Assay concordance between SPA and TR-FRET in high-throughput screening

High-throughput screening (HTS) of large chemical libraries has become the main source of new lead compounds for drug development. Several specialized detection technologies have been developed to facilitate the cost- and time-efficient screening of millions of compounds. However, concerns have been raised, claiming that different HTS technologies may produce different hits, thus limiting trust in the reliability of HTS data. This study was aimed to investigate the reliability of the authors most frequently used assay techniques: scintillation proximity assay (SPA) and homogeneous time-resolved fluorescence resonance energy transfer (TR-FRET). To investigate the data concordance between these 2 detection technologies, the authors screened a large subset of the Schering compound library consisting of 300,000 compounds for inhibitors of a nonreceptor tyrosine kinase. They chose to set up this study in realistic HTS scale to ensure statistical significance of the results. The findings clearly demonstrate that the choice of detection technology has no significant impact on hit finding, provided that assays are biochemically equivalent. Data concordance is up to 90%. The little differences in hit findings are caused by threshold setting but not by systematic differences between the technologies. The most significant difference between the compared techniques is that in the SPA format, more false-positive primary hits were obtained.     

Further comparison of primary hit identification by different assay technologies and effects of assay measurement variability

High-throughput screening (HTS) has grown rapidly in the past decade, with many advances in new assay formats, detection technologies, and laboratory automation. Recently, several studies have shown that the choice of assay technology used for the screening process is particularly important and can yield quite different primary screening outcomes. However, because the screening assays in these previous studies were performed in a single-point determination, it is not clear to what extent the difference observed in the screening results between different assay technologies is attributable to inherent assay variability and day-to-day measurement variation. To address this question, a nuclear receptor coactivator recruitment assay was carried out in 2 different assay formats, namely, AlphaScreen and time-resolved fluorescence resonance energy transfer, which probed the same biochemical binding events but with different detection technologies. For each assay format, 4 independent screening runs in a typical HTS setting were completed to evaluate the run-to-run screening variability. These multiple tests with 2 assay formats allow an unambiguous comparison between the discrepancies of different assay formats and the effects of the variability of assay and screening measurements on the screening outcomes. The results provide further support that the choice of assay format or technology is a critical factor in HTS assay development.     

Efficient hit-finding approaches for histone methyltransferases: the key parameters

For many novel epigenetics targets the chemical ligand space and structural information were limited until recently and are still largely unknown for some targets. Hit-finding campaigns are therefore dependent on large and chemically diverse libraries. In the specific case of the histone methyltransferase G9a, the authors have been able to apply an efficient process of intelligent selection of compounds for primary screening, rather than screening the full diverse deck of 900 000 compounds to identify hit compounds. A number of different virtual screening methods have been applied for the compound selection, and the results have been analyzed in the context of their individual success rates. For the primary screening of 2112 compounds, a FlashPlate assay format and full-length histone H3.1 substrate were employed. Validation of hit compounds was performed using the orthogonal fluorescence lifetime technology. Rated by purity and IC(50) value, 18 compounds (0.9% of compound screening deck) were finally considered validated primary G9a hits. The hit-finding approach has led to novel chemotypes being identified, which can facilitate hit-to-lead projects. This study demonstrates the power of virtual screening technologies for novel, therapeutically relevant epigenetics protein targets.     

The confirmation rate of primary hits: a predictive model

HTS data from primary screening are usually analyzed by setting a cutoff for activity, in order to minimize both false-negative and false-positive rates. An alternative approach, based on a calculated probability of being active, is presented here. Given the predicted confirmation rate derived from this probability, the number of primary positives selected for follow-up can be optimized to maximize the number of true positives without picking too many false positives. Typical cutoff-determining methods are more serendipitous in their nature and not easily optimized in an effort to optimize screening efforts. An additional advantage of calculating a probability of being active for each compound screened is that orthogonal mixtures can be deconvoluted without presetting a deconvolution threshold. An important consequence of using the probability of being active with orthogonal mixtures is that individual compound screening results can be recorded irrespective of whether the assays were performed on single compounds or on cocktails.     

A simple strategy for mitigating the effect of data variability on the identification of active chemotypes from high-throughput screening data

Among the several goals of a high-throughput screening campaign is the identification of as many active chemotypes as possible for further evaluation. Often, however, the number of concentration response curves (e.g., IC(50)s or K(i)s) that can be collected following a primary screen is limited by practical constraints such as protein supply, screening workload, and so forth. One possible approach to this dilemma is to cluster the hits from the primary screen and sample only a few compounds from each cluster. This introduces the question as to how many compounds must be selected from a cluster to ensure that an active compound is identified, if it exists at all. This article seeks to address this question using a Monte Carlo simulation in which the dependence of the success of sampling is directly linked to screening data variability. Furthermore, the authors demonstrate that the use of replicated compounds in the screening collection can easily assess this variability and provide a priori guidance to the screener and chemist as to the extent of sampling required to maximize chemotype identification during the triage process. The individual steps of the Monte Carlo simulation provide insight into the correspondence between the percentage inhibition and eventual IC(50) curves.     

Detecting outliers in species distribution data

Aim

Species distribution data play a pivotal role in the study of ecology, evolution, biogeography and biodiversity conservation. Although large amounts of location data are available and accessible from public databases, data quality remains problematic. Of the potential sources of error, positional errors are critical for spatial applications, particularly where these errors place observations beyond the environmental or geographical range of species. These outliers need to be identified, checked and removed to improve data quality and minimize the impact on subsequent analyses. Manually checking all species records within large multispecies datasets is prohibitively costly. This work investigates algorithms that may assist in the efficient vetting of outliers in such large datasets.

Location

We used real, spatially explicit environmental data derived from the western part of Victoria, Australia, and simulated species distributions within this same region.

Methods

By adapting species distribution modelling (SDM), we developed a pseudo‐SDM approach for detecting outliers in species distribution data, which was implemented with random forest (RF) and support vector machine (SVM) resulting in two new methods: RF_pdSDM and SVM_pdSDM. Using virtual species, we compared eight existing multivariate outlier detection methods with these two new methods under various conditions.

Results

The two new methods based on the pseudo‐SDM approach had higher true skill statistic (TSS) values than other approaches, with TSS values always exceeding 0. More than 70% of the true outliers in datasets for species with a low and intermediate prevalence can be identified by checking 10% of the data points with the highest outlier scores.

Main conclusions

Pseudo‐SDM‐based methods were more effective than other outlier detection methods. However, this outlier detection procedure can only be considered as a screening tool, and putative outliers must be examined by experts to determine whether they are actual errors or important records within an inherently biased set of data.     

An antioxidant screening assay based on oxidant-induced growth arrest in Saccharomyces cerevisiae

This report describes a biological screening system to measure the antioxidant capacity of compounds using the oxidant-induced growth arrest response of Saccharomyces cerevisiae. Alternative methods using the nonphysiological free radical compounds such as diphenylpicrylhydrazyl and azinobis ethylbenzothiaziline-6-sulphonate (ABTS) only provide an indication of the ability of a compound to scavenge oxidants. In contrast, this yeast-based method can also measure the ability of a compound to induce cellular resistance to the damaging effects of oxidants. The screening assay was established against a panel of six physiologically relevant oxidants ranging from reactive oxygen species (hydrogen peroxide, cumene peroxide, linoleic acid hydroperoxide), to a superoxide-generating agent (menadione), reactive nitrogen species (peroxynitrite) and a thiol-oxidizing agent (diamide). The antioxidants ascorbate and gallic acid displayed scavenging activity and induced the resistance of cells against a broad range of oxidants using this assay. Lipoic acid, which showed no scavenging activity and thus would not be detected as an antioxidant using a nonphysiological screen was, however, identified in this assay as providing resistance to cells against a range of oxidants. This assay is high throughput, in the format of a 96-well microtitre plate, and will greatly facilitate the search for effective antioxidants.     

Comparison of assay technologies for a tyrosine kinase assay generates different results in high throughput screening

In today's high-throughput screening (HTS) environment, an increasing number of assay detection technologies are routinely utilized in lead finding programs. Because of the relatively broad applicability of several of these technologies, one is often faced with a choice of which technology to utilize for a specific assay. The aim of this study was to address the question of whether the same compounds would be identified from screening a set of samples in three different versions of an HTS assay. Here, three different versions of a tyrosine kinase assay were established using scintillation proximity assay (SPA), homogeneous time-resolved fluorescence resonance energy transfer (HTR-FRET), and fluorescence polarization (FP) technologies. In this study, 30,000 compounds were evaluated in each version of the kinase assay in primary screening, deconvolution, and dose-response experiments. From this effort, there was only a small degree of overlap of active compounds identified subsequent to the deconvolution experiment. When all active compounds were then profiled in all three assays, 100 and 101 active compounds were identified in the HTR-FRET and FP assays, respectively. In contrast, 40 compounds were identified in the SPA version of the kinase assay, whereas all of these compounds were detected in the HTR-FRET assay only 35 were active in the FP assay. Although there was good correlation between the IC(50) values obtained in the HTR-FRET and FP assays, poor correlations were obtained with the IC(50) values obtained in the SPA assay. These findings suggest that significant differences can be observed from HTS depending on the assay technology that is utilized, particularly in assays with high hit rates.     

RNA as a drug target: methods for biophysical characterization and screening

RNA folds into complex structures that can interact specifically with effector proteins. These interactions are essential for various biological functions. In order to discover small molecules that can affect important RNA-protein complexes, a thorough analysis of the thermodynamics and kinetics of RNA-protein binding is required. This can facilitate the formulation of high-throughput screening strategies and the development of structure-activity relationships for compound leads. In addition to traditional methods, such as filter binding, gel mobility shift assay and various fluorescence techniques, newer methods such as surface plasmon resonance and mass spectrometry are being used for the study of RNA-protein interactions.     

Identification of gap junction blockers using automated fluorescence microscopy imaging

Gap junctions coordinate electrical signals and facilitate metabolic synchronization between cells. In this study, the authors have developed a novel assay for the identification of gap junction blockers using fluorescence microscopy imaging-based high-content screening technology. In the assay, the communication between neighboring cells through gap junctions was measured by following the redistribution of a fluorescent marker. The movement of calcein dye from dye-loaded donor cells to dye-free acceptor cells through gap junctions overexpressed on cell surface membranes was monitored using automated fluorescence microscopy imaging in a high-throughput compatible format. The fluorescence imaging technology consisted of automated focusing, image acquisition, image processing, and data mining. The authors have successfully performed a high-throughput screening of a 486,000- compound program with this assay, and they were able to identify false positives without additional experiments. Selective and pharmacologically interesting compounds were identified for further optimization.     

Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities

Microdeletions and microduplications, not visible by routine chromosome analysis, are a major cause of human malformation and mental retardation. Novel high-resolution, whole-genome technologies can improve the diagnostic detection rate of these small chromosomal abnormalities. Array-based comparative genomic hybridization allows such a high-resolution screening by hybridizing differentially labeled test and reference DNAs to arrays consisting of thousands of genomic clones. In this study, we tested the diagnostic capacity of this technology using approximately 3,500 flourescent in situ hybridization-verified clones selected to cover the genome with an average of 1 clone per megabase (Mb). The sensitivity and specificity of the technology were tested in normal-versus-normal control experiments and through the screening of patients with known microdeletion syndromes. Subsequently, a series of 20 cytogenetically normal patients with mental retardation and dysmorphisms suggestive of a chromosomal abnormality were analyzed. In this series, three microdeletions and two microduplications were identified and validated. Two of these genomic changes were identified also in one of the parents, indicating that these are large-scale genomic polymorphisms. Deletions and duplications as small as 1 Mb could be reliably detected by our approach. The percentage of false-positive results was reduced to a minimum by use of a dye-swap-replicate analysis, all but eliminating the need for laborious validation experiments and facilitating implementation in a routine diagnostic setting. This high-resolution assay will facilitate the identification of novel genes involved in human mental retardation and/or malformation syndromes and will provide insight into the flexibility and plasticity of the human genome.     

Evaluating the utility of the HTRF Transcreener ADP assay technology: A comparison with the standard HTRF assay technology

The HTRF (homogeneous time-resolved fluorescence) Transcreener ADP assay is a new kinase assay technology marketed by Cis-Bio International (Bagnols-Cèze, France). It measures kinase activity by detecting the formation of ADP using a monoclonal antibody and HTRF detection principles. In this article, we compare this technology with a standard HTRF kinase assay using EGFR [L858R/T790M] mutant enzyme as a case study. We demonstrate that the HTRF Transcreener ADP assay generated similar kinetic constants and inhibitor potency compared with the standard HTRF assay. However, the smaller dynamic window and lower Z′ factor of the HTRF Transcreener ADP assay make this format less preferable for high-throughput screening. Based on the assay principle, the HTRF Transcreener ADP assay can detect both kinase and ATPase activities simultaneously. The ability to probe ATPase activity opens up new avenues for assaying kinases with intrinsic ATPase activity without the need to identify substrates, and this can speed up the drug discovery process. However, caution must be exercised because any contaminating ATPase activity will result in an invalid assay. The inability to tolerate high concentrations of ATP in the assay will also limit the application of this technology, especially in compound mechanistic studies such as ATP competition. Overall, the HTRF Transcreener ADP assay provides a new alternative tool to complement existing assay technologies for drug discovery.     

基于Yarn云平台的生物基因多序列比对并行算法

为了解决生物信息学中基因多序列比对的计算速度慢和软件陈旧的问题,提出了基于Yarn(Yet Another Resource Negotiator)云平台的生物基因多序列比对并行计算方法Yarn_clustalW。分析了clustalW算法的数学模型及其面向MapReduce的任务划分方式,Yarn_clustalW中综合考虑了基因的长度和数目,采用一种基于阈值刻度的任务划分方式。利用NCBI的GenBank生物基因数据作为案例程序进行了测试。实验结果表明:Yarn_clustalW比起多序列比对clustalW串行计算方法具有更快的运行时间与加速比,可以使生物科研人员节省很多时间与精力,方便对于药物靶标的发现,缩短生物药物的开发周期。     

Monitoring laboratory performance by statistical analysis of rescreening cervical smears

The rescreening of cervical cytology smears, although inadequate both for checking the reliability of an individual screener and for the detection of false negatives, nonetheless represents an indispensable tool for assessing morphologic diagnostic criteria and monitoring laboratory performance. Interobserver and intraobserver concordance in a given laboratory determine the reliability of diagnostic criteria and disclose the possibility of improving diagnostic consistency. The various aspects of rescreening are discussed, and a simple statistical procedure for a quantitative comparison of screening reproducibility is described. This procedure, with calculation of phi-values and mean prevalence rates, was applied to screening and rescreening data from the Cyt-U-Universitair Cytology Laboratory from 1978 to 1983, in which the morphologic findings in each smear were recorded in detail using the QISO (Quality, Infection, Squamous epithelium and Other abnormalities) coding. The reproducibility of the reported presence of endocervical cells not only steadily improved over the years assessed, but also reached a sufficiently high level that diagnostic variability should not hamper its clinical utility. The same was true of the diagnosis of Trichomonas infection and moderate atypia of squamous cells. On the other hand, the reproducibility of the diagnosis of endometrial cells in smears did not significantly improve. However, since the intraobserver concordance on this criterion was good, it seems likely that the definitions of screeners in this area can still be brought into closer agreement. Conversely, the diagnosis of "abnormal endocervical cells" had such a high level of variability even at the intraobserver level as to question its use as a diagnostic criterion. Similar variability was seen in the distinction between atypical squamous metaplasia and mild dysplasia. Use of this statistical technique for the quality control of cytologic diagnoses frees that assessment from histopathologic control, which does not address the problem of variation within the cytologic or histologic diagnoses themselves.     

Development,validation and pilot screening of an in vitro multi-cellular three-dimensional cancer spheroid assay for anti-cancer drug testing

It has been demonstrated that two-dimensional (2D) monolayer cancer cell proliferation assay for anti-cancer drug screening is a very artificial model and cannot represent the characteristics of three-dimensional (3D) solid tumors. The multi-cellular in vitro 3D tumor spheroid model is of intermediate complexity, and can provide a bridge to the gap between the complex in vivo tumors and simple in vitro monolayer cell cultures. In this study, a simple and cost-effective cancer 3D spheroid assay suitable for small molecule anti-cancer compound screening was developed, standardized and validated on H292 non-small lung cancer cell line. A pilot screening with this assay was performed utilizing a compound library consisting of 41 anti-cancer agents. The traditional 2D monolayer cell proliferation assay was also performed with the same cell line and compounds. A correlational study based on the IC₅₀ values from the 2D and 3D assays was conducted. There is low correlation with the two sets of biological data, suggesting the two screening methods provide different information regarding the potency of the tested drug candidates.     

Microplate orbital mixing improves high-throughput cell-based reporter assay readouts

Reporter assays are commonly used for high-throughput cell-based screening of compounds, cDNAs, and siRNAs due to robust signal, ease of miniaturization, and simple detection and analysis. Among the most widely used reporter genes is the bioluminescent enzyme luciferase, which, when exposed to its substrate luciferin upon cell lysis, yields linear signal over a dynamic range of several orders of magnitude. Commercially available luciferase assay formulations have been developed permitting homogeneous, single-step cell lysis and reporter activity measurements. Assay conditions employed with these formulations are typically designed to minimize well-to-well luminescence variability due to variability in dispensing, evaporation, and incomplete sample mixing. The authors demonstrate that incorporating a microplate orbital mixing step into 96- and 384-well microplate cell-based luciferase reporter assays can greatly improve reporter readouts. They have found that orbital mixing using commercially available mixers facilitates maximal luciferase signal generation from high cell density-containing samples while minimizing variability due to partial cell lysis, thereby improving assay precision. The authors fully expect that widespread availability of mixers with sufficiently small orbits and higher speed settings will permit gains in signal and precision in the 1536-well format as well.     

High-throughput screening: new technology for the 21st century

New technologies in high-throughput screening have significantly increased throughput and reduced assay volumes. Key advances over the past few years include new fluorescence methods, detection platforms and liquid-handling technologies. Screening 100,000 samples per day in miniaturized assay volumes will soon become routine. Furthermore, new technologies are now being applied to information-rich cell-based assays, and this is beginning to remove one of the key bottlenecks downstream from primary screening.