An informatic pipeline for managing high-throughput screening experiments and analyzing data from stereochemically diverse libraries

Integration of flexible data-analysis tools with cheminformatics methods is a prerequisite for successful identification and validation of “hits” in high-throughput screening (HTS) campaigns. We have designed, developed, and implemented a suite of robust yet flexible cheminformatics tools to support HTS activities at the Broad Institute, three of which are described herein. The “hit-calling” tool allows a researcher to set a hit threshold that can be varied during downstream analysis. The results from the hit-calling exercise are reported to a database for record keeping and further data analysis. The “cherry-picking” tool enables creation of an optimized list of hits for confirmatory and follow-up assays from an HTS hit list. This tool allows filtering by computed chemical property and by substructure. In addition, similarity searches can be performed on hits of interest and sets of related compounds can be selected. The third tool, an “S/SAR viewer,” has been designed specifically for the Broad Institute’s diversity-oriented synthesis (DOS) collection. The compounds in this collection are rich in chiral centers and the full complement of all possible stereoisomers of a given compound are present in the collection. The S/SAR viewer allows rapid identification of both structure/activity relationships and stereo-structure/activity relationships present in HTS data from the DOS collection. Together, these tools enable the prioritization and analysis of hits from diverse compound collections, and enable informed decisions for follow-up biology and chemistry efforts.     

A collaborative hit-to-lead investigation leveraging medicinal chemistry expertise with high throughput library design, synthesis and purification capabilities

High throughput screening (HTS) campaigns, where laboratory automation is used to expose biological targets to large numbers of materials from corporate compound collections, have become commonplace within the lead generation phase of pharmaceutical discovery. Advances in genomics and related fields have afforded a wealth of targets such that screening facilities at larger organizations routinely execute over 100 hit-finding campaigns per year. Often, 10(5) or 10(6) molecules will be tested within a campaign/cycle to locate a large number of actives requiring follow-up investigation. Due to resource constraints at every organization, traditional chemistry methods for validating hits and developing structure activity relationships (SAR) become untenable when challenged with hundreds of hits in multiple chemical families per target. To compound the issue, comparison and prioritization of hits versus multiple screens, or physical chemical property criteria, is made more complex by the informatics issues associated with handling large data sets. This article describes a collaborative research project designed to simultaneously leverage the medicinal chemistry and drug development expertise of the Novartis Institutes for Biomedical Research Inc. (NIBRI) and ArQule Inc.'s high throughput library design, synthesis and purification capabilities. The work processes developed by the team to efficiently design, prepare, purify, assess and prioritize multiple chemical classes that were identified during high throughput screening, cheminformatics and molecular modeling activities will be detailed.     

Rating high‐throughput screening results via h‐index

The quantification of both the impact and quality of a scientist's publication record is an essential step in making decisions concerning hiring, promotion, and allocation of funding. In an attempt to resolve this problem, Hirsh proposed the “h‐index,” a single‐number criterion incorporating both the number of publications and the number of citations per publication. This value facilitates rating of a scientist's performance and is now one of the most commonly used matrices. Here, we would like to propose the rating of high‐throughput screening (HTS) result by the h‐index. Rating HTS result is to estimate how the HTS result is preferred by a medicinal chemist. In this study, we applied the h‐index for rating HTS results and observed an enhanced rating of preferred starting points for drug development. In addition, we developed a new index, the maximum common structure (MCS) index, which is more effective than the h‐index. Copyright © 2014 John Wiley & Sons, Ltd.     

High‐Throughput Bioassays using “Dip‐and‐Go” Multiplexed Electrospray Mass Spectrometry

A multiplexed system based on inductive nanoelectrospray mass spectrometry (nESI‐MS) has been developed for high‐throughput screening (HTS) bioassays. This system combines inductive nESI and field amplification micro‐electrophoresis to achieve a “dip‐and‐go” sample loading and purification strategy that enables nESI‐MS based HTS assays in 96‐well microtiter plates. The combination of inductive nESI and micro‐electrophoresis makes it possible to perform efficient in situ separations and clean‐up of biological samples. The sensitivity of the system is such that quantitative analysis of peptides from 1–10 000 nm can be performed in a biological matrix. A prototype of the automation system has been developed to handle 12 samples (one row of a microtiter plate) at a time. The sample loading and electrophoretic clean‐up of biosamples can be done in parallel within 20 s followed by MS analysis at a rate of 1.3 to 3.5 s per sample. The system was used successfully for the quantitative analysis of BACE1‐catalyzed peptide hydrolysis, a prototypical HTS assay of relevance to drug discovery. IC₅₀ values for this system were in agreement with LC‐MS but recorded in times more than an order of magnitude shorter.     

High throughput screening for neurodegeneration and complex disease phenotypes

High throughput screening (HTS) for complex diseases is challenging. This stems from the fact that complex phenotypes are difficult to adapt to rapid, high throughput assays. We describe the recent development of high throughput and high-content screens (HCS) for neurodegenerative diseases, with a focus on inherited neurodegenerative disorders, such as Huntington's disease. We describe, among others, HTS assays based on protein aggregation, neuronal death, caspase activation and mutant protein clearance. Furthermore, we describe high-content screens that are being used to prioritize hits identified in such HTS assays. These assays and screening approaches should accelerate drug discovery for neurodegenerative disorders and guide the development of screening approaches for other complex disease phenotypes.     

Molecular graph convolutions: moving beyond fingerprints

Molecular “fingerprints” encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph—atoms, bonds, distances, etc.—which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.     

Peptide display in functional genomics

The completion of the human genome project has opened novel scientific avenues in functional genomics, structural genomics and proteomics. These areas have a common goal: the identification of all the proteins acting and cross-talking in a single cell at a defined moment of its lifecycle. The expansion of these areas in bioscience has been facilitated by the rapid development of high throughput screening (HTS) methods which has, in turn, attracted the business community to make investments in this novel business segment of biotechnology. By using these HTS methods, the hope is that novel targets will be validated much more rapidly speeding up the development of novel drugs. Numerous techniques and tools have emerged over the past decade for the identification of small target-specific molecular ligands that exploit a common feature: the exploration of molecular diversity using combinatorial methods. While chemists developed new methods for rapidly and efficiently synthesising and screening large collections of small molecules, biologists used recombinant DNA techniques for selecting displayed repertoires. To this end, the discovery of new low molecular weight peptides is becoming increasingly important, not only as molecular tools for the understanding of protein-protein interactions but also for the generation of lead compounds.     

ADLOC: An Aptamer‐Displacement Assay Based on Luminescent Oxygen Channeling

Functional nucleic acids, such as aptamers and allosteric ribozymes, can sense their ligands specifically, thereby undergoing structural alterations that can be converted into a detectable signal. The direct coupling of molecular recognition to signal generation enables the production of versatile reporters that can be applied as molecular probes for various purposes, including high‐throughput screening. Here we describe an unprecedented type of a nucleic acid‐based sensor system and show that it is amenable to high‐throughput screening (HTS) applications. The approach detects the displacement of an aptamer from its bound protein partner by means of luminescent oxygen channeling. In a proof‐of‐principle study we demonstrate that the format is feasible for efficient identification of small drug‐like molecules that bind to a protein target, in this case to the Sec7 domain of cytohesin. We extended the approach to a new cytohesin‐specific single chain DNA aptamer, C10.41, which exhibits a similar binding behavior to cytohesins but has the advantage of being more stable and easier to synthesize and to modify than the RNA‐aptamer M69. The results obtained with both aptamers indicate the general suitability of the aptamer‐displacement assay based on luminescent oxygen channelling (ADLOC) for HTS. We also analyzed the potential for false positive hits and identified from a library of 18 000 drug‐like small molecules two compounds as strong singlet‐oxygen quenchers. With full automation and the use of commercially available plate readers, we estimate that the ADLOC‐based assay described here could be used to screen at least 100 000 compounds per day.     

Enrichment of high-throughput screening data with increasing levels of noise using support vector machines, recursive partitioning, and laplacian-modified naive bayesian classifiers

High-throughput screening (HTS) plays a pivotal role in lead discovery for the pharmaceutical industry. In tandem, cheminformatics approaches are employed to increase the probability of the identification of novel biologically active compounds by mining the HTS data. HTS data is notoriously noisy, and therefore, the selection of the optimal data mining method is important for the success of such an analysis. Here, we describe a retrospective analysis of four HTS data sets using three mining approaches: Laplacian-modified naive Bayes, recursive partitioning, and support vector machine (SVM) classifiers with increasing stochastic noise in the form of false positives and false negatives. All three of the data mining methods at hand tolerated increasing levels of false positives even when the ratio of misclassified compounds to true active compounds was 5:1 in the training set. False negatives in the ratio of 1:1 were tolerated as well. SVM outperformed the other two methods in capturing active compounds and scaffolds in the top 1%. A Murcko scaffold analysis could explain the differences in enrichments among the four data sets. This study demonstrates that data mining methods can add a true value to the screen even when the data is contaminated with a high level of stochastic noise.     

High‐Throughput Screening in Olefin‐Polymerization Catalysis: From Serendipitous Discovery Towards Rational Understanding

High–throughput‐screening (HTS) tools and methods are used more and more, especially in industry, in the search for new, selective organometallic catalysts. In most cases, the approach is, in essence, empirical, and the strategy is to increase the number of experiments that can be run at a given place in a given time. Highly miniaturized, parallel reaction setups have been implemented for the rapid assessment of whether novel catalysts resulting from the structural amplification of a basic framework are “good” or “bad” with respect to the properties of interest, and, depending on the response, worthy of a subsequent, more‐careful evaluation. In this article, we demonstrate that it is possible to utilize these state‐of‐the‐art HTS platforms with a different strategy: the rapid generation of reliable kinetic data for mechanistic studies in view of a thorough understanding and rational catalyst design. Ziegler–Natta‐type catalytic olefin polymerization will be used throughout as an example.

     

SAR modeling: effect of experimental ambiguity

The applicability of SAR (structure-activity relationship) techniques to data obtained using high throughput screening (HTS) and toxicogenomic techniques is explored. The reason for this study derives from the fact that for economical and time considerations HTS bioassays may consist of single determinations, i.e. lack of duplication. This introduces an element of uncertainty. Using two different data bases of fairly complex biological phenomena (allergic contact dermatitis in humans and the induction of mutations in Salmonella), it is demonstrated that the resulting SAR models can tolerate up to 20% ambiguity in the experimental data.     

High throughput screening informatics

High throughput screening (HTS), an industrial effort to leverage developments in the areas of modern robotics, data analysis and control software, liquid handling devices, and sensitive detectors, has played a pivotal role in the drug discovery process, allowing researchers to efficiently screen millions of compounds to identify tractable small molecule modulators of a given biological process or disease state and advance them into high quality leads. As HTS throughput has significantly increased the volume, complexity, and information content of datasets, lead discovery research demands a clear corporate strategy for scientific computing and subsequent establishment of robust enterprise-wide (usually global) informatics platforms, which enable complicated HTS work flows, facilitate HTS data mining, and drive effective decision-making. The purpose of this review is, from the data analysis and handling perspective, to examine key elements in HTS operations and some essential data-related activities supporting or interfacing the screening process, and outline properties that various enabling software should have. Additionally, some general advice for corporate managers with system procurement responsibilities is offered.     

The use of immortalized cell lines in GPCR screening: the good, bad and ugly

For most membrane-bound molecular targets, including G protein linked receptors (GPCRs), the optimal approach in drug discovery involves the use of cell based high throughput screening (HTS) technologies to identify compounds that modulate target activity. Most GPCRs have been cloned and can therefore be routinely expressed in immortalized cell lines. These cells can be easily and rapidly grown in unlimited quantities making them ideal for use in current HTS technologies. A significant advantage of this approach is that immortalized recombinant cells provide a homogenous background for expression of the target which greatly facilitates consistency in screening, thus allowing for a better understanding of the mechanism of action of the interacting compound or drug. Nonetheless, it is now evident that numerous disparities exist between the physiological environment of screening systems using recombinant cells and natural tissues. This has lead to a problem in the validity of the pharmacological data obtained using immortalized cells in as much as such cells do not always reflect the desired clinical efficacy and safety of the compounds under examination. This brief review discusses these issues and describes how they influence the discovery of drugs using modern HTS.     

A HTS Assay for the Detection of Organophosphorus Nerve Agent Scavengers

A new pro‐fluorescent probe aimed at a HTS assay of scavengers is able to selectively and efficiently cleave the P? S bond of organophosphorus nerve agents and by this provides non‐toxic phosphonic acid has been designed and synthesised. The previously described pro‐fluorescent probes were based on a conventional activated P? Oaryl bond cleavage, whereas our approach uses a self‐immolative linker strategy that allows the detection of phosphonothioase activity with respect to a non‐activated P? Salkyl bond. Further, we have also developed and optimised a high‐throughput screening assay for the selection of decontaminants (chemical or biochemical scavengers) that could efficiently hydrolyse highly toxic V ‐type nerve agents. A preliminary screening, realised on a small α‐nucleophile library, allowed us to identify some preliminary “hits”, among which pyridinealdoximes, α‐oxo oximes, hydroxamic acids and, less active but more original, amidoximes were the most promising. Their selective phosphonothioase activity has been further confirmed by using PhX as the substrate, and thus they offer new perspectives for the synthesis of more potent V nerve agent scavengers.     

Cheminformatics in MS-based environmental exposomics: Current achievements and future directions

Compound annotation using MS/MS data is the major bottleneck in interpretation of mass spectrometry data during non-targeted screening and suspect screening exposomics studies. Apart from compound identification using available databases or mass spectral libraries, the true challenge comes when completely new compounds have to be identified. Along with recent advances in MS instrumentation that set grounds to a new revolutionary age in environmental exposomics, a multitude of cheminformatics annotation approaches has been developed. Herein, we review the basic principles of the cutting-edge cheminformatics MS-based approaches employed in eco-exposome annotation.We give a solid background discussing the eco-exposome concept in relation to the advances in MS instrumentation, and define the three crucial cheminformatics tasks used in the eco-exposome annotation: molecular formula assignment, compound prioritization and compound annotation. The basic principles of compound annotation are discussed, which are based on three approaches of utilizing structural information inherent to MS data. These involve direct, indirect and joint annotation approaches. We assess their performance through the ability to annotate eco-exposome constituents. We discuss future perspectives and give directions to new annotation strategies and performance evaluation protocols aiming to solve current issues hampering the incorporation of cheminformatics annotation approaches in regular eco-exposome annotation workflows.     

Measuring intracellular calcium fluxes in high throughput mode

The measurement of intracellular calcium fluxes in real time is widely applied within the pharmaceutical industry to measure the activation of G-protein coupled receptors (GPCRhyp;s), either for pharmacological characterisation or to screen for new surrogate ligands. Initially restricted to G(q) coupled GPCRs, the introduction of promiscuous and chimeric G-proteins has further widened the application of these assays. The development of new calcium sensitive dyes and assays has provided sensitive, homogeneous assays which can be readily applied to high throughput screening (HTS). In this paper we describe the full automation of this assay type using a fluorometric imaging plate reader (FLIPR ) integrated into a Beckman/Sagian system to establish a simple robotic system that is well suited for the current medium throughput screening in this area of lead discovery. Using a recently completed HTS we discuss important determinants for FLIPR based screening, highlight some limitations of the current approach, and look at the requirements for future automated systems capable of keeping up with expanding compound files.     

Targeting chemical inputs and optimising HTS for agrochemical discovery

In vivo high throughput screening (HTS) has been adopted by most of the larger crop protection companies as an important tool for the discovery of new agrochemicals. There has been a paradigm shift in capabilities from screening a few thousand compounds a year to several hundred thousand and the quantity of screening sample required has fallen dramatically. The unifying goal now bringing together screens and inputs is the need to maximise the flow of useful information from HTS and thereby minimise the time taken to discover robust leads and new products. This review examines the positive changes that have occurred towards targeted design and selection of chemical inputs for agrochemical discovery over the last ten years and corresponding developments in HTS assays, data analysis and the logistics of compound storage and dispensing.     

临近闪烁分析法在高通量筛选中的应用

起源于放射性免疫分析的临近闪烁分析法(scintillation proximity assay,SPA)是一种均相、灵敏、快速和简便的基于闪烁载体的分析平台。该平台可用于筛选药物靶点的先导化合物和研究其生理过程。由于无需分离,易于固定药物靶点和检测其活性,SPA成为一种重要的高通量筛选方法。由于放射性标记分子和亲和标签分子的多样化和商业化、以及液闪计数器和液相操作等技术的发展,SPA已经广泛用于受体结合、高通量药物筛选、酶分析、放射性免疫分析、蛋白质-蛋白质相互作用和细胞水平分析等方面。本文阐述了SPA原理,讨论了其关键技术(包括闪烁载体、液闪计数器和放射性标记分子),分析了其评价体系;同时简述了SPA分析的发展, 并介绍了其在高通量筛选中的应用实例, 归纳了存在的问题,给出了未来的发展趋势。目前,基于SPA和荧光分析方法已成为高通量药物筛选的热点研究领域, 这些筛选技术的革新必然提升我们对细胞体系生物学的全面理解和促进先导化合物筛选过程的显著进步。     

Impact of molecule-based magnetic materials: A critical outlook

A critical outlook of the field of molecular magnetic materials is presented. This article is inspired by an international symposium devoted to the “Design, Characterization and Modelling of Molecule-Based Magnetic Materials (DCM4-II)” that took place at Strasbourg (France), from May 28th to June 1st, within the E-MRS 2007 Spring Meeting (Symposium R) organized by the European Materials Research Society in collaboration with the European Science Foundation. A series of papers linked to this symposium are published in this issue and in the previous issue (Volume 11, Issue 4) of Solid State Sciences.     

Design considerations for high-throughput screening and in vitro diagnostic assays

This paper reviews the several different factors that must be considered during the development of assays for high throughput screening (HTS) or in vitro diagnostic (IVD) applications. The reader is introduced to the terminology used in assay development as well as the statistical approaches for evaluating the data. The review is intended to serve as a tutorial to biotechnology, pharmaceutical and clinical professionals, the academic researcher, as well as a guide for established investigators of HTS and IVD. This review is not a comprehensive treatise in its scope or content, but is meant to introduce the reader to key concepts of assay development. Elementary mathematical and statistical tools for designing robust assays and data management are described. While certain design concepts overlap HTS and IVDs, others are more pertinent to one or the other topic. An overview of the regulatory requirements for IVDs is included in the context of the United States Food and Drug Administration. Quality concepts and high content screening are also briefly described. The review does not focus upon any particular assay technology nor does it provide detailed laboratory procedures on specific assays. The references cited are not exhaustive, but meant to steer the reader toward a general status report of the various technologies discussed. The information presented in this review is not intended to replace the judgment of the experienced laboratory scientist. However, this review should assist the scientific professional in executing well designed assays and being aware of design considerations.