Spectroscopic, crystallographic and computational studies of the formation and isomerization of cyclic acetals and ketals of pentonolactones

Clarifying the Use of Benzylidene Protecting Group for D-(+)-Ribono-1,4-Lactone, an Essential Building Block in the Synthesis of C-Nucleosides

In the last two years, nucleosides analogues, a class of well-established bioactive compounds, have been the subject of renewed interest from the scientific community thanks to their antiviral activity. The COVID-19 global pandemic, indeed, spread light on the antiviral drug Remdesivir, an adenine C-nucleoside analogue. This new attention of the medical community on Remdesivir prompts the medicinal chemists to investigate once again C-nucleosides. One of the essential building blocks to synthetize these compounds is the D-(+)-ribono-1,4-lactone, but some mechanistic aspects linked to the use of different carbohydrate protecting groups remain unclear. Here, we present our investigations on the use of benzylidene as a ribonolactone protecting group useful in the synthesis of C-purine nucleosides analogues. A detailed 1D and 2D NMR structural study of the obtained compounds under different reaction conditions is presented. In addition, a molecular modeling study at the B3LYP/6-31G* level of theory with the SM8 solvation model for CHCl₃ and DMSO to support the obtained results is used. This study allows for clarifying mechanistic aspects as the side reactions and structural rearrangements liked to the use of the benzylidene protecting group.

Crystal structure of (+)-N-[(1R,5S,6S,9S)-5-hydroxy-methyl-3,3,9-trimethyl-8-oxo-2,4,7-trioxabi-cyclo-[4.3.0]nonan-9-yl]acetamide

In the title compound, C12H19NO6, the six-membered 1,3-dioxane ring adopts a chair-like conformation. The seat of this chair, containing two O atoms, is essentially planar, with a maximum deviation of 0.0021 (12) Å. The five-membered oxolane ring cis-fused to the 1,3-dioxane ring adopts an envelope form. The bridgehead C atom at the flap, which is bonded to the tetra-substituted C atom of the oxolane ring, deviates from the mean plane of other ring atoms by 0.539 (4) Å. In the crystal, classical O-H⋯O and N-H⋯O hydrogen bonds link the mol-ecules into a sheet structure enclosing an R 4 (4)(24) graph-set motif. Weak inter-molecular C-H⋯O inter-actions support the sheet formation.

Evaluation of fluoropyruvate as nucleophile in reactions catalysed by N-acetyl neuraminic acid lyase variants: scope, limitations and stereoselectivity

The catalysis of reactions involving fluoropyruvate as donor by N-acetyl neuraminic acid lyase (NAL) variants was investigated. Under kinetic control, the wild-type enzyme catalysed the reaction between fluoropyruvate and N-acetyl mannosamine to give a 90 : 10 ratio of the (3R,4R)- and (3S,4R)-configured products; after extended reaction times, equilibration occurred to give a 30 : 70 mixture of these products. The efficiency and stereoselectivity of reactions of a range of substrates catalysed by the E192N, E192N/T167V/S208V and E192N/T167G NAL variants were also studied. Using fluoropyruvate and (2R,3S)- or (2S,3R)-2,3-dihydroxy-4-oxo-N,N-dipropylbutanamide as substrates, it was possible to obtain three of the four possible diastereomeric products; for each product, the ratio of anomeric and pyranose/furanose forms was determined. The crystal structure of S. aureus NAL in complex with fluoropyruvate was determined, assisting rationalisation of the stereochemical outcome of C-C bond formation.

DFT/MM modeling of the five-membered ring in 3,6-anhydrogalactose derivatives and its influence on disaccharide adiabatic maps

Different conformations of methyl 3,6-anhydro-4-O-methyl-alpha-d-galactoside (1) and 3,6-anhydro-4-O-methylgalactitol (2) were studied by molecular mechanics (using the program mm3) and by quantum mechanical (QM) methods at the B3LYP/6-31+G( * *) and MP2/6-311++G( * *) levels, with and without solvent emulation. In 2, where the five-membered ring is free to move, two main stable conformations of this ring were found, identified as North (N) and South (S). The latter appears to be more stable, by either calculation, though the energy difference is reduced when emulating solution behavior. In order to find out the possible influence of a glycosidic bond over its shape, and to explain the marked NMR chemical shift displacements observed by opening of the ring, the adiabatic maps of two disaccharides carrying an analog of beta-galactoside linked to O-4 of 1 and 2 were generated. It was shown that the characteristics of the 3,6-AnGal terminal influence the characteristics of the map, especially at lower dielectric constants. On the other hand, different glycosidic angles also promote distinct stable conformations of the five-membered ring, changing from N to S, or even variants. Comparison with experimental results leads to the idea of highly flexible disaccharides, with variable values for both the five-membered ring and the glycosidic angles.

Looking glass inhibitors: efficient synthesis and biological evaluation of d-deoxyfuconojirimycin

1,6-Dideoxygalactostatin, the mirror image of 1-deoxy-L-fuconojirimycin, was efficiently prepared from 2,3-O-isopropylidene-L-lyxonolactone in four steps and evaluated as a glycosidase inhibitor.

Iodomethyl group as a hydroxymethyl synthetic equivalent: application to the syntheses of D-manno-hept-2-ulose and l-fructose derivatives

The one-carbon elongation of aldoses to ketoses using iodomethyllithium as the key reagent in the homologation step is exemplified by the preparation of two carbohydrates of chemical and biological interests: d-manno-hept-2-ulose from d-mannose and l-fructose from l-arabinose.

The 7-nitroindole nucleoside as a photochemical precursor of 2'-deoxyribonolactone: access to DNA fragments containing this oxidative abasic lesion

On the basis of molecular modeling studies, the 7-nitroindole nucleoside 1 was selected as a suitable photochemical precursor for photochemical generation of the C1' deoxyribosyl radical under irradiation, which led to 2'-deoxyribonolactone. The nitro-indole nucleoside derivatives 1a and 1b were prepared and their conformation was determined by X-ray crystallography and NMR spectroscopy. The photoreaction of these nucleosides gave the corresponding deoxyribonolactone derivatives efficiently, with release of 7-nitrosoindole. This reaction was successfully applied to synthesis of oligonucleotides containing the deoxyribonolactone lesion.

The biosynthesis of erythroascorbate in Saccharomyces cerevisiae and its role as an antioxidant

This study investigated the ability of the yeast Saccharomyces cerevisiae to synthesize ascorbate and its 5-carbon analogue erythroascorbate from a variety of precursors, and their importance as antioxidants in this organism. Studies of ascorbate and analogues in micro-organisms have been reported previously, but their function as antioxidants have been largely ignored. Ascorbate and erythroascorbate concentrations in yeast extracts were measured spectrophotometrically, and their levels and identity were checked using liquid chromatography-electrospray mass spectrometry. The yeast was readily able to synthesize ascorbate from L-galactono-1,4-lactone or erythroascorbate from D-arabinose and D-arabino-1,4-lactone, whereas L-gulono-1,4-lactone was a much poorer substrate for ascorbate biosynthesis. In untreated cells, the concentration of ascorbate-like compounds was below the level of detection of the methods of analysis used in this study (approximately 0.1 mM). Intracellular ascorbate and erythroascorbate were oxidized at high concentrations of tert-butylhydroperoxide, but not hydrogen peroxide. Their synthesis was not increased in response to low levels of stress, however, and preloading with erythroascorbate did not protect glutathione levels during oxidative stress. This study provides new information on the metabolism of ascorbate and erythroascorbate in S. cerevisiae, and suggests that erythroascorbate is of limited importance as an antioxidant in S. cerevisiae.