Dual-purpose sample trap for on-line strong cation-exchange chromatography/reversed-phase liquid chromatography/tandem mass spectrometry for shotgun proteomics. Application to the human Jurkat T-cell proteome

A dual-purpose sample-trapping column is introduced for the capacity enhancement of proteome analysis in on-line two-dimensional nanoflow liquid chromatography (strong cation-exchange chromatography followed by reversed-phase liquid chromatography) and tandem mass spectrometry. A home-made dual trap is prepared by sequentially packing C18 reversed-phase (RP) particles and SCX resin in a silica capillary tubing (1.5 cm x 200 microm I.D. for SCX, 0.7 cm x 200 microm for RP) ended with a home-made frit and is connected to a nanoflow column having a pulled tip treated with an end frit. Without having a separate fraction collection and concentration process, digested peptide mixtures were loaded directly in the SCX part of the dual trap, and the SCX separation of peptides was performed with a salt step elution initiated by injecting only 8 microL of NH4HCO3 solution from the autosampler to the dual trap. The fractionated peptides at each salt step were directly transferred to the RP trap packed right next to the SCX part for desalting, and a nanoflow LC-MS-MS run was followed. During the sample loading-SCX fractionation-desalting, flow direction was set to bypass the analytical column to prevent contamination. The entire 2D-LC separation and MS-MS analysis were automated. Evaluation of the technique was made with an injection of 15 microg peptide mixtures from human Jurkat T-cell proteome, and the total seven salt step cycles followed by each RPLC run resulted in an identification of 681 proteins.     

High-Throughput Analysis of Sofalcone in Human Plasma by Use of Automated 96-Well Protein Precipitation and LC-MS-MS

A sensitive and selective method for the determination of sofalcone in human plasma was established by use of protein precipitation and liquid chromatography-tandem mass spectrometry. Plasma samples were transferred into 96-well plate using an automated sample handling system and spiked with 10 L of 2 g mL^–1 internal standard solution (d₃-sofalcone). 0.5 mL of acetonitrile was added to the 96-well plate and the plasma samples were then vortexed for 30 sec. After centrifugation, the supernatant was transferred into another 96-well plate and completely evaporated at 40 °C under a stream of nitrogen. The dry residue was reconstituted with mobile phase. All sample transfer and protein precipitation was automated through the application of both the PerkinElmer MultiPROBE II HT and TOMTEC Quadra 96 workstation. The limit of quantitation of sofalcone was 2 ng mL^–1 using a sample volume of 0.2 mL for the analysis. The reproducibility of the method was evaluated by analyzing five samples at nine quality control (QC) levels over the nominal concentration range from 2 ng mL^–1 to 1000 ng mL^–1. Validation of the method showed that the assay has good precision and accuracy. Sofalcone and internal standard produced a protonated precursor ion ([M+H]⁺) at m/z 451 and 454, and both gave a corresponding product ion at m/z 315. The high sample throughput of the method has been successfully applied to a pharmacokinetic study of sofalcone in human plasma.     

RELATIVE REACTIVITIES OF THE EXCITED STATES OF FUROCOUMARINS FOR [2+2] PHOTOCYCLOADDITION REACTION WITH TETRAMETHYLETHYLENE

Abstract— The Stern-Volmer constants for fluorescence quenching by tetramethylethylene decrease in the order DMC ≫ DHP > F-2 > 8-MOP. The same order was observed for the quantum yields of [2+2] cycloaddition reaction with tetramethylethylene on direct irradiation. In [2+2] photocycloaddition of F-2 with tetramethylethylene in ethanol, the ratio of quantum yields deduced from singlet and triplet states of F-2; φ₃⁰/φ₁⁰, is about 5. The excited triplet state is the reactive state for the [2+2] photocycloaddition of F-2 with tetramethylethylene in solution but the excited singlet state of F-2 becomes very important in biological conditions.     

Determination of Glimepiride in Human Plasma by LC-MS-MS and Comparison of Sample Preparation Methods for Glimepiride

A sensitive and selective method for quantitation of glimepiride in human plasma was established using liquid chromatography-electrospray ionization tandem mass spectrometry. Three different methods for the sample preparation of glimepiride and an internal standard were investigated (liquid-liquid extraction, solid-phase extraction and protein precipitation). Glipizide was used as an internal standard. Compounds were separated on a C₁₈ column with 80% acetonitrile and 20% deionized water (adjusted to pH 3.5 with acetic acid), as mobile phase at a flow rate of 200 L min^–1. By use of multiple reaction monitoring mode in MS-MS with liquid-liquid extraction and solid-phase extraction, glimepiride and glipizide were detected without severe interference from the human plasma matrix. Glimepiride produced a protonated precursor ion ([M+H]⁺) at m/z 491 and a corresponding product ion at m/z 352, and the internal standard produced a protonated precursor ion ([M+H]⁺) at m/z 446 and a corresponding product ion at m/z 321. The limit of quantitation was 0.1 ng mL^–1, 0.5 ng mL^–1 and 1.0 ng mL^–1 when using liquid-liquid extraction, solid-phase extraction and protein precipitation, respectively. The validation, reproducibility, stability, and recovery of the different sample preparation methods were comparable and all the methods gave reliable results. The method has been successfully applied to pharmacokinetic study of glimepiride in human plasma.     

Efficient chemoselective deprotection of silyl ethers using catalytic 1-chloroethyl chloroformate in methanol

Fast and chemoselective desilylation of silyl-protected alcohols was achieved using a catalytic amount of 1-chloroethyl chloroformate in methanol. With a minimal amount of 1-chloroethyl chloroformate as the source for anhydrous HCl, extremely efficient cleavage of silyl ethers of primary and secondary alcohols was accomplished, and chemoselective deprotection of one silyl ether in the presence of another silyl or other acid-labile group was possible through controlling the amount of the chloroformate and reaction time.     

Ruthenium‐catalyzed formal alkyl group transfer: Synthesis of quinolines from nitroarenes and alkylammonium halides

Nitroarenes are reductively cyclized with an array of tetraalkylammonium halides and trialkylarnmonium chlorides in the presence of a catalytic amount of a ruthenium catalyst along with tin(II) chloride dihydrate at 180° to afford the corresponding quinolines in moderate to good yields. The addition of tin(II) chloride dihydrate is necessary for the effective formation of quinolines and toluene is the solvent of choice. A reaction pathway involving initial reduction of nitroarenes to anilines and conversion of alkylammonium halides to alkylamines, alkyl group transfer from alkylamines to anilines to form an imine, dimerization of imine, and heteroannulation is proposed for this catalytic process.     

Two organometallic fragments inclusioned in a 1,3-alternate calix[4]arene tetraphosphane: evidence for transition metal-arene interaction through the cavity

The preparation of an 1,3-alternate calix[4]arene tetraphosphane ligand, 25,26,27,28-tetrakis{2-(diphenylphosphino)ethoxy}calix[4]arene (4), is described. Ligand 4 is obtained in four steps in 17% overall yield. Reaction of 4 with AgBF4 produced the encapsulated two silver complex [Ag2{(P,P,P,P)-tetraphencalix[4]arene}](BF4)2. The solid-state structure shows that the encapsulated silver undergoes a substantial pi-interaction by two opposite arene rings. Rhodation of 4 employing [Rh(cot)2]BF4 yielded the encapsulated complex with a bent coordination mode. Two organometallic fragments inclusioned inside a 1,3-alternate calix[4]arene tetraphosphane was also achieved by the reaction of 4 with [PtH(PPh3)2 (thf)]+. Full characterization includes X-ray structural studies of compounds 4-6.     

Electronic structure and field emission of multiwalled carbon nanotubes depending on growth temperature

The electronic structure of multiwalled carbon nanotubes (CNTs) has been investigated, depending on the growth temperature, using synchrotron X-ray photoelectron spectroscopy (XPS) and field emission measurements. The vertically aligned CNTs are grown via pyrolysis of ferrocene and acetylene in a broad temperature range 600-1000 degrees C. The CNTs have a cylindrical structure with a uniform diameter of 20 nm. As growth temperature increases, due to an improved crystallinity of the graphitic sheets, the width of the XPS C 1s peak becomes narrower and the intensity of the valence band increases. Field emission from the as-grown CNTs exhibits a large enhancement of current density with growth temperature, strongly correlated with the electronic structure revealed by XPS.     

Scaffold-based molecular design with a graph generative model

Searching for new molecules in areas like drug discovery often starts from the core structures of known molecules. Such a method has called for a strategy of designing derivative compounds retaining a particular scaffold as a substructure. On this account, our present work proposes a graph generative model that targets its use in scaffold-based molecular design. Our model accepts a molecular scaffold as input and extends it by sequentially adding atoms and bonds. The generated molecules are then guaranteed to contain the scaffold with certainty, and their properties can be controlled by conditioning the generation process on desired properties. The learned rule of extending molecules can well generalize to arbitrary kinds of scaffolds, including those unseen during learning. In the conditional generation of molecules, our model can simultaneously control multiple chemical properties despite the search space constrained by fixing the substructure. As a demonstration, we applied our model to designing inhibitors of the epidermal growth factor receptor and show that our model can employ a simple semi-supervised extension to broaden its applicability to situations where only a small amount of data is available.

We propose a scaffold-based graph generative model for designing novel drug candidates that include the desired scaffold as a substructure.