Examining the mechanism of action of a kinesin inhibitor using stable isotope labeled inhibitors for cross-linking (SILIC)

It is difficult to determine a chemical inhibitor's binding site in multiprotein mixtures, particularly when high-resolution structural studies are not straightforward. Building upon previous research involving photo-cross-linking and the use of mixtures of stable isotopes, we report a method, Stable Isotope Labeled Inhibitors for Cross-linking (SILIC), for mapping a small molecule inhibitor's binding site in its target protein. In SILIC, structure-activity relationship data is used to design inhibitor analogues that incorporate a photo-cross-linking group along with either natural or 'heavy' stable isotopes. An equimolar mixture of these inhibitor analogues is cross-linked to the target protein to yield a robust signature for identifying inhibitor-modified peptide fragments in complex mass spectrometry data. As a proof of concept, we applied this approach to an ATP-competitive inhibitor of kinesin-5, a widely conserved motor protein required for cell division and an anticancer drug target. This analysis, along with mutagenesis studies, suggests that the inhibitor binds at an allosteric site in the motor protein.     

New Phenylphenalene Derivatives from Water Hyacinth (Eichhornia crassipes)

Water hyacinth (Eichhornia crassipes) is a cause of great concern in terms of environmental and agricultural impacts in many parts of the world. Phytochemical investigation of water hyacinth led to the isolation of six new phenylphenalenes, 2,3‐dihydro‐3,9‐dihydroxy‐5‐methoxy‐4‐phenyl‐1H‐phenalen‐1‐one ( 1 ), 2,3‐dihydro‐8‐methoxy‐9‐phenyl‐1H‐phenalene‐1,4‐diol ( 2 ), 2,3‐dihydro‐4,8‐dimethoxy‐9‐phenyl‐1H‐phenalen‐1‐ol ( 3 ), 2,3‐dihydro‐9‐(4‐hydroxyphenyl)‐8‐methoxy‐1H‐phenalene‐1,4‐diol ( 4 ), 2,6‐dimethoxy‐9‐phenyl‐1H‐phenalen‐1‐one ( 5 ), and 7‐(4‐hydroxyphenyl)‐5,6‐dimethoxy‐1H‐phenalen‐1‐one ( 6 ), together with the four known compounds 7 – 10 . Their structures were elucidated by spectrometric methods including 1D‐ and 2D‐NMR, and MS analysis. These compounds may be involved in allelopathic interactions of water hyacinth with neighboring plants.     

Two Antioxidant Alkaloids from Portulaca oleracea L.

Two alkaloids, oleraceins F and G, were isolated from Portulaca oleracea L., and their structures were determined as methyl (2S)‐6‐[(β‐D ‐glucopyranosyl)oxy]‐2,3‐dihydro‐5‐hydroxy‐1‐[(2E)‐3‐(4‐hydroxy‐3‐methoxyphenyl)prop‐2‐enoyl]‐1H‐indole‐2‐carboxylate and methyl (2S)‐6‐[(β‐D ‐glucopyranosyl)oxy]‐2,3‐dihydro‐5‐hydroxy‐1‐[(2E)‐3‐(4‐hydroxyphenyl)prop‐2‐enoyl]‐1H‐indole‐2‐carboxylate, based on their spectroscopic data. Oleraceins F and G exhibited scavenging activity against 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) radical, with EC₅₀ values of 21.00 and 37.69 μM , respectively.     

Sesquiterpenoids from the Aerial Parts of Inula japonica

Fourteen sesquiterpenoids with an eudesmane C‐atom skeleton, including four new ones, (1β,5α,7β,8β,11β)‐5‐hydroperoxy‐1‐hydroxyeudesm‐4(15)‐eno‐12,8‐lactone ( 1 ), (1β,5α,7β,8β)‐8‐(acetyloxy)‐5‐hydroperoxy‐1‐hydroxycostic acid methyl ester ( 12 ), and a mixture of (1β,3β,4β,7β,8β)‐1,3‐dihydroxyeudesma‐5,11(13)‐dieno‐12,8‐lactone ( 7 ) and (1β,3β,4β,7β,8β,11β)‐1,3‐dihydroxyeudesm‐5‐eno‐12,8‐lactone ( 8 ), were isolated from the aerial parts of Inula japonica (Asteraceae). Their structures were determined by extensive spectroscopic methods, and those of 7 and 12 confirmed by means of single‐crystal X‐ray diffraction analysis.     

Three New Neolignans and One New Phenylpropanoid from the Leaves and Stems of Toona ciliata var. pubescens

Three new neolignans, (7S,8S,7′E)‐4,9‐dihydroxy‐3,7,3′,9′‐tetramethoxy‐8,4′‐oxyneolign‐7′‐ene ( 1 ), (7R,8S,7′E)‐4, 9‐dihydroxy‐3,7,3′,9′‐tetramethoxy‐8,4′‐oxyneolign‐7′‐ene ( 2 ), (7S,8S,7′E)‐5, 9‐dihydroxy‐3,7,3′,5′,9′‐pentamethoxy‐8,4′‐oxyneolign‐7′‐ene ( 3 ), and one new phenylpropanoid, threo‐5‐hydroxy‐3,7‐dimethoxyphenylpropane‐8,9‐diol ( 4 ), were isolated from the leaves and stems of Toona ciliata var. pubescens. Their structures were determined on the basis of spectroscopic analysis, especially 2D‐NMR, HR‐ESI‐MS, and CD data. The antiproliferative activities of these compounds against four tumor cell lines (A549, Colo 205, QGY‐7703, and LOVO) were also evaluated by MTT (=(3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl‐2H‐tetrazolium bromide) method.     

iMatch: a retention index tool for analysis of gas chromatography-mass spectrometry data

A method was developed to employ National Institute of Standards and Technology (NIST) 2008 retention index database information for molecular retention matching via constructing a set of empirical distribution functions (DFs) of the absolute retention index deviation to its mean value. The effects of different experimental parameters on the molecules' retention indices were first assessed. The column class, the column type, and the data type have significant effects on the retention index values acquired on capillary columns. However, the normal alkane retention index (I(norm)) with the ramp condition is similar to the linear retention index (I(T)), while the I(norm) with the isothermal condition is similar to the Kováts retention index (I). As for the I(norm) with the complex condition, these data should be treated as an additional group, because the mean I(norm) value of the polar column is significantly different from the I(T). Based on this analysis, nine DFs were generated from the grouped retention index data. The DF information was further implemented into a software program called iMatch. The performance of iMatch was evaluated using experimental data of a mixture of standards and metabolite extract of rat plasma with spiked-in standards. About 19% of the molecules identified by ChromaTOF were filtered out by iMatch from the identification list of electron ionization (EI) mass spectral matching, while all of the spiked-in standards were preserved. The analysis results demonstrate that using the retention index values, via constructing a set of DFs, can improve the spectral matching-based identifications by reducing a significant portion of false-positives.     

Quantitative characterization of hydroxyl radicals produced by various photocatalysts

Hydroxyl radicals ((·)OH) have been deemed to be the major active species during the photocatalytic oxidation reaction. In this study, (·)OH produced on various semiconductor photocatalysts in aqueous solution under Xenon lamp irradiation was quantitatively investigated by the photoluminescence (PL) technique using coumarin (COU) as a probe molecule. The results indicated that the formation rate of (·)OH on the surface of irradiated commercial Degussa P25 (P25) was much higher than that of other semiconductor. The pH values of the solution and phase structure of TiO(2) significantly influenced the production rate of (·)OH. The acidic pH environment of the solutions and bi-phase structure (anatase and rutile) of TiO(2) were beneficial to enhancing the formation rate of (·)OH. In addition, the formation rate of (·)OH on anatase TiO(2) and P25 was much faster than that of (·)OH on the other semiconductors (such as rutile TiO(2), ZnO, WO(3), CdS, Bi(2)WO(4) and BiOCl, etc.). A new concept "OH-index" was first proposed to compare photocatalytic activity of photocatalysts, which would provide new insight into the investigation of semiconductor photocatalysts.     

A green method for the synthesis of thiochromene derivatives in ionic liquids

Controlling the pH value by changing the negative ion of ionic liquids, the same reactions of aromatic aldehyde, 2‐(2,3‐dihydrothiochromen‐4‐ylidene) malononitrile and malononitrile product unaromatized and aromatized 6H‐benzo[c]thiochromene derivatives in high yields. The nice features of these procedures include mild reactions condition, simple operations, high yields, and environmentally benign. J. Heterocyclic Chem., (2011).     

1-D Selenidoindates {[In2Se5]}∞ directed by chiral metal complex cations of 1,10-phenanthroline

Two 1-D selenidoindates {[M(phen)(3)]In(2)Se(5)·H(2)O}(n) (M = Ni, Fe) were synthesized by a solvothermal method. The 1-D {[In(2)Se(5)](2-)}(n) anion is a new type of single 1-D structure constituted by an alternately fused four-membered In(2)Se(2) ring and five-membered In(2)Se(3) ring. The chalcogenoindates were separated as mechanical racemic mixtures of single enantiomer crystals, in which the R-helix of 1-D InSe anion is directed by the related clockwise (Δ) cations of [M(phen)(3)](2+) or the L-helix of 1-D anion is directed by the related anticlockwise (Λ) cation. The π···π, C···Se, and C-H···Se oriented interactions of metal complex cations with selenidoindate anions play an important role in the formation of the chiral crystals. The embedded [M(phen)(3)](2+) cations improve the optical absorption of the 1-D semiconductor materials.     

Protein's electronic polarization contributes significantly to its catalytic function

Ab initio quantum mechanical/molecular mechanical method is combined with the polarized protein-specific charge to study the chemical reactions catalyzed by protein enzymes. Significant improvement in the accuracy and efficiency of free-energy simulation is demonstrated by calculating the free-energy profile of the primary proton transfer reaction in triosephosphate isomerase. Quantitative agreement with experimental results is achieved. Our simulation results indicate that electronic polarization makes important contribution to enzyme catalysis by lowering the energy barrier by as much as 3 kcal/mol.