Enzymatic synthesis of highly fluorescent 8-azapurine ribosides using a purine nucleoside phosphorylase reverse reaction: variable ribosylation sites

Photophysics, photochemistry and bioimaging application of 8-azapurine derivatives

New 2-aryl-1,2,3-triazolopyrimidines were designed, synthesized, and characterized. Their optical properties were thoroughly studied in the solid phase, in solution and in a biological environment. Density Functional Theory (DFT) based calculations were performed, including the molecular geometry optimization for both the ground state and the first singlet excited state, the prediction of the UV-Vis absorption and fluorescence spectra, the determination of the molecular electrostatic properties and the solvent effect on the optical properties. The emission intensity was revealed to increase in time upon irradiation. Mass spectrometric research, quantum mechanical calculations, and analysis of literature data suggested a possible photo-transformation pathway through the homolytic cleavage of one of the C-Cl bonds upon irradiation with UV light. The structure of the active intermediate was identified by the series of mass spectrometry experiments and via synthesis of putative transformation products. The kinetic parameters measured in different solvents allowed estimating the rate of these photo-transformations. Biological experiments demonstrated that 2-aryl-1,2,3-triazolopyrimidines penetrate cells and selectively accumulate in the cell membrane and the Golgi complex and endoplasmic reticulum. Their unique properties pave the way for new possible applications of fluorescent 8-azapurines in biology and medicine.

Excited-State Proton Transfer in 8-Azapurines I: A Kinetic Analysis of 8-Azaxanthine Fluorescence

A super-continuum white laser with a half-pulse width of ~75 ps was used to observe the kinetics of a postulated excited-state proton transfer in 8-azaxanthine and its 8-methyl derivative. Both compounds exhibited dual emissions in weakly acidified alcoholic media, but only one band was present in aqueous solutions, exhibiting an abnormal Stokes shift (>12,000 cm⁻¹). It was shown that long-wavelength emissions were delayed relative to the excitation pulse within alcoholic media. The rise time was calculated to be 0.4–0.5 ns in both methanol and deuterated methanol. This is equal to the main component of the fluorescence decay in the short-wavelength band (340 nm). Time-resolved emission spectra (TRES) indicated a two-state photo-transformation model in both compounds. Global analysis of the time dependence revealed three exponential components in each compound, one of which had an identical rise-time, with the second attributed to a long-wavelength band decay (6.4 ns for aza-xanthine and 8.3 ns for its 8-methyl derivative). The origin of the third, intermediate decay time (1.41 ns for aza-xanthine and 0.87 ns for 8-methyl-azaxanthine) is uncertain, but decay-associated spectra (DAS) containing both bands suggest the participation of a contact ion pair. These results confirm the model of phototautomerism proposed earlier, but the question of the anomalous isotope effect remains unsolved.

Tricyclic Nucleobase Analogs and Their Ribosides as Substrates and Inhibitors of Purine-Nucleoside Phosphorylases III. Aminopurine Derivatives

Etheno-derivatives of 2-aminopurine, 2-aminopurine riboside, and 7-deazaadenosine (tubercidine) were prepared and purified using standard methods. 2-Aminopurine reacted with aqueous chloroacetaldehyde to give two products, both exhibiting substrate activity towards bacterial (E. coli) purine-nucleoside phosphorylase (PNP) in the reverse (synthetic) pathway. The major product of the chemical synthesis, identified as 1,N2-etheno-2-aminopurine, reacted slowly, while the second, minor, but highly fluorescent product, reacted rapidly. NMR analysis allowed identification of the minor product as N2,3-etheno-2-aminopurine, and its ribosylation product as N2,3-etheno-2-aminopurine-N2--D-riboside. Ribosylation of 1,N2-etheno-2-aminopurine led to analogous N2--d-riboside of this base. Both enzymatically produced ribosides were readily phosphorolysed by bacterial PNP to the respective bases. The reaction of 2-aminopurine-N9- -D-riboside with chloroacetaldehyde gave one major product, clearly distinct from that obtained from the enzymatic synthesis, which was not a substrate for PNP. A tri-cyclic 7-deazaadenosine (tubercidine) derivative was prepared in an analogous way and shown to be an effective inhibitor of the E. coli, but not of the mammalian enzyme. Fluorescent complexes of amino-purine analogs with E. coli PNP were observed.

Why Purine Nucleoside Phosphorylase Ribosylates 2,6-Diamino-8-azapurine in Noncanonical Positions? A Molecular Modeling Study

Protein nucleoside phosphorylase (PNP) is an enzyme that catalyzes a reversible conversion process (ribosylation and phosphorolysis) between nucleobases (purines) and their nucleosides. Experimental studies showed that calf PNP ribosylates purine analogues in specific positions: 2,6-diamino-8-azapurine in position 7 or 8 and 8-azaguanine in position 9 of the triazole ring. The reason for this phenomenon can be a result of different expositions of purine substrates to the channel leading to the binding site. This hypothesis was verified by the application of molecular modeling techniques to two complexes of purine analogues 2,6-diamino-azapurine, calf PNP (pdb-code: 1LVU), and 8-azaguanine, calf PNP (pdb-code: 2AI1). The results obtained with a combination of quantum chemistry, docking, and molecular dynamics methods showed qualitative validity of our hypothesis. Binding free energies of protein-ligand systems showed that most probable binding poses expose N8 nitrogen for 2,6-diamino-8-azapurine and N9 nitrogen for 8-azaguanine into the binding channel and ruled out the exposition of N9 for 2,6-diamino-8-azapurine and N7 for 8-azaguanine, partially in agreement with the experimental data. The other important result obtained in this study is a significantly higher population of the protonated form of crucial residue Glu-201 present in the binding pocket, compared to the standard protonation of free glutamic acid in solution. This result combined with populations of tautomeric forms of both investigated systems strongly suggests that 2,6-diamino-8-azapurine and 8-azaguanine are recognized by proteins with deprotonated and protonated Glu-201 residues, respectively. A comparison of computed binding poses of the investigated ligands to the inhibitors present in crystal structures suggests that the modification of the (S)-PMPDAP inhibitor, in which a 2-(phosphonomethoxy)propyl chain is attached at position 8 instead of position 9, might increase its binding affinity.

Tri-Cyclic Nucleobase Analogs and their Ribosides as Substrates of Purine-Nucleoside Phosphorylases. II Guanine and Isoguanine Derivatives

Etheno-derivatives of guanine, O⁶-methylguanine, and isoguanine were prepared and purified using standard methods. The title compounds were examined as potential substrates of purine-nucleoside phosphorylases from various sources in the reverse (synthetic) pathway. It was found that 1,N²-etheno-guanine and 1,N⁶-etheno-isoguanine are excellent substrates for purine-nucleoside phosphorylase (PNP) from E. coli, while O⁶-methyl-N²,3-etheno-guanine exhibited moderate activity vs. this enzyme. The latter two compounds displayed intense fluorescence in neutral aqueous medium, and so did the corresponding ribosylation products. By contrast, PNP from calf spleens exhibited only modest activity towards 1,N⁶-etheno-isoguanine; the remaining compounds were not ribosylated by this enzyme. The enzymatic ribosylation of 1,N⁶-etheno-isoguanine using two forms of calf PNP (wild type and N243D) and E. coli PNP (wild type and D204N) gave three different products, which were identified on the basis of NMR analysis and comparison with the product of the isoguanosine reaction with chloroacetic aldehyde, which gave an essentially single compound, identified unequivocally as N9-riboside. With the wild-type E. coli enzyme as a catalyst, N9--d- and N7--d-ribosides are obtained in proportion ~1:3, while calf PNP produced another riboside, tentatively identified as N⁶--d-riboside. The potential application of various forms of PNP for synthesis of the tri-cyclic nucleoside analogs is discussed.

An effective and facile synthesis of new blue fluorophores on the basis of an 8-azapurine core

A convenient synthesis of 2-aryl-2,4-dihydro-5H-[1,2,3]triazolo[4,5-d]pyrimidin-5-ones (DTPs) from 3,3-diamino-2-(arylazo)acrylonitriles through a versatile and readily accessible two-step procedure is described. Density functional theory (DFT) calculations were performed to explain the selectivity of the heterocyclization step, which predominantly afforded 6-amino-5-(arylazo)pyrimidin-2(1H)-thiones in chloroform or ethanol, and 2,3-dihydro-1,2,4-triazines in toluene or DMF. Novel 2-aryl-2,4-dihydro-5H-[1,2,3]triazolo[4,5-d]pyrimidin-5-ones were obtained in good yields and showed absorption in the ultraviolet region and good emission in the blue region. The photophysical properties of DTPs were better than those cited in select literature examples of 8-azapurines. Owing to the facile synthesis and good photophysical characteristics in an aqueous medium, the new DTPs should have potential applications as organic fluorophores in fluorescence imaging and materials science.

Tricyclic nitrogen base 1,N6-ethenoadenine and its ribosides as substrates for purine-nucleoside phosphorylases: Spectroscopic and kinetic studies

The title compound is an excellent substrate for E. coli PNP, as well as for its D204N mutant. The main product of the synthetic reaction is N9-riboside, but some amount of N7-riboside is also present. Surprisingly, 1,N⁶-ethenoadenine is also ribosylated by both wild-type and mutated (N243D) forms of calf PNP, which catalyze the synthesis of a different riboside, tentatively identified as N6-β-D-ribosyl-1,N⁶-ethenoadenine. All ribosides are susceptible to phosphorolysis by the E. coli PNP (wild type). All the ribosides are fluorescent and can be utilized as analytical probes.

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.

Site-Selective Ribosylation of Fluorescent Nucleobase Analogs Using Purine-Nucleoside Phosphorylase as a Catalyst: Effects of Point Mutations

Enzymatic ribosylation of fluorescent 8-azapurine derivatives, like 8-azaguanine and 2,6-diamino-8-azapurine, with purine-nucleoside phosphorylase (PNP) as a catalyst, leads to N9, N8, and N7-ribosides. The final proportion of the products may be modulated by point mutations in the enzyme active site. As an example, ribosylation of the latter substrate by wild-type calf PNP gives N7- and N8-ribosides, while the N243D mutant directs the ribosyl substitution at N9- and N7-positions. The same mutant allows synthesis of the fluorescent N7-β-d-ribosyl-8-azaguanine. The mutated form of the E. coli PNP, D204N, can be utilized to obtain non-typical ribosides of 8-azaadenine and 2,6-diamino-8-azapurine as well. The N7- and N8-ribosides of the 8-azapurines can be analytically useful, as illustrated by N7-β-d-ribosyl-2,6-diamino-8-azapurine, which is a good fluorogenic substrate for mammalian forms of PNP, including human blood PNP, while the N8-riboside is selective to the E. coli enzyme.

8-Azapurines as isosteric purine fluorescent probes for nucleic acid and enzymatic research

The 8-azapurines, and their 7-deaza and 9-deaza congeners, represent a unique class of isosteric (isomorphic) analogues of the natural purines, frequently capable of substituting for the latter in many biochemical processes. Particularly interesting is their propensity to exhibit pH-dependent room-temperature fluorescence in aqueous medium, and in non-polar media. We herein review the physico-chemical properties of this class of compounds, with particular emphasis on the fluorescence emission properties of their neutral and/or ionic species, which has led to their widespread use as fluorescent probes in enzymology, including enzymes involved in purine metabolism, agonists/antagonists of adenosine receptors, mechanisms of catalytic RNAs, RNA editing, etc. They are also exceptionally useful fluorescent probes for analytical and clinical applications in crude cell homogenates.

Excited-state proton transfer and phototautomerism in nucleobase and nucleoside analogs: a mini-review

Intermolecular excited-state proton transfer (ESPT) has been observed in several fluorescent nucleobase and/or nucleoside analogs. In the present work, some new examples of ESPT in this class of compounds are presented together with a brief recapitulation of the previously published data. The nucleobases, nucleosides, and their analogs contain many basic and acidic centers and therefore their ESPT behavior may be complex. To interpret the complex data, it is usually necessary to determine the microscopic pK* values for each (or most) of the possible ESPT centers. Typical approach to solve this problem is by analysis of the alkyl derivatives, in which the possibility of the ESPT is reduced. Of particular interest are examples of "phototautomerization via the cation," observed in several systems, which in the neutral media do not undergo ESPT. Protonation of the molecule in the ground state facilitates the two-step phototautomerism in several systems, including formycin A and 2-amino-8-azadenine. Fluorescence of the nucleobase and nucleoside analogs undergoing ESPT is usually solvent-, isotope-, and buffer-ion sensitive, and in some systems the ESPT can be promoted by environmental factors, e.g., the presence of buffer ions. This sensitivity to the microenvironment parameters makes the ESPT systems potentially useful for biological applications.