Uracil Ring Research Articles

Synthesis and structure–activity relationship of uracil nucleotide derivatives towards the identification of human P2Y6 receptor antagonists

P2Y6 receptor (P2Y6-R) is involved in various physiological and pathophysiological events. With a view to set rules for the design of UDP-based reversible P2Y6-R antagonists as potential drugs, we established structure–activity relationship of UDP analogues, bearing modifications at the uracil ring, ribose moiety, and the phosphate chain. For instance, C5-phenyl- or 3-NMe-uridine-5′-α,β-methylene-diphosphonate, 16 and 23, or lack of 2′-OH, in 12–15, resulted in loss of both agonist and antagonist activity toward hP2Y6-R. However, uridylyl phosphosulfate, 19, selectively inhibited hP2Y6-R (IC50 112μM) versus P2Y2/4-Rs. In summary, we have established a comprehensive SAR for hP2Y6-R ligands towards the development of hP2Y6-R antagonists.

Strain Promoted Click Chemistry of 2- or 8-Azidopurine and 5-Azidopyrimidine Nucleosides and 8-Azidoadenosine Triphosphate with Cyclooctynes. Application to Living Cell Fluorescent Imaging.

Strain-promoted click chemistry of nucleosides and nucleotides with an azido group directly attached to the purine and pyrimidine rings with various cyclooctynes in aqueous solution at ambient temperature resulted in efficient formation (3 min to 3 h) of fluorescent, light-up, triazole products. The 2- and 8-azidoadenine nucleosides reacted with fused cyclopropyl cyclooctyne, dibenzylcyclooctyne, or monofluorocyclooctyne to produce click products functionalized with hydroxyl, amino, N-hydroxysuccinimide, or biotin moieties. The 5-azidouridine and 5-azido-2'-deoxyuridine were similarly converted to the analogous triazole products in quantitative yields in less than 5 min. The 8-azido-ATP quantitatively afforded the triazole product with fused cyclopropyl cyclooctyne in aqueous acetonitrile (3 h). The novel triazole adducts at the 2- or 8-position of adenine or 5-position of uracil rings induce fluorescence properties which were used for direct imaging in MCF-7 cancer cells without the need for traditional fluorogenic reporters. FLIM of the triazole click adducts demonstrated their potential utility for dynamic measuring and tracking of signaling events inside single living cancer cells.

On the importance of antiparallel C[dbnd]O⋯C–F interactions in N1-(3-hydroxypropyl)-5-fluorouracilate–Hg(II) complex: A combined X-ray and DFT study

Herein we report the synthesis and X-ray characterization of a neutral mercury(II) complex of composition [Hg(L)2]n (1), [L=N1-(3-hydroxypropyl)-5-fluorouracilate]. The Hg(II) is bound to the N(3) atoms of both ligands in an essentially linear geometry. Mercury also interacts through short contacts with the O(4) atoms of the uracil rings. The two bases are almost coplanar. Surprisingly, two hydroxyl groups from two different units are also weakly bound in apical positions. Single-crystal X-ray crystallography showed that the molecular complex aggregates into a coordination polymer. The packing assemblies observed in the solid state have been analysed and studied by means of theoretical DFT calculations. Unprecedented antiparallel CO⋯C–F interactions are described since they have a strong influence in the crystal packing of the complex. We have also used the Cambridge Structural Database to examine the occurrence of CO⋯C–F interaction in the solid state of X-ray structures.

TiO2 photocatalytic degradation and detoxification of cylindrospermopsin

Abstract Cylindrospermopsin (CYN), a problematic potent cyanotoxin, is produced during harmful algal blooms and its presence in fresh water lakes and rivers is a threat to human health. UV TiO2 photocatalysis leads to the rapid degradation of CYN following pseudo-first-order kinetics. The pseudo-first-order rate constants (k) are strongly dependent on the reaction conditions, including the initial CYN and TiO2 concentrations, light intensity and solution pH. The observed faster degradation under acidic conditions may be due to the enhanced electrostatic attraction between the positive TiO2 surface and the anionic sulfate group in CYN. The degradation is proportional to the light intensity under our experimental conditions. The roles of reactive species, OH, 1O2, e−cb and h+vb were studied by adding the specific scavengers and the results indicate that OH plays a critical role in UV TiO2 photocatalysis of CYN. Detailed product studies using liquid chromatography mass spectrometry (LC/MS) indicate OH mediated degradation pathways predominantly occur via oxidation of the uracil ring in CYN, leading to hydroxylation and ring opened products. ELISA results demonstrate that TiO2 photocatalysis leads to a significant decrease in the biological activity of CYN as a function of treatment time. Our results indicate TiO2 photocatalysis may be applicable for the degradation of CYN and uracil based compounds.

Palladium-mediated dealkylation of N-propargyl-floxuridine as a bioorthogonal oxygen-independent prodrug strategy.

Herein we report the development and biological screening of a bioorthogonal palladium-labile prodrug of the nucleoside analogue floxuridine, a potent antineoplastic drug used in the clinic to treat advanced cancers. N-propargylation of the N3 position of its uracil ring resulted in a vast reduction of its biological activity (~6,250-fold). Cytotoxic properties were bioorthogonally rescued in cancer cell culture by heterogeneous palladium chemistry both in normoxia and hypoxia. Within the same environment, the reported chemo-reversible prodrug exhibited up to 1,450-fold difference of cytotoxicity whether it was in the absence or presence of the extracellular palladium source, underlining the precise modulation of bioactivity enabled by this bioorthogonally-activated prodrug strategy.

Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation.

We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).

Theoretical study of hydrophobicity and hydrophilicity of uracil and its dimers

The influence of hydrophilic and hydrophobic properties of the uracil elementary nucleic acids bases on its solubility and structure in aqueous solution was studied. Complexes of uracil with water molecules (from 1 to 14) were then calculated. The geometrical parameters of the hydrogen bridge of uracil and the changes in the frequency of valence vibrations of the bonds participating directly in hydrogen bond formation were calculated. It is shown that for the hydrogen bonds O(w)...HN(1) and O(w)...HN3 the hydrogen atom can tear, it may lead to tautomeric transformation of uracil. The results obtained having calculated the structure of uracil dimers, formed with the hydrogen bonds, in an isolated state and water solution, energy, dipole moments and the hydrogen bridge parameters made it possible to explain low solubility of uracil in water at room temperature. It is shown that water molecules with increase in their number are located mainly at one side of the plane of a pyrimidine uracil ring, that leads to the formation of stacking. Of two possible variants of stacking formation, the most profitable grouping is when a dipole moment of the formed dimer is equal to zero (anti-parallel stacking).

Kinetics and mechanisms of cylindrospermopsin destruction by sulfate radical-based advanced oxidation processes

Cylindrospermopsin (CYN) is a potent cyanobacterial toxin frequently found in water bodies worldwide raising concerns over the safety of drinking and recreational waters. A number of technologies have been investigated to remove and/or degrade cyanotoxins with advanced oxidation processes (AOPs) being among the most promising and effective for water detoxification. In this study, the degradation of CYN by sulfate radical-based UV-254 nm-AOPs was evaluated. The UV/S2O82− (UV/peroxydisulfate) was more efficient than UV/HSO5− (UV/peroxysulfate) and UV/H2O2 (UV/hydrogen peroxide) processes when natural water samples were used as reaction matrices. The observed UV fluence based pseudo-first-order rate constants followed the expected order of radical quantum yields. The presence of 200 μM natural organic matter (NOM) as carbon slightly inhibited the destruction of CYN; 1.24 mg L−1NO3− (nitrate) had no significant influence on the removal efficiency and 50 μg L−1 Fe2+ [iron (2+)] or Cu2+ [copper (2+)] improved the performance of UV/S2O82−. The addition of tert-butyl alcohol (t-BuOH; hydroxyl radical scavenger) in the reaction yielded byproducts that indicated specific sites in CYN preferentially attacked by sulfate radicals (SRs). The predominant CYN degradation byproduct was P448 consistent with fragmentation of the C5C6 bond of the uracil ring. The subsequent formation of P420 and P392 through a stepwise loss of carbonyl group(s) further supported the fragmentation pathway at C5C6. The byproduct P432 was identified exclusively as mono-hydroxylation of CYN at tricyclic guanidine ring, whereas P414 was detected as dehydrogenation at the tricyclic ring. The elimination of sulfate group and the opening of tricyclic ring were also observed. The possible degradation pathways of CYN by SR-AOP were presented.

Thermodynamics and mechanism of the interaction of willardiine partial agonists with a glutamate receptor: implications for drug development.

Understanding the thermodynamics of binding of a lead compound to a receptor can provide valuable information for drug design. The binding of compounds, particularly partial agonists, to subtypes of the α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptor is, in some cases, driven by increases in entropy. Using a series of partial agonists based on the structure of the natural product, willardiine, we show that the charged state of the ligand determines the enthalpic contribution to binding. Willardiines have uracil rings with pKa values ranging from 5.5 to 10. The binding of the charged form is largely driven by enthalpy, while that of the uncharged form is largely driven by entropy. This is due at least in part to changes in the hydrogen bonding network within the binding site involving one water molecule. This work illustrates the importance of charge to the thermodynamics of binding of agonists and antagonists to AMPA receptors and provides clues for further drug discovery.

(E)-tert-Butyl 2-(5-{[4-(dimethylamino)phenyl]diazenyl}-2,6-dioxo-1H-pyrimid-in-3-yl)acetate dichloromethane monosolvate.

In the title compound, C18H23N5O4·CH2Cl2, the di­chloro­methane solvent mol­ecule is disordered over two sets of sites in a 0.630 (13):0.370 (13) ratio. The dihedral angle between the uracil and phenyl rings is 30.2 (1)°. In the crystal, the principal inter­actions are N—H⋯O hydrogen bonds, which link uracil units across centres of symmetry, forming eight-membered rings with an R 2 2(8) graph-set motif. The structure also displays C—H⋯O and C—H⋯Cl hydrogen bonds. Intra­molecular C—H⋯O short contacts are also observed.

Rationalizing the formation and versatility of multinuclear metal complexes of bis(1-methyluracil-5-yl)methane as hybrids between classical calix[n]arenes and metallacalixaromatics

Metallacalix[n]arenes are a distinct class of metallacyclic compounds consisting of heteroaromatic rings L and square-planar cis-a2MII entities (M=Pt or Pd; a=NH3 or amine; or a2=chelating diamine) instead of methylene bridges as in the classic calix[n]arenes. Here a series of hybrid compounds is described, which simultaneously have bridging –CH2– as well as cis-a2MII units, and uracil containing ligands L. Specifically, L=bis(1-methyluracil-5-yl)methane (1) and in one case a derivative of it, bis(1-methyluracil-5-yl)methylbenzene (2), have been reacted with cis-[a2M(H2O)2]2+ (with a=NH3 or a2=2,2′-bipyridine or bis(pyrazloyl-1-yl)propane) in water and products were isolated. Altogether X-ray crystal structures of eight metallacycles (complexes 3–6, 8–11) of M2L2, M4L2, and M6L6 stoichiometries have been determined as well as a second modification of 1. In all closed metallacycles the 1-methyluracil entities are deprotonated with metals coordinating via N3 positions, and without exception the uracil rings adopt 1,3-alternate conformations. A special feature of ligand 1 in its twofold deprotonated form is its propensity to bind additional metal ions through its exocyclic oxygen functionalities. While O4 sites appear to be favored as secondary metal binding sites, linkage isomerism and involvement of O2 is likewise possible (compounds 4, 9, 10). On the basis of the X-ray crystal structures, a reaction scheme is proposed which accounts for the different stoichiometries observed.

Synthesis and supramolecular assembly of 1,3-bis(1′-uracilyl)-2-propanone

In this research work, we investigated the properties of a novel heterocyclic molecule, named by us U2CO, whose structure consists of two uracil rings connected by a 2-propanone moiety. We studied by UV the spectroscopic characteristics of U2CO as a function of temperature and ionic strength of the solution. Furthermore, dynamic light scattering (DLS) studies conducted on samples containing the uracil-containing derivative indicated the formation of non-covalent supramolecular networks based on multiple U2CO units. These aggregates contained hydrophobic cavities able to encapsulate drugs such as doxorubicin, as evidenced by fluorescence studies. This property, together with the good stability in human serum of U2CO, determined by HPLC analysis, could be an interesting feature in developing new drug delivery systems. Interestingly, UV studies suggested that U2CO is able to form complexes with copper(II) cations, which is a useful characteristic in view of potential anti-oxidant approaches.

Synthesis and in vitro inhibition effect of new pyrido[2,3-d]pyrimidine derivatives on erythrocyte carbonic anhydrase I and II.

In vitro inhibition effects of indolylchalcones and new pyrido[2,3-d]pyrimidine derivatives on purified human carbonic anhydrase I and II (hCA I and II) were investigated by using CO2 as a substrate. The results showed that all compounds inhibited the hCA I and hCA II enzyme activities. Among all the synthesized compounds, 7e (IC50 = 6.79 µM) was found to be the most active compound for hCA I inhibitory activity and 5g (IC50 = 7.22 µM) showed the highest hCA II inhibitory activity. Structure-activity relationships study showed that indolylchalcone derivatives have higher inhibitory activities than pyrido[2,3-d]pyrimidine derivatives on hCA I and hCA II. Additionally, methyl group bonded to uracil ring increases inhibitory activities on both hCA I and hCA II.

Effect of the microhydration on the tautomerism in the anticarcinogenic drug 5-fluorouracil and relationships with other 5-haloderivatives

The 5-fluorouracil (in short 5-FU) mutagenicity was investigated in the isolated state and in the hydrated form through an exhaustive quantum-chemical analysis. The most optimum tautomers of 5-FU were optimized and analyzed. Six of them were related to those of uracils molecule, with the same stability order. The effect of the halogen substitution in position 5 on the uracil ring in the stability of the different tautomers was analyzed. Solvent effects were considered using a variable number (1–10) of explicit water molecules surrounding 5-FU in order to simulate the first hydration shell. More than 100 cluster structures with water were analyzed. A comparative analysis in the different tautomers of the hydration effect on the molecular structure and energetics was carried out. For cases where literature data are available, the computed values were in good agreement with previous experimental and theoretical studies. Depending on the nature of the tautomers, cyclic, distributed, or clustered structures were formed. The deformation and interaction counterpoise (CP)-corrected energies between 5-FU and water molecules were determined. The maximum interaction was found in the enol form T2. The microhydrated environment stabilized remarkably the enol forms T3 and T5 (present in the corresponding nucleoside) more than the canonical keto T1, although this one continues being the most stable. Several relationships with 5-XU derivatives (X=F, Cl, Br, I) between the relative energy of tautomer T2 and the geometric parameters/atomic charges were underlined.

REACTION OF 5,6-DIAMINO-1,3-DIMETHYLURACIL WITH ARYLIDENEACETONES AND ARYLIDENECYCLANONES

The reaction of 5,6-diamino-1,3-dimethyluracil dihydrochloride with mono- and diarylideneacetones and with cyclohexanones give 2,4-disubstituted 1,7,9-triazaspiro[4,5]dec-1-ene-6,8,10-triones. It was found that arylidenecyclopentanones form only 5-azomethines with retention of the amino group at position 6 of the uracil ring. Authors: N. N. Kolos, V. A. Chebanov, and V. D. Orlov. English Translation in Chemistry of Heterocyclic Compounds , 1999, 35 (9), pp 1085-1088 http://link.springer.com/article/10.1007/BF02251801

Simulation of a tetramer form of 5-chlorouracil: The vibrational spectra and molecular structure in the isolated and in the solid state by using DFT calculations

A Raman and FT-IR study of the biomolecule 5-chlorouracil in the solid state was carried out. The unit cell found in the crystal was simulated as a tetramer form by density functional calculations. They were performed to clarify the assignments of the experimentally observed bands in the spectra. Calculations in the monomer form and comparisons with the experimental data in Ar matrix were also carried out. The error in the calculated frequencies was analyzed and reduced by using scaling equations and scaling factors deduced from the uracil molecule. The calculations with the B3LYP method and with the 6-31G(d,p) and 6-311+G(2d,p) basis set, appear in general to be useful, when combining with a scaling equation procedure or with the specific scale factors, for interpretation of the general features of the IR and Raman spectra. The scaled values were used in the reassignment of the IR and Raman experimental bands. Comparison of the results with those determined in uracil and 5-halogenated derivatives were performed. The substitution at 5-position of the uracil ring by a chlorine atom has a little effect on the geometric parameters.

2,2′-Anhydro-1-(3′,5′-di-O-acetyl-β-D-arabinofuranosyl)uracil, a cyclouridine nucleoside with a C4′-endofuranosyl conformation

2,2'-Anhydro-1-(3',5'-di-O-acetyl-β-D-arabinofuranosyl)uracil, C13H14N2O7, was obtained by refluxing 2',3'-O-(methoxymethylene)uridine in acetic anhydride. The structure exhibits a nearly perfect C4'-endo ((4)E) conformation. The best four-atom plane of the five-membered furanose ring is O-C-C-C, involving the C atoms of the fused five-membered oxazolidine ring, and the torsion angle is only -0.4 (2)°. The oxazolidine ring is essentially coplanar with the six-membered uracil ring [r.m.s. deviation = 0.012 (5) Å and dihedral angle = -3.2 (3)°]. The conformation at the exocyclic C-C bond is gauche-trans which is stabilized by various C-H...π and C-O...π interactions.

Collision-induced dissociation mechanisms of [Li(uracil)

The collision-induced dissociation (CID) of the [Li(uracil)](+) complex with Xe is studied by means of quasi-classical trajectory calculations. The potential energy surface is obtained "on the fly" from AM1 semiempirical calculations, supplemented with two-body analytical potentials to model the intermolecular interactions. The simulations show that Li(+) production is the primary channel, in agreement with a previous experimental study [M. T. Rodgers and P. B. Armentrout, J. Am. Chem. Soc., 2000, 122, 8548]. Collision-induced isomerization of [Li(uracil)](+) was found to be very important as well in the 2.5-10 eV collision energy range. Three minor channels are also identified: complex formation between Xe and [Li(uracil)](+), ligand exchange to form LiXe(+), and fragmentations of the uracil ring, which are strongly nonstatistical. Additional quasi-classical trajectory calculations carried out to investigate in more detail the fragmentations of the uracil ring reveal the presence of bifurcations in the potential energy surface, as trajectories starting from a transition state give rise to four different product channels. The integral cross sections for Li(+) production calculated in this work agree well with those obtained in the experiments only for the lowest collision energies, being ∼20 times greater than the experimental values for a collision energy of 10 eV. Finally, the initial translational energy is transferred preferentially to the [Li(uracil)](+) vibrational degrees of freedom, with energy transfer to rotation being modest. The amount of energy transfer to the different degrees of freedom as a function of the collision energy follows quite nicely a model recently proposed by our group.

Thermochemistry of Uracils. Experimental and Computational Enthalpies of Formation of 5,6-Dimethyl-, 1,3,5-Trimethyl-, and 1,3,5,6-Tetramethyluracils

We describe in the current paper an experimental and computational study of three methylated uracils, in particular, the 5,6-dimethyl-, 1,3,5-trimethyl-, and 1,3,5,6-tetramethyl derivatives. The values of the standard (p(0) = 0.1 MPa) molar enthalpies of formation in the gas phase at T = 298.15 K have been determined. The energies of combustion were measured by static bomb combustion calorimetry, and from the results obtained, the standard molar enthalpies of formation in the crystalline state at T = 298.15 K were calculated. The enthalpies of sublimation were determined using the transpiration method in a saturated N(2) stream. Values of -(376.2 ± 2.6), -(355.9 ± 3.0), and -(381.7 ± 2.8) kJ·mol(-1) for the gas-phase enthalpies of formation at T = 298.15 K of 5,6-dimethyluracil, 1,3,5-trimethyluracil, and 1,3,5,6-tetramethyluracil, respectively, were obtained from the experimental thermochemical study. An extended theoretical study with the G3 and the G4 quantum-chemical methods has been carried out for all the possible methylated uracils. There is a very good agreement between experimental and calculated enthalpies of formation for the three derivatives studied. A Free-Wilson analysis on G4-calculated enthalpies of formation has been carried out, and the contribution of methylation in the different positions of the uracil ring has been estimated.

Inhibiting effect of 5-amino-5-methyluracil and its derivatives on the free-radical oxidation of 1,4-dioxane

The antiradical activity of 5-amino-6-methyluracil in the initiated radical-chain oxidation of 1,4-dioxane as a model system was studied quantitatively. The rate constant k7 of its reaction with the peroxyl radical of 1,4-dioxane was measured to be (5.6 ± 1.8) × 105 L mol−1 s−1 at 333 K. The effect of the methyl substituents in the 1- and 3-positions of the uracil ring and in the amino group on the rate constant of inhibition was studied. The strengths of all N-H bonds in the 5-amino-6-methyluracil and its derivatives were calculated in the G3MP2B3 approximation and were compared with the measured rate constants of inhibition. By the example of the reaction of 5-amino-6-uracil with i-PrO2⊙, different attack pathways of the peroxyl radical at the N-H bonds of uracil were analyzed in the UB3LYP/6-311+G(d,p) approximation. The lowest activation barrier (5.8 kJ/mol) was observed for peroxyl radical attack on the (C5)N-H bonds. The site responsible for the inhibition activity of the compound is the amino group.