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6-Ethynylthieno[3,2-d]- and 6-ethynylthieno[2,3-d]pyrimidin-4-anilines as tunable covalent modifiers of ErbB kinases
Abstract not provided
Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking
Abstract not provided
Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil
The structure of bacterial uridine phosphorylase (UPh) belonging to the NP-I family in complex with 6-methyluracil was determined for the first time at 1.17 Å resolution. The structural features of bacterial UPh from the bacterium Vibrio cholerae (VchUPh) responsible for selectivity toward 6-methyluracil acting as a pseudosubstrate were revealed. The repulsion between the hydrophilic hydroxyl group of the active-site residue Thr93 of VchUPh and the hydrophobic methyl group of 6-methyluracil prevents the oxygen atom O4' of the ribose moiety and the phosphate oxygen atom O3P of ribose 1-phosphate from forming hydrogen bonds with OG1-Thr93, which are essential for the enzymatic reaction. This, apparently, makes VchUPh inactive in the enzymatic synthesis of 6-methyluridine from 6-methyluracil. Hence, Thr93 is the residue, the modification of which will allow VchUPh to catalyze the biotechnologically important synthesis of 6-methyluridine from 6-methyluracil. Taking into account high structural homology of the functionally significant regions of bacterial UPhs, this conclusion is also true for other bacterial UPhs. It was demonstrated that bacterial thymidine phosphorylases of the NP-II family cannot bind 6-methyluracil in a proper conformation required for the catalysis because of a close contact between the 6-methyl group and Phe210.
Purine and pyrimidines in sediments from the experimental mohole.
Cytosine, adenine, guanine, thymine and uracil detection in core samples from experimental Mohole
Chlorination studies. IV - The reaction of aqueous hypochlorous acid with pyrimidine and purine bases.
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Prebiotic syntheses of purines and pyrimidines
The results of experimental and theoretical investigations of the prebiotic synthesis of purines and pyramidines are surveyed. Topics examined include the synthesis of purines from HCN via 4,5-disubstituted imidazole derivatives in aqueous solutions or liquid NH3, simultaneous formation of amino acids and purines by electron irradiation of CH4-NH3-H2O mixtures, synthesis of pyrimadines from cynoacetylene, energetics, formation of bases under anhydrous or concentrated conditions, formation of bases under dilute conditions, Fischer-Tropsch-type reactions, and the role of activated intermediates. It is pointed out that the precursor compounds have been detected in the interstellar medium, on Titan, and in other solar-system bodies, and that solar-nebula HCN concentrations of the order of 1-10 mM have been estimated on the basis of meteorite measurements.
Pyrido[2, 3-d]pyrimidin-7-one inhibitors of cyclin-dependent kinases
Abstract not provided
Structure-Based Prototyping of Allosteric Inhibitors of Human Uridine/Cytidine Kinase 2 (UCK2)
Pyrimidine nucleotide biosynthesis in humans is a promising chemotherapeutic target for infectious diseases caused by RNA viruses. Because mammalian cells derive pyrimidine ribonucleotides through a combination of de novo biosynthesis and salvage, combined inhibition of dihydroorotate dehydrogenase (DHODH; the first committed step in de novo pyrimidine nucleotide biosynthesis) and uridine/cytidine kinase 2 (UCK2; the first step in salvage of exogenous nucleosides) strongly attenuates viral replication in infected cells. However, while several pharmacologically promising inhibitors of human DHODH are known, to date there are no reports of medicinally viable leads against UCK2. Here we use structure-based drug prototyping to identify two classes of promising leads that non-competitively inhibit UCK2 activity. In the process we have identified a hitherto unknown allosteric site at the inter-subunit interface of this homotetrameric enzyme. By reducing the kcat of human UCK2 without altering its KM, these new inhibitors have the potential to enable systematic dialing of the fractional inhibition of pyrimidine salvage to achieve the desired antiviral effect with minimal host toxicity.
Distinct Purine Distribution in Carbonaceous Chondrites
Carbonaceous chondrite meteorites are known to contain a diverse suite of organic compounds, many of which are essential components of biochemistry. Amino acids, which are the monomers of proteins, have been extensively studied in such meteorites (e.g. Botta and Bada 2002; Pizzarello et aI., 2006). The origin of amino acids in meteorites has been firmly established as extraterrestrial based on their detection typically as racemic mixtures of amino acids, the presence of many non-protein amino acids, and non-terrestrial values for compound-specific deuterium, carbon, and nitrogen isotopic measurements. In contrast to amino acids, nucleobases in meteorites have been far less studied. Nucleobases are substituted one-ring (pyrimidine) or two-ring (purine) nitrogen heterocyclic compounds and serve as the information carriers of nucleic acids and in numerous coenzymes. All of the purines (adenine, guanine, hypoxanthine, and xanthine) and pyrimidines (uracil) previously reported in meteorites are biologically common and could be interpreted as the result of terrestrial contamination (e.g. van del' Velden and Schwartz, 1974.) Unlike other meteoritic organics, there have been no observations of stochastic molecular diversity of purines and pyrimidines in meteorites, which has been a criterion for establishing extraterrestrial origin. Maltins et al. (2008) performed compound-specific stable carbon isotope measurements for uracil and xanthine in the Murchison meteorite. They assigned a non-terrestrial origin for these nucleobases; however, the possibility that interfering indigenous molecules (e.g. carboxylic acids) contributed to the 13C-enriched isotope values for these nucleobases cannot be completely ruled out. Thus, the origin of these meteoritic nucleobases has never been established unequivocally. Here we report on our investigation of extracts of II different carbonaceous chondrites covering various petrographic types (Cl, CM, and CR) and degrees of aqueous alteration (l, 2, and 3) and one ureilite. Analysis via liquid chromatography coupled with electrospray triple-stage mass spectrometry or orbitrap mass spectrometry employed a targeted approach for analysis focused on the five canonical RNA/DNA nucleobases as well as 14 non-canonical pyrimidines and purines, which have bcen observed under plausible prebiotic reactions.
The Formation of Nucleobases from the UV Irradiation of Astrophysical Ice Analogs
Nucleobases are the fundamental information bearing components of both RNA and DNA. They are central to all known terrestrial life and they are generally conserved between species. Biological nucleobases can be divided into two groups based on the N-heterocyclic molecules pyrimidine (uracil, cytosine, and thymine) and purine (adenine and guanine) respectively. Do date, no experimental conditions have been determined that could produce both pyrimidines and purines together, abiotically, in a ter-restrial environment or an early terrestrial analog. Organic materials produced in extraterrestrial envi-ronments may have been delivered to the primitive earth by comets and meteorites and may have contrib-uted to the emergence of life. To date, some, but not all nucleobases have been detected in meteorites and their isotopic signatures may be consistent with an extraterrestrial origin. Earlier work in our lab demonstrated that it is possible to produce all of the pyrimidine group nucleobases from the UV-irradiation of pyrimidine in astrophysically relevant ice analogs. Here we report our most recent work, which studied the formation of the purine group nucleobases under similar conditions.
Role of Human DNA Polymerase kappa in Extension Opposite from a cis-syn Thymine Dimer
Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase {Kappa} (Pol{Kappa}), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Pol{Kappa} in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Pol{Kappa} in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.
Identification of a non-competitive inhibitor of Plasmodium falciparum aspartate transcarbamoylase
Highlights: • A novel inhibitor of the malarial ATC is described. • X-ray data show that it binds close to the active site. • Kinetic analysis of the mode of inhibition is presented. • An allosteric mechanism of inhibition is proposed. • An initial structure activity relationship is described. Aspartate transcarbamoylase catalyzes the second step of de-novo pyrimidine biosynthesis. As malarial parasites lack pyrimidine salvage machinery and rely on de-novo production for growth and proliferation, this pathway is a target for drug discovery. Previously, an apo crystal structure of aspartate transcarbamoylase from Plasmodium falciparum (PfATC) in its T-state has been reported. Here we present crystal structures of PfATC in the liganded R-state as well as in complex with the novel inhibitor, 2,3-napthalenediol, identified by high-throughput screening. Our data shows that 2,3-napthalediol binds in close proximity to the active site, implying an allosteric mechanism of inhibition. Furthermore, we report biophysical characterization of 2,3-napthalenediol. These data provide a promising starting point for structure based drug design targeting PfATC and malarial de-novo pyrimidine biosynthesis.
Synthesis and structural characterization of different topological coordination polymers based on tunable Cu{sub 4}Br{sub 4-m}I{sub m} secondary building units and macrocyclic azacalixaromatics
The coordination self-assembly between the macrocyclic ligand tetraazacalix[4]pyrimidine (TAPM) with cubane-like copper halides (Cu{sub 4}X{sub 4}) produced five coordination polymers 1-5 {l_brace}Cu{sub 4}Br{sub 4-m}I{sub m}(TAPM){r_brace}{sub n} (m=0 (1), 1 (2), 2 (3), 3 (4) and 4 (5)). X-ray single crystal analysis revealed that the Br:I ratio in the Cu{sub 4}X{sub 4} cores serves as a controlling factor to fine-tune the geometries of Cu{sub 4}X{sub 4} and therefore induce the conformation variation of tetraazacalix[4]pyrimidine. Consequently, two different topological nets, dia and lcs, were successfully constructed based on tetrahedrally coordinated Cu{sub 4}X{sub 4} secondary building units and the flexible macrocyclic quadridentate ligand TAPM. The structure details of 1-5 as porous materials are analyzed, which shows a solvent accessible volume within the range of 27-35%. Compounds 1-5 exhibit luminescence properties with the peak maximum at around 476-488 nm. -- Graphical Abstract: Five luminescent coordination polymers 1-5 were obtained via the reaction of tetrahedral Cu{sub 4}Br{sub 4-m}I{sub m} SBUs and a flexible macrocyclic ligand tetraazacalix[4] pyrimidine (TAPM), wherein the Br/I ratio serves as a controlling factor to fine-tune the geometries of Cu{sub 4}Br{sub 4-m}I{sub m} and induce the conformation variation of TAPM, thus constructing two different dia and lcs topological nets. Display Omitted Research highlights: > The ratio of Br/I in the Cu{sub 4}X{sub 4} cores fine-tunes the geometries of Cu{sub 4}X{sub 4}. > Variation of Cu{sub 4}X{sub 4} induces the conformation change of the ligand TAPM. > Two different coordination polymeric structures were successfully constructed. > The five coordination polymers show good luminescent properties.