A comparative molecular field analysis (CoMFA) study using semiempirical, density functional, ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands

The Comparative Molecular Field Analysis (CoMFA) was developed to investigate a three-dimensional quantitative structure activity relationship (3D-QSAR) model of ligands for the sigma 1 receptor. The starting geometry of sigma-1 receptor ligands was obtained from the Tripos force field minimizations and conformations were decided from DISCOtech using the SYBYL 6.8. program. The structures of 48 molecules were fully optimized at the ab initio HF/3-21G* and semiempirical AM1 calculations using GAUSSIAN 98. The electrostatic charges were calculated using several methods such as semiempirical AM1, density functional B3LYP/3-21G*, and ab initio HF/3-21G*, MP2/3-21G* calculations within GAUSSIAN 98. Using the optimized geometries, the CoMFA results derived from the HF/3-21G method were better than those from AM1. The best CoMFA was obtained from HF/3-21G* optimized geometry and charges (R2 = 0.977). Using the optimized geometries, the CoMFA results derived from the HF/3-21G methods were better than those from AM1 calculations. The training set of 43 molecules gave higher R2 (0.989-0.977) from HF/3-21G* optimized geometries than R2 (0.966-0.911) values from AM1 optimized geometries. The test set of five molecules also suggested that HF/3-21G* optimized geometries produced good CoMFA models to predict bioactivity of sigma 1 receptor ligands but AM1 optimized geometries failed to predict reasonable bioactivity of sigma 1 receptor ligands using different calculations for atomic charges.     

Mass analyzed threshold ionization spectroscopy of 7-azaindole cation

The vibrationally resolved mass analyzed threshold ionization (MATI) spectra of jet-cooled 7-azaindole have been recorded by ionizing via four different intermediate levels. The adiabatic ionization energy of this molecule is determined to be 65 462±5 cm⁻¹, which is greater than that of indole by 2871 cm⁻¹. The vibrational spectra of 7-azaindole in the S₁ and D₀ states have been successfully assigned by comparing the measured frequencies with those of indole as well as the predicted values from the ab initio calculations. Detailed analysis on the MATI spectra shows that the structure of the cation is somewhat different from that of this species in the neutral S₁ state.     

Effect of particle size in preparative reversed-phase high-performance liquid chromatography on the isolation of epigallocatechin gallate from Korean green tea

To isolate epigallocatechin gallate (EGCG) of catechin compounds from Korean green tea (Bosung, Chonnam), a C18 reversed-phase preparative column (250x22 mm) packed with packings of three different sizes (15, 40-63, and 150 microm) was used. The sample extracted with water was partitioned with chloroform and ethyl acetate to remove the impurities including caffeine. The mobile phases in this experiment were composed of 0.1% acetic acid in water, acetonitrile, methanol and ethyl acetate. The injection volume was fixed at 400 microl and the flow rate was increased as the particle size becomes larger. The isolation of EGCG with particle size was compared at a preparative scale and the feasibility of separation of EGCG at larger particle sizes was confirmed. The optimum mobile phase composition for separating EGCG was experimentally obtained at the particle sizes of 15 and 40-63 microm in the isocratic mode, but EGCG was not purely separated at the particle size of 150 microm.     

Effective isolation of magnesium lithospermate B and its inhibition of aldose reductase and fibronectin on mesangial cell line

We developed an effective isolation method of magnesium lithospermate B from Salviae miltiorrhizae Radix and found for the first time that magnesium lithospermate B shows strong in vitro inhibition (IC50=0.04 microM) of aldose reductase (AR), 2.5 times than that of clinically used epalrestat (IC50=0.1 microM) and accumulation of fibronectin dose dependently.     

Decarbopalladation of pi-allylpalladium intermediates formed from palladium-catalyzed arylations of 3-allen-1-ols

[reaction: see text] Unusual palladium-catalyzed arylative fragmentations of acyclic 3-allen-1-ols were observed. Oxidative addition of Pd(0) to aryl halides would form the arylpalladium halides, which added to the central carbon of allenes via carbopalladation to form the pi-allylpalladium intermediates. The pi-allylpalladium intermediates would be reductively eliminated via carbon-carbon cleavage to give the arylated dienes and the alpha-hydroxyalkylpalladium intermediates, which were further reductively eliminated to the corresponding aldehydes.     

Isolation of rice allergenic cDNA clones from a rice cDNA library by immunoscreening with a polyclonal antibody specific to 16 kD rice allergenic protein

Clinical cases of type-1 hypersensitive reaction to rice (Oryza sativa) have been reported in western countries as well as in Japan. Among rice proteins, 14-16 kD globulin proteins encoded by multiple gene family have been identified as major rice allergens. In this study, a rice cDNA library was constructed using lambda UniZap vector and screened with a rat anti-16 kD globulin protein polyclonal antibody in order to isolate Korean rice allergenic cDNA clones. Five independent cDNA clones, termed RAK1-5, were obtained after second rounds of plaque assay and immunoblot analysis. These clones encoded 13-19 kD recombinant proteins upon IPTG induction, which were identified by the polyclonal antibody in immunoblot analysis. DNA sequencing analysis showed that RAK1-4 have 99% sequence homology with RA5b, and RAK5 is closely related with RA14c. This result indicated that RA5b gene is widely distributed in our cDNA library among other possible rice allergenic genes, and more study is needed to isolate heterogeneous or novel rice allergen genes.     

Folding and unfolding kinetics of DNA hairpins in flowing solution by multiparameter fluorescence correlation spectroscopy

Dynamic equilibrium between the folded and unfolded conformations of single stranded DNA hairpin molecules containing polythymine hairpin loops was investigated using simultaneous two-beam fluorescence cross-correlation spectroscopy and single beam autocorrelation spectroscopy. The hairpins were end-labeled with a fluorescent dye and a quencher, such that folding and unfolding of the DNA hairpin primary structure caused the dye fluorescence to fluctuate on the same characteristic time scale as the folding and unfolding reaction. These fluctuations were observed as the molecules flowed sequentially between two spatially offset, microscopic detection volumes. Cross-correlation analysis of fluorescence from the two detection volumes revealed the translational diffusion and flow properties of the hairpins, as well as the average molecular occupancy of the two volumes. Autocorrelation analysis of the fluorescence from the individual detection volumes revealed the kinetics of hairpin folding and unfolding, with the parameters relating to diffusion, flow, and molecular occupancy constrained to the values determined from the cross-correlation analysis. This allowed unambiguous characterization of the folding and unfolding kinetics, without the need to determine the hydrodynamic properties by analyzing a separate control sample. The analysis revealed nonexponential relaxation kinetics and DNA size-dependent folding times characteristic of dynamic heterogeneity in the DNA hairpin-forming mechanism.     

Polymerizable benzophenone derivatives for labeling vinyl acetate‐butylacrylate latex particles

We describe the synthesis and characterization of three new polymerizable benzophenone derivatives [2‐acryloxy‐5‐methyl benzophenone ( 8 ), 4′‐dimethylamino‐2‐acryloxy‐5‐methyl benzophenone ( 9 ), and 4′‐dimethylamino‐2‐(β‐acryloxyethyl)oxy‐5‐methyl benzophenone ( 10 )]. We show that these monomers can successfully be incorporated into vinyl acetate (VAc) copolymer latex particles. These particles were prepared by semicontinuous emulsion polymerization and mini‐emulsion polymerization of VAc with butylacrylate (BA) for VAc/BA = 4/1 by weight. The two monomers 9 and 10 bearing the 4′‐dimethylamino group satisfy the important spectroscopic criteria required of a dye to serve as an acceptor chromophore for nonradiative energy transfer from phenanthrene (Phe) as the donor. Their UV absorption spectra suggest significant overlap with the emission spectrum of Phe, which can be incorporated into P(VAc‐co‐BA) latex through copolymerization with 9‐acryloxymethyl Phe ( 2 ). In addition, these chromophores provide a window in their absorption spectra for excitation of the Phe chromophore at 300 nm. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 3001–3011, 2002     

Four New Lariciresinol‐Based Lignan Glycosides from the Roots of Rhus javanica var. roxburghiana

The four new lariciresinol‐based lignan glycosides, (?)‐lariciresinol 4′‐(6″‐O‐feruloyl‐β‐D ‐glucopyranoside) ( 1 ), (?)‐lariciresinol 4′‐(4″,6″‐di‐O‐feruloyl‐β‐D ‐glucopyranoside) ( 2 ), 5,5′‐dimethoxylariciresinol 4′‐(4″,6″‐di‐O‐feruloyl)‐β‐D ‐glucopyranoside) ( 3 ), and 4‐O‐[α‐(1,2‐dihydroxyethyl)syringyl]‐5,5′‐dimethoxylariciresinol 4′‐(4″,6″‐di‐O‐feruloyl‐β‐D ‐glucopyranoside) ( 4 ), together with two known ones, lariciresinol 4′‐β‐D ‐glucopyranoside) ( 5 ) and tortoside B ( 6 ), were isolated from the BuOH extract of Rhus javanica var. roxburghiana roots, and their structures were established by means of various spectroscopic techniques.