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A mutation in Arabidopsis cytochrome b5 reductase identified by high-throughput screening differentially affects hydroxylation and desaturation.

As a model for analyzing the production of novel fatty acids in oilseeds, we used the genetic and molecular techniques available for Arabidopsis to characterize modifying mutations affecting the accumulation of hydroxy fatty acids in the seeds of Arabidopsis plants that express a transgene for the castor bean fatty acid hydroxylase, FAH12. We developed a high-throughput analytical system and used it to identify three complementation classes of mutations with reduced hydroxy fatty acid accumulation from among Arabidopsis M3 seed samples derived from chemical mutagenesis. We identified one of the mutations by positional cloning as a single base pair change in a gene encoding NADH:cytochrome b5 reductase (CBR1, At5g17770). When expressed in yeast, the mutant form of the enzyme was less active and less stable than the wild-type enzyme. Characterization of homozygous mutant lines with and without the FAH12 transgene (FAH12 cbr1-1 and cbr1-1, respectively) indicated that the only detectable consequence of the cbr1-1 mutation was on desaturase and hydroxylase reactions in the developing seed. The leaf and root fatty compositions, as well as the growth, development and seed production of mutant plants were indistinguishable from wild type. Interestingly, while the cbr1-1 mutation reduced the accumulation of hydroxy fatty acids in seeds by 85%, the effects on 18:1 and 18:2 desaturation reactions were much less (<25% and <60%, respectively). These results suggest that there is competition in developing seeds among the several reactions that utilize reduced cytochrome b5.

Amino Acid Sequence↗

Technology for high-throughput screens: the present and future using zebrafish.

The zebrafish is a popular vertebrate model organism with similar organ systems and gene sequences to humans. Zebrafish embryos are optically transparent enabling organ visualisation, which can be complemented with gene expression analysis at the transcript and protein levels. Furthermore, zebrafish can be treated with small molecules and drugs in a microtitre plate format for high-throughput analysis and for the identification and validation of drugs. High-throughput methodologies for use in zebrafish include phenotype-based visualisation, transcript studies using low-density DNA microarrays and proteomic analysis. These technologies offer significant whole-organism biological value in the drug discovery and drug development pipeline.

Animals↗

Inhibition of lethal endotoxin shock with an L-pyridylalanine containing metalloproteinase inhibitor selected by high-throughput screening of a new peptide library.

Gelatinase B/MMP-9 fulfills crucial regulator or effector functions in disease states and may be pharmacologically targeted by specific inhibitors. The characteristics of cleavages of a natural gelatinase B substrate were simulated and amino acids with zinc-ion chelating side-groups were employed to design a library of peptide-based inhibitors. Here, we extend previous findings of combinatorial chemical synthesis and subsequent library deconvolution with a recently established high-throughput technology. This enabled us to study MMP inhibitors with two zinc-binding groups and to identify a new L-pyridylalanine-containing gelatinase B inhibitor. The peptide analog was found to inhibit, almost to the same degree, the neutrophil enzymes collagenase 2/ MMP-8 and MMP-9 and the monocytic tumor necrosis factor-alpha (TNF-alpha) converting enzyme (TACE/ADAM-17) in vitro and to protect mice against lethal endotoxinemia in vivo. These data illustrate the usefulness of the screening platform for protective inhibitor discovery and complement recent insights in the pathogenesis and treatment of shock syndromes.

ADAM Proteins↗

A new reporter gene system suited for cell-free protein synthesis and high-throughput screening in small reaction volumes.

The properties of M-hirudin as a new reporter gene system were examined using rabbit reticulocyte lysate for cell-free protein expression. In contrast to the luciferase gene, in vitro translation of M-hirudin is highly robust against changes in concentrations of K+ (and Rb+). In addition, M-hirudin can be detected very sensitively using a reasonably priced fluorimetric thrombin assay. To show that the new reporter gene system is well suited for (u)HTS-applications, cell-free synthesis as well as the fluorimetric assay of M-hirudin were carried out in nanotiter and microtiter plates, respectively.

Animals↗

High-throughput screening for soluble recombinant expressed kinases in Escherichia coli and insect cells.

We have constructed a dual expression vector for the production of recombinant proteins in both Escherichia coli and insect cells. In this vector, the baculoviral polyhedrin promoter was positioned upstream of the bacteriophage T7 promoter and the lac operator. This vector, designated pBEV, was specifically designed to exploit the advantages that both hosts would provide. This vector also facilitates one-stop cloning, thereby simplifying the expression process for automation, and the development of a high-throughput method for protein expression. Utilizing the multi-system vector pBEV, a high-throughput process was developed with expression in deep-well blocks and purification in micro-titer plates enabling the identification of expression and solubility in both E. coli and insect cells. In this study, using pBEV, we have successfully expressed and purified multiple human kinases produced in E. coli and insect cells. Our results validate expression screening as a strategy to rapidly triage proteins identifying the optimum expression system and conditions for production.

Animals↗

A practical high-throughput screening system for enantioselectivity by using FTIR spectroscopy.

For the first time FTIR spectroscopy has been applied to the measurement of enantiomeric purity. The underlying concept is based on the use of pseudo-enantiomers that are (13)C-labeled at appropriate positions. Upon applying Lambert-Beer's law in the determination of the concentrations of both enantiomers, the ee values are accessible, accuracy to within +/-5 % of the true values being possible. The application of a commercially available high-throughput FTIR system results in a slightly decreased accuracy (+/-7% for the ee values), but this allows a throughput of up to 10000 samples per day. The method is of interest in the area of combinatorial symmetric catalysis and directed evolution of enantioselective enzymes.

Journal Article↗

Fluorescence detection-based functional assay for high-throughput screening for MraY.

We have developed a novel assay specific to MraY, which catalyzes the first membrane step in the biosynthesis of bacterial cell wall peptidoglycan. This was accomplished by using UDP-MurNAc-N(epsilon)-dansylpentapeptide, a fluorescent derivative of the MraY nucleotide substrate, and a partially purified preparation of MraY solubilized from membranes of an Escherichia coli overproducing strain. Two versions of the assay were developed, one consisting of the high-pressure liquid chromatography separation of the substrate and product (dansylated lipid I) and the other, without separation and adapted to the high-throughput format, taking advantage of the different fluorescence properties of the nucleotide and lipid I in the reaction medium. The latter assay was validated with a set of natural and synthetic MraY inhibitors.

Anti-Bacterial Agents↗

Fast monolithic micellar liquid chromatography: an alternative drug permeability assessing method for high-throughput screening.

Several methods estimating the partitioning over biological membranes and thus the biological activity of potential oral drug molecules have been developed and are described in the literature. A previous study suggested that fast micellar liquid chromatography on a monolithic column could be one of them. For a set of diverse pharmaceuticals, retention by this fast chromatographic method was determined, besides other parameters also thought or established to describe oral permeability or absorption, e.g., from the Caco-2 permeability method. In view of a high-throughput determination of membrane permeability, a study was made of which information fast micellar liquid chromatography is providing and to what degree this system can replace other methods, i.e., deliver similar information. The retention with this fast method, which is mainly based on hydrophobic interactions, proved useful to sort substances into classes of Caco-2 and percent intestinal absorption.

Caco-2 Cells↗

A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombination.

BACKGROUND: Cre-loxP recombination refers to the process of site-specific recombination mediated by two loxP sequences and the Cre recombinase protein. Transgenic experiments exploit integrative recombination, where a donor plasmid carrying a loxP site and DNA of interest integrate into a recipient loxP site in a target genome. Unfortunately, integrative recombination is highly inefficient because the insert is flanked by two loxP sites, which themselves become targets for Cre and lead to subsequent excision of the insert. A small number of mutations have been discovered in parts of the loxP sequence, specifically the spacer and inverted repeat segments, that increase the efficiency of integrative recombination. In this study we introduce a high-throughput in vitro assay to rapidly detect novel loxP spacer mutants and describe the sequence characteristics of successful recombinants. RESULTS: We created synthetic loxP oligonucleotides that contained a combination of inverted repeat mutations (the lox66 and lox71 mutations) and mutant spacer sequences, degenerate at 6 of the 8 positions. After in vitro Cre recombination, 3,124 recombinant clones were identified by sequencing. Included in this set were 31 unique, novel, self-recombining sequences. Using network visualization tools, we recognized 12 spacer sets with restricted promiscuity. We observed that increased guanine content at all spacer positions save for position 8 resulted in increased recombination. Interestingly, recombination between identical spacers was not preferred over non-identical spacers. We also identified a set of 16 pairs of loxP spacers that reacted at least twice with another spacer, but not themselves. Further, neither the wild-type P1 phage loxP sequence nor any of the known loxP spacer mutants appeared to be kinetically favoured by Cre recombinase. CONCLUSION: This study approached loxP spacer mutant screening in an unbiased manner, assuming nothing about candidate loxP sites save for the conserved 4 and 5 spacer positions. Candidate sites were free to recombine with any other sequence in the pool of all possible sites. The subset of loxP sites identified here are candidates for in vivo serial recombination as they have already demonstrated limited promiscuity with other loxP spacer and stability in the presence of Cre.

Bacteriophage P1↗

High-throughput screen for detecting antimycobacterial agents.

A simple, robust assay system which can be used to screen for inhibitors of mycobacterial growth has been developed. A strain of the rapidly growing saprophyte Mycobacterium aurum is used as the test organism. Inhibition of its growth is highly predictive of activity against Mycobacterium tuberculosis, which cannot itself be used in screening because of its growth characteristics and highly infectious nature. The viability of M. aurum in the presence of a test sample is monitored by measuring the uptake of radiolabelled uracil into the cells. In a microtiter plate format, the screen has the potential for testing several thousand samples per day.

Antitubercular Agents↗

Fluorometric high-throughput screening for inhibitors of cytochrome P450.

Rapid screening for cytochrome P450 inhibitors is part of the current paradigm for avoiding development of drugs likely to give clinical pharmacokinetic drug-drug interactions and associated toxicities. We have developed microtiter plate-based, direct, fluorometric assays for the activities of the principal human drug-metabolizing enzymes, CYP1A2, CYP2C8, CYP2C9, CYP2C19, CYP2D6, and CYP3A4, as well as for CYP2A6, which is an important enzyme in environmental toxicology. These assays are rapid and compatible with existing high-throughput assay instrumentation. For CYP1A2, CYP2C8, CYP2C9, CYP2C19, and CYP2D6, the potency of enzyme inhibition (IC50) is consistent regardless of the probe substrate or assay method employed. In contrast, CYP3A4 inhibition for an individual inhibitor shows significant differences in potency (>300-fold) depending on the probe substrate being used. We have investigated these differences through the use of several structurally distinct fluorescent substrates for CYP3A4 and several classical substrate probes (e.g., testosterone, nifedipine, and midazolam), with a panel of known, clinically significant, CYP3A4 inhibitors. The use of multiple probe substrates appears to be needed to characterize the inhibition potential of xenobiotics for CYP3A4.

Coumarins↗

Invited review: Identifying new mouse models of cardiovascular disease: a review of high-throughput screens of mutagenized and inbred strains.

The mouse is a proven model for studying human disease. Many strains exist that exhibit either natural or engineered genetic variation and thereby enable the elucidation of pathways involved in the development of cardiovascular disease. Although those mouse models have been fundamental to advancing our knowledge base, we are still at an early stage in understanding how genes contribute to complex disorders. There remains a need for new animal models that closely represent human disease. To expedite their development, we have established the Center for New Mouse Models of Heart, Lung, Blood, and Sleep Disorders at The Jackson Laboratory. We are using a phenotype-driven approach to identify mutations leading to atherosclerosis, hypertension, obesity, blood disorders, lung dysfunction, thrombosis, and disordered sleep. Our high-throughput, comprehensive phenotyping draws from two sources for new models: 1) the natural variation among over 40 inbred mouse strains and 2) chemically induced, whole-genome mutagenized mice. Here, we review our cardiovascular screens and present some hypertensive, obese, and cardiovascular models identified with this approach.

Animals↗

High throughput screening technologies for direct cyclic AMP measurement.

A study comparing five different cAMP detection technologies in terms of sensitivity, robustness, and feasibility for HTS is presented. In this report, the following methods are described: a nonhomogeneous DELFIA, and the homogeneous methods based on time-resolved fluorescence (HTRF), luminescent singlet oxygen channeling or ALPHAScreen, FP, and high-affinity enzyme complementation. DELFIA had the highest sensitivity, whereas ALPHAScreen and HTRF shared several advantages, including high sensitivity, broad dynamic range, and minimal reagent addition steps. For G(s)-coupled antagonist screens, we found HTRF and ALPHAScreen the more sensitive and HTS-compatible techniques.

Animals↗

Sol-gel encapsulated enzyme arrays for high-throughput screening of biocatalytic activity.

We developed versatile low-cost arrays of sol-gel-encapsulated enzymes (referred to as solzymes) suitable for repeated assays of bioactivity or enzyme inhibition. Sol-gel microstructures containing active enzymes were stabilized on glass at moderate pH and room temperature without harsh calcination. A multi-well bilayer of polydimethylsiloxane was used to support the solzyme array and contain the reaction medium. Each of the 147 microwells has a working volume of 5 muL and contains 50 mug of immobilized enzyme. The solzyme arrays maintained high activity through repeated applications and exhibited superior thermostability compared to soluble enzymes. Among the enzymes used were lipases, glucose oxidase, and horseradish peroxidase. Twenty different lipases and proteases were also used to prepare a hydrolase array, for which bromthymol blue served as a generic indicator of activity. The relative activities of the encapsulated hydrolases correlated closely with those of the soluble hydrolases, illustrating that sol-gel encapsulation preserved the hierarchy of enzyme activity. The development of solzyme arrays paves the way to higher throughput screening of diverse proteins and enzymes, including those that are available only in trace amounts.

Biosensing Techniques↗

Promoter analysis in mycobacteria using xyIE reporter assays and its implication in high throughput screening.

Understanding the molecular biology of Mycobacterium tuberculosis has become the focus of recent studies in infectious diseases. Here, we describe a spectrophotometric method for quantitative analysis of promoters in mycobacteria. The assay is a modification of the xyIE reporter assay, which uses an inexpensive substrate, catechol. The distinguishing feature of this protocol is that cells are grown by patching on agar plates, and directly used in the assays. The absorption measurements of the cell suspension at 375 nm in the presence and absence of the substrate are used for obtaining xyIE activity and for normalization of the assay values respectively. These features make the assay system directly amenable for high throughput analyses.

Catechol 2,3-Dioxygenase↗

High-throughput screening for the identification of small-molecule inhibitors of retinoblastoma protein phosphorylation in cells.

The tumor suppressor protein, pRb, regulates progression through the G1 phase of the cell cycle by its ability to bind to and regulate the activity of a variety of transcription factors. This function of pRb is disabled through its phosphorylation by the cyclin-dependent kinase (CDK) family of serine/threonine kinases. In many human cancers, genetic alteration such as loss of CDK inhibitor function and deregulated G1 cyclin expression leads to inappropriate phosphorylation and hence inactivation of this tumor suppressor. Identification of cell-permeable small molecules that block pRb phosphorylation in these tumors could therefore lead to development of an effective anticancer treatment. As a result, we have developed a high-throughput assay to detect changes in the level of pRb phosphorylation in cells. Signal detection is by a time-resolved fluorescence-based cellular immunosorbant assay on a fixed monolayer of cells. This comprises a mouse monoclonal antibody that recognizes the phosphorylated form of serine 608 on pRb, a known site of CDK phosphorylation, and a Europium-labeled secondary antibody for signal detection. The assay is reproducible and amenable to automation and has been used to screen 2000 compounds in a search for cell-permeable small molecules that will block pRb phosphorylation.

Animals↗

A fully automated [35S]GTPgammaS scintillation proximity assay for the high-throughput screening of Gi-linked G protein-coupled receptors.

The diversity of physiological functions mediated by the GPCR superfamily provides a rich source of molecular targets for drug discovery programs. Consequently, a variety of assays have been designed to identify lead molecules based on ligand binding or receptor function. In one of these, the binding of [(35)S]GTPgammaS, a nonhydrolyzable analogue of GTP, to receptor-activated G-protein alpha subunits represents a unique functional assay for GPCRs and is well suited for use with automated HTS. Here we compare [(35)S]GTPgammaS scintillation proximity binding assays for two different G(i)-coupled GPCRs, and describe their implementation with automated high-throughput systems.

Automation↗

Immunoassays based on microelectrodes arrayed on a silicon chip for high throughput screening of liver fibrosis markers in human serum.

A novel immunoassays for screening of disease markers in human serum are presented by miniaturizing interdigitated array (IDA) of microelectrodes via micro electro-mechanical system (MEMS) on a silicon chip for multi-channel electrochemical measurement. Different selected antibodies (Abs) are incorporated site-specifically into the electrochemically deposited polypyrrole (PPy) formed on the IDA of the silicon chip, which was characterized by fluorescence microscope photo and the electrochemical quartz crystal microbalance (EQCM) measurements. The selective recognition of Ab to the corresponding antigen (Ag) is monitored through the measurable conductivity change, which is directly visualized by cyclic voltammograms (CVs) in presence of the redox probe, Fe (CN)6(3-/4-). By using the strategy presented here, three liver fibrosis markers, hyaluronic acid (HA), lamin (LN) and collagen type IV (IV-C), are detected simultaneously and specifically at the surface of the chip with calibration curves, y = 21.75 + 0.84x (R = 0.995), y = 57.54 + 0.47x (R = 0.999) and y = 37.92 + 0.28x (R = 0.999), separately. Either the standard or the serum samples can be detected at ng/mL concentration level in a tiny amount of volume, approximately 50 microL. The chip-based immunoassay shows the advantages of high sensitivity, good specificity, high throughput, low sample consumption, and the stability offered via batch production by MEMS as well, which is expected to benefit the multi-target screening of desired clinical analytes.

Biomarkers↗