Exploring the Effect of Bioisosteric Replacement of Carboxamide by a Sulfonamide Moiety on N‐Glycosidic Torsions and Molecular Assembly: Synthesis and X‐ray Crystallographic Investigation of N‐(β‐D‐Glycosyl)sulfonamides as N‐Glycoprotein Linkage Region Analogues

N‐Glycoprotein linkage region constituents, 2‐acetamido‐2‐deoxy‐β‐D ‐glucopyranose (GlcNAc) and asparagine (Asn) are conserved among all the eukaryotes. To gain a better understanding for nature’s choice of GlcNAcβAsn as linkage region constituents and inter‐ and intramolecular carbohydrate–protein interactions, a detailed systemic structural study of the linkage region conformation is essential. Earlier crystallographic studies of several N‐(β‐glycopyranosyl)alkanamides showed that N‐glycosidic torsion, ?_N, is influenced to a larger extent by structural variation in the sugar part than that of the aglycon moiety. To explore the effect of the bioisosteric replacement of a carboxamide group by a sulfonamide moiety on the N‐glycosidic torsions as well as on molecular assembly, several glycosyl methanesulfonamides and glycosyl chloromethanesulfonamides were synthesized as analogues of the N‐glycoprotein linkage region, and crystal structures of seven of these compounds have been solved. A comparative analysis of this series of crystal structures as well as with those of the corresponding alkanamido derivatives revealed that N‐glycosidic torsion, ?_N, does not alter significantly. Methanesulfonamido and chloromethanesulfonamido derivatives of GlcNAc display a different aglycon conformation compared to other sulfonamido analogues. This may be due to the cumulative effect of the direct hydrogen bonding between N1 and O1′ and C? H???O interactions of the aglycon chain, revealing the uniqueness of the GlcNAc as the linkage sugar.     

A Bacterial Chitinase Acts as Catalyst for Synthesis of the N‐Linked Oligosaccharide Core Trisaccharide by Employing a Sugar Oxazoline Substrate

A chitinolytic enzyme, chitinase A1 from Bacillus circulans WL‐12, was found to catalyze a glycosyl‐transferring reaction to form the N‐linked oligosaccharide core structure, Man(β1‐4)‐GlcNAc(β1‐4)‐GlcNAc, by employing Man(β1‐4)‐GlcNAc‐oxazoline as glycosyl donor. When the reaction was carried out in the presence of 20 v/v% acetone, the trisaccharide was obtained in 32% yield. It has been shown for the first time that a chitinase behaves like an endo‐β‐N‐acetylglucosaminidase in spite of low structural similarity between them.     

Propargyl mediated intramolecular aglycon delivery (IAD): applications to the synthesis of core N-glycan oligosaccharides

The use of propargyl mediated intramolecular aglycon delivery (IAD) for the synthesis of the key Manβ(1→4)GlcNAc linkage of N-glycan oligosaccharides, including the core N-glycan pentasaccharide, is investigated. Isomerisation of a 2-O-progargyl group of manno thioglycoside donors to an allene is followed by iodonium ion mediated mixed acetal formation with the 4-OH of protected GlcNAc acceptors, and subsequent intramolecular glycosylation occurs with complete control of anomeric stereochemistry to form the Manβ(1→4)GlcNAc linkage. A variety of linear and convergent approaches (1+2, 3+1, 3+2) to the core pentasaccharide are investigated as means of probing the generality and limitations of this type of intramolecular aglycon delivery for the formation of β-mannoside linkages in complex oligosaccharides.     

A QM/MM Investigation of the Catalytic Mechanism of Metal‐Ion‐Independent Core 2 β1,6‐N‐Acetylglucosaminyltransferase

β1,6‐GlcNAc‐transferase (C2GnT) is an important controlling factor of biological functions for many glycoproteins and its activity has been found to be altered in breast, colon, and lung cancer cells, in leukemia cells, in the lymhomonocytes of multiple sclerosis patients, leukocytes from diabetes patients, and in conditions causing an immune deficiency. The result of the action of C2GnT is the core 2 structure that is essential for the further elongation of the carbohydrate chains of O‐glycans. The catalytic mechanism of this metal‐ion‐independent glycosyltransferase is of paramount importance and is investigated here by using quantum mechanical (QM) (density functional theory (DFT))/molecular modeling (MM) methods with different levels of theory. The structural model of the reaction site used in this report is based on the crystal structures of C2GnT. The entire enzyme–substrate system was subdivided into two different subsystems: the QM subsystem containing 206 atoms and the MM region containing 5914 atoms. Three predefined reaction coordinates were employed to investigate the catalytic mechanism. The calculated potential energy surfaces discovered the existence of a concerted S_N2‐like mechanism. In this mechanism, a nucleophilic attack by O6 facilitated by proton transfer to the catalytic base and the separation of the leaving group all occur almost simultaneously. The transition state for the proposed reaction mechanism at the M06‐2X/6‐31G** (with diffuse functions on the O1′, O5′, O_Glu, and O6 atoms) level was located at C1? O6=1.74 Å and C1? O1=2.86 Å. The activation energy for this mechanism was estimated to be between 20 and 29 kcal mol^?1, depending on the method used. These calculations also identified a low‐barrier hydrogen bond between the nucleophile O6H and the catalytic base Glu320, and a hydrogen bond between the N‐acetamino group and the glycosidic oxygen of the donor in the TS. It is proposed that these interactions contribute to a stabilization of TS and participate in the catalytic mechanism.     

Approaches towards the core pentasaccharide in N-linked glycans

This review focuses on the progresses and challenges in the preparation of Man3GlcNAc2 (M3) which is the core structure in the N-glycan biological pathway. Representative methods and recent reported findings, especially research advances in chemoenzymatic synthesis, are highlighted.     

Conversion of Complex Sialooligosaccharides into Polymeric Conjugates and their Anti-Influenza Virus Inhibitory Potency

ABSTRACT

To investigate the specificity of various influenza virus strains we have prepared polyacrylic type conjugates of undecasaccharide (Neu5Acα2-6Galβ1-4GlcNAcβ1-2Manα1)₂-3,6Manβ1-4GlcNAcβ1-4GlcNAc (YDS), and trisaccharides 6‵-sialyl-N-acetyllactosamine (6‵SLN), 6‵-sialyllactose (6‵SL), and 3‵-sialyllactose (3‵SL). Free oligosaccharides were transformed to glycosylamine-1-N-glycyl derivatives by sequential action of NH₄HCO₃, chloroacetic anhydride, and aqueous NH₃. The known derivatization protocol has been optimized for these sialooligosaccharides. Coupling of obtained amino-spacered derivatives with poly(4-nitrophenyl acrylate) gave rise to two types of conjugates, namely with polyacrylic acid and polyacrylamide backbones; the conversion proceeded quantitatively and without destruction of the oligosaccharides. The content of oligosaccharides in the conjugates was 10, 20, and 30% mol for 3‵SL, 6‵SL, 6‵SLN, and 2, 5 and 10% mol for YDS. Free oligosaccharides and the glycoconjugates were tested as inhibitors of influenza virus adhesion, and also as blockers of virus infectivity in MDCK cell culture. Biantennary YDS demonstrated similar activity to trisaccharide 6‵SLN both as the free form and neoglycoconjugate.     

X-Ray Crystallographic Investigation of Fully Acetylated N-(2-Deoxy-2-Acetamido-β-D-Glucopyranosyl)Alkanamides as N-Glycoprotein Linkage Region Analogs

To understand the structural significance of the linkage region of N-glycoproteins, three title sugar amides have been prepared as analogs and their molecular assembly and crystal structures have been solved to explore the effect of acetyl protection and aglycon variation on the conformation, particularly of the N-glycosidic linkage. Comparative analysis of these structures with those of free sugar amides reported earlier showed that conformation of the amido aglycon moiety is not altered significantly by the masking of hydroxyl groups in the form of acetate. The bifurcated antiparallel pattern involving N?H…O and C?H…O hydrogen bonds, a hallmark of the N-glycoprotein models GlcNAcβNHAc and GlcNAcβAsn, is absent in all of the fully protected title alkanamides. The asymmetric unit of the tri-O-acetylated GlcNAcβNHAc contains two different conformations, in one of which the double-pillared hydrogen bond network involving C1 and C2 acetamido groups is antiparallel, while it is parallel in the other. The co-occurrence of a molecular assembly motif—a double-pillared parallel and antiparallel hydrogen bonding pattern—is hitherto unknown in the crystal structures of N-glycoprotein linkage region models and analogs.     

Synthetic Receptors for the High‐Affinity Recognition of O‐GlcNAc Derivatives

The combination of a pyrenyl tetraamine with an isophthaloyl spacer has led to two new water‐soluble carbohydrate receptors (“synthetic lectins”). Both systems show outstanding affinities for derivatives of N‐acetylglucosamine (GlcNAc) in aqueous solution. One receptor binds the methyl glycoside GlcNAc‐β‐OMe with K_a≈20 000 m ^?1, whereas the other one binds an O‐GlcNAcylated peptide with K_a≈70 000 m ^?1. These values substantially exceed those usually measured for GlcNAc‐binding lectins. Slow exchange on the NMR timescale enabled structural determinations for several complexes. As expected, the carbohydrate units are sandwiched between the pyrenes, with the alkoxy and NHAc groups emerging at the sides. The high affinity of the GlcNAcyl–peptide complex can be explained by extra‐cavity interactions, raising the possibility of a family of complementary receptors for O‐GlcNAc in different contexts.     

A strategy for chromatographic and structural analysis of monosaccharide species from glycoproteins

A general strategy for the chromatographic and structural analysis of the monosaccharide species fucose (Fuc), N-acetylgalactosamine (GalNAc), N-acetylglucosamine (GlcNAc), galactose (Gal), glucose (Glc), mannose (Man), N-acetylneuraminic acid (NANA) present in glycoproteins is described. Qualitative and quantitative aspects for the separation of these glycoprotein monosaccharides (monosaccharide species) using ligand-exchange chromatography (LEC) and high pH anion-exchange chromatography (HPAEC) in combination with pulsed-amperometric detection (PAD), refractive index (RI) and ultraviolet (UV) monitoring are discussed in detail. The conditions for the acidic hydrolysis of glycoproteins and for the liquid chromatographic analyses of glycoprotein monosaccharides using HPAEC and LEC technique were optimised. Furthermore, the characterisation of glycoproteins according to their purity and molecular mass connected with a comparison to biomolecules that are not glycosylated or whose extent of glycosylation is low was carried out by means of matrix-assisted laser-desorption ionisation mass spectrometry (MALDI-MS). The identification of glycoprotein monosaccharides using an on-line coupling liquid chromatography mass spectrometry (LC-MS/MS) was performed by means of their characteristic quasi molecule ions such as (M + NH₄)⁺ and (2M + NH₄)⁺. The different chromatographic and structural methods used in combination with each other were applied to characterise and determine the monosaccharide species of fetuin and a membrane glycoprotein fraction.     

A three‐dimensional hydrogen‐bonded framework in 2‐amino‐6‐(N‐methylanilino)pyrimidin‐4(3H)‐one and a ribbon of fused hydrogen‐bonded rings in 2‐amino‐6‐(N‐methylanilino)‐5‐nitropyrimidin‐4(3H)‐one

The molecular dimensions of both 2‐amino‐6‐(N‐methylanilino)pyrimidin‐4(3H)‐one, C₁₁H₁₂N₄O, (I), and 2‐amino‐6‐(N‐methylanilino)‐5‐nitropyrimidin‐4(3H)‐one, C₁₁H₁₁N₅O₃, (II), are consistent with considerable polarization of the molecular–electronic structures. The molecules of (I) are linked into a three‐dimensional framework by a combination of one N—H...N hydrogen bond, two independent N—H...O hydrogen bonds and one C—H...π(arene) hydrogen bond. The molecules of (II) are linked into ribbons containing three types of edge‐fused ring by the combination of two independent three‐centre N—H...(O)₂ hydrogen bonds.     

A new tricarbonyl­rhenium(I) compound incorporating the tridentate ligand N,N‐bis­picol­yl‐2‐ethano­lamine

The title compound, {[N,N‐bis­(2‐pyridylmeth­yl)­amino]­ethanol‐κ³N,N′,N′′}tricarbonyl­rhenium(I) bromide methanol solvate, [Re(C₁₄H₁₇N₃O)(CO)₃]Br·CH₄O, has been prepared in almost quantitative yield by reacting (NEt₄)₂[Re(CO)₃Br₃] with the ligand N,N‐bis­picol­yl‐2‐ethano­lamine in refluxing methanol. The X‐ray structure revealed that the Re(CO)₃N₃ coordination sphere is highly distorted from octa­hedral geometry and that the Re(CO)₃ core is facial. The coordinated ligand forms two five‐membered rings, with the pyridine rings in a butterfly formation. The OH group is not involved in metal coordination. The packing of the mol­ecule shows a network of classical O⋯H—O and Br⋯H—O, and non‐classical Br⋯H—C and O⋯H—C hydrogen bonds between the methanol solvate mol­ecules, the metal complex cations and the bromide anions.     

Synthesis of modular building blocks using glycosyl phosphate donors for the construction of asymmetric N-glycans

Glycosyl phosphates are known as versatile donors for the synthesis of complex oligosaccharides both chemically and enzymatically. Herein, we report the stereoselective construction of modular building blocks for the synthesis of N-glycan using glycosyl phosphates as donors. We have synthesized four trisaccharide building blocks with orthogonal protecting groups, namely, Manβ2GlcNAc(OAc)₃β6GlcNAc (9), Manβ2GlcNAc-β6GlcNAc(OAc)₃ (15), Manβ2GlcNAc(OAc)₃β4GlcNAc (18) and Manβ2GlcNAcβ4GlcNAc(OAc) (22) for further selective elongation using glycosyltransferases. The glycosylation reaction using glycosyl phosphate was found to be high yielding with shorter reaction time. Initially, The phthalimide protected glucosamine donor was exploited to ensure the formation of β-glycosidic linkage and later converted to the N-acetyl group before the enzymatic synthesis. The selective deprotection of O-benzyl group was performed prior to enzymatic synthesis to avoid its negative interference.     

Preparation of glycopolymer‐substituted gold nanoparticles and their molecular recognition

Glycopolymer‐substituted gold nanoparticles were prepared via living radical polymerization with a reversible addition‐fragmentation chain transfer (RAFT) reagent. Polyacrylamide derivatives with α‐mannose (α‐Man) and N‐acetyl‐β‐glucosamine (β‐GlcNAc) were synthesized and hydrogenated to obtain thiol‐terminated polymer. The thiol‐terminated glycopolymers were mixed with gold nanoparticles to yield the polymer substituted gold nanoparticles with various diameters, which aggregated on addition of saccharide‐recognition proteins (lectins). The aggregation properties were analyzed using transmission electron microscopy and UV spectra. Molecular recognition was studied with E. coli, which induced aggregation of the nanoparticles at the cell periphery. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1412–1421, 2009     

Protecting‐Group‐Controlled Enzymatic Glycosylation of Oligo‐N‐Acetyllactosamine Derivatives

We describe a chemoenzymatic strategy that can give a library of differentially fucosylated and sialylated oligosaccharides starting from a single chemically synthesized tri‐N‐acetyllactosamine derivative. The common precursor could easily be converted into 6 different hexasaccharides in which the glucosamine moieties are either acetylated (GlcNAc) or modified as a free amine (GlcNH₂) or Boc (GlcNHBoc). Fucosylation of the resulting compounds by a recombinant fucosyl transferase resulted in only modification of the natural GlcNAc moieties, providing access to 6 selectively mono‐ and bis‐fucosylated oligosaccharides. Conversion of the GlcNH₂ or GlcNHBoc moieties into the natural GlcNAc, followed by sialylation by sialyl transferases gave 12 differently fucosylated and sialylated compounds. The oligosaccharides were printed as a microarray that was probed by several glycan‐binding proteins, demonstrating that complex patterns of fucosylation can modulate glycan recognition.     

Strong intramolecular O—H⋯O hydrogen bonds in quinaldic acid N‐oxide and picolinic acid N‐oxide

The title compounds contain very short intramolecular hydrogen bonds of the type C—O—H?O—N. The O?O distances are 2.425 (2) Å in picolinic acid N‐oxide (2‐carboxy­pyridine N‐oxide), C₆H₅NO₃, (I), and 2.435 (2) Å in quinaldic acid N‐oxide (2‐carboxy­quinoline N‐oxide), C₁₀H₇NO₃, (II). In (II), this is associated with slight molecular distortion from planarity, while in (I), such an effect cannot be observed because the mol­ecule crystallizes on a mirror plane.     

Two new polymorphs of 4‐(N,N‐dimethyl­amino)­benzoic acid

Two new polymorphs of 4‐(N,N‐dimethyl­amino)­benzoic acid, C₉H₁₁NO₂, resulting from the attempted cocrystallization in ethanol of 4‐(N,N‐dimethyl­amino)­benzoic acid and a mixture of 3‐(N,N‐dimethyl­amino)­benzoic acid and 3‐(3‐pyrid­yl)‐2‐pyridone producing one polymorph, and a mixture of 3‐(N,N‐dimethyl­amino)­benzoic acid and 5‐meth­oxy‐3,3′‐bipyridine producing the second polymorph, have been crystallographically characterized. The primary inter­molecular O—H⋯O hydrogen bonds generate a dimeric acid–acid motif that is present in all three polymorphs.     

The Tn antigen-structural simplicity and biological complexity

Glycoproteins in animal cells contain a variety of glycan structures that are added co‐ and/or posttranslationally to proteins. Of over 20 different types of sugar–amino acid linkages known, the two major types are N‐glycans (Asn‐linked) and O‐glycans (Ser/Thr‐linked). An abnormal mucin‐type O‐glycan whose expression is associated with cancer and several human disorders is the Tn antigen. It has a relatively simple structure composed of N‐acetyl‐D ‐galactosamine with a glycosidic α linkage to serine/threonine residues in glycoproteins (GalNAcα1‐O‐Ser/Thr), and was one of the first glycoconjugates to be chemically synthesized. The Tn antigen is normally modified by a specific galactosyltransferase (T‐synthase) in the Golgi apparatus of cells. Expression of active T‐synthase is uniquely dependent on the molecular chaperone Cosmc, which is encoded by a gene on the X chromosome. Expression of the Tn antigen can arise as a consequence of mutations in the genes for T‐synthase or Cosmc, or genes affecting other steps of O‐glycosylation pathways. Because of the association of the Tn antigen with disease, there is much interest in the development of Tn‐based vaccines and other therapeutic approaches based on Tn expression.     

Cyclic and acyclic products from the reactions between methyl 3‐oxobutanoate and arylhydrazines

The molecules of methyl 3‐(2‐nitrophenylhydrazono)butanoate, C₁₁H₁₃N₃O₄, (I), and methyl 3‐(2,4‐dinitrophenylhydrazono)butanoate, C₁₁H₁₂N₄O₆, (II), both prepared from methyl 3‐oxobutanoate and the corresponding nitrophenylhydrazine, exhibit polarized molecular electronic structures; in each of (I) and (II), the molecules are linked into chains by a single C—H...O hydrogen bond. The molecules of 5‐hydroxy‐3‐methyl‐1‐phenyl‐1H‐pyrazole, C₁₀H₁₀N₂O, (III), prepared by the reaction of methyl 3‐oxobutanoate and phenylhydrazine, are linked into chains by a single O—H...N hydrogen bond. The reaction between methyl 3‐oxobutanoate and 3‐nitrophenylhydrazine yields 5‐hydroxy‐3‐methyl‐1‐(3‐nitrophenyl)‐1H‐pyrazole, (IV), which when crystallized from acetone yields 4‐isopropylidene‐3‐methyl‐1‐(3‐nitrophenyl)‐1H‐pyrazol‐5(4H)‐one, C₁₃H₁₃N₃O₃, (V).     

Crystallographic studies of cinnamamide derivatives as a means of searching for anticonvulsant activity

A cinnamamide (3‐phenylprop‐2‐enamide) core is present in many pharmacologically active compounds. We report three new crystal structures of N‐substituted cinnamamide derivatives which were screened for anticonvulsant activity, namely (R ,S )‐(2E )‐N‐(2‐hydroxypropyl)‐3‐phenylprop‐2‐enamide, C₁₂H₁₅NO₂, ( 1 ), (R ,S )‐(2E )‐N‐(1‐hydroxybutan‐2‐yl)‐3‐phenylprop‐2‐enamide, C₁₃H₁₇NO₂, ( 2 ), and (2E )‐1‐(4‐hydroxypiperidin‐1‐yl)‐3‐phenylprop‐2‐en‐1‐one, C₁₄H₁₇NO₂, ( 3 ). Compounds ( 1 ) and ( 2 ) crystallize in the Pbca space group with one molecule in the asymmetric unit, whereas compound ( 3 ) crystallizes in the P 2₁/c space group with two molecules in the asymmetric unit. All the crystal structures are stabilized by intermolecular O—H…O hydrogen bonds and additionally by N—H…O hydrogen bonds in the structures of ( 1 ) and ( 2 ). The investigated compounds possess fragments that are considered as beneficial for anticonvulsant activity. The conformations of these compounds were analyzed in comparison with the characteristic features of the proposed pharmacophore model of anticonvulsants active in the maximal electroshock test, i.e. a phenyl ring or other hydrophobic unit, an electron‐donor atom and a hydrogen‐bond acceptor/donor domain. In the reported series, two calculated distances fitted the reference model, while the third did not. Structure–activity analysis suggests that anticonvulsant properties may be related to the N‐atom substituent. It is beneficial to combine an electron‐donor atom (e.g. an O atom) with an H atom in the substituent to ensure appropriate interactions with the molecular target. We analyzed the intermolecular interactions in order to find an appropriate spatial arrangement of the important features responsible for anticonvulsant activity.     

Two novel ferrocenyl dipeptide‐like compounds generated via the Ugi four‐component reaction

The Ugi four‐component reaction, a powerful method for the synthesis of diverse dipeptide‐like derivatives in combinatorial chemistry, was used to synthesize (S)‐1′‐{N‐[1‐(anthracen‐9‐yl)‐2‐(tert‐butylamino)‐2‐oxoethyl]‐N‐(4‐methoxyphenyl)carbamoyl}ferrocene‐1‐carboxylic acid dichloromethane disolvate, [Fe(C₆H₅O₂)(C₃₃H₃₁N₂O₃)]·2CH₂Cl₂, (I), and (S)‐2‐(anthracen‐9‐yl)‐N‐tert‐butyl‐2‐[N‐(4‐methylphenyl)ferrocenylformamido]acetamide, [Fe(C₅H₅)(C₃₃H₃₁N₂O₂)], (II). They adopt broadly similar molecular conformations, with near‐eclipsed cyclopentadienyl rings and near‐perpendicular amide planes in their dipeptide‐like chains, one of which is almost coplanar with its attached cyclopentadienyl ring but perpendicular to the aromatic ring bound to the N atom. In the supramolecular structure of (I), a two‐dimensional network is constructed based on molecular dimers and a combination of intermolecular O—H...O, N—H...O and C—H...O hydrogen bonds, forming R₂²(11), R₂²(16), R₂²(22) and C(9) motifs. These two‐dimensional networks are connected by C—H...O and C—H...Cl contacts to create a three‐dimensional framework, where one dichloromethane solvent molecule acts as a bridge between two neighbouring networks. In the packing of (II), classical hydrogen bonds are absent and an infinite one‐dimensional chain is generated via a combination of C—H...O hydrogen bonds and C—H...π interactions, producing a C(7) motif. This work describes a simple synthesis and the supramolecuar structures of ferrocenyl dipeptide‐like compounds and is significant in the development of redox‐active receptors.