High throughput screening for orphan and liganded GPCRs

GPCRs had significant representation in the drug discovery portfolios of most major commercial drug discovery organizations for many years. This is due in part to the diverse biological roles mediated by GPCRs as a class, as well as the empirical discovery that they have proven relatively tractable to the development of small molecule therapeutics. Publication of the human genome sequence in 2001 confirmed GPCRs as the largest single gene superfamily with more than 700 members, furthering the already strong appeal of addressing this target class using efficient and highly parallelized platform approaches. The GPCR research platform implemented at Amgen is used as a case study to review the evolution and implementation of available assays and technologies applicable to GPCR drug discovery. The strengths, weaknesses, and applications of assay technologies applicable to G alpha s, G alpha i and G alpha q-coupled receptors are described and their relative merits evaluated. Particular consideration is made of the role and practice of "de-orphaning" and signaling pathway characterization as a pre-requisite to establishing effective screens. In silico and in vitro methodology developed for rapid, parallel high throughput hit characterization and prioritization is also discussed extensively.     

The regulation of the secondary metabolism of Streptomyces: new links and experimental advances

Streptomycetes and other actinobacteria are renowned as a rich source of natural products of clinical, agricultural and biotechnological value. They are being mined with renewed vigour, supported by genome sequencing efforts, which have revealed a coding capacity for secondary metabolites in vast excess of expectations that were based on the detection of antibiotic activities under standard laboratory conditions. Here we review what is known about the control of production of so-called secondary metabolites in streptomycetes, with an emphasis on examples where details of the underlying regulatory mechanisms are known. Intriguing links between nutritional regulators, primary and secondary metabolism and morphological development are discussed, and new data are included on the carbon control of development and antibiotic production, and on aspects of the regulation of the biosynthesis of microbial hormones. Given the tide of antibiotic resistance emerging in pathogens, this review is peppered with approaches that may expand the screening of streptomycetes for new antibiotics by awakening expression of cryptic antibiotic biosynthetic genes. New technologies are also described that have potential to greatly further our understanding of gene regulation in what is an area fertile for discovery and exploitation     

Discovery of novel targets with high throughput RNA interference screening

High throughput technologies have the potential to affect all aspects of drug discovery. Considerable attention is paid to high throughput screening (HTS) for small molecule lead compounds. The identification of the targets that enter those HTS campaigns had been driven by basic research until the advent of genomics level data acquisition such as sequencing and gene expression microarrays. Large-scale profiling approaches (e.g., microarrays, protein analysis by mass spectrometry, and metabolite profiling) can yield vast quantities of data and important information. However, these approaches usually require painstaking in silico analysis and low-throughput basic wet-lab research to identify the function of a gene and validate the gene product as a potential therapeutic drug target. Functional genomic screening offers the promise of direct identification of genes involved in phenotypes of interest. In this review, RNA interference (RNAi) mediated loss-of-function screens will be discussed and as well as their utility in target identification. Some of the genes identified in these screens should produce similar phenotypes if their gene products are antagonized with drugs. With a carefully chosen phenotype, an understanding of the biology of RNAi and appreciation of the limitations of RNAi screening, there is great potential for the discovery of new drug targets.     

Toward a new generation of therapeutics: artificial cell targeted delivery of live cells for therapy

Scientific evidence in the prevention and treatment of various disorders is accumulating regarding probiotics. The health benefits supported by adequate clinical data include increased resistance to infectious disease, decreased duration of diarrhea, management of inflammatory bowel disease, reduction of serum cholesterol, prevention of allergy, modulation of cytokine gene expression, and suppression of carcinogen production. Recent ventures in metabolic engineering and heterologous protein expression have enhanced the enzymatic and immunomodulatory effects of probiotics and, with time, may allow more active intervention among critical care patients. In addition, a number of approaches are currently being explored, including the physical and chemical protection of cells, to increase probiotic viability and its health benefits. Traditional immobilization of probiotics in gel matrices, most notably calcium alginate and kappa-carrageenan, has frequently been employed, with noted improvements in viability during freezing and storage. Conflicting reports exist, however, on the protection offered by immobilization from harsh physiologic environments. An alternative approach, microencapsulation in "artificial cells," builds on immobilization technologies by combining enhanced mechanical stability of the capsule membrane with improved mass transport, increased cell loading, and greater control of parameters. This review summarizes the current clinical status of probiotics, examines the promises and challenges of current immobilization technologies, and presents the concept of artificial cells for effective delivery of therapeutic bacterial cells.     

Evolution and Operating Experiences with Different Drop‐On‐Demand Systems

Summary: We describe the development of different drop‐on‐demand systems particularly for applications for the liquid handling of biopolymers. Different designs of drop‐on‐demand systems developed by the authors are described. Experiments with these systems show the applicability for pipetting different liquids with different properties. Commercially available systems are also tested. A comparison of the different approaches leads to a discussion of the best fields of application of the different approaches or, alternatively, to the potential further development of the drop‐on‐demand technologies.

Principle setup of the print heads.     

The Royal Society of Chemistry and the delivery of chemistry data repositories for the community

Since 2009 the Royal Society of Chemistry (RSC) has been delivering access to chemistry data and cheminformatics tools via the ChemSpider database and has garnered a significant community following in terms of usage and contribution to the platform. ChemSpider has focused only on those chemical entities that can be represented as molecular connection tables or, to be more specific, the ability to generate an InChI from the input structure. As a structure centric hub ChemSpider is built around the molecular structure with other data and links being associated with this structure. As a result the platform has been limited in terms of the types of data that can be managed, and the flexibility of its searches, and it is constrained by the data model. New technologies and approaches, specifically taking into account a shift from relational to NoSQL databases, and the growing importance of the semantic web, has motivated RSC to rearchitect and create a more generic data repository utilizing these new technologies. This article will provide an overview of our activities in delivering data sharing platforms for the chemistry community including the development of the new data repository expanding into more extensive domains of chemistry data.     

Gene network coherence based on prior knowledge using direct and indirect relationships

Gene networks (GNs) have become one of the most important approaches for modeling biological processes. They are very useful to understand the different complex biological processes that may occur in living organisms. Currently, one of the biggest challenge in any study related with GN is to assure the quality of these GNs. In this sense, recent works use artificial data sets or a direct comparison with prior biological knowledge. However, these approaches are not entirely accurate as they only take into account direct gene–gene interactions for validation, leaving aside the weak (indirect) relationships.We propose a new measure, named gene network coherence (GNC), to rate the coherence of an input network according to different biological databases. In this sense, the measure considers not only the direct gene–gene relationships but also the indirect ones to perform a complete and fairer evaluation of the input network. Hence, our approach is able to use the whole information stored in the networks. A GNC JAVA-based implementation is available at: http://fgomezvela.github.io/GNC/.The results achieved in this work show that GNC outperforms the classical approaches for assessing GNs by means of three different experiments using different biological databases and input networks. According to the results, we can conclude that the proposed measure, which considers the inherent information stored in the direct and indirect gene–gene relationships, offers a new robust solution to the problem of GNs biological validation.     

Combinatorial and high-throughput materials science

There is increasing acceptance of high-throughput technologies for the discovery, development, and optimization of materials and catalysts in industry. Over the years, the relative synchronous development of technologies for parallel synthesis and characterization has been accompanied by developments in associated software and information technologies. This Review aims to provide a comprehensive overview on the state of the art of the field by selected examples. Technologies developed to aid research on complex materials are covered as well as databases, design of experiment, data-mining technologies, modeling approaches, and evolutionary strategies for development. Different methods for parallel synthesis provide single sample libraries, gradient libraries for electronic or optical materials, similar to polymers and catalysts, and products produced through formulation strategies. Many examples illustrate the variety of isolated solutions and document the barely recognized variety of new methods for the synthesis and analysis of almost any material. The Review ends with a summary of success stories and statements on still-present problems and future tasks.     

Methodological approaches for the study of GABA<Subscript>A</Subscript> receptor pharmacology and functional responses

Inhibitory GABA_A receptor ion channels are the target for a wide range of clinically-used therapeutic agents. The complex structural diversity of these ligand-gated channels, revealed by molecular cloning studies, together with increasing requirements for higher-throughput functional assays in drug discovery, has led to the development of a wide range of techniques to examine GABA_A receptor pharmacology and function. In the current article we review some of the methodologies which have contributed to the expansion of knowledge in this field. The techniques include: molecular approaches, immunoprecipitation, and immunopurification to study receptor assembly, structure, and functional expression; in situ hybridization, immunocytochemistry, and autoradiography to examine receptor distribution in native tissues; radioligand binding, site-directed mutagenesis, and electrophysiology to examine pharmacology and allosteric modulation; and patch clamp, ion flux, microphysiometry, and a variety of novel fluorescence-based technologies to examine ion-channel function. The use of gene targetting approaches in transgenic mice has also provided important insights into the role of specific GABA_A receptor subtypes in vivo. The continuing evolution of novel technologies and assay approaches with appropriate sensitivity and resolution to measure subtle modulation of GABA_A ion channels will facilitate ongoing investigation of the physiological functions of these important inhibitory receptors.     

Identifying novel prostate cancer associated pathways based on integrative microarray data analysis

The development and diverse application of microarray and next generation sequencing technologies has made the meta-analysis widely used in expression data analysis. Although it is commonly accepted that pathway, network and systemic level approaches are more reproducible than reductionism analyses, the meta-analysis of prostate cancer associated molecular signatures at the pathway level remains unexplored. In this article, we performed a meta-analysis of 10 prostate cancer microarray expression datasets to identify the common signatures at both the gene and pathway levels. As the enrichment analysis result of GeneGo's database and KEGG database, 97.8% and 66.7% of the signatures show higher similarity at pathway level than that at gene level, respectively. Analysis by using gene set enrichment analysis (GSEA) method also supported the hypothesis. Further analysis of PubMed citations verified that 207 out of 490 (42%) pathways from GeneGo and 48 out of 74 (65%) pathways from KEGG were related to prostate cancer. An overlap of 15 enriched pathways was observed in at least eight datasets. Eight of these pathways were first described as being associated with prostate cancer. In particular, endothelin-1/EDNRA transactivation of the EGFR pathway was found to be overlapped in nine datasets. The putative novel prostate cancer related pathways identified in this paper were indirectly supported by PubMed citations and would provide essential information for further development of network biomarkers and individualized therapy strategy for prostate cancer.     

The CellCard System: a novel approach to assessing compound selectivity for lead prioritization of G protein-coupled receptors

Advances in high throughput screening technologies have led to the identification of many small molecules, "hits", with activities toward the target of interest. And, as the screening technologies become faster and more robust, the rate at which the molecules are identified continues to increase. This evolution of high throughput screening technologies has generated a significant strain on the laboratories involved with the downstream profiling of these hits using cell-based assays. The CellCard System, by enabling multiple targets and/or cell lines to be assayed simultaneously within a single well, provides a platform on which selectivity screening can be quickly and robustly performed. Here we describe two case studies using the beta-lactamase and beta-galactosidase reporter gene systems to characterize G protein-coupled receptor agonist activity. Using these examples we demonstrate how the implementation of this technology enables assay miniaturization without micro-fluidic devices as well as how the inclusion of intra-well controls can provide a means of data quality assessment within each well.     

Molecular site assessment and process monitoring in bioremediation and natural attenuation

A variety of modern biotechnical approaches are available to assist in optimizing and controlling bioremediation processes. These approaches are broad-ranging, and may include genetic engineering to improve biodegradative performance, maintenance of the environment, and process monitoring and control. In addition to direct genetic engineering strategies, molecular diagnostic and monitoring technology using DNA gene probing methods and new quantitative mRNA analytical procedures allows direct analysis of degradative capacity, activity, and response underin situ conditions. Applications of these molecular approaches in process developments for trichloroethylene (TCE), polychlorinated biphenyls (PCB), and polynuclear aromatic hydrocarbons (PAH) bio-oxidation in soils, aquifer sediments, and ground-water treatment reactors have been demonstrated. Molecular genetic technologies permit not only the development of new processes for bioremediation, but also new process monitoring, control strategies, and molecular optimization paradigms that take full advantage of vast and diverse abilities of microorganisms to destroy problem chemicals.     

The fluoride dilemma

The implications of environmental contamination by fluoride on human health call upon the need for the development of monitoring systems for the ‘in situ’ detection of fluoride in contaminated sources and new technologies approaches for their removal. This paper reports recent work on the design of calixpyrrole receptors selective for the fluoride anion. The various steps undertaken for the thermodynamic characterization of these receptors and their anionic complexes are discussed. Thus based on thermodynamic data, the medium and ligand effects on selectivity are quantitatively assessed using representative calixpyrrole derivatives.     

化学计量学方法在脂质组学数据解析中的应用

脂质组学是依赖于分析技术而发展的一门新兴学科,用于全面表征与基因调控、蛋白表达、脂质代谢密切相关的脂质分子,揭示脂质在各种生命活动中的作用机制和代谢途径网络。随着质谱及其联用技术进一步发展和完善,脂质组学逐渐向快速、自动化和高通量的方向发展,而大规模的脂质组数据分析已成为脂质组学研究领域的一大难点。化学计量学主要应用于脂质组学中的基线校正和背景扣除、信号峰识别、同位素分布解析、统计分析等过程,因此,基于化学计量学方法的脂质组学数据自动化解析策略成为研究者关心的热点。该文对近年来化学计量学在脂质组学数据解析中的应用进行了综述,并对基于化学计量学的脂质组学数据解析的未来发展进行了展望。     

Proteomics on a chip: promising developments

The field of proteomics is expanding rapidly due to the completion of the human genome and the realization that genomic information is often insufficient to comprehend cellular mechanisms. This considerable expansion of proteomics towards high-throughput platforms is stressing its current technical capabilities. In recent years, technologies in microfluidic and array technologies have appeared for proteomics. These novel approaches might help solve current technical challenges in proteomics. This review presents a general survey of the recent development in microfluidic and array technologies from a proteomics perspective.     

Integration of genomic data for pharmacology and toxicology using Internet resources

Genome based technologies such as sequencing and gene expression profiling using microarrays are creating massive amounts of data. Results from these studies have provided unique insights into targets, biochemical pathways, and biological systems affected by drug or xenobiotic chemical treatments. Moreover, these genomic technologies offer the potential to identify biomarkers for pharmacological development or toxicological prediction. Nonetheless, microarray studies involving a single compound produce useful although limited data. To gain further power from these individual studies, the ability to combine datasets through integration schemes has become imperative. In the current study, we describe and analyze currently available Internet resources designed to address this problem. Many functionalities, such as ability to cross reference orthologous genes across species or to combine same technology platform data, are present in these resources. Nonetheless, these resources are limited in the number of technology platforms they can support. While the ability to integrate all currently existing gene expression datasets remains enigmatic, the current tools provide a partial solution that may still yield unique insights into the affects of exogenous molecules at the level of gene expression.     

Systematic development and validation of stability indicating micellar electrokinetic chromatography methods for early stage drug candidates

Suitable methods for assessment of purity, potency and stability of new drug substances and drug products are required to be rapidly developed and validated to provide appropriate data for early project development decisions. In order to routinely provide methods of consistent and suitable quality to meet increasingly aggressive timelines, systematic approaches to both develop and validate analytical technologies have been developed. Systematic approaches to evaluate separation parameters such as buffer pH, buffer ionic strength, surfactant concentration, organic modifiers, organic modifier concentration, applied voltage and temperature were evaluated for an early stage drug candidate. Techniques to improve method precision and ruggedness were also examined. Finally, the validation results from the micellar electrokinetic chromatography method utilizing an internal standard were compared against the simultaneously developed high-performance liquid chromatography method.     

DNA microarrays: is there a role for analytical chemistry?

DNA microarrays, or "DNA chips", represent a relatively new technology that is having a profound impact on biology and medicine, yet analytical research into this area is somewhat sparse. This article presents an overview of DNA microarrays and their application to gene expression analysis from the perspective of analytical chemistry, treating aspects of array platforms, measurement, image analysis, experimental design, normalization, and data analysis. Typical approaches are described and unresolved issues are discussed, with a view to identifying some of the contributions that might be made by analytical chemists.     

Applications of Activity‐Based Protein Profiling (ABPP) and Bioimaging in Drug Discovery

Activity‐based protein profiling (ABPP) and bioimaging have been developed in recent years as powerful technologies in drug discovery. Specifically, both approaches can be applied in critical steps of drug development, such as therapy target discovery, high‐throughput drug screening and target identification of bioactive molecules. We have been focused on the development of various strategies that enable simultaneous activity‐based protein profiling and bioimaging studies, thus facilitating an understanding of drug actions and potential toxicities. In this Minireview, we summarize these novel strategies and applications, with the aim of promoting these technologies in drug discovery.