Practical Synthesis of Sugar Monophosphonucleotides

A reliable procedure for the preparation of sugar nucleoside monophosphates is presented, which involves condensation of an activated glycosyl‐1‐H‐phosphonate with an appropriately protected nucleoside and simple end‐product isolation via lithium perchlorate–induced precipitation. The utility of these methods is demonstrated by the preparation of a number of purine‐ and pyrimidine‐based sugar nucleoside monophosphate derivatives.     

Preparation and reactivity of imino glycals: stereocontrolled,divergent approach to imino sugars

The synthesis of 3,4,6-tri-O-acetyl imino D-glucal 2 from D-glucal is reported. This imino glycal participates in a variety of Lewis acid mediated carbon-carbon bond forming reactions by allylic displacement of the C-3 acetate group by added nucleophiles. Allyl silanes, trimethylsilyl enol ethers, alkenes and dialkyl zinc reagents serve as suitable reaction partners. In all the cases studied, the beta-anomer is predominant. Using imino glycal 8, epimeric at C-5, it is established that the configuration at C-5 of the piperidine ring plays a major role in controlling the stereochemical outcome. These results are rationalised by invoking the intermediacy of a conjugated N-acyliminium ion. A short stereocontrolled synthesis of (+)-deoxoprosophylline is achieved using this chemistry. Additionally, imino glucal 2 is transformed into bromo piperidine 16, whose X-ray crystal structure is determined. Bromide 16 participates in palladium catalysed Stille and Suzuki cross-couplings allowing access to C-2 substituted imino sugars 17 and 18. In other studies, imino sugar C-glycosides 21 and 22 are made by combining the Lewis acid mediated carbon-carbon bond forming reactions with stereospecific dihydroxylations.     

Synthesis of nucleoside analogues bearing the five naturally occurring nucleic acid bases built on a 2-oxabicylo[3.1.0]hexane scaffold

Hitherto unknown nucleoside analogues incorporating the five naturally occurring nucleic acid bases built on a 2-oxabicyclo[3.1.0]hexane template were synthesized. The synthesis of these new conformationally restricted nucleoside analogues involved the preparation of a suitable sugar precursor bearing the 2-oxabicyclo[3.1.0]hexane scaffold. This sugar was readily obtained from [(3aS,6aS)-2,2-dimethyl-3a,6a-dihydrofuro[2,3-d][1,3]dioxol-5-yl]methyl benzyl ether (4) following a Simons-Smith-type cyclopropanation reaction. Finally, glycosylation reactions and deprotection provided the nucleoside analogues. Using nucleoside 14 bearing thymine base as a model, we found that the conformation of such nucleoside analogue was restricted toward a (0)T(1) conformation.     

Recognition of base-pairing by DNA polymerases during nucleotide incorporation: the properties of the mutagenic nucleotide dPTP alphaS

The highly mutagenic nucleoside dP (6-(2-deoxy-beta-D-erythro-pentofuranosyl)-3,4-dihydro-6H,8H-pyrimido[4,5-c][1,2]oxazin-2-one) is a bicyclic analogue of N4-methoxy-2'-deoxycytidine. It exists as a mixture of its imino and amino tautomers in solution with a ratio of about 10:1 based on its tautomeric constant. The bicyclic nature of the heterocycle P restrains the amino substituent in an anti conformation and permits effective Watson-Crick base-pairing using either tautomer. The specificity of incorporation of dP by the 3'-5'-exonuclease-free Klenow fragment of DNA polymerase I (exo-free Klenow) has been studied using the 5'-(1-thio)triphosphate dPTP alphaS in combination with phosphorothioate-specific sequencing of the DNA products. The method provides a convenient qualitative assay for studying nucleotide incorporation and reveals for the first time a potential role for the minor tautomeric forms of the natural DNA bases in base misinsertion (substitution mutagenesis) during replication.     

Molecular orbital studies on nucleoside antibiotics. IV. conformation of 3'-deoxyadenosine (cordycepin) and 3'-amino-3'-deoxyadenosine

PCILO computations have been carried out on the conformation of 3'-deoxyadenosine (cordycepin) and 3'-amino-3'-deoxyadenosine. These nucleoside antibiotics results as a consequence of modification in the sugar part of adenosine. Both C(2')-endo and C(3')-endo sugar puckerings have been considered in the computations and the results obtained indicate that these nucleoside antibiotics have very similar conformational preferences as compared to those of the parent nucleoside adenosine. This similarity which is quite marked in aqueous solution has important biological significance.     

A combination chemical and enzymatic approach for the preparation of azole carboxamide nucleoside triphosphate

Alternative substrates for DNA and RNA polymerases offer an important set of biochemical tools. Many of the standard methods for nucleoside triphosphate synthesis fail in the cases of nonpurine and nonpyrimidine nucleosides. An efficient preparation of the 5'-O-tosylates for both the deoxy- and ribonucleosides enabled preparation of the diphosphate esters by displacement with tris(tetra-n-butylammonium) pyrophosphate. Enzymatic synthesis of the azole carboxamide deoxyribonucleoside triphosphate was based on ATP as the phosphate donor, nucleoside diphosphate kinase as the catalyst, coupled with phosphoenol pyruvate (PEP) and pyruvate kinase as an ATP regeneration system. Ribonucleoside triphosphate synthesis required PEP as the phosphate donor and pyruvate kinase as the catalyst. An optimized purification procedure based upon boronate affinity gel was developed to yield highly purified nucleoside triphosphates. The strategy outlined here provides a new and efficient method for preparation of nucleoside 5'-triphosphate and is likely applicable to a broad variety of base and sugar modified nucleoside analogues.     

Synthesis of novel donor mimetics of UDP-Gal, UDP-GlcNAc, and UDP-GalNAc as potential transferase inhibitors

For the enzymatic transfer of galactose, N-acetylglucosamine, and N-acetylgalactosamine, UDP-Gal (1), UDP-GlcNAc (2), and UDP-GalNAc (3) are employed, and UDP serves as a feedback inhibitor. In this paper the synthesis of the novel UDP-sugar analogues 4, 5, and 6 as potential transferase inhibitors is described. Compounds 4-6 feature C-glycosidic hydroxymethylene linkages between the sugar and nucleoside moieties in contrast to the anomeric oxygens in the natural derivatives 1-3.     

Stereoselective chemical synthesis of sugar nucleotides via direct displacement of acylated glycosyl bromides

[structure: see text]. The use of Leloir glycosyltransferases to prepare biologically relevant oligosaccharides and glycoconjugates requires access to sugar nucleoside diphosphates, which are notoriously difficult to efficiently synthesize and purify. We report a novel stereoselective route to UDP- and GDP-alpha-D-mannose as well as UDP- and GDP-beta-L-fucose via direct displacement of acylated glycosyl bromides with nucleoside 5'-diphosphates.     

Synthesis of Thymidine Dimer Containing Novel (N‐Acetyl)imino Linkage

By starting with 3′‐keto‐5′‐O‐protected thymidine, 3′‐O‐amino‐5′‐t‐butyl‐diphenylsilyl thymidine ( 9 ) was prepared and coupled with 3′‐O‐t‐butyl‐diphenylsilyl‐5′‐formyl thymidine to form a nucleoside dimer ( 11 ) containing oxime linkage. The back bone of this dimer, then, under went reduction followed by acetylation to give an (N‐acetyl)imino linkage, and a novel dinucleotide ( 13 ) was obtained.     

An efficient stereoselective synthesis of (3S,4R)-4-(hydroxymethyl)pyrrolidin-3-ol from (S)-diethylmalate

A concise stereoselective synthesis of an imino sugar, (3S,4R)-4-(hydroxymethyl)pyrrolidin-3-ol from (S)-diethylmalate has been developed in five steps and in overall yield of 28%.     

Synthesis of Disaccharide Nucleosides by the O‐Glycosylation of Natural Nucleosides with Thioglycoside Donors

Disaccharide nucleosides constitute an important group of naturally‐occurring sugar derivatives. In this study, we report on the synthesis of disaccharide nucleosides by the direct O‐glycosylation of nucleoside acceptors, such as adenosine, guanosine, thymidine, and cytidine, with glycosyl donors. Among the glycosyl donors tested, thioglycosides were found to give the corresponding disaccharide nucleosides in moderate to high chemical yields with the above nucleoside acceptors using p‐toluenesulfenyl chloride (TolSCl) and silver triflate (AgOTf) as promoters. The interaction of these promoters with nucleoside acceptors was examined by ¹H NMR spectroscopic experiments.     

Targeting SARS-CoV-2 Polymerase with New Nucleoside Analogues

Despite the fact that COVID-19 vaccines are already available on the market, there have not been any effective FDA-approved drugs to treat this disease. There are several already known drugs that through drug repositioning have shown an inhibitory activity against SARS-CoV-2 RNA-dependent RNA polymerase. These drugs are included in the family of nucleoside analogues. In our efforts, we synthesized a group of new nucleoside analogues, which are modified at the sugar moiety that is replaced by a quinazoline entity. Different nucleobase derivatives are used in order to increase the inhibition. Five new nucleoside analogues were evaluated with in vitro assays for targeting polymerase of SARS-CoV-2.     

Small molecule ligand docking to genotype specific bundle structures of hepatitis C virus (HCV) p7 protein

The genome of hepatitis C virus encodes for an essential 63 amino acid polytopic protein p7 of most likely two transmembrane domains (TMDs). The protein is identified to self-assemble thereby rendering lipid membranes permeable to ions. A series of small molecules such as adamantanes, imino sugars and guanidinium compounds are known to interact with p7. A set of 9 of these small molecules is docked against hexameric bundles of genotypes 5a (bundle-5a) and 1b (bundle-1b) using LeadIT. Putative sites for bundle-5a are identified within the pore and at pockets on the outside of the bundle. For bundle-1b preferred sites are found at the site of the loops. Binding energies are in favour of the guanidinium compounds. Rescoring of the identified poses with HYDE reveals a dehydration penalty for the guanidinium compounds, leaving the adamantanes and imino sugar in a better position. Binding energies calculated by HYDE and those by LeadIT indicate that all compounds are moderate binders.     

5-去氮嘌呤核糖核苷类似物的设计与合成研究进展

综述了近年来有关5-去氮嘌呤核糖核苷类似物作为潜在生物活性(如抗病毒、抗肿瘤等)先导化合物的设计与合成研究进展.指出该类先导物的设计与合成主要基于以下两种途径:一是在去氮嘌呤碱基的4-位或5-位引入不同的取代基;二是在去氮嘌呤碱基的4-位或5-位引入不同取代基的同时,对核苷中的糖基进行修饰.并从这两种途径着手介绍了近年来该领域所取得的主要研究进展.     

Homochiral carbon branched piperidines from carbon branched sugar lactones: 4-C-methyl-deoxyfuconojirimycin (DFJ) and its enantiomer—removal of glycosidase inhibition

The value of readily available 2-C-methyl aldonic acids in short syntheses of carbon branched piperidines containing quaternary centers is demonstrated. The effect of the introduction of a 4-C-methyl group into piperidine imino sugar inhibitors of l-fucosidases and d-galactosidases is reported.     

Synthesis, structure, and sugar dynamics of a 2′-spiroisoxazolidine thymidine analog

Bicyclic nucleoside analogs have shown promise in Antisense and RNA interference strategies. Ribofuranosyl ring conformation is a controlling factor in this regard. We have introduced a spiroisoxazolidine ring at the 2′-position of the sugar to gauge the effect it has on sugar dynamics. Proton relaxation measurements and coupling constant analysis indicate the sugar is locked in the North conformation with substantial sugar rigidity evident.     

CARBOHYDRATES CONTAINING SULFUR

Abstract

Thioglycosides with sulfur as the glycosidic bridge are naturally occurring. They have been examined chemically and also biochemically wherein they aid in establishment of enzyme activity. Sugars and sugar nucleoside derivatives with sulfur—and sometimes selenium and nitrogen—replacing the ring oxygen show interesting chemistry and are of great potential usefulness in medicine as indicated by initial biochemical investigations. Their value in biochemistry as analogs of natural structures is proving of useful interest. Carbohydrates with sulfur at positions other than at the anomeric carbon or with ring involvement have interesting chemical properties. This review presents a general survey of carbohydrates containing sulfur, of their special methods of synthesis, their special chemical properties and reactions and a very brief review of their biochemistry and potential clinical value.     

Novel Synthesis and Structures of Amines and Triazole-Derived Glycoside and Nucleoside Derivatives of Phosphanyl Sugar Analogs

ABSTRACT

3-Methyl-1-phenyl-2-phospholene and 1-phenyl-2-phospholene 1-oxides were converted into 2-bromo-3-hydroxy-3-methyl-1-phenylphospholane and 2-bromo-3-hydroxy-1-phenylphospholane 1-oxide (1-bromo-1,3,4-trideoxy-1,4-C-[(R, S)-phenylphosphinylidene]-glycero-tetrofuranose) by the action of bromine in aqueous medium. The bromo substituent of the phospholane was substituted by treatment with amines or an azide anion to afford novel glycoside derivatives of phosphanyl sugar analogs such as 2-amino-3-hydroxy-1-phenylphospholane (3,4-dideoxy-1,4-C-[(R, S)-phenylphosphinylidene]-glycero-tetrofuranosylamine) and 2-azido-3-hydroxy-3-methyl-1-phenylphospholane 1-oxides with retention of the configuration. The 1,3-dipolar cycloaddition of the 2-azido derivative of the phospholane with alkynes gave 3-hydroxy-3-methyl-1-phenyl-2-(triazol-1′-y1)phospholane 1-oxides as a novel triazole-derived nucleoside of phosphanyl sugar analogs. The structure of the glycoside and nucleoside derivatives of the phosphanyl sugar analogs prepared was deterimined from IR, NMR, and X-ray crystallography analysis.     

Determination of the anomeric configuration of glycosyl esters of nucleoside pyrophosphates by fast-atom bombardment tandem mass spectrometry

Very low energy collision-induced dissociation of the deprotonated molecules of glycosyl esters of nucleoside pyrophosphates results in distinct fragmentation patterns that depend on the cis-trans configuration of the phosphodiester and 2″-hydroxyl groups of the glycosyl residue. In tandem mass spectrometry, sugar nucleotides with cis configuration produce only one, very abundant fragment that corresponds to nucleoside monophosphate, whereas nucleotides with trans configuration give weak signals for the nucleoside di- and monophosphates and their dehydration products. This empirical rule holds for sugar nucleotides that have a free 2″-hydroxyl group and no alternative charge location. Owing to its simplicity, sensitivity, and tolerance of impurities, fast-atom bombardment-tandem mass spectrometry represents a suitable method for determination of the anomeric linkage of glycosyl esters of nucleoside pyrophosphates if the absolute configuration of glycosyl residue is known and the compound fulfills the above-mentioned requirements.     

Oligonucleotides containing 6-aza-2'-deoxyuridine: synthesis, nucleobase protection, pH-dependent duplex stability, and metal-DNA formation

Oligodeoxyribonucleotides containing the nucleoside 6-aza-2'-deoxyuridine z6Ud (1a) were prepared by using solid-phase synthesis. As the pKa value of this nucleoside is 6.8, unwanted side reactions are observed. Consequently, nitrogen-3 was protected (o-anisoyl protection). The phosphoramidite of 1a prepared on this route was as efficient as the building blocks of canonical nucleosides in allowing multiple incorporations into oligonucleotides. Oligonucleotide duplexes containing 1a show a pH dependence of the Tm value. This is caused by nucleobase deprotonation occurring on compound 1a already under neutral conditions. Metal (M)-DNA formation was studied in the presence of Zn+2 ions. It is demonstrated that 6-azauracil-modified duplexes form M-DNA already in neutral medium while alkaline conditions (above pH 8.5) are required for natural DNA. The conformational analysis of the sugar moiety of the nucleoside 1a and its anisoyl derivative 5a shows a preferred N-conformation in solution while an S-conformation for compound 1a was obtained in the solid state (single-crystal X-ray analysis).