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At least 775 records · Page 43Linked to original sources
PubMed2005

A chemoinformatics analysis of hit lists obtained from high-throughput affinity-selection screening.

The high-throughput affinity-selection screening platform SpeedScreen was recently reported by the Novartis Institutes for BioMedical Research as a homogeneous, label-free screening technology with mass-spectrometry readout. SpeedScreen relies on the screening of compound mixtures with various target proteins and uses fast size-exclusion chromatography to separate target-bound from unbound substances. After disintegration of the target-binder complex, the binder molecules are identified by their molecular masses using liquid chromatography/mass spectrometry. The authors report an analysis of the molecular properties of hits obtained with SpeedScreen on 26 targets screened within the past few years at Novartis using this technology. Affinity-based SpeedScreen is a robust high-throughput screening technology that does not accumulate frequent hitters or potential covalent binders. The hits are representative of the most commonly identified scaffold classes observed for known drugs. Validated SpeedScreen hits tend to be enriched on more lipophilic and larger-molecular-weight compounds compared to the whole library. The potential for a reduced SpeedScreen screening set to be used in case only limited protein quantities are available is evaluated. Such a reduced compound set should also maximize the coverage of the high-performing regions of the chemical property and class spaces; chemoinformatics methods including genetic algorithms and divisive K-means clustering are used for this aim.

Chromatography, High Pressure Liquid↗
PubMed2002

Development of a solid-phase binding assay and identification of nonpeptide ligands for the FynB Src homology 2 domain.

The nonreceptor tyrosine kinase FynB is known to be required in the induction of long-term potentiation (LTP), a cellular mechanism for learning and memory. Ligands of the FynB SH2 domain as a possible FynB activator are, thus, of great interest. In this study, a solid-phase ligand binding assay was established to meet the screening requirement of high-throughput and ease of use, and in an attempt to find the specific ligands for the FynB SH2 domain. This assay measures the competitive inhibition of the binding of the biotinylated phosphopeptide (GGSETDDY*AEIID), derived from a binding sequence in human focal adhesion kinase, to the SH2 domain of FynB precoated as a glutathione S-transferase fusion protein on a solid-phase. Using this high-throughput screening method for SH2 ligands, a modest size of chemical library was screened, and two non-peptide compounds, 4-acetamidobenzene sulfinic acid and 1-allylpyridinium 3-sulfonate, were identified by their strong binding affinity to the FynB SH2 domain. This result demonstrates the feasibility of the developed assay in high-throughput screening. Further studies on the molecular structures of the identified SH2-binding ligands will allow presentation of specific models for ligand-domain complexes for improving the ligands and will help to develop a potential lead compound for improving LTP.

Amino Acid Sequence↗
PubMed2002

A high-throughput optical screening method for the optimization of colloidal water oxidation catalysts.

A high-throughput method has been developed for screening and optimization of colloidal water oxidation catalysts. The catalysts are irradiated in parallel by visible light from an overhead projector in solutions containing tris(2,2'-bipyridyl)ruthenium(II) (Ru(bpy)(3)(2+)) and persulfate. The array of reaction solutions is held in a 96-well plate, and absorbance readings are taken intermittently using a bioassay plate reader. The absorbance at 430 nm is indicative of the amount of Ru(bpy)(3)(2+) remaining in solution. The best catalysts give the most persistent absorbance, because the oxygen evolution reaction is kinetically competitive with decomposition of Ru(bpy)(3)(3+). Reagent concentrations were varied using a factorial design-of-experiment approach in order to optimize reaction conditions for a IrO(2).xH(2)O colloidal catalyst. A higher colloid concentration, a lower Ru(bpy)(3)(2+) concentration, and a higher pH buffer doubled the number of turnovers relative to the original conditions. Metal oxide colloids consisting of IrO(2).xH(2)O doped with varying amounts of Pt, Ru, and Os were made using a parallel microwave synthesis technique and were tested both by the parallel screening method and by direct measurement of oxygen evolution. The correlation between the two methods was good, with Ir-Pt-Os oxide compositions showing the highest activity. The effect of adding small amounts of Pt and Os to IrO(2).xH(2)O appears to be predominantly to reduce the particle size of the colloids.

Journal Article↗
PubMedDate not supplied

Development of a high throughput in vitro toxicity screen predictive of high acute in vivo toxic potential.

At an early stage of drug discovery high throughput screens are an invaluable tool to de-select compounds with undesirable properties. A high throughout in vitro toxicity screen has been developed and validated to identify compounds that have a high potential to be acutely toxic in vivo. This screen is based on treating Chinese hamster ovary (CHO) cells with test compounds for 24 h and then determining the degree of cytotoxicity by the reduction of Resazurin. Twenty-six structurally unrelated compounds were chosen that spanned a range of acute LD(50) values and mechanisms of toxicity. The acute LD(50) values (intraperitoneal and intravenous routes) from rat and mouse were taken from the RTECS database. Experimentally derived in vitro IC(35) results were compared to the 'most toxic' (lowest) LD(50) values for each compound. The resulting correlation was statistically significant (r=0.8475). However, due to the scatter of the data points, it was considered not appropriate to rank compounds according to their degree of in vivo toxicity on the basis of the in vitro result. However, by defining cut-off concentrations for both the in vivo (LD(50)) and the in vitro (IC(35)) values it was possible, using the in vitro result (IC(35) <10 microM), to identify compounds that had a high potential to be acutely toxic in vivo ('most toxic' LD(50) <25 micromol/kg). Further development led to a high throughput screen capable of giving a 'Yes', 'No' or 'Borderline' classification as to whether a compound has a high acute in vivo toxic potential. This screen is highly specific (no false positive classifications) and has a sensitivity of approximately 80%. This is deemed acceptable for a first tier toxicity screen at an early stage in the drug discovery process. Transfer of this screen from GlaxoSmithKline UK to sites in Italy, Spain and the USA resulted in very similar findings indicating the inter-laboratory robustness of this screen and therefore the ability to compare results across the GlaxoSmithKline sites.

Animal Testing Alternatives↗
PubMed2006

Application of chemical arrays in screening elastase inhibitors.

Protein chip technology provides a new and useful tool for high-throughput screening of drugs because of its high performance and low sample consumption. In order to screen elastase inhibitors on a large scale, we designed a composite microarray integrating enzyme chip containing chemical arrays on glass slides to screen for enzymatic inhibitors. The composite microarray includes an active proteinase film, screened chemical arrays distributed on the film, and substrate microarrays to demonstrate change of color. The detection principle is that elastase hydrolyzes synthetic colorless substrates and turns them into yellow products. Because yellow is difficult to detect, bromochlorophenol blue (BPB) was added into substrate solutions to facilitate the detection process. After the enzyme had catalyzed reactions for 2 h, effects of samples on enzymatic activity could be determined by detecting color change of the spots. When chemical samples inhibited enzymatic activity, substrates were blue instead of yellow products. If the enzyme retained its activity, the yellow color of the products combined with blue of BPB to make the spots green. Chromogenic differences demonstrated whether chemicals inhibited enzymatic activity or not. In this assay, 11,680 compounds were screened, and two valuable chemical hits were identified, which demonstrates that this assay is effective, sensitive and applicable for high-throughput screening (HTS).

Bromphenol Blue↗
PubMed2000

Direct plasma sample injection in multiple-component LC-MS-MS assays for high-throughput pharmacokinetic screening.

The simultaneous dosing of numerous compounds followed by multiple-component analysis using LC-MS-MS (the N-in-1 approach) has significantly improved the throughput of the drug-screening process. However, plasma samples still need to be extracted before LC-MS-MS analysis, which frequently limits the throughput of the assay. In this work, a high-throughput on-line extraction technique has been developed for multiple-component LC-MS-MS assays using a high-flow column-switching technique. In N-in-1 LC-MS-MS assays, high sensitivity is required since the dose level is generally reduced to minimize drug-drug interactions. In addition, good chromatographic separation is essential to minimize interference and suppression effects. The direct plasma sample injection method developed in this work has successfully met the two requirements for multiple-component LC-MS-MS assays in high-throughput pharmacokinetic screening. Plasma samples containing a large number of potential drug candidates were directly injected onto an extraction column operated under a flow rate sufficiently high to exhibit a turbulent-flow profile. The extracted analytes were then eluted onto an analytical column via column switching for LC-MS-MS analysis. The use of turbulent flow resulted in a faster and more rugged extraction with reduced carryover compared with results obtained under laminar-flow conditions. Meanwhile, the use of a column-switching method maintained the chromatographic resolving power and high sensitivity of the LC-MS-MS assay. Separation efficiency, dynamic range, accuracy, and precision comparable with those of solid-phase extraction have been achieved with the turbulent-flow column-switching technique. As a result, this technique has been successfully and routinely used for high-throughput pharmacokinetic screening.

Animals↗
PubMed2004

Cell-based screening: a high throughput flow cytometry platform for identification of cell-specific targeting molecules.

Targeting of drugs and genes to specific cell types is an emerging paradigm in the treatment of many medical conditions. However, targeting structures such as peptides are susceptible to rapid inactivation in vivo. To address this problem, novel targeting molecules can now be rapidly synthesized using a combinatorial approach. Methods to screen the large libraries created in this process are often lacking or compatible only with solution-based screening. This report describes a high-throughput cell-based method utilizing flow cytometry, capable of rapidly screening large libraries of molecules simultaneously for biological functionality and stability. In this method, each library molecule is attached to a microsphere exhibiting a unique set of optical properties, or "fingerprint", conferring modularity and multiplex capability. We investigated the multiplex capability of our flow cytometric method to determine its capacity for high-throughput screening. Current instrumentation in our laboratory allows the screening of at least 75 unique compounds in a single well, a number comparable to available solution-based assays. In state-of-the-art configuration, however, this methodology can support the screening of up to 1875 compounds per well, achieving high-throughput potential in a single multiwell plate. We also investigated the binding capability of targeted microspheres to adherent target cells. These microspheres exhibited a 12-fold increase in binding over control, untargeted microspheres. Competitive inhibition experiments with soluble ligand confirmed the specificity of microsphere binding. Overall, the methodology proposed here is capable of quickly and effectively screening large libraries of targeting molecules using instrumentation readily available to the greater research community.

Antibodies, Monoclonal↗
PubMed2006

Construction of a high sensitive Escherichia coli alkaline phosphatase reporter system for screening affinity peptides.

An enzyme-linker-peptide fusion protein reporter system was constructed for sensitive analysis of affinity of peptide ligands to their receptor. An E. coli alkaline phosphatase (EAP) mutant enzyme with high catalytic activity was selected as the reporter protein. Interaction of affinity peptide and streptavidin was applied as demonstration of the method. Three affinity peptides, strep-tag I (SI), strep-tag II (SII) and streptavidin binding peptide (SBP) were genetically fused to the C-terminal of EAP respectively, with an insertion of a flexible linker peptide in between. The enzyme activity of the EAP fusions showed no obvious change. After expression and purification, the EAP-affinity peptide fusions were applied to the streptavidin modified surface. Binding of the fusions to the surface through interaction of affinity peptides to streptavidin was indicated by color generated from conversion of the substrate by EAP. The relative affinity and specificity of each affinity peptides to the immobilized streptavidin were then evaluated with high sensitivity and broad detection range. This method may be used for effective high-throughput screening of high affinity peptide from the peptide pool.

Affinity Labels↗
PubMed2004

Reliable high-throughput functional screening with 3-FABS.

An NMR method called 3-FABS has extended the capabilities of NMR, enabling rapid, efficient and reliable high-throughput functional screening for the identification of inhibitors and for measuring their 50% mean inhibition concentration (IC(50)) with accuracy. The substrate is tagged with a CF(3) moiety and (19)F NMR spectroscopy is used for the detection of the substrate and product components. We provide comprehensive insight into 3-FABS, a discussion of its strength and weakness when compared with other HTS techniques and a presentation of some of its applications to the screening of different enzymes and to multiple screening.

Drug Evaluation, Preclinical↗
PubMedDate not supplied

One step screening of retroviral producer clones by real time quantitative PCR.

BACKGROUND: Recombinant retroviruses are obtained from either stably or transiently transfected retrovirus producer cells. In the case of stably producing lines, a large number of clones must be screened in order to select the one with the highest titre. The multi-step selection of high titre producing clones is time consuming and expensive. METHODS: We have taken advantage of retroviral endogenous reverse transcription to develop a quantitative PCR assay on crude supernatant from producing clones. We used Taqman PCR technology, which, by using fluorescence measurement at each cycle of amplification, allows PCR product quantification. Fluorescence results from specific degradation of a probe oligonucleotide by the Taq polymerase 3'-5' exonuclease activity. Primers and probe sequences were chosen to anneal to the viral strong stop species, which is the first DNA molecule synthesised during reverse transcription. The protocol consists of a single real time PCR, using as template filtered viral supernatant without any other pre-treatment. RESULTS: We show that the primers and probe described allow quantitation of serially diluted plasmid to as few as 15 plasmid molecules. We then test 200 GFP-expressing retroviral-producing clones either by FACS analysis of infected cells or by using the quantitative PCR. We confirm that the Taqman protocol allows the detection of virus in supernatant and selection of high titre clones. Furthermore, we can determine infectious titre by quantitative PCR on genomic DNA from infected cells, using an additional set of primers and probe to albumin to normalise for the genomic copy number. CONCLUSION: We demonstrate that real time quantitative PCR can be used as a powerful and reliable single step, high throughput screen for high titre retroviral producer clones.

Animals↗
PubMed1999

The SHAPES strategy: an NMR-based approach for lead generation in drug discovery.

BACKGROUND: Recently, it has been shown that nuclear magnetic resonance (NMR) may be used to identify ligands that bind to low molecular weight protein drug targets. Recognizing the utility of NMR as a very sensitive method for detecting binding, we have focused on developing alternative approaches that are applicable to larger molecular weight drug targets and do not require isotopic labeling. RESULTS: A new method for lead generation (SHAPES) is described that uses NMR to detect binding of a limited but diverse library of small molecules to a potential drug target. The compound scaffolds are derived from shapes most commonly found in known therapeutic agents. NMR detection of low (microM-mM) affinity binding is achieved using either differential line broadening or transferred NOE (nuclear Overhauser effect) NMR techniques. CONCLUSIONS: The SHAPES method for lead generation by NMR is useful for identifying potential lead classes of drugs early in a drug design program, and is easily integrated with other discovery tools such as virtual screening, high-throughput screening and combinatorial chemistry.

IMP Dehydrogenase↗
PubMed2006

In vivo hepatotoxicity study of rats in comparison with in vitro hepatotoxicity screening system.

For the establishment of a high throughput screening system using primary cell cultures, investigation of elucidated toxicities to assess the correlation between in vitro and in vivo hepatotoxicity is necessary in the safety evaluation of the compound. In the previous study, we reported the usability of rat primary cultured hepatocytes for establishment of high throughput screening system. To confirm the reliability of rat primary hepatocytes culture screening system, we conducted a single-dose in vivo study with relatively high dose of hepatotoxicant in rats using 4 reference compounds (acetaminophen, amiodarone, tetracycline, carbon tetrachloride), and investigated histopathological changes and expression of oxidative stress-related proteins by immunohistochemistry. We also carried out a proteomics analysis for estimating the reliable and sensitive biomarkers. Histopathologically, compound-specific hepatotoxicity was detected at 24 hr after administration in all compounds except amiodarone, which is known to induce phospholipidosis. Immunohistochemically, oxidative stress-related proteins were increased within 6 hr after administration in all treated groups. Proteomics analysis revealed several protein biomarkers related to oxidative stress and mitochondrial metabolism-regulation, which had been previously detected by proteomics analysis in in vitro screening system. Oxidative stress-related proteins were considered as useful biomarkers of hepatotoxicity; since they were detected by immunohistochemistry and proteomics analysis prior to appearance of compound-specific histopathological changes detected by light microscopy. Considering the relevance of in vitro system to in vivo system from the aspect of new biomarkers related to the toxicogenomics/toxicoproteomics, in vitro primary cell culture system would be sufficient to detect hepatotoxicity in the early stage of drug discovery.

Acetaminophen↗
PubMed2006

A kinase-focused compound collection: compilation and screening strategy.

Lead identification by high-throughput screening of large compound libraries has been supplemented with virtual screening and focused compound libraries. To complement existing approaches for lead identification at Biogen Idec, a kinase-focused compound collection was designed, developed and validated. Two strategies were adopted to populate the compound collection: a ligand shape-based virtual screening and a receptor-based approach (structural interaction fingerprint). Compounds selected with the two approaches were cherry-picked from an existing high-throughput screening compound library, ordered from suppliers and supplemented with specific medicinal compounds from internal programs. Promising hits and leads have been generated from the kinase-focused compound collection against multiple kinase targets. The principle of the collection design and screening strategy was validated and the use of the kinase-focused compound collection for lead identification has been added to existing strategies.

Combinatorial Chemistry Techniques↗
PubMed2003

High-throughput inhibition screening of major human cytochrome P450 enzymes using an in vitro cocktail and liquid chromatography-tandem mass spectrometry.

A method has been developed for the high-throughput inhibition screening of the major human cytochrome P450 (CYP) enzymes (CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4) using an in vitro substrate cocktail and liquid chromatography-tandem mass spectrometry (LC-MS-MS). A cocktail consisting of the selective substrates phenacetin (CYP1A2), tolbutamide (CYP2C9), omeprazole (CYP2C19), bufuralol (CYP2D6), and midazolam (CYP3A4) was incubated with human liver microsomes. The metabolic reactions were terminated with methanol containing dextrorphan as an internal standard. Following centrifugation, the supernatant was analyzed by LC-MS-MS employing a fast gradient. The concentrations of the substrate metabolites-paracetamol, 4-hydroxytolbutamide, 5-hydroxyomeprazole, 1'-hydroxybufuralol, and 1'-hydroxymidazolam-in each sample were determined by LC-MS-MS in a single assay. The method was validated by incubating known CYP inhibitors (furafylline, CYP1A2; sulfaphenazole, CYP2C9; s-mephenytoin, CYP2C19; quinidine, CYP2D6; and troleandomycin, CYP3A4) with the individual substrates they were known to inhibit and with the substrate cocktail. IC50s (microM) determined using the substrate cocktail were in good agreement with those obtained with individual substrates (furafylline, 2.9 vs. 2.0; sulfaphenazole, 0.75 vs. 0.72; s-mephenytoin, 170 vs. 180; quinidine, 0.17 vs. 0.24; troleandomycin, 2.6 vs. 3.2) and with previously reported values in the literature.

Cytochrome P-450 Enzyme System↗
PubMed2006

Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling.

Flow cytometry allows high-content, multiparameter analysis of single cells, making it a promising tool for drug discovery and profiling of intracellular signaling. To add high-throughput capacity to flow cytometry, we developed a cell-based multiplexing technique called fluorescent cell barcoding (FCB). In FCB, each sample is labeled with a different signature, or barcode, of fluorescence intensity and emission wavelengths, and mixed with other samples before antibody staining and analysis by flow cytometry. Using three FCB fluorophores, we were able to barcode and combine entire 96-well plates, reducing antibody consumption 100-fold and acquisition time to 5-15 min per plate. Using FCB and phospho-specific flow cytometry, we screened a small-molecule library for inhibitors of T cell-receptor and cytokine signaling, simultaneously determining compound efficacy and selectivity. We also analyzed IFN-gamma signaling in multiple cell types from primary mouse splenocytes, revealing differences in sensitivity and kinetics between B cells, CD4+ and CD4- T cells and CD11b-hi cells.

Animals↗
PubMed2006

A novel high-throughput genetic screen for stress-responsive mutants of Arabidopsis thaliana reveals new loci involving stress responses.

Activation sequence-1 (as-1) cognate promoter elements are widespread in the promoters of plant defense-related genes as well as in plant pathogen promoters, and may play important roles in the activation of defense-related genes. The as-1-type elements are highly responsive to multiple stress stimuli such as jasmonic acid (JA), salicylic acid (SA), H(2)O(2), xenobiotics and heavy metals, and therefore provide a unique opportunity for identifying additional signaling components and cross-talk points in the various signaling networks. A single as-1-type cis-element-driven GUS reporter Arabidopsis line responsive to JA, SA, H(2)O(2), xenobiotics and heavy metals was constructed for mutagenesis. A large-scale T-DNA mutagenesis has been conducted in the reporter background, and an efficient high-throughput mutant screen was established for isolating mutants with altered responses to the stress chemicals. A number of mutants with altered stress responses were obtained, some of which appear to identify new components in the as-1-based signal transduction pathways. We characterized a mutant (Delta8L4) with a T-DNA insertion in the coding sequence of the gene At4g24275. The as-1-regulated gene expression and GUS reporter gene expression were altered in the Delta8L4 mutant, but there was no change in the expression of genes lacking as-1 elements in their promoters. The phenotype observed with the Delta8L4 mutant was further verified using RNAi plants for At4g24275 (8L4-RNAi), suggesting the feasibility of use of this high-throughput mutant screening in isolating stress-signaling mutants.

Arabidopsis↗
PubMedDate not supplied

Setup for high-throughput impedance screening of gas-sensing materials.

This paper reports on the setup for a high-throughput impedance measurement system that allows rapid screening of the electrical and dielectrical properties of solid-state sample libraries in variable atmospheres and temperatures. Using multielectrode arrays, most time-consuming steps in the workflow are parallelized. In addition, an approach for automated data evaluation of impedance spectra is presented. For reasons of verification of robust measuring results and reproducibility, screening results of a sample library composed of doped indium(III) oxide as a resistive-type gas-sensing material are discussed on the basis of the determined sensitivities focusing temperature and testing gas gradients.

Journal Article↗
PubMed2002

Past, present and future strategies to study the genetics of body weight regulation.

Genetic advances have made remarkable progress towards our understanding of body weight regulation. Much of our current knowledge has come from the cloning and characterisation of the genes responsible for obesity syndromes in the mouse, and the identification of homologous mutations causing rare forms of obesity in humans. Gene targeting experiments in mice have been instrumental in confirming the importance of many genes in the aetiology of obesity, and the existence of a fundamental physiological pathway that controls energy balance is becoming clear. The genetic determinants that underlie common forms of human obesity are largely polygenic, with most genes producing small effects. Thus, elucidating the many genetic determinants of obesity is a current challenge for modern geneticists. Despite the inherent difficulties, progress has been made through linkage/association studies and a genetic map of quantitative trait loci for human obesity is beginning to emerge. Obesity research is now very much in a transition period. Not so long ago, access to high throughput screening, as well as microarray and proteomic techniques, was prohibitively expensive and available only to the few. In recent years, these technologies have become more accessible to the larger scientific community and, in this paper, we will discuss how such technological advances are likely to drive the next wave of progress in obesity research. For example, large-scale mutagenesis screens in rodents coupled with high throughput screening are likely to emerge as important technologies for identifying genes previously unexpected to be involved in body weight regulation. Furthermore, applications of microarray and proteomic techniques will further refine our understanding of currently known peptides as well as identify novel pathways and molecules which are involved in energy homeostasis.

Agouti Signaling Protein↗