Anomeric Carbon Atom Research Articles

Synthesis of 4-Selenothreofuranose Derivatives via Pummerer-Type Reactions of trans-3,4-Dioxygenated Tetrahydroselenophenes Mediated by a Selenonium Intermediate.

Selenosugars are interesting targets of organic synthesis as they would possess potential biological activities. However, 4-selenotherofuranose derivatives, which have trans configuration for the two dihydroxy substituents at the 2,3-positions and a glycoside bond at the anomeric position, are not available in the current selenosugar library. In this study, racemic 4-selenothreofuranose derivatives were synthesized from trans-3,4-dioxygenated tetrahydroselenophenes in 77–99% yields with the α/β selectivity about 7:3 via oxidation and subsequent seleno-Pummerer rearrangement. The acetoxy group introduced at the anomeric position was then substituted with various nucleophiles, including activated 6-chloropurine, which afforded 4′-selenothreonucleoside derivatives, in the presence of BF3·OEt2 or TMSOTf. The stereochemistry of the selenosugar products was established by 1H NMR spectroscopy as well as X-ray analysis. The similar α/β selectivity observed in the latter glycosylation reaction to that in the former seleno-Pummerer rearrangement suggested the mediation of a common selenonium intermediate (−Se+=C<). It was also suggested that an unexpected interaction between the ester protecting group at the 3-position of the selenofuranose ring and the anomeric carbon atom decreases the α/β selectivity.

Study of the complex-forming ability of polygalacturonic acid with tin ions

Samples of a trisubstituted tin-organic compound with D - (+) - galacturonic acid have been synthesized. A study of the compound was carried out by a semiempirical quantum-chemical method, its structural feature was proved, and alsographs of changes in energy and electronic characteristics are constructed depending on the charge on atoms, the order of bonds, the energy of the boundary molecular orbitals. Computer models of the complex compound of polygalacturonic acid with tin ions were obtained, the centers of nucleophilic and electrophonic attacks, donor-acceptor groups, and the electronic structure were determined. The new synthesized compounds were characterized by 1H, 13C and 119Sn NMR - a method was shown that galacturonic acid acts as a monoanionic fragment and indicates the dynamic behavior of compounds with the participation of the anomeric carbon atom of the ligand.

Understanding the Rate-Limiting Step of Glycogenolysis by Using QM/MM Calculations on Human Glycogen Phosphorylase.

Liver glycogen phosphorylase (GP) is a key enzyme for human health, as its increased activity is associated with type 2 diabetes. The GP catalytic mechanism has been explored by quantum mechanics/molecular mechanics (QM/MM) methods. Herein, we propose a mechanism that proceeds by three steps: 1) it begins with transfer of a hydrogen atom from the phosphate group of the pyridoxal 5'-phosphate (HPO42- -PLP) cofactor to the phosphate substrate; 2) the glycosidic linkage is then cleaved through protonation of the glycosidic oxygen atom by a hydroxy group of the inorganic phosphate group; and 3) an oxygen atom of the phosphate performs a nucleophilic attack on the anomeric carbon atom of glucose, concomitant with the return of a proton from phosphate to PO43- -PLP, which finally leads to formation of the glucose-1-phosphate product and recovers the initial state of the PLP cofactor. The glycosidic bond cleavage and nucleophilic attack from the phosphate group to the glycosyl molecule have the highest activation free energies. The structural properties of the hereby characterized transition states could be very useful in structure-based drug design studies against liver GP.

Kaolin: A Natural Low-Cost Material as Catalyst for Isomerization of Glucose to Fructose

Kaolin was identified as an effective catalyst for isomerization of glucose to fructose in methanol. The methyl-fructoside is obtained as main product through in situ etherification at the anomeric carbon atom, reflecting the bifunctionality of the layered alumosilicate. Using this exceptionally cheap and abundant natural clay (0.16 $/kg), methyl-fructoside is produced with up to 52% yield.

Anti-cancer activity of di- and tri-organotin(IV) compounds with D-(+)-Galacturonic acid on human tumor cells

We have compared the anti-proliferative activity in vitro, of R2SnGala (1-3) [R = Me, n-Bu, Ph] and novel R3SnGala (4, 5) [R = Me, n-Bu] with D-(+)-Galacturonic acid [HGala; Galaq-, q = (2) and (1) for R2SnGala and R3SnGala, respectively] compounds, towards human tumor cell lines of intestinal carcinoma (HCT-116) and breast adenocarcinoma (MCF-7). The new synthesized 4 and 5 compounds were characterized, in solution, by 1H, 13C and 119Sn NMR, that showed that HGala acts as monoanionic moiety and evidenced the dynamic behavior of the compounds, due to inter-conversions involving the anomeric carbon atom of the ligand. Cell viability, apoptosis induction and cell cycle distribution were analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) colorimetric assay and flow cytometry, respectively. The cytotoxicity of the compounds, in the micro-submicromolar range, changed in the order of the organotin(IV) moieties, according to 5 > 3 > 2, while 1 and 4, containing MenSn(IV) (n = 2,3) moieties, were ineffective. Compound 5 showed peculiar cytotoxic effects. It did not cause time dependent inhibition of cell growth nor accumulated into the cells. Cell death induced by the active 2, 3, and 5, was shown to be apoptotic by measuring the exposure of phosphatidylserine to the outer membrane and the loss of mitochondrial potential. All the cytotoxic compounds induced an accumulation of cells in the subG0/G1phase, while only 2 and 3 perturbed the cell cycle confining viable cells in G0/G1phase. Finally, none of the compounds investigated affected the viability of normal intestinal or liver cells, indicating selectivity towards tumor cells.

Does low-energy collision-induced dissociation of lithiated and sodiated carbohydrates always occur at anomeric carbon of the reducing end?

Collision-induced dissociation (CID) tandem mass spectrometry is one of the major methods in the structural determination of carbohydrates. Previous experimental studies and theoretical investigation of lithiated and sodiated underivatized carbohydrates seem to indicate that dehydration reactions and cross-ring dissociation of low-energy CID mainly occur at the anomeric carbon of the reducing end. However, these studies only investigated a few carbohydrates. ESI-MS/MS spectra of [M+Li]+ and [M+Na]+ ions of several 18 O1-labeled monosaccharides and disaccharides at O1 of the reducing end were studied using a linear ion trap mass spectrometer. Dissociations from the losses of both labeled and unlabeled neutral fragments were observed. The branching ratios of dissociations from the losses of unlabeled neutrals for dehydration reactions are larger than that for cross-ring dissociation; lithiated carbohydrates are larger than sodiated carbohydrates, and 1-4 linkages of disaccharides are larger than the other linkages. For some lithiated carbohydrates, dehydration reactions from the losses of unlabeled neutrals have larger branching ratios than that from the losses of labeled neutrals. The fragments from the losses of unlabeled neutrals investigated using MS3 showed that the losses of unlabeled H2 O mainly occur at the reducing monomer for sodiated carbohydrates, but the losses of unlabeled C2 H4 O2 for lithiated carbohydrates can occur at both reducing and nonreducing monomers. The ratio of B1 and Y1 ions to C1 and Z1 ions of disaccharides is related to the cis or trans configuration of the O1 and O2 atoms in the nonreducing monomer. The results are explained by the properties of transition states of dissociation channels. Our data shows that dehydration reactions and cross ring dissociation do not always occur at the anomeric carbon atom of the reducing monomer.

Coiled coil type neoglycoproteins presenting three lactose residues

Scaffold design, synthesis and application are relevant for biomedical research. For example, multivalent interactions, such as those between cell surface glycoproteins and lectins can influence the potency and duration of signalling. The spacing between carbohydrates on their native protein scaffold could be important. Herein, the coiled coil design principle is used to generate synthetic coiled coil type glycoproteins, where three lactose residues are grafted to the coil via N-linkages to asparagine. Molecular modelling indicates that the distance between the galactose anomeric carbon atoms on the neoglycoproteins is ∼30Å. The inclusion of lactose was accommodated in both the final heptad towards the N-terminus, or more centrally in the penultimate heptad. In either case, neither the helicity nor the assembly to the trimeric form was unduly altered by the presence of the disaccharide.

Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review

This article is a review of computational work over the last ∼15 years to elucidate the catalytic mechanisms of three major enzyme classes: glycoside hydrolases, carboxylic ester hydrolases, and thioesterases. The mechanisms of glycoside hydrolases that both invert and retain the configuration of the anomeric carbon atom of the labile glycosidic bond are covered, as is the twisting of the glycosidic bond exerted by members of different glycoside hydrolase families. The hydrolytic mechanisms and substrate binding of five different carboxylic ester hydrolase classes—acetylcholinesterases, butyrylcholinesterases, cocaine esterases, carboxylesterases, and triacylglycerol lipases—are addressed. Finally, the mechanism of members of a thioesterase family with HotDog tertiary structures is covered.

ChemInform Abstract: Direct Umpolung of Glycals and Related 2,3‐Unsaturated N‐Acetylneuraminic Acid Derivatives Using Samarium Diiodide.

The umpolung of glycals with samarium diiodide offers a simple route to novel carbohydrate-derived nucleophilic reagents in a single step using a readily available reductant. The corresponding allyl samarium reagent that arises from the hexose series reacts with ketones at the C3 position with high stereoselectivity; carbon–carbon bond formation takes place only anti to the substituent at the C4 position of the dihydropyran ring. For the sialic acid series, the completely regio- and stereoselective coupling process of the samarium reagent occurs at the anomeric carbon atom and provides a new approach to the α-C-glycosides of N-acetyl neuraminic acid.

Investigation of the rescue mechanism catalyzed by a nucleophile mutant of rice BGlu1

In the present study, the quantum mechanical/molecular mechanical (QM/MM) method was used to investigate the rescue mechanism of an E386G mutant as well as the glycosylation mechanism of the wild rice β-d-glucosidase. E386G mutant experiences an asynchronous collaborative process to glycosylate the anionic formate with an energy barrier of 22.6kcal/mol, while the energy barrier is 25.9kcal/mol for the wild complex. The low energy barrier of the mutated complex suggests that anionic formate might be a good nucleophile to attack the anomeric carbon atom. Both energy barriers can be lowered when the leaving departure releases from the active site, suggesting that the product release, rather than chemistry, contributes to the rate limiting in BGlu1 mutants. Structure analyses also indicate that the external nucleophile has little steric hindrance with pocket residues and adjusts freely to proceed the rescue mechanism of the mutated complex. Our calculations provide a guide for the selectivity of exogenous nucleophiles in the future study of β-glucosidase.

Direct Umpolung of Glycals and Related 2,3‐Unsaturated N‐Acetylneuraminic Acid Derivatives Using Samarium Diiodide

AbstractThe umpolung of glycals with samarium diiodide offers a simple route to novel carbohydrate‐derived nucleophilic reagents in a single step using a readily available reductant. The corresponding allyl samarium reagent that arises from the hexose series reacts with ketones at the C3 position with high stereoselectivity; carbon–carbon bond formation takes place only anti to the substituent at the C4 position of the dihydropyran ring. For the sialic acid series, the completely regio‐ and stereoselective coupling process of the samarium reagent occurs at the anomeric carbon atom and provides a new approach to the α‐C‐glycosides of N‐acetyl neuraminic acid.

Direct umpolung of glycals and related 2,3-unsaturated N-acetylneuraminic acid derivatives using samarium diiodide.

The umpolung of glycals with samarium diiodide offers a simple route to novel carbohydrate-derived nucleophilic reagents in a single step using a readily available reductant. The corresponding allyl samarium reagent that arises from the hexose series reacts with ketones at the C3 position with high stereoselectivity; carbon-carbon bond formation takes place only anti to the substituent at the C4 position of the dihydropyran ring. For the sialic acid series, the completely regio- and stereoselective coupling process of the samarium reagent occurs at the anomeric carbon atom and provides a new approach to the α-C-glycosides of N-acetyl neuraminic acid.

Investigation of Xylose Reversion Reactions That Can Occur during Dilute Acid Pretreatment

Xylose reversion reactions to form xylooligomers represent a potentially important mechanism of sugar loss during dilute acid pretreatment of biomass. We have conducted a study to identify the products that result from these reactions and to determine the kinetics of their formation. A major obstacle is that there are few commercial standards available for xylose disaccharides, which are essential for the identification and quantification of the xylose reversion products formed during these reactions. To overcome this obstacle, we have used GC/MS and NMR analysis of xylose disaccharides isolated by preparative HPLC to identify the reaction products. At the xylose concentration we used (300 g L–1), only xylose disaccharides were observed. As with glucose reversion reactions [Pilath, H. M.; et al. J. Agric. Food Chem. 2010, 58, 6131], the disaccharides contained linkages that involved the anomeric carbon atom of one of the sugar monomers. Eight out of the nine possible disaccharides, including alpha and bet...

PdII‐Catalyzed Spiroketalization of Ketoallylic Diols

A high-yielding stereoselective method for forming spiroketals from simple ketoallylic diols is reported. Employing catalytic [PdCl2(MeCN)2] in THF at 0 °C, these dehydrative cyclization reactions require only mild conditions to produce vinyl-substituted spiroketals in high yields after brief reaction times with water as the only byproduct. Using this method, the stereochemical information embedded at the nucleophile is transmitted "down-the-chain" and efficiently sets the stereochemistry at both the anomeric carbon atom and the newly formed allylic stereocenter.

Supramolecular structure and anomer-selective formation of polyglucuronic acid

Polyglucuronic acids provide a biocompatible matrix for industries ranging from pharmaceuticals to agriculture. Here we provide a method for selectively producing α-polyglucuronic acid, a simple alternative to the oxidation of cellulose or amylose with 2,2,6,6-tetramethylpiperidine-1-oxyl radical (TEMPO) or isolation from bacterial cultures. Atomic force micrographs show the pH-dependent formation and persistence of polyglucuronic acid fibrils, while NMR studies demonstrate the selectivity of the glycosidic linkage. By controlling pH, oligoglucuronate chains are created, with both NMR and AFM data showing the preservation of this linkage in basic medium after formation under acid. Clear evidence for the formation of the C–O–C glycosidic bond comes from peaks in the 13C NMR spectra, revealing a linkage through the anomeric carbon atom and also a linkage with a ring carbon atom.

Mechanism of Brønsted acid-catalyzed conversion of carbohydrates

A comprehensive DFT study of acid-catalyzed glucose and fructose reactions in water covering more than 100 potential reaction paths is performed with the aim to identify the main reaction channels for obtaining such desirable biorefinery platform products as 5-hydroxymethylfurfural (HMF) and levulinic acid (LA). Characteristic for fructose dehydration by Brønsted acids is the preferred protonation of the O2H group at the anomeric carbon atom, which initiates a sequence of facile reactions toward HMF. Further rehydration to LA is more difficult and competes with condensation reactions leading to humins. A very different result is obtained when glucose is the reactant. The preferred protonation site is the O1H hydroxyl group. The associated reaction paths do not lead to the formation of HMF or LA but result in humin precursors and reversion products. Protonation of other sites occurs at a much lower rate. Nevertheless, when glucose is activated at these less reactive sites, it can lead to LA via a reaction mechanism that does not involve the intermediate formation of fructose and HMF. This direct mechanism is argued to be preferred over the conventional sequential conversion scheme. It is concluded that the differences in the reactivity of glucose and fructose in acidic aqueous solutions are dominated by the regioselectivity of the initial protonation step.

Identification of Residues That Confer Sugar Selectivity to UDP-Glycosyltransferase 3A (UGT3A) Enzymes

Recent studies in this laboratory characterized the UGT3A family enzymes, UGT3A1 and UGT3A2, and showed that neither uses the traditional UDP-glycosyltransferase UGT co-substrate UDP-glucuronic acid. Rather, UGT3A1 uses GlcNAc as preferred sugar donor and UGT3A2 uses UDP-Glc. The enzymatic characterization of UGT3A mutants, structural modeling, and multispecies gene analysis have now been employed to identify a residue within the active site of these enzymes that confers their unique sugar preferences. An asparagine (Asn-391) in the UGT signature sequence of UGT3A1 is necessary for utilization of UDP-GlcNAc. Conversely, a phenylalanine (Phe-391) in UGT3A2 favors UDP-Glc use. Mutation of Asn-391 to Phe in UGT3A1 enhances its ability to utilize UDP-Glc and completely inhibits its ability to use UDP-GlcNAc. An analysis of homology models docked with UDP-sugar donors indicates that Asn-391 in UGT3A1 is able to accommodate the N-acetyl group on C2 of UDP-GlcNAc so that the anomeric carbon atom (C1) is optimally situated for catalysis involving His-35. Replacement of Asn with Phe at position 391 disrupts this catalytically productive orientation of UDP-GlcNAc but allows a more optimal alignment of UDP-Glc for sugar donation. Multispecies sequence analysis reveals that only primates possess UGT3A sequences containing Asn-391, suggesting that other mammals may not have the capacity to N-acetylglucosaminidate small molecules. In support of this hypothesis, Asn-391-containing UGT3A forms from two non-human primates were found to use UDP-GlcNAc, whereas UGT3A isoforms from non-primates could not use this sugar donor. This work gives new insight into the residues that confer sugar specificity to UGT family members and suggests a primate-specific innovation in glycosidation of small molecules.

Crystal Structures and Small-angle X-ray Scattering Analysis of UDP-galactopyranose Mutase from the Pathogenic Fungus Aspergillus fumigatus

UDP-galactopyranose mutase (UGM) is a flavoenzyme that catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, which is a central reaction in galactofuranose biosynthesis. Galactofuranose has never been found in humans but is an essential building block of the cell wall and extracellular matrix of many bacteria, fungi, and protozoa. The importance of UGM for the viability of many pathogens and its absence in humans make UGM a potential drug target. Here we report the first crystal structures and small-angle x-ray scattering data for UGM from the fungus Aspergillus fumigatus, the causative agent of aspergillosis. The structures reveal that Aspergillus UGM has several extra secondary and tertiary structural elements that are not found in bacterial UGMs yet are important for substrate recognition and oligomerization. Small-angle x-ray scattering data show that Aspergillus UGM forms a tetramer in solution, which is unprecedented for UGMs. The binding of UDP or the substrate induces profound conformational changes in the enzyme. Two loops on opposite sides of the active site move toward each other by over 10 Å to cover the substrate and create a closed active site. The degree of substrate-induced conformational change exceeds that of bacterial UGMs and is a direct consequence of the unique quaternary structure of Aspergillus UGM. Galactopyranose binds at the re face of the FAD isoalloxazine with the anomeric carbon atom poised for nucleophilic attack by the FAD N5 atom. The structural data provide new insight into substrate recognition and the catalytic mechanism and thus will aid inhibitor design.

Ring Cleavage Reactions of Methyl α-D-Allopyranoside Derivatives with Phenylboron Dichloride and Triethylsilane

In the course of our studies on the regioselective carbon-oxygen bond cleavage of the benzylidene acetal group of hexopyranosides with a reducing agent, we found that a combination of a Lewis acid and a reducing agent triggered a ring-opening reaction of the pyranose ring of methyl α-D-allopyranosides. The formation of an acyclic boronate ester by the attachment of a hydride ion at C-1 indicated that the unexpected endocyclic cleavage of the bond between the anomeric carbon atom and the pyranose ring oxygen atom proceeded via an oxacarbenium ion intermediate produced by the chelation between O5/O6 of the pyranoside and the Lewis acid, followed by nucleophile substitution with a hydride ion at C1.

Structure and properties of the exopolysaccharides produced by Pseudomonas mutabilis T6 and P. mutabilis ATCC 31014

This paper presents a study on the purification, primary structure, and rheological properties of exopolysaccharides isolated from cultures of Pseudomonas mutabilis T6 and P. mutabilis ATCC 31014. Both polymers are exopolysaccharides of d-mannose. The mannan isolated from P. mutabilis T6 contains on average about 5% of residual β- d-glucose, in contrast to the mannan from P. mutabilis ATCC 31014, which contained only trace amounts of residual β- d-glucose (less than 1%). Based on the 13C NMR spectra, all of the remaining carbohydrates in the exopolysaccharides occur in the form of pyranose rings. All of the mannose residues have the α configuration at the anomeric carbon atom while the glucose adopts the β configuration. The reaction of both polysaccharide hydrolysates with an optically active alcohol indicates that all of the sugar residues have the d configuration. We found that the main chain of the exopolysaccharide is composed of mannose residues connected through α-(1→6) linkages, of which a large number are substituted on O2 with d-mannose and the remaining are substituted with di- to pentasaccharide fragments. The rheological properties of the exopolysaccharide isolated from P. mutabilis T6 show that its viscosity is over 30 times greater than that of P. mutabilis ATCC 31014.