High-throughput target discovery using cell-based genetics

High-throughput target discovery requires robust disease models and the ability to rapidly survey the genome for function. In the post-genomics era, there has been a strong emphasis placed upon "gene-to-function" approaches that take advantage of the large amount of gene sequence information now available. Here, we advocate a return to "function-to-gene" approaches as a first step in target discovery (and validation), followed by hypothesis-driven research to validate new targets identified by their activity in cell-based disease models.     

Opportunities and limits of cell-based assay miniaturization in drug discovery

Importance of the field: Miniaturization is a significant driver for many life-science applications and a key technology for personalized medicine. Innovations in microfluidics will make ex vivo testing in in vivo-like environment possible, thus, allowing novel pathways for drug discovery.

Areas covered in this review: This review covers the application of miniaturization technologies, namely microfluidics for cell-based assay development. We highlight the use of microfluidics in sample preparation and clinical trials, review the progress towards in vivo-like test environments and point out practical challenges in the work with microfluidic systems.

What the reader will gain: The reader will gain an overview of the different application areas of miniaturized systems for cell-based assay-methods and the technologies involved in how they can be applied in the drug discovery process is given. Examples of clinical applications are pointed out.

Take home message: Miniaturization is a key technology driver for methodological progress in drug discovery. The enabling nature of this technology is reflected in the multitude of applications covering all aspects of the drug discovery process.     

Opportunities and limits of cell-based assay miniaturization in drug discovery

Importance of the field: Miniaturization is a significant driver for many life-science applications and a key technology for personalized medicine. Innovations in microfluidics will make ex vivo testing in in vivo-like environment possible, thus, allowing novel pathways for drug discovery. Areas covered in this review: This review covers the application of miniaturization technologies, namely microfluidics for cell-based assay development. We highlight the use of microfluidics in sample preparation and clinical trials, review the progress towards in vivo-like test environments and point out practical challenges in the work with microfluidic systems. What the reader will gain: The reader will gain an overview of the different application areas of miniaturized systems for cell-based assay-methods and the technologies involved in how they can be applied in the drug discovery process is given. Examples of clinical applications are pointed out. Take home message: Miniaturization is a key technology driver for methodological progress in drug discovery. The enabling nature of this technology is reflected in the multitude of applications covering all aspects of the drug discovery process.     

The role of genomics in antibacterial target discovery

Complete DNA sequence information has now been obtained for several prokaryotic genomes, defining the entire genetic complement of these organisms. The collection of genomic data has provided new insights into the molecular architecture of bacterial cells, revealing the basic genetic and metabolic structures that support viability of the organisms. Genomic information has also revealed new avenues for inhibition of bacterial growth and viability, expanding the number of possible drug targets for antibiotic discovery. This review examines how genomic sciences and experimental tools are applied to antibacterial target discovery, the necessary first step in the development of new antibiotic classes. Significant advances have been realized in the development of functional genomic, comparative genomic, and proteomic methods for the analysis of completed genomes. The combination of these methods can be used to systematically parse the genome and identify targets worthy of inhibitor screens. Two basic categories of targets emerge from this exercise, comprising in vitro essential targets required for bacterial viability on synthetic media and in vivo essential targets required to establish and maintain infection within a host organism. Current use of genomic information is focused primarily on a definition of all in vitro essential targets that satisfy criteria of selectivity, spectrum, and novelty. As the genomes of additional bacterial pathogens are solved, it will be possible to select in vivo essential targets common to groups of select pathogens (e.g., bacterial agents of community acquired pneumonia) or even pathogen-specific targets. Consideration of host-pathogen interactions, defined at the level of gene expression for each organism, might provide novel therapeutic options in the future.     

Molecular targets in cancer drug discovery: cell-based profiling

The phrase "molecular target-based drug discovery" usually implies an in vitro biochemical assay or battery of assays. One portion of the U.S. National Cancer Institute's drug discovery program, to the contrary, examines molecular targets for cancer therapy in a cell-based format. That approach has a number of significant limitations, but it has produced databases of significant utility on the activities and structures of tested compounds, as well as on molecular characteristics of the cell types used for testing.     

Viral-mediated gene delivery for cell-based assays in drug discovery

Background: Adenovirus, retrovirus and lentivirus-based vectors, originally engineered and optimized for in vivo and ex vivo gene therapy, have become increasingly useful for viral-mediated gene delivery to support in vitro cell-based assays. Viral vectors underpin functional genomics screening of cDNA, shRNA and aptamer libraries, are used for a variety of target validation studies and importantly, for high-throughput cell-based drug discovery and compound profiling assays. The baculovirus/insect cell expression system had gained prevalence as a tool for recombinant protein production when it was observed that recombinant baculovirus vectors too could serve as efficient gene delivery vehicles for a wide range of mammalian cells. Although the use of baculovirus vectors in vivo has lagged behind retroviral, adenoviral and lentiviral vectors, they have gained prominence for development of in vitro cell-based assays due to the ease of generation, broad host range and excellent biosafety profile. There is an increasing emphasis on cell-based assays in high-throughput automated drug discovery laboratories and a variety of commercially available viral-vectors can be used for supporting these assays. Objective: We compare and contrast the current viral-mediated gene delivery vector systems and highlight their suitability for cell-based drug discovery assays. Conclusion: Viral-mediated gene delivery is increasingly being used in support of genome scale target validation studies and cell-based assay development for specific drug target genes such as ion channels, G protein-coupled receptors and intracellular enzymes. The choice of a delivery system over another for a particular application is largely dictated by the cell types and cell lines in use, virus cellular tropism, assay throughput, safety requirements and ease/cost of reagent generation.     

Label-free cell-based assays with optical biosensors in drug discovery

Once viewed solely as a tool for low throughput and kinetic analysis of biomolecular interactions, optical biosensors are gaining widespread uses in drug discovery because of recent advances in instrumentation and experimental design. These advances have expanded the capabilities of optical biosensors to meet the needs at many points in the drug discovery process. Concurrent shifts in drug discovery paradigms have seen the growing use of whole cell systems for drug screens, thus creating both a need in drug discovery and a solution in optical biosensors. This article reviews important advances in optical biosensor instrumentation, and highlights the potential of optical biosensors for drug discovery with an emphasis on whole cell sensing in both high throughput and high content fashions.     

细胞热迁移分析技术及其在靶标发现中的应用进展

细胞热迁移分析(cellular thermal shift assay,CETSA)是一种在细胞或组织中直接研究配体与蛋白结合的生物学技术,其原理是当靶蛋白与药物分子结合时,靶蛋白通常会变得稳定,不容易发生热变性.该技术可以在细胞裂解液、细胞内及组织中检测非标记药物与蛋白质的结合情况.近年来,将CETSA技术与免疫印...     

High throughput P450 inhibition screens in early drug discovery

This review of high throughput (HT) P450 inhibition technologies and their impact on early drug discovery finds the field at a mature stage. The relationship between P450 inhibition and drug-drug interactions is well understood. A wide variety of P450 inhibition detection technologies are readily available off-the-shelf, but what seems still to be missing is a general agreement on how much weight one should give to the various types of early discovery HT P450 inhibition data. Method-dependent potency differences are a cause of concern, and to resolve this issue the authors advocate calibration of the HT methods with a large set of marketed drugs.     

Bioinformatics and cancer target discovery

The convergence of genomic technologies and the development of drugs designed against specific molecular targets provides many opportunities for using bioinformatics to bridge the gap between biological knowledge and clinical therapy. Identifying genes that have properties similar to known targets is conceptually straightforward. Additionally, genes can be linked to cancer via recurrent genomic or genetic abnormalities. Finally, by integrating large and disparate datasets, gene-level distinctions can be made between the different biological states that the data represents. These bioinformatics approaches and their associated methodologies, which can be applied across a range of technologies, facilitate the rapid identification of new target leads for further experimental validation.     

晚期糖基化终末产物受体及其抑制剂的研究进展

晚期糖基化终末产物受体(receptor for advanced glycation end products,RAGE)是一种多配体的膜受体,与配体结合后可启动多条信号通路,引起细胞内氧化应激和炎症反应等,导致细胞功能紊乱。RAGE在糖尿病并发症、炎症、阿尔采末病和肿瘤等疾病的发生和发展中起重要作用。应用可溶性RAGE(sRAGE)、抗RAGE抗体或干扰RAGE与配体结合的抑制剂阻断RAGE的活化,是防治上述疾病的新策略。该文对RAGE配体与疾病的关系和RAGE-配体激活的信号通路进行阐述,并对近年来关于RAGE抑制剂的研究进展进行总结。     

Antibody libraries in drug and target discovery

Antibody libraries have come of age in the generation and evolution of monoclonal antibodies for therapeutic applications. Here, with an emphasis on cancer therapy, several examples are presented that illustrate the ability to design, engineer and select antibody libraries for different rationales in drug and target discovery.     

Rethinking target discovery in polygenic diseases

Despite an extraordinary investment in R&D the yield of successful new drugs has been disproportionately low in recent years, suggesting that the whole process of drug development requires rethinking and reform. Most analyses on this issue focus on molecular target discovery considerations. Target identification is characterized by a surplus of potential targets, but there is a translational bottleneck primarily due to limitations of currently employed target validation platforms. Meanwhile, the clinical entities, to which treatments are directed, are also highly complex in terms of pathophysiologic mechanisms and manifestations. In the present study we discuss the limitations of current molecular target discovery approaches mainly in regard to selectivity and efficacy. We also describe the constraints imposed on drug development by the current diagnostic constructs and the tendency towards dissecting the complex clinical phenotypes to component intermediate phenotypes. Finally, we describe how the reconsideration of molecular and clinical targets in polygenic diseases may lead to new strategies of pharmacological intervention directed against component dysfunctions, rather than the whole complex phenotype. Such strategies involve the combination of single ligands that act selectively on multiple molecules involved in a particular disease, or the employment of "multi-targeted" drugs, i.e. single drug molecules that hit selectively multiple receptors sharing common binding sites.     

The Wnt-dependent signaling pathways as target in oncology drug discovery

Summary Our current understanding of the Wnt-dependent signaling pathways is mainly based on studies performed in a number of model organisms including, Xenopus, Drosophila melanogaster, Caenorhabditis elegans and mammals. These studies clearly indicate that the Wnt-dependent signaling pathways are conserved through evolution and control many events during embryonic development. Wnt pathways have been shown to regulate cell proliferation, morphology, motility as well as cell fate. The increasing interest of the scientific community, over the last decade, in the Wnt-dependent signaling pathways is supported by the documented importance of these pathways in a broad range of physiological conditions and disease states. For instance, it has been shown that inappropriate regulation and activation of these pathways is associated with several pathological disorders including cancer, retinopathy, tetra-amelia and bone and cartilage disease such as arthritis. In addition, several components of the Wnt-dependent signaling pathways appear to play important roles in diseases such as Alzheimer’s disease, schizophrenia, bipolar disorder and in the emerging field of stem cell research. In this review, we wish to present a focused overview of the function of the Wnt-dependent signaling pathways and their role in oncogenesis and cancer development. We also want to provide information on a selection of potential drug targets within these pathways for oncology drug discovery, and summarize current data on approaches, including the development of small-molecule inhibitors, that have shown relevant effects on the Wnt-dependent signaling pathways.     

胚胎干细胞的代谢组学方法在毒理学中的应用进展

胚胎干细胞(ESC)是高度未分化的细胞,具备体外无限增殖和诱导分化成三个胚层细胞的特性,所以胚胎干细胞可以作为一种毒性评价的工具。代谢组学是近年来发展起来的对某一生物或细胞内源性的所有低分子量代谢产物进行定量和定性分析的一门新学科,它以生物体液,细胞提取物,细胞培养液和组织等为研究对象,研究手段主要是核磁共振和质谱。该文综述了胚胎干细胞和代谢组学相关的实验技术及其在毒理学中的应用现状,同时对基于胚胎干细胞的代谢组学在毒理学研究中的应用和发展趋势进行了探讨。     

The application of multi-component reactions in drug discovery

Multi-component reactions (MCRs) enable the facile, automated and high throughput generation of small organic molecules. MCRs have been used to create diversity oriented and biased combinatorial libraries, to accomplish the synthesis of highly complex natural products as well as for the large-scale production of drug candidates. This provides medicinal chemists with a powerful tool to create novel chemical diversity, matching the space of biological targets with relevant chemistry. The discovery of novel MCRs has become an increasingly active area of research, yielding novel chemical scaffolds for drug discovery efforts.     

The heart of drug discovery and development: rational target selection

Critical to the discovery and development of drugs and vaccines is the rational selection of biochemical, immunologic or molecular targets. To understand the rationale for target selection, we review strengths and weaknesses of the four main approaches: whole animal disease models; molecular targeting; epidemiology/observation studies, and genomics. After classifying diseases into those with a relatively stable pathophysiology (e.g., hypertension and gout) versus those with an unstable pathophysiology (e.g., AIDS and influenza) to aid in understanding target selection, we provide examples of successful and unsuccessful selection of drug and vaccine targets, focusing on the molecular and epidemiological/observational approaches. We discuss the reasons that molecular targeting has led to successful control of many diseases, whereas the epidemiological/observational approach has had a checkered history. We also assess the potential power of the genomic approach, specifically the curative versus controlling/preventive strategies. With combined genetic and molecular approaches and judicious use of whole animal models and properly performed epidemiology/observation studies to select the appropriate targets, the future for controlling, preventing and even curing many diseases is very bright indeed.