Regioselective 1-N-Alkylation and Rearrangement of Adenosine Derivatives

Bioorthogonal labeling and profiling of N6-isopentenyladenosine (i6A) modified RNA

Chemical modifications in RNAs play crucial roles in diversifying their structures and regulating numerous biochemical processes. Since the 1990s, several hydrophobic prenyl-modifications have been discovered in various RNAs. Prenyl groups serve as precursors for terpenes and many other biological molecules. The processes of prenylation in different macromolecules have been extensively studied. We introduce here a novel chemical biology toolkit that not only labels i6A, a prenyl-modified RNA residue, by leveraging the unique reactivity of the prenyl group, but also provides a general strategy to incorporate fluorescence functionalities into RNAs for molecular tracking purposes. Our findings revealed that iodine-mediated cyclization reactions of the prenyl group occur rapidly, transforming i6A from a hydrogen-bond acceptor to a donor. Based on this reactivity, we developed an Iodine-Mediated Cyclization and Reverse Transcription (IMCRT) tRNA-seq method, which can profile all nine endogenous tRNAs containing i6A residues in Saccharomyces cerevisiae with single-base resolution. Furthermore, under stress conditions, we observed a decline in i6A levels in budding yeast, accompanied by significant decrease of mutation rate at A37 position. Thus, the IMCRT tRNA-seq method not only permits semi-quantification of i6A levels in tRNAs but also holds potential for transcriptome-wide detection and analysis of various RNA species containing i6A modifications.

From synthesis to the biological effect of isoprenoid 2'-deoxyriboside and 2',3'-dideoxyriboside cytokinin analogues

Isoprenoid cytokinins are a class of naturally occurring plant signaling molecules. A series of prepared compounds derived from isoprenoid cytokinins (isopentenyladenine, trans-zeatin and cis-zeatin) with attached 2'-deoxy-d-ribose or 2',3'-dideoxy-d-ribose at the N⁹ position of the purine were prepared and their biological activities were examined. Different synthetic approaches were employed. The final compounds were characterized with variety of physicochemical methods (TLC, HPLC-MS, and NMR) and their cytokinin activity was determined in classical bioassays such as Amaranthus, tobacco callus, detached wheat leaf senescence and Arabidopsis thaliana root elongation inhibition assay. In addition, compounds were screened for activation of the cytokinin signaling pathway (bacterial receptor, competitive ligand binding and ARR5::GUS assay) to provide a detailed assessment of CK structure-activity relationship. The prepared compounds were found to be non-toxic to human cells and the majority of assays exhibited the highest activity of free bases while 2',3'-dideoxyribosides had very weak or no activity. In contrast to the free bases, all 2'-deoxyriboside derivatives were not toxic to tobacco callus even at the highest tested concentration (10^-4 moL/l) and compound 1 (iPdR) induced betacyanin synthesis at higher concentration even stronger than iP free base in the Amaranthus bioassay. The general cytokinin activity pattern base > riboside >2'-deoxyriboside > 2',3'-dideoxyriboside was distinguished.

Cytotoxicity reduction by O-nicotinoylation of antiviral 6-benzylaminopurine ribonucleosides

One of the promising approaches in the development of nucleoside prodrugs is to use the nucleoside analogs containing lipophilic biodegradable residues, which are cleaved to biologically active forms after metabolic transformations in the cell. The introduction of such fragments makes it possible to reduce the general toxicity of the drug candidate and increase its stability in the cell. In order to study the influence of biodegradable lipophilic groups on antiviral activity and cytotoxicity, in this work we synthesized N⁶-benzyl-2',3',5'-tri-O-nicotinoyl adenosine and N⁶-(3-fluorobenzyl)-2',3',5'-tri-O-nicotinoyl adenosine, derivatives of N⁶-benzyladenosine (BAR) and N⁶-(3-fluorobenzyl)adenosine (FBAR), which had previously shown prominent antiviral activity against human enterovirus EV-A71 but appeared to be cytotoxic. As a result, the obtained fully-O-nicotinoylated BAR and FBAR inhibited reproduction of EV-A71 strains BrCr and 46,973 and manifested significantly lower cytotoxicity compared to non-protected compounds. In addition, we performed enzymatic hydrolysis of the fully-O-nicotinoylated FBAR in the presence of esterases (Cal B and PLE) to investigate metabolic degradation of O-nicotinoylated compounds in cells. As a result, both enzymes hydrolyzed the tested substrate to form the corresponding O-deprotected nucleoside that may suggest the role of hydrolase-type enzymes as general participants of metabolic activation of O-nicotinoylated prodrugs in different cells.

In Vitro and In Vivo Evidence for RNA Adduction Resulting from Metabolic Activation of Methyleugenol

Methyleugenol (ME) is a ubiquitous component in spices and other culinary herbal products. A prevailing theory in ME toxicity is its ability to be metabolically activated by P450 enzymes and sulfotransferases, which initiates sequential reactions of the resulting metabolites with functional biomolecules. The present study aimed at a potential interaction between the reactive metabolites of ME and RNA. Cultured mouse primary hepatocytes were incubated with ME followed by RNA extraction and NaOH and alkaline phosphatase-based RNA hydrolysis. Three adenosine adducts were detected in the hydrolytic mixture by LC-MS/MS. The same adenosine adducts were also detected in hepatic tissues harvested from ME-treated mice. These three adducts were chemically synthesized and structurally characterized by ¹H NMR. Additionally, two guanosine adducts and one cytidine adduct were detected in the in vivo samples. These results provided solid evidence that the reactive metabolites of ME attacked RNA, resulting in RNA adduction.

Inositol Adenophostin: Convergent Synthesis of a Potent Agonist of d-myo-Inositol 1,4,5-Trisphosphate Receptors

d-myo-Inositol 1,4,5-trisphosphate receptors (IP₃Rs) are Ca²⁺ channels activated by the intracellular messenger inositol 1,4,5-trisphosphate (IP₃, 1). The glyconucleotide adenophostin A (AdA, 2) is a potent agonist of IP₃Rs. A recent synthesis of d-chiro-inositol adenophostin (InsAdA, 5) employed suitably protected chiral building blocks and replaced the d-glucose core by d-chiro-inositol. An alternative approach to fully chiral material is now reported using intrinsic sugar chirality to avoid early isomer resolution, involving the coupling of a protected and activated racemic myo-inositol derivative to a d-ribose derivative. Diastereoisomer separation was achieved after trans-isopropylidene group removal and the absolute ribose-inositol conjugate stereochemistry assigned with reference to the earlier synthesis. Optimization of stannylene-mediated regiospecific benzylation was explored using the model 1,2-O-isopropylidene-3,6-di-O-benzyl-myo-inositol and conditions successfully transferred to one conjugate diastereoisomer with 3:1 selectivity. However, only roughly 1:1 regiospecificity was achieved on the required diastereoisomer. The conjugate regioisomers of benzyl derivatives 39 and 40 were successfully separated and 39 was transformed subsequently to InsAdA after amination, pan-phosphorylation, and deprotection. InsAdA from this synthetic route bound with greater affinity than AdA to IP₃R1 and was more potent in releasing Ca²⁺ from intracellular stores through IP₃Rs. It is the most potent full agonist of IP₃R1 known and .equipotent with material from the fully chiral synthetic route.

Synthesis of Triazole-Linked SAM-Adenosine Conjugates: Functionalization of Adenosine at N-1 or N-6 Position without Protecting Groups

More than 150 RNA chemical modifications have been identified to date. Among them, methylation of adenosine at the N-6 position (m⁶A) is crucial for RNA metabolism, stability and other important biological events. In particular, this is the most abundant mark found in mRNA in mammalian cells. The presence of a methyl group at the N-1 position of adenosine (m¹A) is mostly found in ncRNA and mRNA and is mainly responsible for stability and translation fidelity. These modifications are installed by m⁶A and m¹A RNA methyltransferases (RNA MTases), respectively. In human, deregulation of m⁶A RNA MTases activity is associated with many diseases including cancer. To date, the molecular mechanism involved in the methyl transfer, in particular substrate recognition, remains unclear. We report the synthesis of new SAM-adenosine conjugates containing a triazole linker branched at the N-1 or N-6 position of adenosine. Our methodology does not require protecting groups for the functionalization of adenosine at these two positions. The molecules described here were designed as potential bisubstrate analogues for m⁶A and m¹A RNA MTases that could be further employed for structural studies. This is the first report of compounds mimicking the transition state of the methylation reaction catalyzed by m¹A RNA MTases.

Dinucleoside polyphosphates act as 5'-RNA caps in bacteria

It has been more than 50 years since the discovery of dinucleoside polyphosphates (Np_nNs) and yet their roles and mechanisms of action remain unclear. Here, we show that both methylated and non-methylated Np_nNs serve as RNA caps in Escherichia coli. Np_nNs are excellent substrates for T7 and E. coli RNA polymerases (RNAPs) and efficiently initiate transcription. We demonstrate, that the E. coli enzymes RNA 5′-pyrophosphohydrolase (RppH) and bis(5′-nucleosyl)-tetraphosphatase (ApaH) are able to remove the Np_nN-caps from RNA. ApaH is able to cleave all Np_nN-caps, while RppH is unable to cleave the methylated forms suggesting that the methylation adds an additional layer to RNA stability regulation. Our work introduces a different perspective on the chemical structure of RNA in prokaryotes and on the role of RNA caps. We bring evidence that small molecules, such as Np_nNs are incorporated into RNA and may thus influence the cellular metabolism and RNA turnover.

Nicotinamide adenine dinucleotide and coenzyme A serve as a 5′-cap of prokaryotic RNA. Here the authors report that methylated and non-methylated dinucleoside polyphosphates (Np_nNs) exist as Escherichia coli RNA caps which can be cleaved by 5′-pyrophosphohydrolase (RppH) and bis(5′-nucleosyl)-tetraphosphatase (ApaH).

Comparative study of inorganic, boron-rich cluster and organic, phenyl adenosine modifications: synthesis and properties

Background: Nucleoside analogs are important class of chemotherapeutics. One of the original openings in the nucleoside medicinal chemistry was derivatives comprising a boron cluster component. Results: A series of adenosine derivative pairs containing inorganic boron cluster or alternatively its mimic, organic phenyl modification were synthesized and their physicochemical and biological properties compared. Marked effects of boron clusters, which are qualitatively and quantitatively different from the phenyl group effects, were detected. The studied characteristics include syn/ anti conformation, lipophilicity, cytotoxicity and antiviral activity, as well as phosphorylation by adenosine kinase. Conclusion: The obtained results demonstrate usefulness of the boron clusters for tuning properties of biomolecules and prove their potential as modifying units in design of future therapeutics based on nucleoside structures.

Adenosine: Synthetic Methods of Its Derivatives and Antitumor Activity

Since 1929, several researchers have conducted studies in relation to the nucleoside of adenosine (1) mainly distribution identifying, characterizing their biological importance and synthetic chemistry to which this type of molecule has been subjected to obtain multiple of its derivatives. The receptors that interact with adenosine and its derivatives, called purinergic receptors, are classified as A1, A2A, A2B and A3. In the presence of agonists and antagonists, these receptors are involved in various physiological processes and diseases. This review describes and compares some of the synthetic methods that have been developed over the last 30 years for obtaining some adenosine derivatives, classified according to substitution processes, complexation, mating and conjugation. Finally, we mention that although the concentrations of these nucleosides are low in normal tissues, they can increase rapidly in pathophysiological conditions such as hypoxia, ischemia, inflammation, trauma and cancer. In particular, the evaluation of adenosine derivatives as adjunctive therapy promises to have a significant impact on the treatment of certain cancers, although the transfer of these results to clinical practice requires a deeper understanding of how adenosine regulates the process of tumorigenesis.