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

Stereochemistry-dependent thermotropic liquid crystalline phases of monosaccharide-based amphiphiles

Conformational rigidity controls the bulk self-assembly and liquid crystallinity from amphiphilic block molecules to copolymers. The effects of block stereochemistry on the self-assembly have, however, been less explored. Here, we have investigated amphiphilic block molecules involving eight open-chain monosaccharide-based polyol units possessing different stereochemistries, derived from D-glucose, D-galactose, L-arabinose, D-mannose and L-rhamnose (allylated monosaccharides t-Glc*, e-Glc*, t-Gal*, e-Gal*, t-Ara*, e-Ara*, t-Man*, and t-Rha*), end-functionalized with repulsive tetradecyl alkyl chain blocks to form well-defined amphiphiles with block molecule structures. All compounds studied showed low temperature crystalline phases due to polyol crystallization, and smectic (lamellar) and isotropic phases upon heating in bulk. Hexagonal cylindrical phase was additionally observed for the composition involving t-Man*. Cubic phases were observed for e-Glc*, e-Gal*, e-Ara*, and t-Rha* derived compounds. Therein, the rich array of WAXS-reflections suggested that the crystalline polyol domains are not ultra-confined in spheres as in classic cubic phases but instead show network-like phase continuity, which is rare in bulk liquid crystals. Importantly, the transition temperatures of the self-assemblies were observed to depend strongly on the polyol stereochemistry. The findings underpin that the stereochemistry in carbohydrate-based assemblies involves complexity, which is an important parameter to be considered in material design when developing self-assemblies for different functions.

Synthesis of Gentamicins C1, C2, and C2a and Antiribosomal and Antibacterial Activity of Gentamicins B1, C1, C1a, C2, C2a, C2b, and X2

Complementing our earlier syntheses of the gentamicins B1, C1a, C2b, and X2, we describe the synthesis of gentamicins C1, C2, and C2a characterized by methyl substitution at the 6'-position, and so present an alternative access to previous chromatographic methods for accessing these sought-after compounds. We describe the antiribosomal activity of our full set of synthetic gentamicin congeners against bacterial ribosomes and hybrid ribosomes carrying the decoding A site of the human mitochondrial, A1555G mutant mitochondrial, and cytoplasmic ribosomes and establish structure-activity relationships with the substitution pattern around ring I to antiribosomal activity, antibacterial resistance due to the presence of aminoglycoside acetyl transferases acting on the 6'-position in ring I, and literature cochlear toxicity data.

Can Side-Chain Conformation and Glycosylation Selectivity of Hexopyranosyl Donors Be Controlled with a Dummy Ligand?

The use of a phenylthio group (SPh) as a dummy ligand at the 6-position to control the side-chain conformation of a series of hexopyranosyl donors is described. The SPh group limits side-chain conformation in a configuration-specific manner, which parallels that seen in the heptopyranosides, and so influences glycosylation selectivity. With both d- and l-glycero-d-galacto-configured donors, the equatorial products are highly favored as they are with an l-glycero-d-gluco donor. For the d-glycero-d-gluco donor, on the other hand, modest axial selectivity is observed. Selectivity patterns are discussed in terms of the side-chain conformation of the donors in combination with the electron-withdrawing effect of the thioacetal group. After glycosylation, removal of the thiophenyl moiety and hydrogenolytic deprotection is achieved in a single step with Raney nickel.

Influence of Side Chain Conformation on the Activity of Glycosidase Inhibitors

Substrate side chain conformation impacts reactivity during glycosylation and glycoside hydrolysis and is restricted by many glycosidases and glycosyltransferases during catalysis. We show that the side chains of gluco and manno iminosugars can be restricted to predominant conformations by strategic installation of a methyl group. Glycosidase inhibition studies reveal that iminosugars with the gauche,gauche side chain conformations are 6- to 10-fold more potent than isosteric compounds with the gauche,trans conformation; a manno-configured iminosugar with the gauche,gauche conformation is a 27-fold better inhibitor than 1-deoxymannojirimycin. The results are discussed in terms of the energetic benefits of preorganization, particularly when in synergy with favorable hydrophobic interactions. The demonstration that inhibitor side chain preorganization can favorably impact glycosidase inhibition paves the way for improved inhibitor design through conformational preorganization.

Syntheses of Legionaminic Acid, Pseudaminic Acid, Acetaminic Acid, 8-epi-Acetaminic Acid, and 8-epi-Legionaminic Acid Glycosyl Donors from N-Acetylneuraminic Acid by Side Chain Exchange

Metaperiodate cleavage of the glycerol side chain from an N-acetyl neuraminic acid-derived thioglycoside and condensation with the two enantiomers of the Ellman sulfinamide afford two diastereomeric N-sulfinylimines from which bacterial sialic acid donors with the legionaminic and acetaminic acid configurations and their 8-epi-isomers are obtained by samarium iodide-mediated coupling with acetaldehyde and subsequent manipulations. A variation on the theme, with inversion of the configuration at C5, similarly provides two differentially protected pseudaminic acid donors.

Side Chain Conformation and Its Influence on Glycosylation Selectivity in Hexo- and Higher Carbon Furanosides

We describe the synthesis and side chain conformational analysis of a series of four 6-deoxy-2,3,5-tri-O-benzyl hexofuranosyl donors with the d-gluco, l-ido, d-altro, and l-galacto configurations. The conformation of the exocyclic bond of these compounds depends on the relative configuration of the point of attachment of the side chain to the ring and of the two flanking centers and can be predicted on that basis analogously to the heptopyranose analogs. Variable-temperature nuclear magnetic resonance (VT NMR) spectroscopy of the activated donors reveals complex, configuration-dependent mixtures of intermediates that we interpret in terms of fused and bridged oxonium ions arising from participation by the various benzyl ethers. The increased importance of ether participation in the furanoside series compared to the pyranosides is discussed in terms of the reduced stabilization afforded to furanosyl oxocarbenium ions by covalent triflate formation. The stereoselectivities of the four donors are discussed on the basis of the benzyl ether participation model.

Unusual C-C bond cleavage of an α-trifloxy Sialic acid hemiacetal under Lattrell-Dax conditions

We describe the novel oxidative fragmentation of methyl (5-acetamido-4,7,8,9-tetra-O-acetyl-5-deoxy-3-O-trifluoromethanesulfonyl-β-D-erythro-L-gluco-2-nonulopyranos)onate 2 on stirring with sodium nitrite in DMF to give the novel 3-acetamido-2,5,6,7-tetra-O-acetyl-d-glycero-d-galacto-heptono-1,4-lactone 3 in excellent yield. Stirring of the same triflate with sodium carbonate on the other hand affords the novel methyl (5-acetamido-7,8,9-tri-O-acetyl-3,6-anhydro-5-deoxy-d-manno-3-ene-2-nonulos)onate 19 also in excellent yield. Reduction of the heptono lactone with sodium borohydride followed by acetylation gives a peracetylated aminodeoxyheptitol 6 that adopts the zig zag conformation of its carbon backbone.

Influence of ring size in conformationally restricted ring I analogs of paromomycin on antiribosomal and antibacterial activity

In order to further investigate the importance of the conformation of the ring I side chain in aminoglycoside antibiotic binding to the ribosomal target several derivatives of paromomycin were designed with conformationally locked side chains. By changing the size of the appended ring between O-4' and C-6' used to restrict the motion of the side chain, the position of the C-6' hydroxy group was fine tuned to probe for the optimal conformation for inhibition of the ribosome. While the changes in orientation of the 6'-hydroxy group cannot be completely dissociated from the size and hydrophobicity of the conformation-restricting ring, overall, it is apparent that the preferred conformation of the ring I side chain for interaction with A1408 in the decoding A site of the bacterial ribosome is an ideal gt conformation, which results in the highest antimicrobial activity as well as increased selectivity for bacterial over eukaryotic ribosomes.

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 S_N2 character in the displacement reaction.

Side Chain Conformation Restriction in the Catalysis of Glycosidic Bond Formation by Leloir Glycosyltransferases, Glycoside Phosphorylases, and Transglycosidases

Carbohydrate side chain conformation is an important factor in the control of reactivity at the anomeric center, ie, in the making and breaking of glycosidic bonds, whether chemically or, for hydrolysis, by glycoside hydrolases. In nature glycosidic bond formation is catalyzed out by glycosyltransferases (GTs), glycoside phosphoryases, and transglycosidases. By analysis of 118 crystal structures of sugar nucleotide dependent (Leloir) GTs, 136 crystal structures of glycoside phosphorylases, and 54 crystal structures of transglycosidases bound to hexopyranosides or their analogs at the donor site (-1 site), we determined that most enzymes that catalyze glycoside synthesis, be they GTs, glycoside phosphorylases or transglycosidases, restrict their substrate side chains to the most reactive gauche,gauche (gg) conformation to achieve maximum stabilization of the oxocarbenium ion-like transition state for glycosyl transfer. The galactose series deviates from this trend, with α-galactosyltransferases preferentially restricting their substrates to the second-most reactive gauche,trans (gt) conformation, and β-galactosyltransferases favoring the least reactive trans,gauche (tg) conformation. This insight will help progress the design and development of improved, conformationally-restricted GT inhibitors that take advantage of these inherent side chain preferences.

Influence of substitution at the 5α-Position on the side chain conformation of glucopyranosides

We describe the preparation of methyl 5α-methyl-α-d-glucopyranoside and of 5α-fluoro-β-d-glucopyranose per acetate and the NMR-based conformational analysis of their side chains. Both the 5α-methyl and 5α-fluoro substituents increase the population of the gauche,gauche side chain conformer to the extent that it becomes the predominant conformation. In the 5α-methyl series this is attributed to steric effects, whereas in the 5α-fluoro series the optimization of attractive gauche effects is the more likely reason.

En Route to the Transformation of Glycoscience: A Chemist's Perspective on Internal and External Crossroads in Glycochemistry

Carbohydrate chemistry is an essential component of the glycosciences and is fundamental to their progress. This Perspective takes the position that carbohydrate chemistry, or glycochemistry, has reached three crossroads on the path to the transformation of the glycosciences, and illustrates them with examples from the author's and other laboratories. The first of these potential inflexion points concerns the mechanism of the glycosylation reaction and the role of protecting groups. It is argued that the experimental evidence supports bimolecular SN2-like mechanisms for typical glycosylation reactions over unimolecular ones involving stereoselective attack on naked glycosyl oxocarbenium ions. Similarly, it is argued that the experimental evidence does not support long-range stereodirecting participation of remote esters through bridged bicyclic dioxacarbenium ions in organic solution in the presence of typical counterions. Rational design and improvement of glycosylation reactions must take into account the roles of the counterion and of concentration. A second crossroads is that between mainstream organic chemistry and glycan synthesis. The case is made that the only real difference between glycan and organic synthesis is the formation of C-O rather than C-C bonds, with diastereocontrol, strategy, tactics, and elegance being of critical importance in both areas: mainstream organic chemists should feel comfortable taking this fork in the road, just as carbohydrate chemists should traveling in the opposite direction. A third crossroads is that between carbohydrate chemistry and medicinal chemistry, where there are equally many opportunities for traffic in either direction. The glycosciences have advanced enormously in the past decade or so, but creativity, input, and ingenuity of scientists from all fields is needed to address the many sophisticated challenges that remain, not the least of which is the development of a broader and more general array of stereospecific glycosylation reactions.