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PubMed2006

High-throughput screening, metabolomics and drug discovery.

The science of metabolomics has the potential to deliver wide-reaching benefits to the currently embattled pharmaceutical industry. Current applications for this field center around toxicological profiling and biomarker studies; however, the ability of metabolomics to quantitatively assess pharmacologically induced changes in biological systems at the phenotype level suggests that there would be value in its adoption at much earlier phases of the drug-discovery process. As is argued herein, this approach could be coupled with a re-organization of early drug-discovery paradigms to reduce both the rates of attrition and the costs of bringing a drug to market.

Animals↗
PubMed2006

Comparison of allele specific oligonucleotide-polymerase chain reaction and direct sequencing for high throughput screening of ABL kinase domain mutations in chronic myeloid leukemia resistant to imatinib.

To identify a fast and sensitive method for screening for mutations in patients with imatinib- resistant chronic myeloid leukemia (CML), we compared allele specific oligonucleotide- polymerase chain reaction (ASO-PCR) assay with conventional direct sequencing. Among the 68 imatinib resistant CML patients studied, 18 amino acid substitutions were detected in 44 patients by two assays. The sensitivity of ASO-PCR was superior to that of direct sequencing as it could detect one mutant allele in 100 approximately 100,000 wild type sequences. The fastness, simplicity, and sensitivity of ASO-PCR assays will be useful for routine monitoring of mutations, especially for frequently identified mutations.

Alleles↗
PubMed2006

[High throughput screening and analysis of prostate cancer-related genes through mining databases].

BACKGROUND & OBJECTIVE: Investigation of differentially expressed genes in prostate cancer tissues may help to understand the molecular mechanism of prostate cancer and provide diagnostic markers or new targets for therapy. The Cancer Genome Anatomy Project (CGAP) public database provides an unprecedented opportunity for cancer researchers to mine genes differentially expressed in cancer tissues by bioinformatic methods. This study was to explore the feasibility of incorporating the Internet-available Serial Analysis of Gene Expression (SAGE) and cDNA databases to find human prostate cancer-related genes. METHODS: SAGE digital gene expression displayer (DGED) and cDNA DGED were used to analyze differentially expressed (>5 folds) genes in malignant prostate tissues compared with normal prostate tissues. The SAGE tags were filtered by their confidence and our 3 criteria. To test the confidence of tags of virtual digital analysis for gene identification, the modified GLGI (generation of longer cDNA fragments from SAGE tags for gene identification) was used to get the cDNA 3' end downstream of 20 tags. Main functions of all candidate genes and their relations to prostate cancer were annotated. RESULTS: Fifty-three differentially expressed genes were screened out by SAGE DGED, 26 of them were up-regulated and 27 were down-regulated in prostate cancer; 28 differentially expressed genes were got by cDNA DGED, 15 of them were up-regulated and 13 were down-regulated in prostate cancer. CONCLUSION: Reasonable use of public databases by the Internet-available tools is a simple, effective approach to get cancer-related genes, and might provide useful clues for further investigation although the results require experimental validation.

DNA, Complementary↗
PubMed2006

Robust regression for high throughput drug screening.

Effective analysis of high throughput screening (HTS) data requires automation of dose-response curve fitting for large numbers of datasets. Datasets with outliers are not handled well by standard non-linear least squares methods, and manual outlier removal after visual inspection is tedious and potentially biased. We propose robust non-linear regression via M-estimation as a statistical technique for automated implementation. The approach of finding M-estimates by Iteratively Reweighted Least Squares (IRLS) and the resulting optimization problem are described. Initial parameter estimates for iterative methods are important, so self-starting methods for our model are presented. We outline the software implementation, done in Matlab and deployed as an Excel application via the Matlab Excel Builder Toolkit. Results of M-estimation are compared with least squares estimates before and after manual editing.

Algorithms↗
PubMed2003

Rapid assays for quantitating cytokine gene expression without target amplification.

Many drug discovery efforts are focused on finding candidates that alter gene expression of the cytokines involved in inflammation, allergy, and cell-mediated immunity. Current methods used to evaluate gene expression such as northern blot and RT-PCR are laborious, time-consuming, expensive, and are not conducive to high throughput screening. High Performance Signal Amplification (HPSA( trade mark )) gene expression assays quantitate mRNA targets directly from cell lysate samples using DNA probe hybridization and fluorescent signal amplification. The assay format eliminates the need for RNA purification prior to testing and does not involve target amplification. The 96 or 384-well microplate formats allow the method to be run manually, by a workstation approach, or with full automation. Cellular mRNA levels are quantitated relative to a standard curve comprised of highly purified in vitro RNA calibrators. The analytical sensitivity is in the low attomole (10(-18) mole) range. This technique was used to monitor the transcription patterns of mRNA encoding TNF-alpha, IL-1beta, and Interferon-gamma in human cell lines or primary PBMC treated with inducers such as PMA, ionomycin, and endotoxin. The specificity, precision and reproducibility of the assay are sufficient to provide a reliable screening system. The HPSA gene expression assay system offers a rapid and convenient alternative to more cumbersome, expensive methods.

Cytokines↗
PubMed2000

A strategy for primary high throughput cytotoxicity screening in pharmaceutical toxicology.

PURPOSE: Recent advances in combinatorial chemistry and high throughput screens for pharmacologic activity have created an increasing demand for in vitro high throughput screens for toxicological evaluation in the early phases of drug discovery. METHODS: To develop a strategy for such a screen, we have conducted a data mining study of the National Cancer Institute's Developmental Therapeutics Program (DTP) cytotoxicity database. RESULTS: Using hierarchical cluster analysis, we confirmed that the different tissues of origin and individual cell lines showed differential sensitivity to compounds in the DTP Standard Agents database. Surprisingly, however, approaching the data globally, linear regression analysis showed that the differences were relatively minor. Comparison with the literature on acute toxicity in mice showed that the predictive power of growth inhibition was marginally superior to that of cell death. CONCLUSIONS: This datamining study suggests that in designing a strategy for high throughput cytotoxicity screening: a single cell line, the choice of which may not be critical, can be used as a primary screen; a single end point may be an adequate measure and a cut off value for 50% growth inhibition between 10(-6) and 10(-8) M may be a reasonable starting point for accepting a cytotoxic compound for scale up and further study.

Animals↗
PubMed2004

Development of a sensitive and HTS-compatible reporter gene assay for functional analysis of human adenosine A2a receptors in CHO-K1 cells.

Adenosine A2a receptor, a member of the G protein-coupled receptor superfamily, has been demonstrated to be an important pharmacological target. It couples to stimulatory G protein and activates adenylate cyclase upon agonist stimulation. Here we attempted to stably transfect Chinese hamster ovary (CHO-K1) cells, which lack any known subtypes of adenosine receptors, with recombinant human adenosine A2a receptors (hA2aR). Rapid down-regulation of hA2aR in a clonal cell line, CHOA2a-2, was observed over a short period of time in culture. This is consistent with other groups' findings of low expression and poor G protein coupling of this receptor in several cell systems. To facilitate pharmacological profiling for hA2aR ligand, we introduced a cyclic AMP response element (CRE)-linked beta-galactosidase reporter gene into CHOA2a-2 cells to generate a stable cell line, CHOA2a-2CREbetagal#26. Robust cyclic AMP signal amplification was obtained using a colorimetric assay measuring beta-galactosidase activity. The EC(50) of 5'-N-ethylcarboxamidoadenosine (NECA), a potent A2a agonist, for inducing beta-galactosidase activity was 23.3 +/- 3.5 nM, similar to 22.7 +/- 3.9 nM, which was the NECA EC(50) in the direct measurement of cyclic AMP of CHOA2a-2 cells in early culture. Subsequently we validated this assay for high throughput screening for hA2aR agonists. The Z' factor for robotic assay performance was 0.79 +/- 0.03, the ratio of signal/noise was 157 +/- 36, and the ratio of signal/background was 10.6 +/- 1.2, demonstrating that this assay is well suitable for quality high throughput screening. High throughput screening of Johnson & Johnson libraries uncovered a couple of distinct series of nonadenosine small molecules, in addition to adenosine analogues, as potential hA2aR agonists with EC(50) values of 2-6 microM. Preliminary characterization of those compounds was presented.

Adenosine A2 Receptor Agonists↗
PubMed1999

Functional genomics in cancer research: identification of target genes of the Epstein-Barr virus nuclear antigen 2 by subtractive cDNA cloning and high-throughput differential screening using high-density agarose gels.

In the past, the identification and isolation of phenotype-associated genes was a difficult and time-consuming task. However, recent improvements of methods that are designed to isolate differentially expressed genes have remarkably speeded up the process of target gene isolation. The ultimate goal of functional genomics is to apply these technologies to clone phenotype-associated genes irrespective of the availability of probes (e.g., antibodies) and an intimate knowledge of biological background. We demonstrate the use of a novel subtractive cDNA cloning approach for the isolation and characterization of target genes of the Epstein-Barr virus nuclear antigen 2 (EBNA2). Two different subtractive cDNA libraries specific for two different time periods following activation of a conditional estrogen receptor/EBNA2 (ER/EBNA2) fusion protein were generated. Comparison of the two libraries by cross-hybridization experiments allowed the differentiation between direct and indirect target genes of EBNA2 and led to the identification of a novel direct target gene of EBNA2.

Cloning, Molecular↗
PubMed2006

A novel tracing algorithm for high throughput imaging Screening of neuron-based assays.

High throughput neuron image processing is an important method for drug screening and quantitative neurobiological studies. The method usually includes detection of neurite structures, feature extraction, quantification, and statistical analysis. In this paper, we present a new algorithm for fast and automatic extraction of neurite structures in microscopy neuron images. The algorithm is based on novel methods for soma segmentation, seed point detection, recursive center-line detection, and 2D curve smoothing. The algorithm is fully automatic without any human interaction, and robust enough for usage on images with poor quality, such as those with low contrast or low signal-to-noise ratio. It is able to completely and accurately extract neurite segments in neuron images with highly complicated neurite structures. Robustness comes from the use of 2D smoothening techniques and the idea of center-line extraction by estimating the surrounding edges. Efficiency is achieved by processing only pixels that are close enough to the line structures, and by carefully chosen stopping conditions. These make the proposed approach suitable for demanding image processing tasks in high throughput screening of neuron-based assays. Detailed results on experimental validation of the proposed method and on its comparative performance with other proposed schemes are included.

Algorithms↗
PubMed1999

High-throughput polymorphism screening and genotyping with high-density oligonucleotide arrays.

A highly reliable and efficient technology has been developed for high-throughput DNA polymorphism screening and large-scale genotyping. Photolithographic synthesis has been used to generate miniaturized, high-density oligonucleotide arrays. Dedicated instrumentation and software have been developed for array hybridization, fluorescent detection, and data acquisition and analysis. Specific oligonucleotide probe arrays have been designed to rapidly screen human STSs, known genes and full-length cDNAs. This has led to the identification of several thousand biallelic single-nucleotide polymorphisms (SNPs). Meanwhile, a rapid and robust method has been developed for genotyping these SNPs using oligonucleotide arrays. Each allele of an SNP marker is represented on the array by a set of perfect match and mismatch probes. Prototype genotyping chips have been produced to detect 400, 600 and 3000 of these SNPs. Based on the preliminary results, using oligonucleotide arrays to genotype several thousand polymorphic loci simultaneously appears feasible.

Genetic Markers↗
PubMed2004

Screening and synthesis: high throughput technologies applied to parasitology.

High throughput technologies continue to develop in response to the challenges set by the genome projects. This article discusses how the techniques of both high throughput screening (HTS) and synthesis can influence research in parasitology. Examples of the use of targeted and phenotype-based HTS using unbiased compound collections are provided. The important issue of identifying the protein target(s) of bioactive compounds is discussed from the synthetic chemist's perspective. This article concludes by reviewing recent examples of successful target identification studies in parasitology.

Animals↗
PubMed2005

Layered peptide arrays: high-throughput antibody screening of clinical samples.

High-throughput methods to detect and quantify antibodies in sera and other patient specimens have use for many clinical and laboratory studies, including those associated with cancer detection, microbial exposures, and autoimmune diseases. We developed a new technique, termed layered peptide array (LPA), to serve as a screening tool to detect antibodies in a highly multiplexed format. We demonstrate here that a prototype LPA was capable of producing approximately 5000 measurements per experiment and appeared to be scalable to higher throughput levels. Sera and saliva from Sjögren's syndrome patients served as a test set to examine antibody titers in clinical samples. The LPA platform exhibited both a high sensitivity (100%) and high specificity (94%) for correctly identifying SSB antigen-positive samples. The multiplex capability of the platform was also confirmed when serum and saliva samples were analyzed for antibody reactivity to several peptides, including Sjögren's syndrome antigens A and B. The data indicate that LPA analysis will be a useful method for a number of screening applications.

Antibodies↗
PubMed2001

An automated fluorescent single strand conformation polymorphism technique for high throughput mutation screening.

OBJECTIVE: To develop a high throughput mutational detection method by multiple fluorescence-labeled polymerase chain reaction (PCR) products. METHODS: A total of 27 known mutations including 22 substitutions, 3 insertions (1, 2 and 7 bp) and 2 deletions (1 and 2 bp) in the hepatocyte nuclear factor (HNF)-4 alpha, glucokinase and HNF-1 alpha genes were tested. During nested PCR, amplified fragments were labeled with three fluorescent dyes. PCR products were visualized with an ABI-377 fluorescence sequencer using 5% glycerol or 10% sucrose in non-denaturing gel conditions. RESULTS: Twenty-five of 27 variants (93%) could be detected by combining 5% glycerol and 10% sucrose gel matrix conditions. Twenty-two of 27 (82%) and 18 of 27 (67%) variants were identified using 5% glycerol and 10% sucrose conditions, respectively. CONCLUSION: This fluorescence-based PCR single strand conformation polymorphism technique represents a simple, non-hazardous, time-saving and sensitive method for high throughput mutation detection.

Basic Helix-Loop-Helix Leucine Zipper Transcriptio↗
PubMed2001

Cell-based assay for high-throughput quantitative screening of CFTR chloride transport agonists.

Drug discovery by high-throughput screening is a promising approach to develop new therapies for the most common lethal genetic disease, cystic fibrosis. Because disease-causing mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) protein produce epithelial cells with reduced or absent Cl(-) permeability, the goal of screening is to identify compounds that restore cell Cl(-) transport. We have developed a rapid, quantitative screening procedure for analysis of CFTR-mediated halide transport in cells with the use of a conventional fluorescence plate reader. Doubly transfected cell lines were generated that express wild-type or mutant CFTR together with a yellow fluorescent protein (YFP)-based halide sensor. CFTR function was assayed from the time course of cell fluorescence in response to extracellular addition of 100 mM I(-) followed by forskolin, resulting in decreased YFP fluorescence due to CFTR-mediated I(-) entry. Cell lines were chosen, and conditions were optimized to minimize basal halide transport to maximize assay sensitivity. In cells cultured on 96-well plastic dishes, the assay gave reproducible halide permeabilities from well to well and could reliably detect a 2% activation of CFTR-dependent halide transport produced by low concentrations of forskolin. Applications of the assay are shown, including comparative dose-dependent CFTR activation by genistein, apigenin, 8-cyclopentyl-1,3-dipropylxanthine, IBMX, 8-methoxypsoralen, and milrinone as well as activation of alternative Cl(-) channels. The fluorescence assay and cell lines should facilitate the screening of novel CFTR activators and the characterization of alternative Cl(-) channels and transporters.

Animals↗
PubMed2006

High-throughput pKa screening and prediction amenable for ADME profiling.

Recent technological advances have made it possible for several new pK(a) assays to be used in drug screening. In this review, a critical overview is provided of current new methodologies for high-throughput screening and prediction of pK(a). Typical applications of using pK(a )constants and charge state for absorption, distribution, metabolism and excretion (ADME) profiling and quantitative structure-activity relationship modelling complements the methodological comparisons and discussions. The experimental methods discussed include high-throughput screening of pK(a) by multiplexed capillary with ultraviolet absorbance detection on a 96-capillary format instrument, capillary electrophoresis and mass spectrometry (CEMS) based on sample pooling, determination of pK(a) by pH gradient high-performance liquid chromatography, and measurement of pK(a) by a mixed-buffer liner pH gradient system. Comparisons of the different experimental assays are made with emphasis on the newly developed CEMS method. The current status and recent progress in computational approaches to pK(a) prediction are also discussed. In particular, the accuracy limits of simple fragment-based approaches as well as quantum mechanical methods are addressed. Examples of pK(a) prediction from in-house drug candidates as well as commercially available drug molecules are shown and an outline is provided for how drug discovery companies can integrate experiments with computational approaches for increased applications for ADME profiling.

Animals↗
PubMed2003

Identification of active-site inhibitors of MurG using a generalizable, high-throughput glycosyltransferase screen.

MurG is a glycosyltransferase involved in the biosynthesis of bacterial peptidoglycan. It is a potentially important antibiotic target, but no inhibitors of the enzyme have been reported. In general, inhibitors of glycosyltransferases have been difficult to design. Furthermore, no glycosyltransferase inhibitors have been identified through high-throughput screening, perhaps because appropriate screens for glycosyltransferase inhibition have not been developed. In this manuscript, we describe the development of a high-throughput screen for MurG that was used to screen a 50 000 compound library for inhibitors. The screen, which can be generalized to other glycosyltransferases, led to the identification of a family of active-site directed MurG inhibitors. The family of inhibitors contains a five-membered heterocyclic core that appears to function as a diphosphate mimic with respect to the presentation of substituents. We discuss the implications of this result and the utility of the screen for identifying inhibitors of other glycosyltransferases.

Anti-Bacterial Agents↗
PubMed2006

Development of a Drosophila seizure model for in vivo high-throughput drug screening.

An important application of model organisms in neurological research has been to identify and characterise therapeutic approaches for epilepsy, a recurrent seizure disorder that affects > 1% of the human population. Proconvulsant-treated rodent models have been widely used for antiepileptic drug discovery and development, but are not suitable for high-throughput screening. To generate a genetically tractable model that would be suitable for large-scale, high-throughput screening for antiepileptic drug candidates, we characterized a Drosophila chemical treatment model using the GABA(A) receptor antagonist picrotoxin. This proconvulsant, delivered to Drosophila larvae via simple feeding methods suitable for automated screening, generated robust generalised seizures with lethality occurring at doses between 0.3 and 0.5 mg/mL. Electrophysiological analysis of CNS motor neuron output in picrotoxin-treated larvae revealed generalised seizures within minutes of drug exposure. At subthreshold doses for seizure induction, picrotoxin produced an increased frequency of motor neuron action potential bursting, indicating that CNS GABAergic transmission regulates patterned activity. Mutants in the Drosophila Rdl GABA(A) receptor are resistant to picrotoxin, confirming that seizure induction occurs via a conserved GABA(A) receptor pathway. To validate the usefulness of this model for in vivo drug screening, we identified several classes of neuroactive antiepileptic compounds in a pilot screen, including phenytoin and nifedipine, which can rescue the seizures and lethal neurotoxicity induced by picrotoxin. The well-defined actions of picrotoxin in Drosophila and the ease with which compounds can be assayed for antiseizure activity makes this genetically tractable model attractive for high-throughput in vivo screens to identify novel anticonvulsants and seizure susceptibility loci.

Amino Acid Sequence↗