Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis

Cytochrome P450 (CYP) is deeply involved in the metabolism of chemicals including pharmaceuticals. Therefore, polymorphisms of this enzyme have been widely studied to avoid unfavorable side effects of drugs in chemotherapy. In this work, we performed computational analysis of the mechanism of the decrease in enzymatic activity for three typical polymorphisms in CYP 2C9 species: *2, *3, and *5. Based on the equilibrated structure obtained by molecular dynamics simulation, the volume of the binding pocket and the fluctuation of amino residues responsible for substrate holding were compared between the wild type and the three variants. Further docking simulation was carried out to evaluate the appropriateness of the binding pocket to accommodate substrate chemicals. Every polymorphic variant was suggested to be inferior to the wild type in enzymatic ability from the structural viewpoint. F‐G helices were obviously displaced outward in CYP2C9*2. Expansion of the binding pocket, especially the space near F′ helix, was remarkable in CYP2C9*3. Disappearance of the hydrogen bond between K helix and β4 loop was observed in CYP2C9*5. The reduction of catalytic activity of those variants can be explained from the deformation of the binding pocket and the consequent change in binding mode of substrate chemicals. The computational approach is effective for predicting the enzymatic activity of polymorphic variants of CYP. This prediction will be helpful for advanced drug design because calculations forecast unexpected change in drug efficacy for individuals. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Generation and development of RNA ligase ribozymes with modular architecture through "design and selection"

In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed "design and selection," new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.     

Ionic liquid salt bridge based on tributyl(2-methoxyethyl)phosphonium bis(pentafluoroethanesulfonyl)amide for stable liquid junction potentials in highly diluted aqueous electrolyte solutions

A moderately hydrophobic ionic liquid, tributyl(2-methoxyethyl)phosphonium bis(pentafluoroethanesulfonyl)amide ([TBMOEP⁺][C₂C₂N⁻]), shows a very stable liquid junction potential upon contact with an aqueous solution whose ionic strength is as low as 1 μmol dm⁻³. The stability with the maximum excursion of the potential within ±0.5 mV for 30 min is very promising for accurate determination of pH and other single ion activities potentiometrically.     

Medicinal Flowers. XXXI. Acylated oleanane-type triterpene saponins, Sasanquasaponins I-V, with antiallergic activity from the flower buds of Camellia sasanqua

The methanolic extract and its 1-butanol-soluble fraction from the flower buds of Camellia sasanqua THUNB. were found to show inhibitory activities on the release of β-hexosaminidase from rat basophile leukemia (RBL-2H3) cells. From the 1-butanol-soluble fraction, five new acylated oleanane-type triterpene saponins, sasanquasaponins I-V, were isolated together with a known saponin and their chemical structures were elucidated on the basis of chemical and physicochemical evidence. The principal saponin constituents, sasanquasaponins I-III, with an acyl group at the 22-position of the aglycon part showed the inhibitory effects on the release of β-hexosaminidase and some structure-activity relationships were reported.     

Facile synthesis of optically active oxindoles by copper-catalyzed asymmetric monotosylation of prochiral 1,3-diols

A facile synthetic method toward optically active 3,3-disubstituted oxindoles with excellent enantioselectivity was achieved using chiral copper-catalyzed desymmetrization of prochiral 1,3-diols. The monotosylated product was transformed into oxindole derivatives efficiently.     

Virtually complete E-selective alpha,beta-unsaturated ester synthesis by Hg(OTf)2-catalyzed hydration of sec-ethoxyalkynyl acetate

The reaction of alkyl-substituted sec-ethoxyalkynyl acetates with water catalyzed by Hg(OTf)2 afforded alpha,beta-unsaturated esters in excellent yield with high catalytic turnover up to 1000 times under very mild reaction conditions with virtually complete E-selectivity, superior even to that of the HWE reaction.     

Marine diterpenoids with a briarane skeleton from the Okinawan soft coral Pachyclavularia violacea

Five new briarane-type diterpenoids, pachyclavulides E (5), F (6), G (7), H (8) and I (9), were isolated from the Okinawan soft coral Pachyclavularia violacea. The structures of these compounds were elucidated based on the results of spectroscopic analysis. Compound 5 showed a weak growth-inhibitory activity in vitro toward cancer cells.     

Application to Photocatalytic H2 Production of a Whole‐Cell Reaction by Recombinant Escherichia coli Cells Expressing [FeFe]‐Hydrogenase and Maturases Genes

A photocatalytic H₂ production system using an inorganic–bio hybrid photocatalyst could contribute to the efficient utilization of solar energy, but would require the development of a new approach for preparing a H₂‐forming biocatalyst. In the present study, we constructed a recombinant strain of Escherichia coli expressing the genes encoding the [FeFe]‐hydrogenase and relevant maturases from Clostridium acetobutylicum NBRC 13948 for use as a biocatalyst. We investigated the direct application of a whole‐cell of the recombinant E. coli. The combination of TiO₂, methylviologen, and the recombinant E. coli formed H₂ under light irradiation, demonstrating that whole cells of the recombinant E. coli could be employed for photocatalytic H₂ production without any time‐consuming and costly manipulations (for example, enzyme purification). This is the first report of the direct application of a whole‐cell reaction of recombinant E. coli to photocatalytic H₂ production.     

Modification of Wide‐Band‐Gap Oxide Semiconductors with Cobalt Hydroxide Nanoclusters for Visible‐Light Water Oxidation

Cobalt‐based compounds, such as cobalt(II) hydroxide, are known to be good catalysts for water oxidation. Herein, we report that such cobalt species can also activate wide‐band‐gap semiconductors towards visible‐light water oxidation. Rutile TiO₂ powder, a well‐known wide‐band‐gap semiconductor, was capable of harvesting visible light with wavelengths of up to 850 nm, and thus catalyzed water oxidation to produce molecular oxygen, when decorated with cobalt(II) hydroxide nanoclusters. To the best of our knowledge, this system constitutes the first example that a particulate photocatalytic material that is capable of water oxidation upon excitation by visible light can also operate at such long wavelengths, even when it is based on earth‐abundant elements only.