A fully automated nanoelectrospray tandem mass spectrometric method for analysis of Caco-2 samples

Caco-2 cells offer a means to rapidly screen permeability of drug candidates, allowing pharmaceutical companies to eliminate candidates unable to cross the intestinal barrier early in the discovery process. This screening process is typically performed by conventional liquid chromatography/tandem mass spectrometry (LC/MS/MS), which can require time-consuming method development. An alternative to LC/MS/MS, automated nanoelectrospray tandem mass spectrometry (nanoESI-MS/MS), is introduced. This novel approach requires an off-line ZipTip desalting step followed by automated nanoESI-MS/MS, using the NanoMate 100 and ESI Chip. In addition to reduced method development time, automated nanoESI-MS/MS also offers no carry-over between samples, low sample consumption, and ease-of-use as compared with conventional pulled-capillary nanoelectrospray. Furthermore, the infusion system described has the potential to be high-throughput. A comparison of Caco-2 samples analyzed both by LC/MS/MS and by automated nanoESI-MS/MS is presented. The permeability and recovery data of the two compounds analyzed in this study obtained from conventional LC/MS/MS and by automated nanoESI-MS/MS were in excellent agreement.     

The development of an 18-locus Y-STR system for forensic casework

The aim of the present work was to improve the discriminatory potential, and hence the probative value, of Y-STR-based testing by extending the set of Y chromosome STR loci available for forensic casework. In accordance with the requirements of a Y chromosome multiplex analytical system developed specifically for forensic casework use, we have sought to maximize the number of loci able to be co-amplified, ensure appropriate assay sensitivity (1–2 ng of input genomic DNA), balance inter-locus signals and minimize confounding female DNA artifacts. Two Y chromosome STR systems, multiplex I (MPI) and multiplex II (MPII), have been developed which permit the robust co-amplification of 18 Y-STRs. The loci include DYS19, DYS385(a) and (b), DYS388, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS425, DYS434, DYS437, DYS438, DYS439, Y-GATA-C4, Y-GATA-A7.1 (DYS460) and Y-GATA-H4. The two multiplex systems are robust over a wide range of primer, magnesium, and DNA polymerase concentrations and perform well under a variety of cycling conditions. Complete male haplotypes can be obtained with as little as 100–250 pg of template DNA. Although a limited number of female DNA artifacts are observed in mixed stains in which the male DNA comprises 1/100 of the total, the male profile is easily discernible. Slightly modified versions of MPI and MPII demonstrate a significant reduction in female artifacts. Thus, it may not be necessary to employ a differential extraction strategy to obtain a male haplotype (or haplotypes in the case of multiple male donors) in cases of sexual assault. The potential utility of MPI and MPII for forensic casework is exemplified by their ability to dissect out the male haplotype in post-coital vaginal swabs and to determine the number of male donors in mixed semen stains.This study has emphasized the need for novel Y-STR multiplexes developed for forensic use to undergo a series of validation exercises that go beyond simply optimizing the PCR reaction conditions. Specifically, stringent performance checks on their efficacy need to be carried out using casework-type specimens in order to determine potential confounding effects from female DNA.     

Fourier transform infrared studies of alternate acid-amine Langmuir-Blodgett films with pyroelectric properties

FTIR-RAIRS and ATR techniques are shown to provide a powerful means of investigating the molecular behaviour responsible for the pyroelectric properties of organic monolayer assemblies on silicon and aluminised glass. Spectral changes, associated with either proton transfer or head group rearrangement, are well correlated with the level of pyroelectric response for two different devices. The technique promises to be extremely important for the elucidation of the microscopic properties of molecular electronic devices.     

5-Ethoxy-3-(trichloromethyl)-1,2,4-oxadiazole

5-Ethoxy-3-(trichloromethyl)-1, 2, 4-oxadiazole (V) was synthesized to elucidate the chemistry involved in the preparation of the hitherto unreported alkoxy-1, 2, 4-oxadiazoles and to determine the effect of the isosteric replacement of sulfur by oxygen on antifungal activity. Heating the “amino-oxime” tautomer II of trichloroacetamidoxime with ethyl chloroformate furnished exclusively the O-acylated product III. The trans configuration of III accounts for its resistance to cyclize under a variety of conditions, in contrast to the general behaviour of acylated amidoximes. Pyrolysis of III at 160° yielded IV which exists in the keto form. Refluxing IV with ethyl iodide in the presence of silver oxide gave an isomeric mixture which was separated by v.p.c. to give V and VI. Compound V retained 60% of the overall activity of the corresponding sulfur analog.     

Extended Hückel MO calculations of the conformation of several amino acids

The conformation of the amino acid residues, glycine, alanine, proline, and phenylalanine have been predicted from molecular orbital calculations of appropriate model compounds. Using the current main chain rotation convention (, ) the principle conformations were found to be glycine (0, 0), alanine (240, 240), proline (120, 330) and phenylalanine (30, 330). Several secondary conformations were also found for glycine. A comparison of the predicted conformations is in good agreement with experimental data on comparable residues or model compounds.Supported by National Institutes of Health Grants No. FR 5409-07 and GM 16312-01.Recipient of a Public Health Service Research Career Development Award AM 1159-01.     

Rapid synthesis of α-ketoamides using microwave irradiation-simultaneous cooling method

Microwave-assisted acyl chloride-isonitrile condensation and CaCO₃-mediated hydrolysis constitute a one-pot, 2-minute process to prepare α-ketoamides.     

A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins

Peptides bind to class II major histocompatibility complex (MHC) proteins in an extended conformation. Pockets in the peptide binding site spaced to accommodate peptide side chains at the P1, P4, P6, and P9 positions have been previously characterized and help to explain the obtained peptide binding specificity. However, two peptides differing only at P10 have significantly different binding affinities for HLA-DR1. The structure of HLA-DR1 in complex with the tighter binding peptide shows that the peptide binds in the usual polyproline type II conformation, but with the P10 residue accommodated in a shallow pocket at the end of the binding groove. HLA-DR1 variants with polymorphic residues at these positions were produced and found to exhibit different side chain specificity at the P10 position. These results define a new specificity position in HLA-DR proteins.     

Biomimetic cycloaddition approach to tropolone natural products via a tropolone ortho-quinone methide

[reaction: see text] A study toward a possible biomimetic hetero Diels-Alder reaction is reported between humulene and a novel tropolone ortho-quinone methide. A suitable tropolone ortho-quinone methide precursor has been prepared from 3-methyl-2-furoate. Heating the ortho-quinone methide precursor gave a tropolone ortho-quinone methide, which in the presence of humulene underwent a hetero Diels-Alder reaction to give a deoxy analogue of epolone B.     

Gene expression analysis for high throughput screening applications

To meet growing needs for high throughput gene expression profiling, we established a new automated high throughput TaqMan RT-PCR method for quantitative mRNA expression analysis. In this method, the Allegro( trade mark ) (Zymark) system conducts all sample tracking and liquid handling steps, and ABI PRISM 7900 HT (Applied Biosystems) is used to conduct real-time determination of the C(t) value when amplification of PCR products is first detected and accumulation of inhibitory PCR products is unlikely to occur. The ABI PRISM 7900 HT Sequence Detection System features a real-time PCR instrument with 384-well-plate compatibility and robotic loading, and continuous wavelength detection, which enables the use of multiple fluorophores in a single reaction. The Allegro System offers an assembly line approach with a modular design that allows reconfiguration of the components to accommodate variations in the assay flow. In the present study, we have established and validated a new automated High Throughput (HT) TaqMan RT-PCR- based method for quantitative mRNA expression analysis. The data demonstrate that HT-Taqman PCR is a powerful tool that can be used for measuring low concentrations of mRNA, and is highly accurate, reproducible, and amenable to high throughput analysis. Results suggest that HT-TaqMan is a reliable method for the quantification of low-expression genes and a powerful tool with HT capability for target identification/validation, structure-activity relationship (SAR) study, compound selection for efficacy studies, and biomarker identification in drug discovery and development.     

Ion spray-tandem mass spectrometry of supramolecular coordination complexes

Double-helical [M₂L₂] ⁿ⁺, triple-helical [M₂L₃] ⁿ⁺, and toroidal [M₃L₃] ⁿ⁺ (M = Cu, Co, Fe, Ni, La, Eu, Gd, Tb, or Lu) supramolecular complexes have been fully characterized by ion spray mass spectrometry (IS-MS). The IS-MS spectra from pure acetonitrile solutions reflect the nature of the cations present in solution with conservation of the charge state and allow an efficient qualitative speciation of the compounds. The mass spectrometry results can be correlated with other powerful techniques (nuclear magnetic resonance and electronic spectroscopy) for the characterization of supramolecular complexes in solution, Structural information is obtained by collision-induced dissociation, which strongly depends on the metal ions used in the supramolecular complexes and on the various connectivities and topologies of the ligands. When the ligand contains 3,5dimethoxybenzyl groups bound to the benzimidazole rings, the partial fragmentation of the complexes is associated with a decrease of the total charge of the complexes and the appearance of the characteristic fragment at m/z 151 that corresponds to the 3,5-dimethoxybenzyl cation. A detailed analysis of the fragmentation pathways of these supramolecular complexes suggests that the metal-nitrogen coordination bonds are very strong in the gas phase.