

Correction for 'Model molecules to classify CHO hydrogen-bonds' by Amol M. Vibhute et al., Chem. Commun., 2018, 54, 4629-4632.

Model molecules to classify CHO hydrogen-bonds.

We developed a set of conformationally locked molecules each of which makes a single CHO H-bond/short contact and has different electron density at the acceptor oxygen atom. The downfield shift of the 1H NMR signals due to the hydrogen involved in the CHO H-bond varied from 0.93-1.6 ppm, and the magnitude of Δδ is in correlation with the hybridization state of the acceptor oxygen and with the CHO H-bond strengths quantified using a computational method.

A Sugar-Based Gelator for Marine Oil-Spill Recovery.

Marine oil spills constitute an environmental disaster with severe adverse effects on the economy and ecosystem. Phase-selective organogelators (PSOGs), molecules that can congeal oil selectively from oil-water mixtures, have been proposed to be useful for oil-spill recovery. However, a major drawback lies in the mode of application of the PSOG to an oil spill spread over a large area. The proposed method of using carrier solvents is impractical for various reasons. Direct application of the PSOG as a solid, although it would be ideal, is unknown, presumably owing to poor dispersion of the solid through the oil. We have designed five cheap and easy-to-make glucose-derived PSOGs that disperse in the oil phase uniformly when applied as a fine powder. These gelators were shown to selectively congeal many oils, including crude oil, from oil-water mixtures to form stable gels, which is an essential property for efficient oil-spill recovery. We have demonstrated that these PSOGs can be applied aerially as a solid powder onto a mixture of crude oil and sea water and the congealed oil can then be scooped out. Our innovative mode of application and low cost of the PSOG offers a practical solution to oil-spill recovery.

Synthesis of dimeric analogs of adenophostin A that potently evoke Ca2+ release through IP3 receptors.

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are tetrameric intracellular channels through which many extracellular stimuli initiate the Ca2+ signals that regulate diverse cellular responses. There is considerable interest in developing novel ligands of IP3R. Adenophostin A (AdA) is a potent agonist of IP3R and since some dimeric analogs of IP3R ligands are more potent than the corresponding monomer; we considered whether dimeric AdA analogs might provide agonists with increased potency. We previously synthesized traizolophostin, in which a simple triazole replaced the adenine of AdA, and showed it to be equipotent to AdA. Here, we used click chemistry to synthesize four homodimeric analogs of triazolophostin, connected by oligoethylene glycol chains of different lengths. We evaluated the potency of these analogs to release Ca2+ through type 1 IP3R and established that the newly synthesized dimers are equipotent to AdA and triazolophostin.

A versatile glycosylation strategy via Au(iii) catalyzed activation of thioglycoside donors.

Among various methods of chemical glycosylations, glycosylation by activation of thioglycoside donors using a thiophilic promoter is an important strategy. Many promoters have been developed for the activation of thioglycosides. However, incompatibility with substrates having alkenes and the requirement of a stoichiometric amount of promoters, co-promoters and extreme temperatures are some of the limitations. We have developed an efficient methodology for glycosylation via the activation of thioglycoside donors using a catalytic amount of AuCl3 and without any co-promoter. The reaction is very fast, high-yielding and very facile at room temperature. The versatility of this method is evident from the facile glycosylation with both armed and disarmed donors and sterically demanding substrates (acceptors/donors) at ambient conditions, from the stability of the common protecting groups, and from the compatibility of alkene-containing substrates during the reaction.

Correction: A versatile glycosylation strategy via Au(iii) catalyzed activation of thioglycoside donors.

[This corrects the article DOI: 10.1039/C6SC00633G.].

Triazolophostins: a library of novel and potent agonists of IP3 receptors.

IP3 receptors are channels that mediate the release of Ca(2+) from the intracellular stores of cells stimulated by hormones or neurotransmitters. Adenophostin A (AdA) is the most potent agonist of IP3 receptors, with the ß-anomeric adenine contributing to the increased potency. The potency of AdA and its stability towards the enzymes that degrade IP3 have aroused interest in AdA analogs for biological studies. The complex structure of AdA poses problems that have necessitated optimization of synthetic conditions for each analog. Such lengthy one-at-a-time syntheses limit access to AdA analogs. We have addressed this problem by synthesizing a library of triazole-based AdA analogs, triazolophostins, by employing click chemistry. An advanced intermediate having all the necessary phosphates and a ß-azide at the anomeric position was reacted with various alkynes under Cu(i) catalysis to yield triazoles, which upon deprotection gave triazolophostins. All eleven triazolophostins synthesized are more potent than IP3 and some are equipotent with AdA in functional analyses of IP3 receptors. We show that a triazole ring can replace adenine without compromising the potency of AdA and provide facile routes to novel AdA analogs.

Strength from weakness: conformational divergence between solid and solution states of substituted cyclitols facilitated by CH···O hydrogen bonding.

We have investigated the conformational preferences of a series of cyclitol derivatives, namely mono- and diesters of 1,2:5,6-di-O-isopropylidene-myo-inositol and 1,2:5,6-di-O-cyclohexylidene-myo-inositol, in both solid and solution states. The solid-state conformations were determined by single-crystal X-ray analysis. The solution-state conformations were determined by using NMR. The experimental (3)J(HH) values were applied in the Haasnoot-Altona equation to calculate the dihedral angle (ϕ) between the respective vicinal protons. By fixing the dihedral angle between different sets of vicinal protons, the molecules were energy-minimized by MM2 method to visualize their conformation in solution. As the solvent polarities can influence the conformational preference, we have determined the conformations of these molecules in various solvents of different polarities such as benzene-d6, chloroform-d, acetonitrile-d3, acetone-d6, methanol-d4, and DMSO-d6. All of the compounds adopted boat conformations in solution irrespective of the solvents, acyl groups, or alkylidene protecting groups. This conformation places H6 and O3 of the cyclitol ring in proximity, such that an intramolecular CH···O hydrogen bond between them stabilizes this otherwise unstable conformation. However, in the solid state, several intermolecular CH···O hydrogen bonds force these molecules to adopt the chair conformation. This study uncovers the role of weak noncovalent interactions in influencing the molecular conformations differentially in different states.

Regioselectivity among six secondary hydroxyl groups: selective acylation of the least reactive hydroxyl groups of inositol.

We report the first, general and selective acylation of the least reactive hydroxyl group among six secondary hydroxyl groups of inositol in high yield, using very cheap and easy-to-make H(2)SO(4)-silica as the catalyst, providing easy access to bioactive molecules.

Strength from weakness: opportunistic CH···O hydrogen bonds differentially dictate the conformational fate in solid and solution states.

We show that the CH···O hydrogen bond can be opportunistic to differentially dictate the conformation of cyclitols in solution and solid states. While several intermolecular CH···O stabilize the chair-conformation in the solid, single intramolecular CH···O stabilizes an otherwise unfavorable boat-conformation in solutions analogous to the boat-conformation of cis-1,4-cyclohexanediols by OH···O bonds.