pyrimidinones and pyrimidine

Pyrido[2,3-

Topics: Chemistry Techniques, Synthetic; Molecular Structure; Pyrimidines; Pyrimidinones; Structure-Activity Relationship

Photolyases (PHRs) repair ultraviolet (UV)-induced DNA photoproducts into normal bases. In this study, we measured the conformational changes upon photoactivation and photorepair processes of a PHR and its specific substrates, (6-4)PHR and a pyrimidine(6-4)pyrimidone photoproduct ((6-4)PP), by light-induced difference Fourier transform infrared (FT-IR) spectroscopy. The single-stranded DNA with (6-4)PP (ss(6-4)PP) was used as a substrate and the resultant FT-IR spectra were compared with the previous results on double-stranded DNA with (6-4)PP (ds(6-4)PP). In the excess amount of substrate to the enzyme, different ss(6-4)PP photorepair FT-IR signals were obtained in an illumination time-dependent manner. As reported for ds(6-4)PP, the early stages of the photoreaction involve the changes in the ss(6-4)PP only, while the late stages of the reaction involve the ss(6-4)PP repair-associated changes and dissociation from (6-4)PHR. From these spectra, difference spectra originating from the binding/dissociation spectrum were extracted. The signals of the C═O stretches of (6-4)PP and repaired thymines in the single- and double-stranded DNA were tentatively assigned. The C═O stretches of (6-4)PP were observed at frequencies that reflect single- and double-stranded DNA environments in aqueous solution, reflecting the different hydrogen-bonding environments. The conformational changes of PHR upon binding of ss(6-4)PP and ds(6-4)PP were similar, suggesting that the conformational change is limited to the (6-4)PP binding pocket region. We interpreted that ds(6-4)PP may be bound together without any special mechanism for flipping out.

Topics: Animals; Deoxyribodipyrimidine Photo-Lyase; DNA; DNA Breaks, Double-Stranded; DNA Repair; DNA, Single-Stranded; Pyrimidines; Pyrimidinones; Spectroscopy, Fourier Transform Infrared; Ultraviolet Rays; Xenopus laevis; Xenopus Proteins

Sequence dependence of the (6-4) photoproduct conformational landscape when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending, and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing different upstream and downstream flexibilities. Moreover, REST2 simulations allow us to probe structures possibly important for damaged DNA recognition.

Topics: DNA; Molecular Dynamics Simulation; Nucleic Acid Conformation; Photochemical Processes; Pyrimidines; Pyrimidinones

AZD3965, a pyrole pyrimidine derivative, is a potent and orally bioavailable inhibitor of monocarboxylate transporter 1 (MCT1), currently in a Phase I clinical trial in UK for lymphomas and solid tumors. There is currently no published assay for AZD3965. The objectives of this study were to develop and validate a LC/MS/MS assay for quantifying AZD3965 in mouse plasma and tumor tissue. Protein precipitation with 0.1% formic acid in acetonitrile was used for sample preparation. Chromatographic separation was achieved on a C18 column followed by tandem mass spectrometry detection in multiple reaction monitoring mode with utilizing Atmospheric Pressure Chemical Ionization. AR-C155858 was used as the internal standard. The inter-day and intra-day precision and accuracy of quality control samples evaluated in plasma and tumor tissue were less than ±7% of the nominal concentrations. The extraction recovery, matrix effect and stability values were all within acceptable levels. Sample dilution integrity, accessed by diluting plasma spiked with AZD3965 10-fold with blank plasma, was 101%. The lower limit of quantification (LLOQ) and upper limit of quantification (ULOQ) were 0.15 ng/mL and 12 μg/mL, respectively, in plasma. The assay of AZD3965 in tumor tissue was also validated with good precision and accuracy. The LLOQ was 0.15 ng/mL in tumor tissue. This assay was successfully applied to pharmacokinetic and murine 4T1 breast tumor xenograft studies of AZD3965 in mice.

Topics: Acetonitriles; Animals; Atmospheric Pressure; Breast Neoplasms; Cell Line, Tumor; Chromatography, Liquid; Female; Heterografts; Mice; Plasma; Pyrimidines; Pyrimidinones; Reproducibility of Results; Tandem Mass Spectrometry; Thiophenes; Uracil

Structural features are of major importance for the formation of mutagenic photoproducts in DNA. It was recently reported that lack of constraints between two adjacent nucleosidic units prevents the conversion of pyrimidine (6-4) pyrimidone photoproducts into their Dewar valence isomers. We here report that this is not the case for the thymidine photoproducts which, although unconstrained, are quantitatively converted into photolysis products identified as Dewar valence isomers by mass spectrometry and NMR and infrared spectroscopies.

Topics: Dinucleoside Phosphates; DNA; DNA Damage; Isomerism; Magnetic Resonance Spectroscopy; Molecular Structure; Photochemistry; Photolysis; Pyrimidines; Pyrimidinones; Ultraviolet Rays

Fatty acid binding protein 4 (FABP4) is the most well-characterized FABP isoform. FABP4 regulates inflammatory pathways in adipocytes and macrophages and is involved in both inflammatory diseases and tumor formation. FABP4 expression was recently reported for glioblastoma, where it may participate in disease malignancy. While FABP4 is a potential molecular imaging target, with the exception of a tritium labeled probe there are no reports of other nuclear imaging probes that target this protein. Here we designed and synthesized a nuclear imaging probe, [123I]TAP1, and evaluated its potential as a FABP4 targeting probe in in vitro and in vivo assays. We focused on the unique structure of a triazolopyrimidine scaffold that lacks a carboxylic acid to design the TAP1 probe that can undergo facilitated delivery across cell membranes. The affinity of synthesized TAP1 was measured using FABP4 and 8-anilino-1-naphthalene sulfonic acid. [125I]TAP1 was synthesized by iododestannylation of a precursor, followed by affinity and selectivity measurements using immobilized FABPs. Biodistributions in normal and C6 glioblastoma-bearing mice were evaluated, and excised tumors were subjected to autoradiography and immunohistochemistry. TAP1 and [125I]TAP1 showed high affinity for FABP4 (Ki = 44.5±9.8 nM, Kd = 69.1±12.3 nM). The FABP4 binding affinity of [125I]TAP1 was 11.5- and 35.5-fold higher than for FABP3 and FABP5, respectively. In an in vivo study [125I]TAP1 displayed high stability against deiodination and degradation, and moderate radioactivity accumulation in C6 tumors (1.37±0.24% dose/g 3 hr after injection). The radioactivity distribution profile in tumors partially corresponded to the FABP4 positive area and was also affected by perfusion. The results indicate that [125I]TAP1 could detect FABP4 in vitro and partly in vivo. As such, [125I]TAP1 is a promising lead compound for further refinement for use in in vivo FABP4 imaging.

Topics: Adipose Tissue; Animals; Autoradiography; Carboxylic Acids; Cell Line; Cell Line, Tumor; Fatty Acid-Binding Proteins; Immunohistochemistry; Iodine Radioisotopes; Male; Mice; Mice, Inbred BALB C; Protein Binding; Pyrimidines; Pyrimidinones; Rats; Rats, Sprague-Dawley; Tissue Distribution; Triazoles

4(3H)-Pyrimidinone is observed in nature in equilibrium with other tautomeric forms, mimicking the tautomeric equilibrium in pyrimidine nucleobases. In this work, the enthalpy of formation in the gaseous phase of 4(3H)-pyrimidinone was derived from the combination of the enthalpy of formation in the crystalline phase, obtained by static bomb combustion calorimetry, and the enthalpy of sublimation, obtained by Knudsen effusion. The gaseous phase enthalpy of formation of 4(3H)-pyrimidinone was interpreted in terms of isodesmic reactions that consider the enthalpic effects of hydroxypyridines and pyrimidine. After comparison of the experimental and computational results, the same type of isodesmic reactions was used to study the substituent effects of the hydroxyl functional group of 2-, 4-, and 5-hydroxypyrimidines. The influence of aromaticity on the energetics of hydroxypyrimidines was evaluated using the variation of nucleus-independent chemical shifts for several reactions. The influence of intramolecular hydrogen bonds was investigated using the quantum theory of atoms in molecules and the geometric rule of Baker and Hubbard to identify hydrogen bonds. The energetic results obtained were also interpreted in terms of an in plane anomeric effect in the pyrimidine ring.

Topics: Calorimetry; Hydrogen Bonding; Pyridines; Pyrimidines; Pyrimidinones; Thermodynamics

Pyrimidine (6-4) pyrimidone photoproduct (6-4PP), a common DNA photolesion formed under solar irradiation, was indicated to hydrolyze under strong basic conditions, breaking the N3-C4 bond at the 5'-thymine. The reanalysis of this reaction revealed that the resulting water adduct may not be stable as previously proposed; it readily undergoes an esterification reaction induced by the 5-OH group at 6-4PP to form a five-membered ring, eliminating a molecule of ammonia.

Topics: Deamination; DNA; Hydrolysis; Magnetic Resonance Spectroscopy; Pyrimidines; Pyrimidinones; Thymine

The mechanism by which the hypothetical oxetane/azetidine intermediate formed during the photochemical process leading to pyrimidine (6-4) pyrimidone photoproducts when DNA is submitted to UV radiation opens is investigated computationally by DFT using a 5'-TT-3' dinucleoside monophosphate as a structural model. First, the feasibility of an intramolecular mechanism involving one proton transfer inducing opening of the oxetane ring is examined. It results in a very high Gibbs energy of activation (+166 kJ mol(-1)) and quite a low Gibbs energy of reaction (-35 kJ mol(-1)). The protonation state of the phosphate group is shown to have little effect while the bulk effect of an aqueous environment modeled by the Polarizable Continuum Model method lowers slightly the activation barrier (by about 10-20 kJ mol(-1)), not enough to explain the fact that the oxetane intermediate is not observed experimentally. Then the catalytic effect of water molecules on the reaction pathway is studied by including either 1 or 2 assisting water molecules in the chemical system. The resulting activation barrier is considerably lowered and in the most favorable situation - a phosphate group deprotonated and 2 assisting water molecules - the Gibbs energy activation is as low as +44 kJ mol(-1) and the Gibbs energy of reaction is quite favorable: -79 kJ mol(-1), suggesting that in biological systems the oxetane ring opening process proceeds with explicit intervention of water molecules from the environment.

Topics: DNA; Ethers, Cyclic; Models, Molecular; Protons; Pyrimidines; Pyrimidinones; Thermodynamics; Thymine; Ultraviolet Rays; Water

In the present work, a combined experimental and computational study for the optimized molecular structural parameters, FT-IR spectra, thermo-chemical parameters, total dipole moment and HOMO-LUMO energy gap for 2-chloro-5-(2,5-dimethoxy-benzylidene)-1,3-diethyl-dihydro-pyrimidine-4,6(1H,5H)-dione have been investigated using B3LYP/6-311G basis set. Our calculated results have showed that the investigated compound possesses a dipole moment of 4.9 Debye and HOMO-LUMO energy gap of 3 eV which indicate high recommendations for photovoltaic devices fabrication.

Topics: Kinetics; Models, Molecular; Molecular Conformation; Pyrimidines; Pyrimidinones; Quantum Theory; Spectroscopy, Fourier Transform Infrared; Thermodynamics; Vibration

Coupling reaction between electron-rich 2-morpholino-4(3H)-pyrimidinone and nucleophilic side chains of several natural α-amino acids promoted by phosphonium salt has been developed to prepare new optically active pyrimidin-4-yl amino acids. The best results were obtained using a two-step method through the easily available benzotriazolyl-1-oxy intermediate. A detailed optimization study of this reaction is discussed.

Topics: Amino Acids; Morpholinos; Organophosphonates; Pyrimidines; Pyrimidinones; Salts

A molecular simplification approach of previously reported 2-arylpyrazolo[3,4-c]quinolin-4-ones was applied to design 2-arylpyrazolo[4,3-d]pyrimidin-7-one derivatives as new human A(3) adenosine receptor antagonists. Substituents with different lipophilicity and steric hindrance were introduced at the 5-position of the bicyclic scaffold (R(5) = H, Me, Et, Ph, CH(2)Ph) and on the 2-phenyl ring (OMe, Me). Most of the synthesized derivatives were highly potent hA(3) adenosine receptor antagonists, the best being the 2-(4-methoxyphenyl)pyrazolo[4,3-d]pyrimidin-7-one (K(i) = 1.2 nM). The new compounds were also highly selective, being completely devoid of affinity toward hA(1), hA(2A), and hA(2B) adenosine receptors. On the basis of the recently published human A(2A) receptor crystallographic information, we propose a novel receptor-driven hypothesis to explain both A(3) AR affinity and A(3) versus A(2A) selectivity profiles of these new antagonists.

Topics: Adenosine A2 Receptor Antagonists; Adenosine A3 Receptor Antagonists; Amino Acid Sequence; Animals; CHO Cells; Cricetinae; Cricetulus; Humans; Models, Molecular; Molecular Conformation; Molecular Sequence Data; Protein Binding; Pyrazoles; Pyrimidines; Pyrimidinones; Receptor, Adenosine A2A; Receptor, Adenosine A3; Substrate Specificity; Triazines; Triazoles

Mutagenic pyrimidine-pyrimidone (6-4) photoproducts are one of the main DNA lesions induced by solar UV radiation. These lesions can be photoreversed by (6-4) photolyases. The originally published repair mechanism involves rearrangement of the lesion into an oxetane intermediate upon binding to the (6-4) photolyase, followed by light-induced electron transfer from the reduced flavin cofactor. In a recent crystallographic study on a (6-4) photoproduct complexed with (6-4) photolyase from Drosophila melanogaster no oxetane was observed, raising the possibility of a non-oxetane repair mechanism. Using quantum-chemical calculations we find that in addition to repair via an oxetane, a direct transfer of the hydroxyl group results in reversal of the radical anion (6-4) photoproduct. In both mechanisms, the transition states have high energies and correspond to avoided crossings of the ground and excited electronic states. To study whether the repair can proceed via these state crossings, the excited-state potential energy curves were computed. The radical excitation energies and accessibility of the nonadiabatic repair path were found to depend on hydrogen bonds and the protonation state of the lesion. On the basis of the energy calculations, a nonadiabatic repair of the excited (6-4) lesion radical anion via hydroxyl transfer is probable. This repair mechanism is in line with the recent structural data on the (6-4) photolyase from D. melanogaster .

Topics: Animals; Deoxyribodipyrimidine Photo-Lyase; DNA; DNA Repair; Drosophila melanogaster; Electrons; Pyrimidines; Pyrimidinones; Quantum Theory; Ultraviolet Rays

A new reaction of 4-arylidene-3-methylisoxazol-5(4H)-one or 4-arylidene-2-phenyloxazol-5(4H)-one with 2,6-diaminopyrimidin-4(3H)-one is described and a number of new pyrido[2,3-d]pyrimidine-4,7-dione derivatives are synthesized. This protocol has the advantages of good yields, broad substrate scope and simple work-up.

Topics: Microwaves; Models, Molecular; Pyridones; Pyrimidines; Pyrimidinones; Solvents; Temperature

All the nine 1,3-dialkylated-pyrimidin-2,4-diones investigated are active against all the 59 human tumor cell lines. Compounds 2, 3, 4, and 6 show significant anti-cancer activities at some specific cell lines while compounds 7 and 9 exhibit anti-cancer activities against more number of cell lines. The structure-activity relationship studies indicate that the presence of piperidine/pyrrolidine at the end of C-6 chain, benzoyl group at C-5, and benzyl groups at N-1, N-3 of the pyrimidine ring increases the anti-cancer activities of these molecules.

Topics: Antineoplastic Agents; Cell Line, Tumor; Drug Screening Assays, Antitumor; Humans; Neoplasms; Piperidines; Propanolamines; Pyrimidines; Pyrimidinones; Pyrrolidines; Structure-Activity Relationship

Sunscreens are known to protect against sunlight-induced erythema and sunburn, but their efficiency at protecting against skin cancer is still a matter of debate. Specifically, the capacity of sunscreens to prevent or reduce tissue and DNA damage has not been thoroughly investigated. The present study was undertaken to assess the ability of a chemical broad-spectrum sunscreen to protect human skin against tissue and DNA damage after solar UV radiation. Engineered human skin was generated and either treated or not with a broad-spectrum SPF 30 sunscreen and exposed to increasing doses of simulated sunlight (SSL). Immediately after irradiation, histological, immunohistochemical, and molecular quantitative analyses were performed. The unprotected irradiated engineered human skin showed significant epidermal disorganization accompanied by a complete absence of laminin deposition. The sunscreen prevented SSL-induced epidermal damage at low doses and allowed laminin deposition at almost all SSL doses tested. The frequencies of cyclobutane pyrimidine dimers, pyrimidine (6-4) pyrimidone photoproducts, and photooxidative lesions measured by alkaline gel electrophoresis and radioimmunoassay were significantly reduced by the sunscreen. Thus, tissue and DNA damage may provide excellent quantitative end points for assessing the photoprotective efficacy of sunscreens.

Topics: Adolescent; Adult; Cells, Cultured; Cyclobutanes; Dimerization; DNA Damage; Dose-Response Relationship, Radiation; Female; Humans; Immunohistochemistry; Keratinocytes; Laminin; Pyrimidines; Pyrimidinones; Radioimmunoassay; Skin; Sunscreening Agents; Ultraviolet Rays

Ultraviolet light induces damage to DNA, with the majority of the damage expressed as the formation of cyclobutane dimers and pyrimidine-pyrimidone (6-4) photoproducts. The (6-4) photoproducts have been implicated as important UV light-induced premutagenic DNA lesions. The most abundant of the (6-4) products is the thymine-cytosine pyrimidine-pyrimidone (6-4) photoproduct, or TC (6-4) product. The structure of the TC (6-4) product was deduced by proton NMR, IR, and fast atom bombardment mass spectroscopy, and the product was found to differ from the previously described photoadduct, Thy(6-4)Pyo, by the presence of an amino group at the 5 position of the 5' pyrimidine. The implications of this structure on DNA base pairing and the induction of ultraviolet light-induced mutations are discussed.

Topics: Cytosine; DNA; Magnetic Resonance Spectroscopy; Photochemistry; Pyrimidines; Pyrimidinones; Spectrophotometry, Atomic; Spectrophotometry, Infrared; Thymine; Ultraviolet Rays

Topics: Chemistry, Pharmaceutical; Glucosides; Humans; Pyrimidines; Pyrimidinones

Topics: Glucosides; Humans; Pyrimidines; Pyrimidinones