A novel synthesis of 2-deoxy-α-glycosides

The key step of the synthesis involves the reaction of glycals [3,4,6-tri-O-acetyl-d-glucal (1), the new glycal derivative 4-O-acetyl-1,5-anhydro-2,6-dideoxy-3-C-methyl-3-O-methyl-l-ribo-hex-l-enitol (2), and 3-acetamido-4,6,-di-O-acetyl-1,5-anhydro-2,3-dideoxy-d-arabino-hex-l-enitol (3)] with 1.5 molar equivalents of several alcohols in the presence ofN-bromosuccinimide in acetonitrile to give mainly the corresponding 2-bromo-2-deoxy-α-glycopyranosides (4-21). The glycopyranosides (4-8 and16-21) from1 and3 have the α-d-manno configuration and those (10-15) from2 have the α-l-altro configuration. The yields are high from1, virtually quantitative from2, and moderate from3. Debromination of the 2-bromo-2-deoxy compounds with tributylstannane and a radical initiator gives the corresponding 2-deoxy-α-glycopyranosides (22-38) in quantitative yields. In particular, the branched-chain glycal2 reacts with alcohols to give exclusively the corresponding α-glycopyranosides (27-32) of cladinose in strikingly high overall yields. The stereoselectivity and regiospecificity of the bromination reaction are described. 1,3-Dibromo-5,5-dimethylhydantoin andN-bromoacetamide are also found to be useful for the reaction.     

The synthesis of 2-acetamido-2-deoxy-6-O-β-d-mannopyranosyl-d-glucose

4,6-Di-O-acetyl-2,3-O-carbonyl-α-d-mannopyranosyl bromide was condensed with benzyl 2-acetamido-3,4-di-O-acetyl-2-deoxy-α-d-glucopyranoside in the presence of silver carbonate to give crystalline benzyl 2-acetamido-3,4-di-O-acetyl-2-deoxy-6-O-(4,6-di-O-acetyl-2,3-O-carbonyl-β-d-mannopyranosyl)-α-d-glucopyranoside in 32% yield. Removal of the protective O-acetyl and cyclic carbonate groups gave the crystalline benzyl α-glycoside of the disaccharide, which was catalytically hydrogenolyzed to yield the crystalline, title compound. Proof of the anomeric configuration of the interglycosidic linkage was obtained by comparison of the physical, spectral, and chromatographic properties of the disaccharide and its derivatives with those of the previously prepared α-d-linked analog.     

Stereoselective synthesis of β-arabino glycosyl sulfones as potential inhibitors of mycobacterial cell wall biosynthesis

A series of β-arabino glycosyl sulfones with varying alkyl chain lengths were synthesised in a stereoselective fashion as putative mimics of decaprenolphosphoarabinose (DPA), and as potential inhibitors of mycobacterial cell wall biosynthesis. Biological testing against Mycobacterium bovis BCG revealed low to moderate anti-mycobacterial activity with marked dependence on alkyl chain length, which was maximal for a C-12 chain.     

Stereoselective reduction of 2-azido-1-phenylethanone derivatives by whole cells of marine-derived fungi applied to synthesis of enantioenriched β-hydroxy-1,2,3-triazoles

Several marine-derived fungi were evaluated by the bioreduction of 2-azido-1-phenylethanone 1, and the strains A. sydowii CBMAI 935 and M. racemosus CBMAI 847 were selected for the reduction of 2-azido-1-phenylethanone derivatives 2–4. Whole cells of A. sydowii CBMAI 935 promoted the reduction of 2-azido-1-phenylethanones 1–4 with high selectivities to yield the (S)-2-azido-1-phenylethanols 1a–4a. Bioreduction of compounds 1–4 by M. racemosus CBMAI 847 led to (R)-2-azido-1-phenylethanols for 1, 2 and 4 and (S)-2-azido-1-phenylethanol 3. Enantiomerically enriched 2-azido-1-phenylethanols 1a–4a and phenylacetylene 5 were applied in the synthesis of β-hydroxy-1,2,3-triazoles using CuSO₄ and sodium ascorbate leading to regioselective formation of enantioenriched 1,4-disubstituted 1,2,3-triazole compounds 1b–4b.     

Biocatalytic synthesis of base-modified 2′-deoxy-β-D-ribonucleosides with bacterial whole cells

Whole-cell syntheses of representative modified purine and pyrimidine 2-deoxy--D-ribonucleosides are described. The transglycosylation reactions were carried out at 55¡C using the thermostable bacteria, Bacillus stearothermophilus. These transformations were efficient and gave yields close to or greater than 50% (conversions >70%).     

One-pot enzymatic synthesis of deoxy-thymidine-diphosphate (TDP)-2-deoxy-α-d-glucose using phosphomannomutase

Production of deoxy-thymidine-diphosphate (TDP)-sugars as substrates of glycosyltransferases, has been one of main hurdles for combinatorial antibiotic biosynthesis, which combines sugar moiety with aglycon of various antibiotics. Here, we report the one-pot enzymatic synthesis of TDP-2-deoxy-glucose employing high efficient TMP kinase (TMK; E.C. 2.7.2.12), acetate kinase (ACK; E.C. 2.7.1.21), and TDP-glucose synthase (TGS; E.C. 2.7.7.24) with phosphomannomutase (PMM; E.C. 5.4.2.8). In this study, replacing phosphoglucomutase (PGM; E.C. 5.4.2) by PMM from Escherichia coli gave four times higher specific activity on 2-deoxy-6-phosphate glucose, suggesting that the activity on 2-deoxy-glucose-6-phosphate was mainly affected by PMM activity, not PGM activity. Using an in vitro system starting from TMP and 2-deoxy-glucose-6-phosphate glucose, TDP-2-deoxy-glucose (63% yield) was successfully synthesized. Considering low productivity of NDP-sugars from cheap starting materials, this paper showed how production of NDP-sugars could be enhanced by controlling mutase activity.     

1,3,5-Tri-O-acetyl-2-deoxy- α, β-D-ERYTHRO-Pentofuranose from 2-Deoxy-D-ERYTHRO-Pentose

Abstract

A convenient, high-yield synthesis of 1,3,5-tri-O-acetyl-2-deoxy-α. β-D-erythro-pentofuranose from 2-deoxy-D-erythro-pentose is described.     

Specificity of β1,4-galactosyltransferase inhibition by 2-naphthyl 2-butanamido-2-deoxy-1-thio-β-D-glucopyranoside

Inhibitors of Galactosyltransferase (GalT) have the potential of reducing the amounts of adhesive carbohydrates on secreted and cell surface-bound glycoproteins. We recently found a potent inhibitor of β4GalT, 2-naphthyl 2-butanamido-2-deoxy-1-thio-β-D-glucopyranoside (compound 612). In this work, we have tested compound 612 for the specificity of its inhibition and examined its effect on GalT, and on GlcNAc- and GalNAc-transferases in homogenates of different cell lines, as well as on recombinant glycosyltransferases. Compound 612 was found to be a specific inhibitor of β4GalT. The specificity of recombinant human β3GalT5 that also acts on GlcNAc-R substrates, revealed similarities to bovine milk β4GalT. However, 612 was a poor substrate and not an inhibitor for β3GalT5. To further determine the specific structures responsible for the inhibitory property of 612, we synthesized (2-naphthyl)-2-butanamido-2-deoxy-β-D-glucopyranosylamine (compound 629) containing nitrogen in the glycosidic linkage, and compared it to other naphthyl and quinolinyl derivatives of GlcNAc as substrates and inhibitors. Compound 629 was a substrate for both β4GalT and β3GalT5. This suggests that properties of 612 other than the presence of the naphthyl ring alone were responsible for its inhibitory action. The results suggest a usefulness of 612 in specifically blocking the synthesis of type 2 chains and thus epitopes attached to type 2 chains. In addition, 612 potently inhibits β4GalT in cell homogenates and thus allows assaying β3GalT activity in the presence of β4GalT.     

A short synthesis of 4-deoxy-4-fluoroglucosaminides: Methylumbelliferyl N-acetyl-4-deoxy-4-fluoro-β-D-glucosaminide

A convenient method of synthesis of 1,6-anhydro-4-deoxy-2-O-tosyl-4-fluoro-β-D-glucopyranose by fusion of 1,6;3,4-dianhydro-2-O-tosyl-β-D-galactopyranose with 2,4,6-trimethylpyridinium fluoride was found. By a successive action of ammonia, methyl trifluoroacetate, and acetic anhydride, the resulting compound was transformed into 1,6-anhydro-3-O-acetyl-2,4-dideoxy-2-trifluoroacetamido-4-fluoro-β-D-glucopyranose, which was converted into 3,6-di-O-acetyl-2,4-dideoxy-2-trifluoroacetamido-4-fluoro-αD-glucopyranosyl fluoride by the reaction with HF/Py. The resulting fluoride was further used as a glycosyl donor in the synthesis of methylumbelliferyl N-acetyl-4-deoxy-4-fluoro-β-D-glucosaminide.     

High-yield enzymatic synthesis of O-allyl β-d-galactopyranoside

A high-yield synthesis of O-allyl β-d-galactopyranoside was carried out by the use of Aspergillus oryzae β-galactosidase. The reaction was carried out employing p-nitrophenyl β-d-galactopyranoside as the donor and a large excess of allyl alcohol as the acceptor. The molar yield was 65.6%, corresponding to an improvement of 41.3% with respect to the best results previously reported with other systems, and of 80.2% with respect to the results obtained using the same enzyme.     

Inducible synthesis of β-galactosidase inKluyveromyces fragilis

Lactose,d-galactose, andl-arabinose induce the synthesis of β-galactosidase inKluyveromyces fragilis. Lactose is the best inducer with a maximum effect at 1.4 mm. The induced synthesis of the enzyme in glycerol grown stationary phase cells is triggered within 30 min of inducer addition, the full induction being achieved within subsequent 30–40 min.     

A method for the synthesis of C-(2-deoxy-β-glycosyl) arenes

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(2) was converted by a Wittig reaction into a mixture of (

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(4,5). Selective deprotection of the 5,6-O-isopropylidene group in compounds 4 and 5 followed by selective silylation at position 6 afforded the separate

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8a–d and the corresponding E-isomers (9a–d). Iodonium-ion-induced cyclization of compounds 8c and 9a-c furnished stereoselectively the

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10a–c. Full deprotection of compounds 10a–c and the O-acetylation led to compounds 11a–c, which on treatment with tributyltin hydride-azobisisobutyromnitrile yielded and the title compounds (12a–c).     

Discovery of β-d-2′-deoxy-2′-dichlorouridine nucleotide prodrugs as potent inhibitors of hepatitis C virus replication

Discovery of sofosbuvir has radically changed hepatitis C treatment and nucleoside/tide NS5B inhibitors are now viewed as one of the key components in combination therapies with other direct-acting antiviral agents. As part of our program to identify new nucleoside inhibitors of HCV replication, we now wish to report on the discovery of β-d-2′-deoxy-2′-dichlorouridine nucleotide prodrugs as potent inhibitors of HCV replication. Although, cytidine analogues have long been recognized to be metabolized to both cytidine and uridine triphosphates through the action of cytidine deaminase, uridine analogues are generally believed to produce exclusively uridine triphosphate. Detailed investigation of the intracellular metabolism of our newly discovered uridine prodrugs, as well as of sofosbuvir, has now revealed the formation of both uridine and cytidine triphosphates. This occurs, not only in vitro in cell lines, but also in vivo upon oral dosing to dogs.     

Outer membrane β-barrel structure prediction through the lens of AlphaFold2

Most proteins found in the outer membrane of gram-negative bacteria share a common domain: the transmembrane β-barrel. These outer membrane β-barrels (OMBBs) occur in multiple sizes and different families with a wide range of functions evolved independently by amplification from a pool of homologous ancestral ββ-hairpins. This is part of the reason why predicting their three-dimensional (3D) structure, especially by homology modeling, is a major challenge. Recently, DeepMind's AlphaFold v2 (AF2) became the first structure prediction method to reach close-to-experimental atomic accuracy in CASP even for difficult targets. However, membrane proteins, especially OMBBs, were not abundant during their training, raising the question of how accurate the predictions are for these families. In this study, we assessed the performance of AF2 in the prediction of OMBBs and OMBB-like folds of various topologies using an in-house-developed tool for the analysis of OMBB 3D structures, and barrOs. In agreement with previous studies on other membrane protein classes, our results indicate that AF2 predicts transmembrane β-barrel structures at high accuracy independently of the use of templates, even for novel topologies absent from the training set. These results provide confidence on the models generated by AF2 and open the door to the structural elucidation of novel transmembrane β-barrel topologies identified in high-throughput OMBB annotation studies or designed de novo.