A computer program for automated data evaluation to support in vitro higher-throughput screening for drug metabolism and pharmacokinetics attributes

With the advances in analytical techniques, higher-throughput screening for drug metabolism and pharmacokinetics (DMPK) attributes has become an integral part of drug discovery. However, as the number of compounds increases, the volume of data that needs to be processed and evaluated increases exponentially. As a result, a major challenge for the analytical chemist is how to quickly process the vast amount of data so as to keep up with the throughput of the screening assay. We have developed a customized computer program for automated evaluation of the liquid chromatography/tandem mass spectrometric (LC/MS/MS) data generated from the in vitro DMPK screening assays. This program performs automatic data processing and quality control. It identifies analytical anomalies, such as low internal standard intensity and poor reproducibility of replicates. All analytical anomalies for individual compounds are summarized into an 'E-Log' in a color-coded format for reviewing. With the use of this program and other supporting software, data processing and evaluation for up to 100 compounds are accomplished in several minutes.     

Analysis of one-dimensional gels and two-dimensional Serwer-type gels on the basis of the extended Ogston model using personal computers

This report presents the stand-alone computer application ELPHOFIT, a software package for the analysis of gel electrophoretic data based on Ferguson plots. Either conventional one-dimensional gels or two-dimensional agarose gels (Serwer-type) can be evaluated. Special emphasis is on the latter gel type, which has been applied previously for the separation of DNA, intact viruses and polydisperse meningitis vaccines. ELPHOFIT is designed for Macintosh PCs and for the IBM XT, AT, PS/2 and compatibles. The program operates interactively with the user, who determines the course of evaluation. Data input is in the format of files providing values of gel electrophoretic migration distances or particle mobility (absolute or relative). Data processing involves a simultaneous least-square curve fitting algorithm (Newton-Gauss, Marquardt-Levenberg) which uses equations derived from the extended Ogston model. Functions are fit to the database by adjusting their variables, representing physical parameters of the gel and the electrophoresed particle. The program output consists of tables and graphics accompanied by an explanatory text providing the following information: (i) radius and free mobility of the electrophoresed particle, (ii) fiber radius, length and volume, mean or median pore radius of the gel, (iii) linear Ferguson plots, (iv) iso-free-mobility/iso-size nomogram for two-dimensional gels, (v) confidence ellipses, (vi) required parameters for image processing program GELFIT and (vii) goodness-of-fit and other statistical parameters, such as standard errors, dependency values, root-mean-square (RMS) error and determination coefficient. Other features of the program are (i) simulation of Serwer-type two-dimensional electrophoresis, (ii) standardization according to size, or size and free mobility, (iii) the conversion of particle radii to molecular (or particle) weight and vice versa, (iv) interconversion of DNA size specifications, i.e. the number of base pairs and the geometric mean radii, (v) computation of gel concentration for optimal resolution of two components, (vi) option to obtain a session record, (viii) option to establish a data output file containing the information of generated graphics (IBM only) and (ix) a text editing facility, e.g., for creating data files. Graphics (Macintosh version, PICT format) and text output files (both IBM and Macintosh versions, standard ASCII format) generated by ELPHOFIT are compatible with commercially available software.     

A rapid and precise computer-aided method for the spectrophotometric determination of substances in solution

The Newton—Raphson iteration method for the solution of mass-balance equations is used. Given accurate spectrophotometric data (absorbances, absorptivities) and equilibrium constants, this procedure permits rapid determination of substances in solution. The program is convenient to use and gives satisfactory results on a number of systems. The pyridoxal hydrochloride system was selected for evaluation of equilibrium constants and molar absorptivities from spectrophotometric and potentiometric data and was then used as the main test of the SPEDEAD program (SPEctrophotometric DEtermination by Absorbance Data).     

Program DEIMOS32 for gamma-ray spectra evaluation

The main features of a program for gamma-ray spectra analysis in the Windows environment are described. The program allows handling of HPGe multichannel pulse-height spectra produced by many commercial instruments. It performs the analysis using an interactive manual or automatic mode of evaluation. Results are directed to a number of different output files. The performance of the evaluation can be affected by selecting only regions with prescribed type of peaks. The calibration of the detector efficiency is included. Identification of isotopes and the calculation of their absolute activities are possible. Data can be edited in an internal text editor.     

Systematic evaluation of new chiral stationary phases for supercritical fluid chromatography using a standard racemate library

A systematic approach to the evaluation of new chiral stationary phases (CSPs) for supercritical fluid chromatography (SFC) using a standard library of racemic analytes is described. A standard library of racemic analytes representing a variety of functional group classes was assembled from a mixture of proprietary and commercial compounds. The library is dispensed and stored in a convenient 96-well microplate format to facilitate ease of use, and to minimize the amount of analyte required for analysis. Automated SFC screening was performed on both established CSPs in common use, as well as a group of six recently commercialized CSPs. Screening results were archived in a structure-searchable database that allows convenient comparison of performance data to determine which CSPs shows the best performance.     

hCB2 ligand-interaction landscape: cysteine residues critical to biarylpyrazole antagonist binding motif and receptor modulation

The human cannabinoid 2 GPCR (hCB2) is a prime therapeutic target. To define potential cysteine-related binding motifs critical to hCB2-ligand interaction, a library of hCB2 cysteine-substitution mutants and a novel, high-affinity biarylpyrazole hCB2 antagonist/inverse agonist (AM1336) functionalized to serve as a covalent affinity probe to target cysteine residues within (or in the microenvironment of) its hCB2 binding pocket were generated. The data provide direct experimental demonstration that both hCB2 TMH7 cysteines [i.e., C7.38(284) and C7.42(288)] are critical to optimal hCB2-AM1336 binding interaction and AM1336 pharmacological activity in a cell-based functional assay (cAMP formation). Elongating the AM1336 aliphatic side chain generated another novel?hCB2 inverse agonist that binds covalently and selectively to C7.42(288) only. Identification of specific cysteine residues critical to hCB2 ligand interaction and function informs the structure-based design of hCB2-targeted medicines.     

Computer reconstructed gas and liquid chromatograms

This paper describes a Lab Basic II program which allows the reconstruction of GLC-chromatograms on a Hewlett-Packard 2648A graphics terminal, starting from raw data gathered by the HP-3354A Laboratory Data System. The introduction of a considerable number of automatic parameter selections restricts user's interventions. The program can be run in terminal mode or be recalled as a post-analysis program when working in autocall mode.     

A program for the processing of analytical data (DPP)

Computer-assisted interactive data presentation and analysis facilities are needed to handle the vast amount of information produced by automated instruments. The data processing program, DPP, presented here in a FORTRAN-77 program designed to solve this problem. The program is equipped with a leading verb command language for input and job scheduling, thus providing an efficient and user-friendly operator/program interface, and with a data-base organization that accommodates a wide variety of data structures. Data presentation and analysis procedures include tabulation and plotting, regression analysis, non-linear least-squares fitting, polynomial fitting, principal component analysis, hierarchal clustering and non-hierarchal clustering. Data matrices with up to 10 000 data points, distributed over a maximum of 3000 variables and 3000 samples, can be examined. Because of the open-ended structure of the program, it is straightforward to incorporate additional data analysis procedures when they are needed. Recent applications are discussed.     

Molecular all-photonic encoder-decoder

In data processing, an encoder can compress digital information for transmission or storage, whereas a decoder recovers the information in its original form. We report a molecular triad consisting of a dithienylethene covalently linked to two fulgimide photochromes that performs as an all-photonic single-bit 4-to-2 encoder and 2-to-4 decoder. The encoder compresses the information contained in the four inputs into two outputs. The inputs are light of four different wavelengths that photoisomerize the fulgimide, dithienylethene, or both. The outputs are absorbance at two wavelengths. The two decoder inputs are excitation at two wavelengths, whereas the four outputs, which recover the information compressed into the inputs, are absorbance at two wavelengths, transmittance at one wavelength, and fluorescence emission. The molecule can be cycled through numerous encoder and decoder functions without significant photodecomposition. Molecular photonic encoders and decoders could potentially be used for labeling and tracking of nano- and microscale objects as well as for data manipulation.     

Novel method for evaluation of chemicals based on ligand-dependent recruitment of GFP labeled coactivator to estrogen receptor displayed on bacterial magnetic particles

We established a novel method to evaluate endocrine disrupting chemicals (EDCs) by assembling the estrogen receptor-ligand binding domain (ERLBD) and GFP labeled coactivator on magnetic nanoparticles. EDC can promote or inhibit coactivator recruitment to the ligand-ERLBD complex. ERLBD was displayed on the surface of nano-sized bacterial magnetic particles (BacMPs) produced by the magnetic bacterium, Magnetospirillum magneticum AMB-1. Our method resulted in 38 molecules of ERLBD molecules on a BacMPs with diameter of 75 nm. Furthermore, ligand-dependent recruitment assays of GFP labeled coactivator to ERLBD-BacMPs was performed by measuring the fluorescence intensity. 17β-estradiol (E2), estriol, diethylstilbestrol, zeralenone (full agonist), octylphenol (partial agonist) and ICI 182,780 (antagonist) were evaluated by this method. Full agonists tested showed increased fluorescence with increasing agonist concentration. Octylphenol had lower fluorescence intensity than E2. ICI 182,780 did not produce any fluorescence. The method developed in this study can evaluate the estrogenic potential of chemicals by discriminating whether they are an ER full agonist, partial agonist, or antagonist. Finally, this method is amenable adaptation into a high throughput format by using automated magnetic separation.     

Computer-aided method for simultaneous determination of substances in solution by spectrophotometry

A computer program, LESSDAD (East-Squares Spectrophotometric Determination by Absorbance Data), is described for computation of the best set of analytical concentrations of two ligands and/or metal ions from absorbance measurements. A least-squares method is used to calculate the concentrations from the pH of the solution, spectrophotometric data (experimental absorbances and known molar absorptivities) and the relevant equilibrium constants. The Newton-Raphson iteration is used to solve the mass-balance equations. The program is rapid and convenient to use and gives satisfactory results on a number of systems.     

Synthesis of N1-phenethyl substituted indole derivatives as new melatoninergic agonists and antagonists

The potency of new indolic N1-phenethyl substituted melatoninergic ligands with and without methyl groups in the alpha and beta position of the alkanamidoethyl side chain was examined using the pigment aggregation response in a clonal line of Xenopus laevis melanophores. The non 5-OMe substituted compounds, 8a--e, are all weak antagonists while introduction of the 5-OMe group, 9a--e, increases both agonist and antagonist activity except for 9c (R=C3H7), which is only an agonist and 9e (R=c-C4H7), which is only an antagonist. Introduction of an alpha-methyl group into the 5-OMe derivatives, 14a-e, reduces the agonist potency while introduction of a beta-methyl group has only a small effect on either the agonist or antagonist potency. Double beta-methyl substitution of the 5-OMe derivatives, 20a--e, generally increases the agonist potential (20c, R=C3H7 is the most potent agonist of the compounds described) and decreases the antagonist potency, except for 20a (R=CH3), which is the most potent antagonist of this series of compounds.     

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank,which uses dihedral angles as independent variables

We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein–DNA complex, a protein–tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.     

Porting a peak search program to A PC,non-linear fit testing

The University of Alberta SLOWPOKE Facility has a need for an automated peak searching program. This need was solved by porting and modifying the source code to the Nuclear Data Basic Physics package program. This paper deals specifically with the testing of the non-linear fitting part of the program, which was extensively modified.     

Development of new expanded editions of the Gamma-ray Spectrum Catalogues in electronic format

A program has been developed at the INEL to produce new enhanced editions of the original Gamma-ray Spectrum Catalogues for presentation in electronic format. This program has produced the first version of the Catalogues in CD-ROM format and will offer them on the Internet through the Gamma-ray Spectrometry Center Web Site at INEEL. The original content of the Catalogues has been expanded to include integrated decay scheme drawings, tables of related decay data, and updated material on the techniques of gamma-ray spectrometry. All of the original spectral plots, gamma-ray energy and intensity data, and text were converted to digital format, related decay data from the Evaluated Nuclear Structure Data File (ENSDF) and decay scheme graphics were then added, and all data converted to the Adobe Acrobat (PDF) format. Follow-on versions of the catalogues are being expanded to include prompt neutron capture and n-n' spectra and spectra representing the response of large-volume Ge detectors. Large-volume Ge detector spectra will be calculated, using Monte Carlo and parametric fitting techniques presently under development. Examples of content and details of the advanced technology applied to produce these new volumes will be presented. Services and content of the Gamma-ray Spectrometry Center Web Site will also be described.     

A Microtiter Plate Assay for Sulfonamides

Abstract

Sulfamethoxazole, sulfisoxazole, and sulfadiazine are sulfonamides used in the treatment of several infectious diseases. Several studies have demonstrated that the amino substituent plays an important role in both the toxicity and the therapeutic effect of these drugs. In view of these findings, a rapid and convenient method of analysis would be useful for monitoring selected patients receiving these drugs. With the increasing use of microtiter plate methodology in the clinical laboratory, an assay based upon the Bratton-Marshall reaction with the amino substituent was adapted to the microtiter plate format. The results indicate that the microtiter plate assay for sulfonamides retains the sensitivity and linearity necessary for analysis of sulfonamides in biological fluids at clinically relevant concentrations. The assay is simple, rapid, convenient, and suitable for monitoring procedures where only the measurement of the active drug concentration is required.