High-content siRNA screening for target identification and validation

Background: Automated microscopy and image analysis have progressed tremendously over the past 10 years and opened up a new era of high-content screening. In parallel, RNA interference (RNAi) has revolutionized the functional analysis of genes. Objective: The focus of this review is screening of RNAi libraries, and in particular in screening of short interfering RNA (siRNA) libraries for target identification and validation in mammalian cell systems. Methods: Recent literature of high-content siRNA screening in oncology, in intracellular trafficking and infection biology, and in neurobiology is reviewed and placed in the context of a discussion on hit verification. Results/conclusion: Various methods have been established for the application of RNAi in mammalian cells also, which allows efficient and reproducible silencing of individual genes to gain functional information on each individual gene. Complex multi-parametric cell-based assays, combined with both technologies, provide an extraordinary valuable tool to help understand biological and pathological processes in a systematic way and discover new targets for pharmaceutical exploitation.     

Screening protocol for the identification of modulators by immunofluorescent cell‐based assay

High‐throughput assays are a common strategy for the identification of compounds able to modulate a certain cellular activity. Here, we show an automatized analysis platform for the quantification of nuclear foci as inhibitory effect of compounds on a target protein labeled by fluorescent antibodies. Our experience led us to a fast analysis platform that combines cell‐based assays, high‐content screening, and confocal microscopy, with an automatic and user‐friendly statistical analysis of plate‐based assays including positive and negative controls, able to identify inhibitory effect of compounds tested together with the Z‐prime and Window of individual plate‐based assays to assess the reliability of the results. The platform integrates a web‐based tool implemented in Pipeline Pilot and R, and allows computing the inhibition values of different parameters obtained from the high‐content screening and confocal microscopy analysis. This facilitates the exploration of the results using the different parameters, providing information at different levels as the number of foci observed, the sum of intensity of foci, area of foci, etc, the detection and filtering of outliers over the assay plate, and finally providing a set of statistics of the parameters studied together with a set of plots that we believe significantly helps to the interpretation of the assay results.     

Drug target identification and quantitative proteomics

The emerging technologies in proteomic analysis provide great opportunity for the discovery of novel therapeutic drug targets for unmet medical needs through delivering of key information on protein expression, post-translational modifications and protein–protein interactions. This review presents a summary of current quantitative proteomic concepts and mass spectrometric technologies, which enable the acceleration of target discovery. Examples of the strategies and current technologies in the target identification/validation process are provided to illustrate the successful application of proteomics in target identification, in particular for monoclonal antibody therapies. Current bottlenecks and future directions of proteomic studies for target and biomarker identification are also discussed to better facilitate the application of this technology.     

An industry perspective on drug target validation

Pushing the pharmaceutical industry to improve its performance, are years of poor returns on investment in research and development as well as the patients’ advocacy for their unmet medical needs. Pulling on our industry, we find an exploding scientific knowledge of disease mechanisms and the translation of this information into treatments by innovative biotechnology companies. Those companies that manage best these push–pull forces – in particular, the therapies provided by biotechnology – will succeed in creating the innovative medicines of tomorrow.     

Principles of early drug discovery

Developing a new drug from original idea to the launch of a finished product is a complex process which can take 12-15 years and cost in excess of $1 billion. The idea for a target can come from a variety of sources including academic and clinical research and from the commercial sector. It may take many years to build up a body of supporting evidence before selecting a target for a costly drug discovery programme. Once a target has been chosen, the pharmaceutical industry and more recently some academic centres have streamlined a number of early processes to identify molecules which possess suitable characteristics to make acceptable drugs. This review will look at key preclinical stages of the drug discovery process, from initial target identification and validation, through assay development, high throughput screening, hit identification, lead optimization and finally the selection of a candidate molecule for clinical development.     

Applications of CRISPR genome editing technology in drug target identification and validation

Introduction: The analysis of pharmaceutical industry data indicates that the major reason for drug candidates failing in late stage clinical development is lack of efficacy, with a high proportion of these due to erroneous hypotheses about target to disease linkage. More than ever, there is a requirement to better understand potential new drug targets and their role in disease biology in order to reduce attrition in drug development. Genome editing technology enables precise modification of individual protein coding genes, as well as noncoding regulatory sequences, enabling the elucidation of functional effects in human disease relevant cellular systems.

Areas covered: This article outlines applications of CRISPR genome editing technology in target identification and target validation studies.

Expert opinion: Applications of CRISPR technology in target validation studies are in evidence and gaining momentum. Whilst technical challenges remain, we are on the cusp of CRISPR being applied in complex cell systems such as iPS derived differentiated cells and stem cell derived organoids. In the meantime, our experience to date suggests that precise genome editing of putative targets in primary cell systems is possible, offering more human disease relevant systems than conventional cell lines.     

秀丽隐杆线虫在医药学领域的应用和进展

模式生物秀丽隐杆线虫 (Caenorhabditis elegans) 对基础生物学研究贡献卓著。随着功能基因组时代的到来, 线虫被视为可借以探明人类致病基因或致病相关因子, 寻找可能的药物靶点的强大工具。这得益于线虫的丰富的可利用生物学信息, 灵活多样的遗传学可操作性, 简易的培养维持条件, 尤其是其独特的生理特点适合于大规模化学药物的体内筛选或全基因组功能研究。本文将从新药研发的角度总结线虫的特点, 与人类基因的同源性, 讨论以线虫为技术平台的药物研发主要方法, 以及成功案例, 并探讨线虫在医药学领域的发展热点。     

Functional genomic and high-content screening for target discovery and deconvolution

Introduction: Functional genomic screens apply knowledge gained from the sequencing of the human genome toward rapid methods of identifying genes involved in cellular function based on a specific phenotype. This approach has been made possible through advances in both molecular biology and automation. The utility of this approach has been further enhanced through the application of image-based high-content screening: an automated microscopy and quantitative image analysis platform. These approaches can significantly enhance the acquisition of novel targets for drug discovery.

Areas covered: Both the utility and potential issues associated with functional genomic screening approaches are discussed in this review, along with examples that illustrate both. The considerations for high-content screening applied to functional genomics are also presented.

Expert opinion: Functional genomic screening and high-content screening are extremely useful in the identification of new drug targets. However, the technical, experimental, and computational parameters have an enormous influence on the results. Thus, although new targets are identified, caution should be applied to the interpretation of screening data in isolation. Genomic screens should be viewed as an integral component of a target identification campaign that requires both the acquisition of orthogonal data, as well as a rigorous validation strategy.     

G-蛋白偶联受体的功能测定和高通量药物筛选

G 蛋白偶联受体家族是药物开发中最大的一类药物靶点 ,高通量药物筛选是开发药物早期阶段的最重要工具之一。根据G 蛋白偶联受体与配体结合及激发的信号通路 ,人们设计了各种可行的功能测试方法 ,用于G 蛋白偶联受体为药靶的高通量药物筛选 ,如 :微体积荧光数字图像测定技术 (Fluorometicmicrovolumeassaytechnology ,FMAT)、荧光偏振 (Fluoresencepolarization ,FP)、竞争性ELISA (Com petitiveenzyme linkedimmunosorbent)、闪烁邻近测定法(Scintillation proximityassay ,SPA)、载黑色素细胞测定法(Melanophoreassay)、报告基因测定法 (Reportergeneassay)和钙离子测定法等测定方法。在这些方法中 ,报告基因测定法和钙离子测定法占了主导地位。非放射性、无需底物和辅助剂的报告基因测定方法和荧光钙离子指示剂的钙离子测定方法可能是将来G 蛋白偶联受体的功能分析和高通量药物筛选的发展方向     

微型细菌回复突变试验方法的建立及验证

目的 建立高通量评价药物遗传毒性的微型细菌回复突变（Ames）试验。方法 采用平皿掺入法进行标准Ames试验,采用6孔板掺入法进行微型Ames试验,两试验均设置阴性对照组和阳性对照组,2组又分别分为代谢活化和非活化2个亚组,各组培养基中分别加入菌液（鼠伤寒沙门菌组氨酸缺陷型菌株：TA97、TA98、TA100、TA102和TA1535）,活化组加大鼠肝微粒体酶（S9）混合液,阳性对照组再加入阳性诱变剂：Dexon（-S9）,应用于TA97、TA98和TA102;NaN₃（-S9）,应用于TA100和TA1535;2-AA（+S9）,应用于TA97、TA98、TA100、TA102和TA1535。凝固后37℃温箱培养约48 h,计数各组回变菌落数。结果 在标准Ames试验中,阴性对照组各个菌株回变菌落数均在本实验室自发回变菌落数正常值范围内。在两试验中,阳性对照组所诱导的回变菌落数均是阴性对照组的2倍以上,标准试验细菌回变菌落数约为微型试验的5倍。结论 在6孔板上进行微型细菌回复突变试验,大大减少了受试物的用量,提高了筛选速度。本实验室建立的微型细菌回复突变试验背景数据,用于遗传毒理的检测是高效可靠的。     

RNAi: for functional analysis and target validation

The third annual conference on discovery on target, organised by the Cambridge Healthtech Institute was held on 19 – 20 October 2005, in Boston. More than 300 delegates from both academic and industrial institutes attended the meeting. The presentations provided insights into understanding the RNA interference technology as a useful tool to identify and validate new targets for therapeutic intervention. Discussions focused in the design of siRNA for effective gene silencing, RNAi screens to identify new targets, RNAi delivery and the in vivo validation of targets using this technology.     

Current possibilities and unresolved issues of drug target validation in Mycobacterium tuberculosis

Introduction: Target driven drug discovery is a long and arduous task requiring a huge investment of time, energy and resources. Therefore, it is very important to select targets which provide the maximum chance of obtaining inhibitors that will be efficacious in animal models and finally in tuberculosis (TB) patients.

Areas covered: The article discusses the necessity for new targets in Mycobacterium tuberculosis (Mtb) drug discovery and how the functional redundancy of putative targets in Mtb adds a new dimension to the complexity of validation. The article also reviews survival kinetics using conditional knockout (KO) or knockdown (KD) strains and discusses how this has provided crucial information on target vulnerability. Furthermore, the article also comments on how the chemical validation of new targets using specific inhibitors has greatly supplemented the genetic validation efforts.

Expert opinion: Because of complexity of pathogenesis of TB, the putative drug targets need to be validated under multiple physiological conditions. Target protein depletion can mimic chemical inhibition and, therefore, will be a valuable tool in predicting the vulnerability of a target. Conditional KO or KD makes it possible to study the phenotypes of Mtb strains under a variety of physiological states. The phenotype of these strains should also be tested in animal models which mimic human TB more closely. Finally, inhibitors with confirmed mode of action can be important tools for validating Mtb drug targets.     

化合物药物活性的高通量筛选

介绍高通量药物筛选系统的组成及其相关技术。结合国家药物筛选中心的工作,详细介绍了化合物药物活性的高通量筛选的４ 个组成部分及其在药物发现过程中的作用。高通量药物筛选系统是一个涉及多个学科的、以分子生物学、新型检测技术技术为基础的新型药物发现系统。高通量药物筛选系统的顺利开展可以加速我国的新药研究     

新药研发过程中毒理学研究方法的进展--毒性的原因和早期毒性筛选

毒性已成为新药开发过程中淘汰的主要原因。近年来制药和生物技术工业的研究人员开发了多种新技术以便在药物发现和开发过程中尽早确定化合物的安全特性。笔者首先对药物毒性产生的原因如药靶的特异性、药物的分子结构、药物代谢和代谢动力学等方面进行了分析，再介绍了近几年早期毒性筛选的新技术，包括预测模型、体外高通量毒性筛选、活性代谢产物的检测、高内涵筛选技术、动物实验。     

药物高通量筛选的设计与实施

本文在简要介绍药物高通量筛选体系的基础上,就组建高效能的高通量筛选体系需要关注的因素,如作用靶点、测试方法、检测方法与作用靶点的匹配、关键参数、效能评价等进行了重点阐述,为高通量筛选体系的设计和实施提供了有益的借鉴。     

Using reverse docking for target identification and its applications for drug discovery

ABSTRACT

Introduction: In contrast to traditional molecular docking, inverse or reverse docking is used for identifying receptors for a given ligand among a large number of receptors. Reverse docking can be used to discover new targets for existing drugs and natural compounds, explain polypharmacology and the molecular mechanism of a substance, find alternative indications of drugs through drug repositioning, and detecting adverse drug reactions and drug toxicity.

Areas covered: In this review, the authors examine how reverse docking methods have evolved over the past fifteen years and how they have been used for target identification and related applications for drug discovery. They discuss various aspects of target databases, reverse docking tools and servers.

Expert opinion: There are several issues related to reverse docking methods such as target structure dataset construction, computational efficiency, how to include receptor flexibility, and most importantly, how to properly normalize the docking scores. In order for reverse docking to become a truly useful tool for the drug discovery, these issues need to be adequately resolved.     

Uncovering genetic relationships using small molecules that selectively target yeast cell cycle mutants

Genetic analysis in budding yeast has shown that multiple G1 cyclins and cyclin-dependent kinases control cell cycle entry, polarized growth, and spindle pole duplication. The G1 cyclins Cln1 and Cln2 associate with the cyclin-dependent kinase Cdc28 to facilitate cell cycle progression and development of the cleavage apparatus. We have developed a chemical genetic approach toward the discovery of compounds that target G1 control pathways by screening for compounds that selectively kill a yeast strain lacking the G1 cyclins Cln1 and Cln2. A class of small molecules was identified that is highly toxic toward the cln1 Delta cln2 Delta double mutant and has relatively little effect on wild-type yeast. We call these compounds 'clinostatins' for their selectivity toward the cln1/2 deletion strain. Clinostatins were used in a genome-wide chemical synthetic lethality screen to identify other genes required for growth in the presence of the drug. Other deletions that were sensitive to the drug include members of the protein kinase C(PKC)-dependent MAP kinase pathway. These results suggest an approach for combining chemical synthetic lethality and chemical genomic screens to uncover novel genetic interactions that can be applied to other eukaryotic pathways of interest.     

Using grid techniques for drug target identification

The completion of the sequencing of the human genome has opened an unprecedented opportunity in the discovery of novel drug targets for disease therapy. However, one of the major challenges facing the drug discovery community is the expanding of data and the need of large-scale computational power in a collaborative environment. Grid techniques can present an architectural framework that aims to provide access to heterogeneous resources in a secure, reliable and scalable manner across various administrative boundaries for drug discovery, which has been a promising strategy for solving large-scale problems in modern pharmaceutical R&D. In this review, we discuss the current applications of Grid technology in drug target protein identification process; and an overview of drug target discovery system architecture, focusing in particular on the data manager service system architecture is also proposed.     

DNA microarray technology for target identification and validation

1. Microarrays, a recent development, provide a revolutionary platform to analyse thousands of genes at once. They have enormous potential in the study of biological processes in health and disease and, perhaps, microarrays have become crucial tools in diagnostic applications and drug discovery. 2. Microarray based studies have provided the essential impetus for biomedical experiments, such as identification of disease-causing genes in malignancies and regulatory genes in the cell cycle mechanism. Microarrays can identify genes for new and unique potential drug targets, predict drug responsiveness for individual patients and, finally, initiate gene therapy and prevention strategies. 3. The present article reviews the principles and technological concerns, as well as the steps involved in obtaining and analysing of data. Furthermore, applications of microarray based experiments in drug target identifications and validation strategies are discussed. 4. To exemplify how this tool can be useful, in the present review we provide an overview of some of the past and potential future aspects of microarray technology and present a broad overview of this rapidly growing field.