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.

Synthesis of Ribose - Oleic Acid Esters in the Presence- and Absence of Candida antarctica Lipase B.

D-ribose-oleic acid esters were produced with or without a biocatalyst, using in the same organic media, dimethyl sulfoxide (DMSO): tert-butanol (TBU) or 2-methyl-2-butanol (2M2B). The yield of the ester product was above 90% in both of the reactions. The biocatalyst used was lipase B of Candida antarctica. Molecular characterization was performed by using all the analytical methods available: IR, 1H-NMR and 13C-NMR, HSQC, and ESI-MS.

Microbial and enzymatic strategies for the production of L-ribose.

L-Ribose is a non-naturally occurring pentose that recently has become known for its potential application in the pharmaceutical industry, as it is an ideal starting material for use in synthesizing L-nucleosides analogues, an important class of antiviral drugs. In the past few decades, the synthesis of L-ribose has been mainly undertaken through the chemical route. However, chemical synthesis of L-ribose is difficult to achieve on an industrial scale. Therefore, the biotechnological production of L-ribose has gained considerable attention, as it exhibits many merits over the chemical approaches. The present review focuses on various biotechnological strategies for the production of L-ribose through microbial biotransformation and enzymatic catalysis, and in particular on an analysis and comparison of the synthetic methods and different enzymes. The physiological functions and applications of L-ribose are also elucidated. In addition, different sugar isomerases involved in the production of L-ribose from a number of sources are discussed in detail with regard to their biochemical properties. Furthermore, analysis of the separation issues of L-ribose from the reaction solution and different purification methods is presented.Key points • l -Arabinose, l -ribulose and ribitol can be used to produce l -ribose by enzymes. • Five enzymes are systematically introduced for production of l -ribose. • Microbial transformation and enzymatic methods are promising for yielding l -ribose.

Regioselective 5'-position phosphorylation of ribose and ribonucleosides: phosphate transfer in the activated pyrophosphate complex in the gas phase.

Herein, we present a rapid, efficient and regioselective phosphorylation method at the 5'-position of unprotected ribose and ribonucleosides with pyrophosphate in the gas phase, which involves the formation of anionic complexes via electrospray ionization and collisional activation to induce phosphorylation within the complexes.

Design, synthesis, cholinesterase inhibition and molecular modelling study of novel tacrine hybrids with carbohydrate derivatives.

A series of hybrids containing tacrine linked to carbohydrate-based moieties, such as d-xylose, d-ribose, and d-galactose derivatives, were synthesized by the nucleophilic substitution between 9-aminoalkylamino-1,2,3,4-tetrahydroacridines and the corresponding sugar-based tosylates. All compounds were found to be potent inhibitors of both acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) in the nanomolar IC50 scale. Most of the d-xylose derivatives (6a-e) were selective for AChE and the compound 6e (IC50 = 2.2 nM for AChE and 4.93 nM for BuChE) was the most active compound for both enzymes. The d-galactose derivative 8a was the most selective for AChE exhibiting an IC50 ratio of 7.6 for AChE over BuChE. Only two compounds showed a preference for BuChE, namely 7a (d-ribose derivative) and 6b (d-xylose derivative). Molecular docking studies indicated that the inhibitors are capable of interacting with the entire binding cavity and the main contribution of the linker is to enable the most favorable positioning of the two moieties with CAS, PAS, and hydrophobic pocket to provide optimal interactions with the binding cavity. This finding is reinforced by the fact that there is no linear correlation between the linker size and the observed binding affinities. The majority of the new hybrids synthesized in this work do not violate the Lipinski's rule-of-five according to FAF-Drugs4, and do not demonstrated predicted hepatotoxicity according ProTox-II.

Synthesis of ENA Nucleotides and ENA Oligonucleotides.

2'-O,4'-C-Ethylene-bridged nucleic acid (ENA) is a sugar-modified oligonucleotide with an ethylene bridge between the 2'-oxygen and 4'-carbon of ribose. ENA not only has as high binding affinity to complementary RNA as conventional bridged/locked nucleic acid, but also has much higher nuclease resistance in plasma, which makes it a promising candidate for antisense therapeutics. This unit presents detailed protocols for the synthesis and characterization of ENA nucleosides and oligonucleotides. © 2018 by John Wiley & Sons, Inc.

Synthesis of tRNA analogues containing a terminal ribose locked in the South conformation to study tRNA-dependent enzymes.

We report here the synthetic route of two constrained dinucleotides and the determination of the sugar puckering by NMR analyses of the starting nucleosides. Enzymatic ligation to microhelix-RNAs provide access to tRNA analogues containing a 3' terminal A76 locked in South conformation. Biological evaluation of our tRNA analogues has been performed using amino-acyl tRNA-dependent transferase FemXWv, which mediates non-ribosomal incorporation of amino acids into the bacterial cell wall. We have shown that our tRNA analogues inhibited the aminoacyl transfer reaction catalyzed by FemXWv with IC50s of 10 and 8 µM. These results indicate that FemXWv displays a moderate preference for tRNAs containing a terminal A76 locked in the South conformation and that a South to North switch in the conformation of the terminal ribose might contribute to the release of the uncharged tRNAAla product of the aminoacyl transfer reaction catalyzed by FemXwv.

Substoichiometric ribose methylations in spliceosomal snRNAs.

Sequencing-based profiling of ribose methylations is a new approach that allows for experiments addressing dynamic changes on a large scale. Here, we apply such a method to spliceosomal snRNAs present in human whole cell RNA. Analysis of solid tissue samples confirmed all previously known sites and demonstrated close to full methylation at almost all sites. Methylation changes were revealed in biological experimental settings, using T cell activation as an example, and in the T cell leukemia model, Jurkat cells. Such changes could impact the dynamics of snRNA interactions during the spliceosome cycle and affect mRNA splicing efficiency and splicing patterns.

Synthesis and in vitro antiproliferative activities of (5-aryl-1,2,4-oxadiazole-3-yl) methyl d-ribofuranosides.

The emergence of multidrug resistance cell lines is one of the major obstacles in the success of cancer chemotherapeutic treatment. Therefore, it remains a big challenge the development of new and effective drugs to defeat cancer. The presence of nitrogen heterocycles in the architectural design of drugs has led to the discovery of new leading compounds. Herein, we report the synthesis, characterization and in vitro antiproliferative activity against six cancer cell lines of d-ribofuranoside derivatives bearing a 1,2,4-oxadiazolic ring, with the aim of developing new active compounds. Most of these derivatives exhibit significant antiproliferative activities in the micromolar range. Noteworthy, the most potent compound of the series showed better selectivity towards the more resistant colon cancer cell line WiDr.

Synthesis of isomeric analogues of S-ribosylhomocysteine analogues with homocysteine unit attached to C2 of ribose.

LuxS (S-ribosylhomocysteinase; EC 4.4.1.21) is an enzyme that catalyzes the cleavage of the thioether linkage in the catalytic pathway of S-ribosylhomocysteine (SRH) which produces homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD). DPD is the precursor of the signaling molecules known as autoinducer 2 (AI-2) responsible for the bacterial quorum sensing (QS) identified as cell to cell communication. Inhibitors of LuxS should be able to interfere with its catalytic pathway thus preventing the formation of the autoinducer molecules. In this work, the synthesis of 2-deoxy-2-bromo-SRH analogues was attempted by the coupling of the corresponding 2-bromo-2-deoxypentafuranosyl sugars with the homocysteinate anion. The displacement of the bromide from C2 rather than the expected substitution of the mesylate group from C5 was observed leading to a novel isomeric analogue of SRH in which Hcy moiety is attached to a ribose ring via C2-sulfur bond.

Synthesis of Nucleosides through Direct Glycosylation of Nucleobases with 5-O-Monoprotected or 5-Modified Ribose: Improved Protocol, Scope, and Mechanism.

Simplifying access to synthetic nucleosides is of interest due to their widespread use as biochemical or anticancer and antiviral agents. Herein, a direct stereoselective method to access an expansive range of both natural and synthetic nucleosides up to a gram scale, through direct glycosylation of nucleobases with 5-O-tritylribose and other C5-modified ribose derivatives, is discussed in detail. The reaction proceeds through nucleophilic epoxide ring opening of an in situ formed 1,2-anhydrosugar (termed "anhydrose") under modified Mitsunobu reaction conditions. The scope of the reaction in the synthesis of diverse nucleosides and other 1-substituted riboside derivatives is described. In addition, a mechanistic insight into the formation of this key glycosyl donor intermediate is provided.

Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs.

Ribose is the central molecular subunit in RNA, but the prebiotic origin of ribose remains unknown. We observed the formation of substantial quantities of ribose and a diversity of structurally related sugar molecules such as arabinose, xylose, and lyxose in the room-temperature organic residues of photo-processed interstellar ice analogs initially composed of H2O, CH3OH, and NH3 Our results suggest that the generation of numerous sugar molecules, including the aldopentose ribose, may be possible from photochemical and thermal treatment of cosmic ices in the late stages of the solar nebula. Our detection of ribose provides plausible insights into the chemical processes that could lead to formation of biologically relevant molecules in suitable planetary environments.

TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth.

Recent synthetic efforts aimed at reconstructing the beginning of life on our planet point at the plausibility of scenarios fueled by extraterrestrial energy sources. In the current work we show that beyond nucleobases the sugar components of the first informational polymers can be synthesized in this way. We demonstrate that a laser-induced high-energy chemistry combined with TiO2 catalysis readily produces a mixture of pentoses, among them ribose, arabinose and xylose. This chemistry might be highly relevant to the Late Heavy Bombardment period of Earth's history about 4-3.85 billion years ago. In addition, we present an in-depth theoretical analysis of the most challenging step of the reaction pathway, i.e., the TiO2-catalyzed dimerization of formaldehyde leading to glycolaldehyde.

Highly regio- and diastereoselective, acidic clay supported intramolecular nitrile oxide-alkene cycloaddition on D-ribose derived nitriles: an efficient synthetic route to isoxazoline fused five and six membered carbocycles.

An efficient synthetic route to isoxazoline fused carbocycles from carbohydrate scaffolds that comprise of free hydroxyl group(s) is described with high regio- and stereoselectivity. Montmorillonite K-10/chloramine T oxidation and in situ intramolecular nitrile oxide-alkene cycloaddition (INOC) of D-ribose derived oximes have been developed for the diversity oriented synthesis of isoxazoline fused five and six membered carbocycles.

Life Origination Hydrate Theory (LOH-Theory) and the explanation of the biological diversification.

The Life Origination Hydrate Theory (LOH-Theory) considers the life origination process as a sequence of thermodynamically caused regular and inevitable chemical transformations regulated by universal physical and chemical laws. The LOH-Theory bears on a number of experimental, thermodynamic, observation, and simulation researches. N-bases, riboses, nucleosides, and nucleotides and DNAs and RNAs are formed repeatedly within structural cavities of localizations of underground and underseabed honeycomb CH4-hydrate deposits from CH4 and nitrate and phosphate ions that diffused into the hydrate structures; proto-cells and their agglomerates originated from these DNAs and from the same minerals in the semi-liquid soup after liquation of the hydrate structures. Each localization gave rise to a multitude of different DNAs and living organisms. The species diversity is caused by the spatial and temporal repeatability of the processes of living matter origination under similar but not identical conditions, multiplicity of the DNA forms in each living matter origination event, variations in the parameters of the native medium, intraspecific variations, and interspecific variations. The contribution of the last to the species diversity is, likely, significant for prokaryotes and those eukaryotes that are only at low steps of their biological organization; however, in the light of the LOH-Theory, of available long-term paleontological investigations, and of studies of reproduction of proliferous organisms, we conclude that, in toto, the contribution of interspecific variations to the species diversity was earlier overestimated by some researchers. The reason of this overestimation is that origination of scores of «spores¼ of different organisms in any one event and multiple reproductions of such events in time and Earth's space were not taken into consideration.

Examination of the influence of C5-hydroxymethyl group and configurations of hydroxyl groups at C2, C3, and C4 stereocentres on the N-glycosidic torsion: synthesis and X-ray crystallographic investigation of N-(D-ribopyranosyl)alkanamides as N-glycoprotein linkage region analogs.

N-Linked glycosylation is not only present in eukaryotes but also occurs in archaea and bacteria and is mainly characterized by the ß-glucosylamine linkage to the asparagine (GlcNAcßAsn). Earlier crystallographic studies aimed at understanding the structural significance of the linkage region constituents revealed that N-glycosidic torsion, ϕN is influenced considerably by variation in the glycan part as compared to the aglycon moiety. The ϕN value observed for XylßNHAc deviated maximum as compared to that of the model compound, GlcNAcßNHAc. The present work was undertaken to assess the influence of ribose on the N-glycosidic torsions and molecular assembly. Several ribopyranosyl alkanamides have been synthesized and crystal structures of three of them have been solved. A comprehensive crystal structure analysis of ribosyl alkanamides along with xylosyl and arabinosyl alkanamides showed the wide range of deviations in their ϕN values as compared to the negligible deviation shown by hexopyranosyl alkanamides. This study revealed the importance of C5-hydroxymethyl group and hydroxyl group configurations at C2, C3, and C4 stereocentres in controlling the N-glycosidic torsions.

[N6-dipeptide derivatives of the N12-ribosyl-indolo[2,3-a]carbazole].

N6-derivatives of N12-ribosyl-indolo[2,3-a]pirrolo[3,4-c]carbazole-5,7-dione are synthesized as potential antitumor agents, in which an atom of N6-pyrrole part of heterocycle is included into the dipeptide residual of the general formula >N6-(CH2)n-CO-Ala/ßAla-OMe (n = 2 or 3). These compounds are derived by reacting of 13-methyl-12-(2,3,4-three-O-acetyl-ß-D-ribopyranosyl)indolo[2,3-a]furano[3,4-c] carbazole-5,7-dione with dipeptides, having an unreplaced N-amino end-group, in DMF at 130°C, wherein the nitrogen atom of peptide amino group replaces oxygen O6 in furan ring of heterocycle and is embedded in imide nitrogen atom of pyrrole N6. The ability of the obtained compounds to inhibit growth of SKOV3 human ovarian carcinoma cells was studied, only derivative with radical >N6-(CH2)3-CO-L-Ala-OMe showed cytotoxic activity with an inhibitory concentration of IC50 = 8 µM.

Advances in chemical synthesis of structurally modified bioactive RNAs.

Methods for the chemical synthesis of RNA have been available for almost half century, and presently, RNA could be chemically synthesized by automated synthesizers, using protected ribonucleosides preactivated as phosphoramidites, which has already been covered by many reviews. In addition to advancement on synthetic methods, a variety of modifications have also been made on the synthesized oligonucleotides, and previous reviews on the general synthesis of RNAs have not covered this area. In this tutorial review, three types of modifications have been summarized standing at the viewpoint of medicinal chemistry: (1) modifications on nucleobase, comprising substituent introduction and replacement with pseudobase; (2) modifications on ribose, consisting of modifications on the 2', 3' or 5'-position, alternation of configuration, and conformational restriction on ribose; (3) modifications on internucleoside linkages, including amide, formacetal, sulfide, sulfone, ether, phosphorothiolate and phosphorothioate linkages. Synthetic methods achieving these modifications along with the functions or values of these modifications have also been discussed and commented on.

Synthesis and biological activity of substituted 4H-1,4-benzothiazines, their sulfones, and ribofuranosides.

The present article describes the synthesis of new 4H-1,4-benzothiazines via condensation and oxidative cyclization of substituted 2-aminobenzenethiols with ß-diketones/ß-ketoesters in dimethyl sulfoxide. The oxidation of these synthesized 4H-1,4-benzothiazines with 30% hydrogen peroxide in glacial acetic acid yielded 4H-1,4-benzothiazine sulfones and the reaction of these synthesized benzothiazines with sugar (ß-D-ribofuranose-1-acetate-2,3,5-tribenzoate) afforded the new ribofuranosides. These compounds were evaluated for their antioxidant and antimicrobial activities (using broth microdilution method). The structural assignments of the synthesized compounds were made on the basis of elemental analyses and spectroscopic data.

O-Aryl α,ß-d-ribofuranosides: synthesis & highly efficient biocatalytic separation of anomers and evaluation of their Src kinase inhibitory activity.

A series of peracetylated O-aryl α,ß-d-ribofuranosides have been synthesized and an efficient biocatalytic methodology has been developed for the separation of their anomers which was otherwise almost impossible by column chromatographic or other techniques. The incubation of 2,3,5-tri-O-acetyl-1-O-aryl-α,ß-d-ribofuranoside with Lipozyme® TL IM immobilized on silica led to the selective deacetylation of only one acetoxy group, viz the C-5'-O-acetoxy group of the α-anomer over the other acetoxy groups derived from the two secondary hydroxyl groups present in the molecule and also over three acetoxy groups (derived from one primary and two secondary hydroxyls of the ß-anomer). This methodology led to the easy synthesis of both, α- and ß-anomers of O-aryl d-ribofuranosides. All the arylribofuranosides were screened for inhibition of Src kinase. 1-O-(3-Methoxyphenyl)-ß-d-ribofuranoside exhibited the highest activity for inhibition of Src kinase (IC(50)=95.0µM).