Synthesis, stereochemistry confirmation and biological activity evaluation of a constituent from Isodon excisus

A synthesis and stereochemistry confirmation of a constituent recently isolated from the whole plant Isodon excisus is reported. An enantioselective catalytic boron-mediated reduction of an α-bromoketone was utilized in the key synthetic transformation. The methodology described herein was also used for the synthesis of the natural product's enantiomer and several derivatives. In addition, the compounds were evaluated for inhibitory activity in a caspase induction assay. The natural product was found to be devoid of activity, but several derivatives had moderate inhibitory activity (EC₅₀<1 μM).     

Synthesis and Structure of MnCl2(HDpyF) (HDpyF = N,N′‐di(2‐pyridyl)formamidine): New Crystallographic Disorder and Bonding Mode of the HDpyF Ligand

The reaction of N,N′‐di(2‐pyridyl)formamidine (HDpyF) with MnCl₂‐4H₂O afforded the complex MnCl₂(HDpyF), which was characterized by X‐ray crystallography. The HDpyF ligand chelates to the Mn(II) center through the first and the third nitrogen atoms to form a six‐membered ring, leaving the second and the fourth nitrogen atoms uncoordinated. The HDpyF ligand is crystallographically disordered such that two different molecules can be solved. The neutral HDpyF ligand adopts the new s‐cis‐syn‐s‐trans conformation.     

Model Studies of DNA Photorepair: Enthalpy of Cleavage of a Pyrimidine Dimer Measured by Photothermal Beam Deflection Calorimetry

Abstract— The enzyme DNA photolyase mediates the repair of pyrimidine dimers. This repair step, a net retro [²+2] reaction, proceeds through either the cation or anion radical of the pyrimidine dimer. In order to understand how electron transfer makes the repair process possible, its energetics have been examined by photothermal beam deflection calorimetry, fluorescence quenching and quantum yield studies. The enthalpy for the cleavage reaction of cis-syn 1,3-dimethylthymine dimer itself was found to be -19 kcal/mol. In addition, from the redox potentials, the enthalpies for the cleavage reactions of the dimer cation radical and the anion radical were determined to be -19 kcal/mol and -28 kcal/mol, respectively.     

Catalytic Pyrolysis of Methane

Methane decomposition over metal oxides/SiO₂ surface was investigated. At 1400 K obtained product distribution of this decomposition varied with metal oxide used. The effectiveness of these catalysts has been discussed in terms of activity and C₂ selectivity. ThO₂/SiO₂ was found to be the most effective catalyst for the catalytic decomposition of methane. Positive catalytic effect of ThO₂/SiO₂ on the pyrolysis has also been confirmed at 1073 K. At low reaction conversions, ethane and ethylene are found as major products. Yields of ethylene and other unsaturated products are sensitively inhibited by NO impurities in the methane. A reaction mechanism has been proposed to account observed experimental results.     

Electron Paramagnetic Resonance Study of Radical Pairs and Isolated Radicals Trapped in Irradiated Long-Chain Hydrocarbons at Low Temperatures

The intrinsic characteristics of radical pairs produced in squalane and in cetane receiving high gamma-dose are extensively studied with the EPR technique at temperatures from 77°K up to 150°K. The spectra of the paired radicals occur at g=4 with a very low transition probability in contrast to that of isolated radicals which appear at g=2 A well-resolved hyperfine spectrum corresponding to the species (CH₃CH₂.CH₂CH₃) is observed in cetane. The isothermal decay rates of radical pairs in cetane below 100°K are significantly slow; however, the decay kinetics at 150°K is first order with rate constant=1.86 min^?1. A relatively slower decay rate is obtained for isolated radicals suggesting that the decay mechanism of paired radicals is through geminate recombination. The relative inter-radical distance in radical pairs is known from a decay curve as a function of temperature. The yields of radical pairs are low in both matrices, only few percents of those of isolated radicals. The formation mechanisms of paired radicals with direct radiolytic bond scission process are discussed in connection with the experimental observations.     

Determination of unbound cefamandole in rat blood by microdialysis and microbore liquid chromatography

To analyze unbound cefamandole in rat blood, a method combing microdialysis with microbore liquid chromatography has been developed. A microdialysis probe was inserted into the jugular vein/right atrium of male Sprague-Dawley rats to examine the unbound cefamandole level in the rat blood following cefamandole administration (50 mg/kg, i.v.). The dialysates were directly submitted to a liquid chromatographic system. Samples were eluted with a mobile phase containing acetonitrile-methanol-100 mM monosodium phosphate (pH 5.0; 15:20:65, v/v). The UV wavelength was set at 270 nm for monitoring the analyte. Using the retrograde method, at infusion concentrations of 1 microg/mL of cefamandole, the in vivo microdialysis recoveries were 55.44% for the rat blood (n = 6). Intra- and inter-assay accuracy and precision of the analyses were < or = 10% in the range of 0.1-10 microg/mL. Pharmacokinetic parameters were calculated from the recovery-corrected dialysate concentrations of cefamandole vs time data. The elimination half-life (t1/2,beta) was 21.6 +/- 1.6 min. The results suggest that the pharmacokinetics of unbound cefamandole in blood following cefamandole administration (50 mg/kg, i.v., n = 5) fit best to the two-compartmental model.     

A sensitive and specific method for the determination of total ribavirin in human red blood cells by liquid chromatography-tandem mass spectrometry

A sensitive and specific method using high-performance liquid chromatography (LC)-tandem mass spectrometry (MS) for the analysis of total ribavirin in human red blood cells (RBC) is developed and validated. The method involves the addition of an internal standard and perchloric acid, the conversion of ribavirin phosphorylated metabolites to ribavirin, purification with a solid-phase exchange cartridge, and LC-MS-MS analysis. The MS-MS is selected to monitor m/z 245-113 for ribavirin and m/z 250-113 for [13C]ribavirin using positive electrospray ionization. The calibration curve is linear over a concentration of 100-10,000 ng/mL with a limit of quantitation of 100 ng/mL. Mean interassay accuracy for quality control (QC) at 100, 1000, and 10,000 ng/mL are 101.8%, 99.4%, and 98.8%, respectively. Mean interassay precision (%CV) for QC at 100, 1000, and 10,000 ng/mL are 5.0%, 5.0%, and 2.5%, respectively. Extractibility of total ribavirin from RBC is confirmed with RBC obtained from a [(14)C]ribavirin-dosed monkey. The method is used to determine the free and total ribavirin concentration in human RBC obtained from hepatitis C patients treated with ribavirin.     

The influences of solid-phase organic constituents on the partition of aliphatic and aromatic organic contaminants

The influence of natural organic matter (NOM) constituents on contaminant distribution coefficients was evaluated by determining the Koc values of aromatic and aliphatic organic compounds (solutes) with clays modified with both aromatic- and aliphatic-rich organic constituents. The studied compounds consisted of naphthalene, phenanthrene, n-pentane, and 2,3,4-trimethylmethane; the solid samples comprised two clays with little organic content, kaolinite and Ca-montmorillonite. Two aliphatic surfactants and three aromatic dyes, sorbed to the clays, served as reference NOM constituents. For solutes of comparable water solubilities, the organic-carbon normalized distribution coefficients (Koc) of the aliphatic solutes between sorbed aliphatic organic matter and aqueous solution slightly exceed those of the aromatic solutes. By contrast, the aromatic solutes exhibited higher Koc values than did the aliphatic compounds with sorbed aromatic-rich organic matter. The difference in Koc values could be attributed to either comparable solubility parameters or the difference in the chemical structure between nonionic organic solutes and specific components of the simulated NOM. The much higher Koc values observed for the aromatic solutes indicate that the NOM composition is a major factor determining the NOC environmental distribution.     

Protein family classification and functional annotation

With the accelerated accumulation of genomic sequence data, there is a pressing need to develop computational methods and advanced bioinformatics infrastructure for reliable and large-scale protein annotation and biological knowledge discovery. The Protein Information Resource (PIR) provides an integrated public resource of protein informatics to support genomic and proteomic research. PIR produces the Protein Sequence Database of functionally annotated protein sequences. The annotation problems are addressed by a classification-driven and rule-based method with evidence attribution, coupled with an integrated knowledge base system being developed. The approach allows sensitive identification, consistent and rich annotation, and systematic detection of annotation errors, as well as distinction of experimentally verified and computationally predicted features. The knowledge base consists of two new databases, sequence analysis tools, and graphical interfaces. PIR-NREF, a non-redundant reference database, provides a timely and comprehensive collection of all protein sequences, totaling more than 1,000,000 entries. iProClass, an integrated database of protein family, function, and structure information, provides extensive value-added features for about 830,000 proteins with rich links to over 50 molecular databases. This paper describes our approach to protein functional annotation with case studies and examines common identification errors. It also illustrates that data integration in PIR supports exploration of protein relationships and may reveal protein functional associations beyond sequence homology.