Synthesis Of Nucleosides Research Articles

Mild Approach to Nucleoside Analogues via Photoredox/Cu-Catalyzed Decarboxylative C-N Bond Formation. Total Synthesis of Oxetanocin A.

The conventional N-glycosylation methods for nucleoside synthesis usually require strongly acidic or basic conditions. Here we report the decarboxylative C(sp3)-N coupling of glycosyl N-hydroxyphthalimide esters with nucleobases via dual photoredox/Cu catalysis, which offered a mild approach to nucleoside analogues. A total synthesis of oxetanocin A, an antiviral natural product containing an oxetanose moiety, has been achieved by using this method.

Advances in the Synthesis of Spirocyclic Nucleosides

AbstractThe nucleosides are the building blocks for nucleic acids and composed of a five-carbon sugar bearing either pyrimidine or purine nucleobase. The biological properties of nucleosides can be tailored by chemically modifying the five-carbon sugar to influence its sugar pucker. The spirocyclic scaffold is an indispensable scaffold in more than ten approved drugs, and its inherent three-dimensionality makes it an ideal modification to influence the sugar pucker and biological properties of nucleosides. However, the introduction of spirocyclic scaffold is often synthetically challenging due to increase in synthetic steps and stereocenters. The present review highlights the advances in synthetic methodologies developed during the past decades for accessing various members of the spiro-functionalized nucleoside family.1 Introduction2 C-1′-Spirocyclic Nucleosides3 C-2′-Spirocyclic Nucleosides4 C-3′-Spirocyclic Nucleosides5 C-4′-Spirocyclic Nucleosides6 Miscellaneous Spirocyclic Nucleosides7 Conclusion and Future Perspectives

Bioprocess development to produce a hyperthermostable S-methyl-5'-thioadenosine phosphorylase in Escherichia coli.

Nucleoside phosphorylases are important biocatalysts for the chemo-enzymatic synthesis of nucleosides and their analogs which are, among others, used for the treatment of viral infections or cancer. S-methyl-5'-thioadenosine phosphorylases (MTAP) are a group of nucleoside phosphorylases and the thermostable MTAP of Aeropyrum pernix (ApMTAP) was described to accept a wide range of modified nucleosides as substrates. Therefore, it is an interesting biocatalyst for the synthesis of nucleoside analogs for industrial and therapeutic applications. To date, thermostable nucleoside phosphorylases were produced in shake flask cultivations using complex media. The drawback of this approach is low volumetric protein yields which hamper the wide-spread application of the thermostable nucleoside phosphorylases in large scale. High cell density (HCD) cultivations allow the production of recombinant proteins with high volumetric yields, as final optical densities >100 can be achieved. Therefore, in this study, we developed a suitable protocol for HCD cultivations of ApMTAP. Initially, optimum expression conditions were determined in 24-well plates using a fed-batch medium. Subsequently, HCD cultivations were performed using E. coli BL21-Gold cells, by employing a glucose-limited fed-batch strategy. Comparing different growth rates in stirred-tank bioreactors, cultivations revealed that growth at maximum growth rates until induction resulted in the highest yields of ApMTAP. On a 500-mL scale, final cell dry weights of 87.1-90.1 g L-1 were observed together with an overproduction of ApMTAP in a 1.9%-3.8% ratio of total protein. Compared to initially applied shake flask cultivations with terrific broth (TB) medium the volumetric yield increased by a factor of 136. After the purification of ApMTAP via heat treatment and affinity chromatography, a purity of more than 90% was determined. Activity testing revealed specific activities in the range of 0.21 ± 0.11 (low growth rate) to 3.99 ± 1.02 U mg-1 (growth at maximum growth rate). Hence, growth at maximum growth rate led to both an increased expression of the target protein and an increased specific enzyme activity. This study paves the way towards the application of thermostable nucleoside phosphorylases in industrial applications due to an improved heterologous expression in Escherichia coli.

Introduction of pseudo-base benzimidazole derivatives into nucleosides via base exchange by a nucleoside metabolic enzyme

In alternate organic synthesis, biocatalysis using enzymes provides a more stereoselective and cost-effective approach. Synthesis of unnatural nucleosides by nucleoside base exchange reactions using nucleoside-metabolizing enzymes has previously shown that the 5-position recognition of pyrimidine bases on nucleoside substrates is loose and can be used to introduce functional molecules into pyrimidine nucleosides. Here we explored the incorporation of purine pseudo bases into nucleosides by the base exchange reaction of pyrimidine nucleoside phosphorylase (PyNP), demonstrating that an imidazole five-membered ring is an essential structure for the reaction. In the case of benzimidazole, the base exchange proceeded to give the deoxyribose form in 96 % yield, and the ribose form in 23 % yield. The reaction also proceeded with 1H-imidazo[4,5-b]phenazine, a benzimidazole analogue with an additional ring, although the yield of nucleoside was only 31 %. Docking simulations between 1H and imidazo[4,5-b]phenazine nucleoside and the active site of PyNP (PDB 1BRW) supported our observation that 1H-imidazo[4,5-b]phenazine can be used as a substrate by PyNP. Thus, the enzymatic substitution reaction using PyNP can be used to incorporate many purine pseudo bases and benzimidazole derivatives with various functional groups into nucleoside structures, which have potential utility as diagnostic or therapeutic agents.

Plasma Metabolomics Predicts Chemotherapy Response in Advanced Pancreatic Cancer.

Pancreatic cancer (PC) is one of the deadliest cancers. Developing biomarkers for chemotherapeutic response prediction is crucial for improving the dismal prognosis of advanced-PC patients (pts). To evaluate the potential of plasma metabolites as predictors of the response to chemotherapy for PC patients, we analyzed plasma metabolites using high-performance liquid chromatography-mass spectrometry from 31 cachectic, advanced-PC subjects enrolled into the PANCAX-1 (NCT02400398) prospective trial to receive a jejunal tube peptide-based diet for 12 weeks and who were planned for palliative chemotherapy. Overall, there were statistically significant differences in the levels of intermediates of multiple metabolic pathways in pts with a partial response (PR)/stable disease (SD) vs. progressive disease (PD) to chemotherapy. When stratified by the chemotherapy regimen, PD after 5-fluorouracil-based chemotherapy (e.g., FOLFIRINOX) was associated with decreased levels of amino acids (AAs). For gemcitabine-based chemotherapy (e.g., gemcitabine/nab-paclitaxel), PD was associated with increased levels of intermediates of glycolysis, the TCA cycle, nucleoside synthesis, and bile acid metabolism. These results demonstrate the feasibility of plasma metabolomics in a prospective cohort of advanced-PC patients for assessing the effect of enteral feeding as their primary source of nutrition. Metabolic signatures unique to FOLFIRINOX or gemcitabine/nab-paclitaxel may be predictive of a patient's response and warrant further study.

Chemoenzymatic Synthesis of arabino-Configured Bicyclic Nucleosides

AbstractA convergent route for the synthesis of a new class of bicyclic nucleosides has been developed. The synthetic route to the corresponding arabino-configured uracil and thymine bicyclic nucleosides proceeds in 24 and 27% overall yields, respectively, starting from 1,2,5,6-di-O-isopropylidene-α-d-glucofuranose. This synthetic protocol includes some crucial steps such as Vorbrüggen base coupling and chemo-enzymatic regioselective acetylation of the primary hydroxyl group by using Lipozyme® TL IM where it was found that Lipozyme® TL IM could be recovered and reused for selective acetylation without losing its selectivity.

DMAP and TBPP-mediated synthesis of urea-substituted nucleobases and nucleosides

Urea-functionalized nucleobases and nucleosides have emerged as versatile compounds with potential applications in a wide range of fields. Conventionally, the synthesis of urea involves the reaction of isocyanates with nucleobases and nucleosides. In contrast, this study presents a novel and efficient one-pot method for the synthesis of urea-substituted nucleobases and nucleosides without the use of isocyanates. The reaction was carried out in the presence of DMAP and TBPP, resulting in moderate to good yields of various urea-substituted nucleobases and nucleosides. Notably, N6-(N-threonyl-carbonyl)adenosine was also synthesized using this method. Furthermore, the synthesized compounds with adenine scaffold were evaluated for their binding affinity to adenosine receptors, but none of them exhibited binding, indicating a need for further modifications. These findings hold great promise for the facile synthesis of urea-functionalized nucleobases and nucleosides with potential applications in various fields.

Chemistry of NH2OH and its related species in the ISM

ABSTRACT Hydroxylamine (NH2OH) is a key precursor of both the formation of amino acids and the concurrent synthesis of pyrimidine and purine nucleosides. Recently, NH2OH was detected towards the quiescent molecular cloud G+0.693-0.027, which is located in the Galactic Centre. In this study, we construct the chemical network for NH2OH and its related species via quantum chemical calculations, and simulate their chemistry using the astrochemical code Nautilus in isothermal models and shock models. According to the disagreement distance formula and molecular abundance ratios, we acquire the best-fitting isothermal model T18 and the best-fitting C-shock model S2, respectively. Of these two models, S2 is more suitable for G+0.693-0.027 due to its reproduction of abundances of all considered molecules. From the model, we found that NH2OH and CH3NH2 are mainly formed on grain surfaces, while HNCN and CH2NH, which are the post-shock tracers, are produced by both gas-phase and grain-surface reactions. Our chemical modelling also agrees with the observed abundances or upper limits of NH2OH and its related species towards IRAS 16293-2422 B and Sgr B2(N). Moreover, we predict that NH2OH and the undiscovered species H2NO and HNOH are of high abundance, thus are detectable in cold clouds and pre-stellar cores, and in G+0.693-0.027, respectively.

The 2′-C-methylribonucleoside of 5-aza-7-deaza-7-iodoguanine: Hydrogen and halogen bonding in nucleoside crystals, synthesis and physical properties

The single-crystal X-ray structure of the 5-aza-7-deaza-7-iodoguanine 2′-C-methylribonucleoside 1 is described. The nucleoside was synthesized by stereoselective nucleobase anion glycosylation, yielding the protected nucleoside (70%), which was then deprotected to 1. By the same route, the non-iodinated 2′-C-methylribonucleoside 2 was obtained. In solution, the CD-spectrum of the iodinated 2′-C-methylribonucleoside 1 displays an almost mirror-like Cotton effect compared to the non-halogenated 2, revealing the strong impact of the iodo substituent to the molecule. Suzuki-Miyaura cross-coupling of 1 with pyrene boronic acid yielded a dye conjugate. The pyrene conjugate shows solvent dependent exciplex fluorescence. From the single-crystal X-ray structure of 1, conformational parameter were determined in solid state. The molecule shows anti conformation, a C3’-endo (N) sugar pucker and an antiperiplanar orientation of the 5′‑hydroxyl group. Apart from classical hydrogen bonds, nucleoside 1 possesses a halogen bond from the iodo substituent to the sugar oxygen O3’. A Hirshfeld surface analysis supports this finding. Nucleoside 1 forms a regular, tightly packed structure with stacking interactions between nucleobases and among sugar residues. A comparison of crystal packing of the iodinated 2′-C-methylribonucleoside 1 with the corresponding ribo- and 2′-deoxyribonucleosides demonstrates that halogen bonding depends on the sugar structure and determines the connectivity in crystal layers.

A Unifying Concept for the Prebiotic Formation of RNA Pyrimidine Nucleosides

AbstractThe question of how nucleosides might have formed as essential precursor molecules on the early Earth is one of the many challenges associated with the origin of life. In this context, the prebiotic synthesis of pyrimidine nucleosides is controversially discussed. For the pyrimidines, two at first glance contradictory prebiotically plausible reaction pathways have been proposed, based on either oxazole or isoxazole chemistry. This study shows that these two reaction sequences can be merged under prebiotically reasonable conditions, suggesting that both pathways could have co‐existed and possibly interacted. The key precursor 3‐aminoisoxazole was found to react with the key intermediate of the oxazole route (ribo‐2‐(methylthio)oxazoline), to form a ribo‐isoxazole‐oxazoline hybrid structure, which collapses upon reductive N−O bond cleavage to give the nucleoside cytidine. The data suggest that different, interacting prebiotically plausible chemical pathways may have created the key molecules of life on the early Earth.

Production of Modified Nucleosides in a Continuous Enzyme Membrane Reactor

Nucleoside analogues are important compounds for the treatment of viral infections or cancers. While (chemo-)enzymatic synthesis is a valuable alternative to traditional chemical methods, the feasibility of such processes is lowered by the high production cost of the biocatalyst. As continuous enzyme membrane reactors (EMR) allow the use of biocatalysts until their full inactivation, they offer a valuable alternative to batch enzymatic reactions with freely dissolved enzymes. In EMRs, the enzymes are retained in the reactor by a suitable membrane. Immobilization on carrier materials, and the associated losses in enzyme activity, can thus be avoided. Therefore, we validated the applicability of EMRs for the synthesis of natural and dihalogenated nucleosides, using one-pot transglycosylation reactions. Over a period of 55 days, 2'-deoxyadenosine was produced continuously, with a product yield >90%. The dihalogenated nucleoside analogues 2,6-dichloropurine-2'-deoxyribonucleoside and 6-chloro-2-fluoro-2'-deoxyribonucleoside were also produced, with high conversion, but for shorter operation times, of 14 and 5.5 days, respectively. The EMR performed with specific productivities comparable to batch reactions. However, in the EMR, 220, 40, and 9 times more product per enzymatic unit was produced, for 2'-deoxyadenosine, 2,6-dichloropurine-2'-deoxyribonucleoside, and 6-chloro-2-fluoro-2'-deoxyribonucleoside, respectively. The application of the EMR using freely dissolved enzymes, facilitates a continuous process with integrated biocatalyst separation, which reduces the overall cost of the biocatalyst and enhances the downstream processing of nucleoside production.

Revisiting Purine Nucleoside Cholinesterase Inhibitors - An Experimental Glycon Structure/Activity Relationship Study.

A new family of purine nucleoside cholinesterase inhibitors was disclosed by us, with potency and selectivity over acetylcholinesterase or butyrylcholinesterase controlled by tuning structural and stereochemical features of nucleosides with perbenzylated glycosyl moieties. Design, synthesis, and biological evaluation of new purine nucleosides were used to investigate glycon protecting group pattern required for anticholinesterase activity and selectivity. Regioselective chemistry to introduce methyl/benzyl groups in glycon donors and Nglycosylation was used to acquire the target nucleosides. Evaluation of their biological potential and selectivity as cholinesterase inhibitors was performed. Synthetic strategies chosen resulted in high glycon donor's overall yield and regio- and stereoselectivity was found in N-glycosylation reaction. Some of the new nucleosides are cholinesterase inhibitors and selectivity for butyrylcholinesterase was also achieved. N-glycosylation reaction was stereoselective for the β-anomers while regioselectivity was achieved for the N9 isomers when glycon positions 2 and 3 were methylated. Cholinesterase inhibition was found when the 2,3-di-O-benzyl-4-O-methyl pattern is present in the sugar moiety. Amongst the new compounds, the two most promising ones showed micromolar inhibition (mixed inhibition), being one of them selective for butyrylcholinesterase inhibition.

Modular Total Synthesis of Antibacterial Nucleosides

Key words antibacterial nucleosides - modular synthesis - Fisher glycosylation

Human tear metabolites associated with nucleoside-signalling pathways in bacterial keratitis

ObjectiveThe study aimed to profile and quantify tear metabolites associated with bacterial keratitis using both untargeted and targeted metabolomic platforms. MethodsUntargeted metabolomic analysis using liquid-chromatography-Q Exactive-HF mass-spectrometry explored tear metabolites significantly associated with bacterial keratitis (n = 6) compared to healthy participants (n = 6). Differential statistics and principal component analysis determined meaningful metabolite differences between cases and controls. Purines and nucleosides were further quantified and compared between 15 cases and 15 controls in the targeted metabolomic platform using TSQ quantum access triple quadrupole mass spectrometry. Compound quantification was done by plotting the calibration curves and the difference in the compound levels was evaluated using the Wilcoxon rank-sum test. ResultsIn the untargeted analysis, 49 tear metabolites (27 upregulated and 22 downregulated) were differentially expressed between cases and controls. The untargeted analysis indicated that the purine metabolism pathway was the most affected by bacterial keratitis. Metabolite quantification in the targeted analysis further confirmed the upregulation of xanthine (P = 0.02) and downregulation of adenine (P < 0.0001), adenosine (P < 0.0001) and cytidine (P < 0.0001) in the tears of participants with bacterial keratitis compared to that of healthy participants. ConclusionsBacterial keratitis significantly changes the tear metabolite profile, including five major compound classes such as indoles, amino acids, nucleosides, carbohydrates, and steroids. This study also indicates that tear fluids can be used to map the metabolic pathways and uncover metabolic markers associated with bacterial keratitis. Conceivably, the inhibition of nucleoside synthesis may contribute to the pathophysiology of bacterial keratitis because nucleosides are required for maintaining cellular energy homeostasis and immune adaptability.

Studies on enzymatic transglycosylation catalyzed by bacterial Nucleoside deoxyribosyltransferase II and Nucleoside phosphorylase for the synthesis of pyrimidine 2′-Deoxyribonucleosides containing modified heterocyclic base

A comparative analysis of enzymatic transglycosylation reactions catalyzed by Lactobacillus leichmannii NDT II and Escherichia coli PNP in the presence of various glycosyl donors and under different conditions was performed to synthesize modified 2ʹ-deoxynucleosides. Substitution of Escherichia coli PNP with Lactobacillus leichmannii NDT II allowed the synthesis of various deoxynucleosides from different glycosyl donors in 39–100% yields. The replacement of thymidine as a commonly used NDT substrate with 7-Methyl-2′-deoxyguanosine as a novel glycosyl-donor allowed the enzymatic synthesis of 2′-deoxycytidine derivatives and 5-substituted 2′-deoxyuridine derivatives, which is essential for further elaboration of eco-friendly technologies for synthesis of base-modified nucleosides.

N-Fluoroalkylated Morpholinos - a New Class of Nucleoside Analogues.

The first concise and efficient synthesis of some fluorine-containing morpholino nucleosides has been developed. One synthetic strategy was based on the oxidative ring cleavage of the vicinal diol unit of uridine, cytidine adenosine and guanosine derivatives, followed by cyclisation of the dialdehyde intermediates by double reductive amination with fluorinated primary amines to obtain various N-fluoroalkylated morpholinos. Another approach involved cyclisation of the diformyl intermediates with ammonia source, followed by dithiocarbamate formation and desulfurization-fluorination with diethylaminosulfur trifluoride yielding the corresponding morpholine-based nucleoside analogues with a N-CF3 element in their structure.

Research progress on application of multi-enzyme-catalyzed cascade reactions in enzymatic synthesis of natural products

As a biocatalyst, enzyme has the advantages of high catalytic efficiency, strong reaction selectivity, specific target products, mild reaction conditions, and environmental friendliness, and serves as an important tool for the synthesis of complex organic molecules. With the continuous development of gene sequencing technology, molecular biology, genetic manipulation, and other technologies, the diversity of enzymes increases steadily and the reactions that can be catalyzed are also gradually diversified. In the process of enzyme-catalyzed synthesis, the majority of common enzymatic reactions can be achieved by single enzyme catalysis, while many complex reactions often require the participation of two or more enzymes. Therefore, the combination of multiple enzymes together to construct the multi-enzyme cascade reactions has become a research hotspot in the field of biochemistry. Nowadays, the biosynthetic pathways of more natural products with complex structures have been clarified, and secondary metabolic enzymes with novel catalytic activities have been identified, discovered, and combined in enzymatic synthesis of natural/unnatural molecules with diverse structures. This study summarized a series of examples of multi-enzyme-catalyzed cascades and highlighted the application of cascade catalysis methods in the synthesis of carbohydrates, nucleosides, flavonoids, terpenes, alkaloids, and chiral molecules. Furthermore, the existing problems and solutions of multi-enzyme-catalyzed cascade method were discussed, and the future development direction was prospected.

Synthesis and Antimicrobial Activity of Some New Pyrimidine Nucleosides and Their Analogs

Synthesis and Antimicrobial Activity of Some New Pyrimidine Nucleosides and Their Analogs

Synthesis of N‐Glycosides by Silver‐Assisted Gold Catalysis

AbstractThe synthesis of N‐glycosides from stable glycosyl donors in a catalytic fashion is still challenging, though they exist ubiquitously in DNA, RNA, glycoproteins, and other biological molecules. Herein, silver‐assisted gold‐catalyzed activation of alkynyl glycosyl carbonate donors is shown to be a versatile approach for the synthesis of purine and pyrimidine nucleosides, asparagine glycosides and quinolin‐2‐one N‐glycosides. Thus synthesized nucleosides were subjected to the oxidation–reduction sequence for the conversion of Ribf‐ into Araf‐ nucleosides, giving access to nucleosides that are otherwise difficult to synthesize. Furthermore, the protocol is demonstrated to be suitable for the synthesis of 2’‐modified nucleosides in a facile manner. Direct attachment of an asparagine‐containing dipeptide to the glucopyranose and subsequent extrapolation to afford the dipeptide disaccharide unit of chloroviruses is yet another facet of this endeavor.

Synthesis of N-Glycosides by Silver-Assisted Gold Catalysis.

The synthesis of N-glycosides from stable glycosyl donors in a catalytic fashion is still challenging, though they exist ubiquitously in DNA, RNA, glycoproteins, and other biological molecules. Herein, silver-assisted gold-catalyzed activation of alkynyl glycosyl carbonate donors is shown to be a versatile approach for the synthesis of purine and pyrimidine nucleosides, asparagine glycosides and quinolin-2-one N-glycosides. Thus synthesized nucleosides were subjected to the oxidation-reduction sequence for the conversion of Ribf- into Araf- nucleosides, giving access to nucleosides that are otherwise difficult to synthesize. Furthermore, the protocol is demonstrated to be suitable for the synthesis of 2'-modified nucleosides in a facile manner. Direct attachment of an asparagine-containing dipeptide to the glucopyranose and subsequent extrapolation to afford the dipeptide disaccharide unit of chloroviruses is yet another facet of this endeavor.