Cyclic Nucleoside Research Articles

Nucleotides and nucleotide derivatives as signal molecules in plants

Abstract In reaction to a stimulus, signaling molecules are made, generate a response, and are then degraded. Nucleotides are classically associated with central metabolism and nucleic acid biosynthesis, but there are a number of nucleotides and nucleotide derivatives in plants to which this simple definition of a signaling molecule applies in whole or at least in part. These include cytokinins, chloroplast guanosine tetraposphate (ppGpp), as well as extracellular canonical nucleotides such as extracellular adenosine triphosphate (eATP) or nicotinamide adenine dinucleotide (eNAD+). In addition, there is a whole series of compounds derived from NAD+ such as adenosine diphosphate (ADP) ribose (ADPR), ATP-ADPR dinucleotides and their hydrolysis products (e.g. pRib-AMP) as well as different variants of cyclic ADPR (cADPR, 2'-cADPR, 3'-cADPR). Furthermore, cyclic nucleotides such as 3',5'-cAMP or 2',3'-cyclic nucleoside monophosphates. Interestingly, some of these compounds have recently been shown to play a central role in pathogen defense. In this review, we highlight these exciting new developments. We also review nucleotide derivatives that are considered candidates for signaling molecules, for example purine deoxynucleosides, for which the evidence base is still rather thin, and discuss more controversial cases.

Recent Synthesis of Nucleoside Phosphonate Analogs Using Olefin Cross-metathesis.

Nucleotide analogs known as acyclic and cyclic nucleoside phosphonates (ANPs and CNPs, respectively) have a variety of biological properties, including antibacterial, antiviral, antiparasitic, antineoplastic, and immunomodulatory. A strong reaction that has emerged in the last several decades has fundamentally changed our knowledge of the chemistry of nucleoside phosphonates. In particular, Olefin cross-metathesis (CM) has been a potent and practical synthesis route to produce functionalized olefins from essential alkene precursors. This review describes recent synthesis examples of ANPs and CNPs analogs using the Ru-catalyzed olefin cross-metathesis reactions. Olefin cross-metathesis reactions are performed in the olefinic parts of nucleoside and phosphonate produced by Grubbs, Hoveyda-Grubbs, and Nolan. This review presents a synthetic overview of a few chosen nucleosides with biological significance. Their biological activity results are briefly discussed.

Dehydration promotes phosphoramidate-linked amino acidyl and peptido adenosine conjugates.

Cyclic nucleoside phosphates have been shown previously to be adequately activated to oligomerise under dry conditions. Herein, it is demonstrated that 3',5'-cyclic adenosine monophosphate (3',5'-cAMP) and glycine when subjected to dehydration under alkaline conditions form phosphoramidate-linked conjugates. Solid-state reaction mechanisms investigated by DFT suggest why the reaction does not occur efficiently in the aqueous phase.

Synthesis and Conformational Analyses of Cyclonucleoside Having 13-Membered Ring Bridging Nucleobase and 5'-Position via a Linker Containing Sulfonamide.

A cyclic nucleoside has been designed and synthesized to serve as a conformationally fixed building block for the development of functional oligonucleotides. The bridge was introduced between the nucleobase and the 5'-position to fix the rotation around the C4'-C5' bond, the base orientation, and the sugar puckering all at once. The 13-membered cyclic structure was introduced using a sulfonamide linkage, which retains an N-H group that can be used to attach an additional nucleoside moiety. The sulfonamide linkage was formed through the end-to-end cyclization of an intermediate that contained both a sulfonyltriazole and amino groups. Both 1H NMR and computational studies revealed that the sugar conformation, base orientation, and γ torsion angle were S-type, anti, and trans, respectively. As such, cyclic nucleosides show promise for introducing these specific distorted conformations into functional nucleic acids.

Nonenzymatic Template-Directed Primer Extension Using 2'-3' Cyclic Nucleotides Under Wet-Dry Cycles.

RNA World Hypothesis is centred around the idea of a period in the early history of life's origin, wherein nonenzymatic oligomerization and replication of RNA resulted in functional ribozymes. Previous studies in this endeavour have demonstrated template-directed primer extension using chemically modified nucleotides and primers. Nonetheless, similar studies that used non-activated nucleotides led to the formation of RNA only with abasic sites. In this study, we report template-directed primer extension with prebiotically relevant cyclic nucleotides, under dehydration-rehydration (DH-RH) cycles occurring at high temperature (90 °C) and alkaline conditions (pH 8). 2'-3' cyclic nucleoside monophosphates (cNMP) resulted in primer extension, while 3'-5' cNMP failed to do so. Intact extension of up to two nucleotide additions was observed with both canonical hydroxy-terminated (OH-primer) and activated amino-terminated (NH2-primer) primers. We demonstrate primer extension reactions using both purine and pyrimidine 2'-3' cNMPs, with higher product yield observed during cAMP additions. Further, the presence of lipid was observed to significantly enhance the extended product in cCMP reactions. In all, our study provides a proof-of-concept for nonenzymatic primer extension of RNA, using intrinsically activated prebiotically relevant cyclic nucleotides as monomers.

Ecological Insights Into Community Interactions, Assembly Processes and Function in the Denitrifying Phosphorus Removal Activated Sludge Driven by Phosphorus Sources.

The microbial characteristics in the wastewater treatment plants (WWTPs) strongly affect their optimal performance and functional stability. However, a cognitive gap remains regarding the characteristics of the microbial community driven by phosphorus sources, especially co-occurrence patterns and community assembly based on phylogenetic group. In this study, 59 denitrifying phosphorus removal (DPR) activated sludge samples were cultivated with phosphorus sources. The results suggested that homogeneous selection accounted for the largest proportion that ranged from 35.82 to 64.48%. Deterministic processes dominated in 12 microbial groups (bins): Candidatus_Accumulibacter and Pseudomonas in these bins belonged to phosphate-accumulating organisms (PAOs). Network analysis revealed that species interactions were intensive in cyclic nucleoside phosphate-influenced microbiota. Function prediction indicated that cyclic nucleoside phosphates increased the activity of enzymes related to denitrification and phosphorus metabolism and increased the α-diversity of microorganism but decreased the diversity of metabolic function. Based on these results, it was assumed that cyclic nucleoside phosphates, rather than inorganic phosphates, are the most available phosphorus source for majority microorganisms in DPR activated sludge. The study revealed the important role of phosphorus source in the construction and assembly of microbial communities and provided new insights about pollutant removal from WWTPs.

A simple electroanalysis of polyG RNA in mixtures with 3′,5′-cyclic guanosine monophosphate achieved by selective desorption of the monomers from the electrode surface

• A simple label-free technique for analysis of nucleic acid polymerization mixtures. • The technique is based on selective removal of interfering monomers from electrode. • Monomers are removed by treatment with a surfactant or water at elevated temperature. Previously it has been shown that cyclic nucleoside monophosphates can spontaneously polymerize to form RNA oligonucleotides under conditions simulating prebiotic conditions on Archean Earth. The most efficient polymerization was documented with 3′,5′-cyclic guanosine monophosphate (cGMP). In this work a method for fast detection of short polyG RNAs present in a large overabundance of cGMP, modeling conditions in the non-enzymatic nucleotide polymerization mixtures, is presented. The method is based on electrochemical measurements of guanine (G) oxidation signals yielded by RNA oligomers adsorbed onto the surface of a pyrolytic graphite electrode (PGE). To avoid false positive results arising from the G oxidation signals due to co-adsorbed cGMP, a method for selective removal of the monomers from the electrode surface has been devised. In the first step, both cGMP and RNAs are co-adsorbed onto the PGE surface. In the second step, the cGMP is selectively desorbed using treatments in solutions of different tested surfactants (SDS, Tween 20 or Triton X-100), or by washing in deionized water at elevated temperature. We show that this new approach is suitable for selective analysis of products of polymerization reactions from mixtures of their building blocks.

Antiviral nucleoside analogs.

The minireview surveys the modification of native nucleosides as a result of which huge libraries of nucleoside analogs of various structures were synthesized. Particular attention is paid to the synthesis of the so-called prodrug forms of nucleoside analogs which ensure their penetration into the cell and metabolism to active 5'-triphosphate derivatives. All the best known antiviral cyclic nucleoside analogs approved for the treatment of HIV infections, hepatitis B, C, and influenza since the 1960s, as well as those in various stages of clinical trials in recent years, are listed. Nucleoside analogs that have shown the ability to inhibit the replication of SARS-CoV and MERS-CoV are discussed, including remdesivir, approved by the FDA for emergency use in the fight against COVID-19.

Elucidating cyclic AMP signaling in subcellular domains with optogenetic tools and fluorescent biosensors.

The second messenger 3',5'-cyclic nucleoside adenosine monophosphate (cAMP) plays a key role in signal transduction across prokaryotes and eukaryotes. Cyclic AMP signaling is compartmentalized into microdomains to fulfil specific functions. To define the function of cAMP within these microdomains, signaling needs to be analyzed with spatio-temporal precision. To this end, optogenetic approaches and genetically encoded fluorescent biosensors are particularly well suited. Synthesis and hydrolysis of cAMP can be directly manipulated by photoactivated adenylyl cyclases (PACs) and light-regulated phosphodiesterases (PDEs), respectively. In addition, many biosensors have been designed to spatially and temporarily resolve cAMP dynamics in the cell. This review provides an overview about optogenetic tools and biosensors to shed light on the subcellular organization of cAMP signaling.

CAMPS derivatives. A minireview over synthetic medicinal chemistry

Cyclic nucleosides belonging to the cAMPS system can exert antagonistic or agonistic effects on the cAMP/PKA type 1 inhibitory pathway affecting T-lymphocyte replications. The stereochemistry at the phosphorus atom in the phosphate group is important for the expressed selectivity. The two stereoisomers at the phosphorus atom in the phosphate arise by selective replacements of one of the oxygens pendant from the phosphorus atom by a sulfur atom. Methods for the preparation of cAMPS derivatives as stereochemical mixtures at the phosphorus atom and separation of stereoisomers have been developed into highly stereoselective syntheses. Methods for halogenation in the purine 8-position afford corresponding halides. Heteronucleophilic substitution of the halides afford corresponding amines, ethers or sulfides. Transition metal catalysis for carbylation of the 8-halides affords simple and efficient routes for the preparation of 8-aryl, 8-hetaryl or 8-alkyl cAMPS derivatives. Preparations of prodrugs for improved cell membrane penetration are described. The prodrugs are S-alkylated derivatives which are constructed for selective cleavage of the SP bond by an esterase to regenerate the bioactive cAMPS species at the site of the desired action.

Revisiting and Redesigning Light-Activated Cyclic-Mononucleotide Phosphodiesterases

As diffusible second messengers, cyclic nucleoside monophosphates (cNMPs) relay and amplify molecular signals in myriad cellular pathways. The triggering of downstream physiological responses often requires defined cNMP gradients in time and space, generated through the concerted action of nucleotidyl cyclases and phosphodiesterases (PDEs). In an approach denoted optogenetics, sensory photoreceptors serve as genetically encoded, light-responsive actuators to enable the noninvasive, reversible, and spatiotemporally precise control of manifold cellular processes, including cNMP metabolism. Although nature provides efficient photoactivated nucleotidyl cyclases, light-responsive PDEs are scarce. Through modular recombination of a bacteriophytochrome photosensor and the effector of human PDE2A, we previously generated the light-activated, cNMP-specific PDE LAPD. By pursuing parallel design strategies, we here report a suite of derivative PDEs with enhanced amplitude and reversibility of photoactivation. Opposite to LAPD, far-red light completely reverts prior activation by red light in several PDEs. These improved PDEs thus complement photoactivated nucleotidyl cyclases and extend the sensitivity of optogenetics to red and far-red light. More generally, our study informs future efforts directed at designing bacteriophytochrome photoreceptors.

The extreme C terminus of the Pseudomonas aeruginosa effector ExoY is crucial for binding to its eukaryotic activator, F-actin

Bacterial nucleotidyl cyclase toxins are potent virulence factors that upon entry into eukaryotic cells are stimulated by endogenous cofactors to catalyze the production of large amounts of 3'5'-cyclic nucleoside monophosphates. The activity of the effector ExoY from Pseudomonas aeruginosa is stimulated by the filamentous form of actin (F-actin). Utilizing yeast phenotype analysis, site-directed mutagenesis, functional biochemical assays, and confocal microscopy, we demonstrate that the last nine amino acids of the C terminus of ExoY are crucial for the interaction with F-actin and, consequently, for ExoY's enzymatic activity in vitro and toxicity in a yeast model. We observed that isolated C-terminal sequences of P. aeruginosa ExoY that had been fused to a carrier protein bind to F-actin and that synthetic peptides corresponding to the extreme ExoY C terminus inhibit ExoY enzymatic activity in vitro and compete with the full-length enzyme for F-actin binding. Interestingly, we noted that various P. aeruginosa isolates of the PA14 family, including highly virulent strains, harbor ExoY variants with a mutation altering the C terminus of this effector. We found that these naturally occurring ExoY variants display drastically reduced enzymatic activity and toxicity. Our findings shed light on the molecular basis of the ExoY-F-actin interaction, revealing that the extreme C terminus of ExoY is critical for binding to F-actin in target cells and that some P. aeruginosa isolates carry C-terminally mutated, low-activity ExoY variants.

Synthesis of Cyclic and Acyclic Pyrimidine Nucleosides Analogues with Anticipated Antiviral Activity.

A convenient method for preparation of cyclic and acyclic nucleosides was achieved by alkylation of 6-(2,4-dichlorophenoxymethyl) pyrimidine-2,4-dione (1) with a variety of acyclic and cyclic activated sugar analogues, namely (2-acetoxyethoxy)methyl acetate (3), 2-(acetoxymethoxy)propane-1,3-diyl dibenzoate (4), benzyloxymethyl acetate (5), 2-acetoxy-5-(benzoyloxymethyl)tetrahydrofuran-3,4-diyl dibenzoate (12), 5-chloro-2-((4-chlorobenzoyloxy)methyl) tetrahydrofuran-3-yl 4-chlorobenzoate (13) and 2-(acetoxymethyl)-6-bromotetrahydro-2H-pyran-3,4,5-triyl triacetate (14), respectively. Deprotection of the synthesized nucleosides was achieved by using methanolic ammonia. The structures of the newly synthesized nucleoside analogues were fully characterized by analytical methods (mass spectrometry, 1H NMR, 13C NMR, and elemental analysis).

Microwave in glycosylation reaction: design, and synthesis of highly substituted nicotinonitrile nucleosides

An efficient and rapid regiospecific approach for the synthesis of cyclic and acyclic nucleosides of 2-oxonicotinonitriles was performed. Whereas, glycosylation of 2-oxonicotinonitriles 1a, b with peracetylated sugars (namely, peracetylated glucose, galactose and ribose) under MWI tolerated exclusively the desired N-nucleosides 2a, b, 4a, b and 6a, b in significant yields (75–86%) and in short reaction time (5–7 min.). The same products were obtained under the conventional conditions, using halo-sugar with low yields in hard conditions. Similarly, the acyclic nucleosides 8a, b and 9a, b were obtained under MWI and conventional conditions via reaction of 1a, b with 4-bromo butyl acetate and 2-acetoxyethoxymethyl bromide. Finally, deprotection of the latter blocked N-nucleosides was performed via treatment with aqueous methanolic solution containing a catalytic amount of triethyl amine to give the desired free nucleosides 3a, b, 5a, b, 7a, b, 10a, b and 11a, b, respectively. The free nucleosides (3a, b, 5a, b, 7a, b and 11a, b) were evaluated against Gram (+ ve) bacteria, Gram (–ve) bacteria and one pathogenic Fungi namely, Aspergillus flavus. Good results were obtained for compounds 7a, b and 11a, b compared with the used standard drugs (Cefotaxime and Dermatin).

One flask synthesis of 2′,3′-cyclic nucleoside monophosphates from unprotected nucleosides using activated cyclic trimetaphosphate

The 2′,3′-cyclic nucleoside monophosphates (2′,3′-cNMPs) of adenosine, guanosine, cytidine, and uridine were prepared in good yield in a one pot reaction from unprotected ribonucleosides and activated trimetaphosphate in the presence of N-methylimidazole, 4-nitroimidazole and MgCl2.

Synthesis of some novel S-alkylated and S-glycosylated hydantoin derivatives containing pyrene moiety

3-Aryl-5-[(Z)-pyrenylmethylene]-2-alkylthiohydantoins and 3-Aryl-5-[(Z)-pyrenylmethylene]-2-(D-glycosyl)-2-thiohydantoins functionalized with different aromatic and glycoside substituents have been synthesized by the reaction of (Z)-3-(4-methoxyphenyl)-5-[(pyren-8-yl)methylene]-2-thiohydantoin with alkyl halides, cyclic and acyclic nucleosides via various routes with moderate to good yields and characterized by 1H, 13C NMR and mass spectra and elemental analysis

Synthesis of Pyridone-based Nucleoside Analogues as Substrates or Inhibitors of DNA Polymerases

ABSTRACTThe synthesis and characterization of novel acyclic and cyclic pyridone-based nucleosides and nucleotides is described. In total, seven nucleosides and four nucleotides were synthesized. None of the tested nucleosides showed inhibitory properties against Klenow exo- polymerase and M.MuLV and HIV-1 reverse transcriptases. The nucleotides containing 4-chloro- and 4-bromo-2-pyridone as a nucleobase were accepted by the Klenow fragment, but at the expense of fidelity and extension efficiency.

A Chemoenzymatic Route To Prepare Acyclic Nucleoside Analogues

AbstractAcyclic nucleosides are potential antiviral and antitumor agents. In this work, their preparation through a novel chemoenzymatic procedure involving the N‐alkylation of a nucleobase and subsequent aldol condensation catalyzed by a dihydroxyacetone phosphate‐dependant aldolase (Rabbit Muscle Aldolase, RAMA) is described.

First-principles DFT study of cyclic and acyclic nucleoside phosphonates

In this paper, we have studied the properties and successfully explained the effectiveness of nucleoside phosphonates as antiviral agents. Working within the framework of first-principles density functional theory (DFT) using the B3LYP functional and the 6-311+G(d,p) basis set, the structural, energetics, and electronic properties of cyclic and acyclic nucleoside phosphonates were determined. Conceptual DFT was used to determine chemical parameters. By comparing the reactivities with those of the competing natural nucleotide during diphosphorylation, we show that, as is, commonly believed, the drugs act by terminating the viral DNA chain. A good correlation has been obtained between the experimental biological activity and the computed DFT-based global chemical reactivity descriptors.

ChemInform Abstract: Medicinal Chemistry of Fluorinated Cyclic and Acyclic Nucleoside Phosphonates

ChemInform Abstract: Medicinal Chemistry of Fluorinated Cyclic and Acyclic Nucleoside Phosphonates