Full-speed mammalian genetics: in vivo target validation in the drug discovery process

The Validation of Nematode-Specific Acetylcholine-Gated Chloride Channels as Potential Anthelmintic Drug Targets

New compounds are needed to treat parasitic nematode infections in humans, livestock and plants. Small molecule anthelmintics are the primary means of nematode parasite control in animals; however, widespread resistance to the currently available drug classes means control will be impossible without the introduction of new compounds. Adverse environmental effects associated with nematocides used to control plant parasitic species are also motivating the search for safer, more effective compounds. Discovery of new anthelmintic drugs in particular has been a serious challenge due to the difficulty of obtaining and culturing target parasites for high-throughput screens and the lack of functional genomic techniques to validate potential drug targets in these pathogens. We present here a novel strategy for target validation that employs the free-living nematode Caenorhabditis elegans to demonstrate the value of new ligand-gated ion channels as targets for anthelmintic discovery. Many successful anthelmintics, including ivermectin, levamisole and monepantel, are agonists of pentameric ligand-gated ion channels, suggesting that the unexploited pentameric ion channels encoded in parasite genomes may be suitable drug targets. We validated five members of the nematode-specific family of acetylcholine-gated chloride channels as targets of agonists with anthelmintic properties by ectopically expressing an ivermectin-gated chloride channel, AVR-15, in tissues that endogenously express the acetylcholine-gated chloride channels and using the effects of ivermectin to predict the effects of an acetylcholine-gated chloride channel agonist. In principle, our strategy can be applied to validate any ion channel as a putative anti-parasitic drug target.

Personalized medicine: changing the paradigm of drug development

Despite an increased investment in research and development, there has been a steady decline in the number of drugs brought to market over the past 40 years. The tools of personalized medicine are refining diseases into molecular categories, and future therapeutics may be dictated by a patient's molecular profile relative to these categories. The adoption of a personalized medicine approach to drug development may improve the success rate by minimizing variability during each phase of the drug development process. This chapter describes the current paradigm of drug development and then discusses how molecular profiling/personalized medicine might be used to improve upon this paradigm.

Transmembrane and ubiquitin-like domain containing 1 (Tmub1) regulates locomotor activity and wakefulness in mice and interacts with CAMLG

Tmub1 (C7orf21/HOPS) encodes a protein containing a ubiquitin-like domain. Tmub1 is highly expressed in the nervous system. To study its physiological function, we generated mice with Tmub1 deleted by homologous recombination. The knockout mice were grossly normal and viable. In a comprehensive behavioral testing battery, the only knockout phenotype displayed was a strong increase in home cage locomotor activity during the dark phase (subjective day) of the light∶dark (L∶D) cycle. There were no changes in activity during the light period. There were no changes in locomotor activity observed in other assays, e.g. novel open-field. The increase in dark phase locomotor activity persisted during a seven day D∶D (complete darkness) challenge, and remained largely confined to the normally dark period. Telemetric recording in freely moving subjects for one 24 hr L∶D cycle, revealed the same increase in locomotor activity in the dark phase. In addition, EEG analysis showed that the knockout mice exhibited increased waking and decreased NREM & REM times during the dark phase, but the EEG was otherwise normal. Using lacZ as a reporter we found Tmub1 expression prominent in a few brain structures including the thalamus, a region known to drive wakefulness and arousal via its projections to the cortex. We identified calcium modulating cyclophilin ligand CAMLG/CAML as a binding partner by a yeast two-hybrid screen of a brain library. The interaction of Tmub1 and CAMLG was confirmed by co-immunoprecipitation assays in HEK cells. The two proteins were also found to be co-localized to the cytoplasm when expressed in HEK cells. Both Tmub1 and CAMLG have been recently described in the regulation of membrane trafficking of specific receptors. Taken together our results implicate Tmub1 in the regulation of locomotor activity and wakefulness and suggest that Tmub1 binds to and functions together with CAMLG.

Large-scale gene trapping in C57BL/6N mouse embryonic stem cells

We report the construction and analysis of a mouse gene trap mutant resource created in the C57BL/6N genetic background containing more than 350,000 sequence-tagged embryonic stem (ES) cell clones. We also demonstrate the ability of these ES cell clones to contribute to the germline and produce knockout mice. Each mutant clone is identified by a genomic sequence tag representing the exact insertion location, allowing accurate prediction of mutagenicity and enabling direct genotyping of mutant alleles. Mutations have been identified in more than 10,000 genes and show a bias toward the first intron. The trapped ES cell lines, which can be requested from the Texas A&M Institute for Genomic Medicine, are readily available to the scientific community.

Drug discovery paradigms: past, present, future - a centennial symposium of the American Society for Pharmacology and Experimental Therapeutics

BACKGROUND

The American Society for Pharmacology and Experimental Therapeutics (ASPET) celebrated its centennial during the April 2008 Experimental Biology meeting held in San Diego, CA, USA.

OBJECTIVES

This report summarizes a centennial symposium on past, present and future paradigms in drug discovery. The John Langley (1905) concept of 'receptive substances' initiated a cascade of cardinal discoveries for pharmacology. During the following 100 years, receptors achieved the status of well-defined multifunctional cellular proteins mediating all drug effects. The G-protein-coupled receptors (GPCRs) were discussed in relation to multiple targets they represent for clinically used or new medicines. The development of inbred and transgenic animal strains is a fundamental twentieth century achievement for biological research activities. Progress in treating CNS disorders still awaits breakthrough treatments. Drug development remains a risky and expensive venture; improvements are expected from emerging biomarker and translational medicine technologies. Future clinical research has to document the benefits that new medications provide to concerned stakeholders.

CONCLUSIONS

We wish ASPET a new century of great achievements and acknowledge the dedication of several generations of colleagues, many of whom are our 'unsung heroes'. They have left us a precious heritage to be pursued with passion in the quest for better medicines.

Learning and memory impairment in Eph receptor A6 knockout mice

Genetic inhibition of the ephrin receptor (EphA6) in mice produced behavioral deficits specifically in tests of learning and memory. Using a fear conditioning training paradigm, mice deficient in EphA6 did not acquire the task as strongly as did wild type (WT) mice. When tested in the same context 24h later, knockout (KO) mice did not freeze as much as WT mice indicating reduced memory of the consequences of the training context. The KO mice also displayed less freezing when presented with the conditioning stimulus (CS) in a separate context. In the hidden platform phase of the Morris water maze (MWM) task, KO mice did not reach the same level of proficiency as did WT mice. KO mice also exhibited less preference for the target quadrant during a probe trial and were significantly impaired on an initial reversal of the platform. These findings suggest that EphA6, in line with a number of other Eph receptors and their ephrin ligands, is involved in neural circuits underlying aspects of learning and memory.

The Potential of Bioartificial Tissues in Oncology Research and Treatment

This review article addresses the relevance and potential of bioartificial tissues in oncologic research and therapy and reconstructive oncologic surgery. In order to translate the findings from basic cellular research into clinical applications, cell-based models need to recapitulate both the 3D organization and multicellular complexity of an organ but at the same time accommodate systematic experimental intervention. Here, tissue engineering, the generation of human tissues and organs in vitro, provides new perspectives for basic and applied research by offering 3D tissue cultures resolving fundamental obstacles encountered in currently applied 2D and 3D cell culture systems. Tissue engineering has already been applied to create replacement structures for reconstructive surgery. Applied in vitro, these complex multicellular 3D tissue cultures mimic the microenvironment of human tissues. In contrast to the currently available cell culture systems providing only limited insight into the complex interactions in tissue differentiation, carcinogenesis, angiogenesis and the stromal reaction, the more realistic (micro)environment afforded by the bioartificial tissuespecific 3D test systems may accelerate the progress in design and development of cancer therapies.

Drug discovery and delivery in the 21st century

Drug discovery in the late 20th century has increasingly focused on the definition and characterization of the macromolecular substrates that serve as targets for drug design. The advent of genomics and the molecular biology revolution has permitted both the definition of new targets and the characterization of the genetic basis of disease states. The introduction of powerful new technologies should greatly accelerate the pace of new drug discovery. Although genomics, both human and nonhuman, should in principle increase the number of potential drug targets and provide a greater understanding of cellular events contributing to the pathology of disease this has yet to occur in practice, primarily because of the underlying complexity of cellular signaling processes. The emerging discipline of systems biology is attempting to bring both order and understanding to these signaling processes. Genomics has, however, impacted on drug discovery in ways that are important beyond a mere increase in potential drug target numbers. Genomics has provided the tools of contemporary drug discovery, the pharmacogenomic pathways to personalized medicine, and has greatly influenced the nature of synthetic organic chemistry, a discipline that is still the cornerstone of contemporary drug discovery. In the future, genomics and the tools of molecular biology will have a corresponding impact on drug delivery processes and mechanisms through introduction of drug delivery machines capable of both synthesis and activation by disease-specific signals. Such machines will be based on a synthetic genome, using an expanded genetic code, and designed for specific drug synthesis and delivery and activation by a pathological signal. This essay is based upon a lecture of the same title presented at the Faculty of Medicine, Kuwait University during a visit in the spring of 2005. It is intended, as was the lecture, to be a broad, descriptive and speculative overview rather than a comprehensive and detailed review.

Preparation of poly(ethylene glycol)-introduced cationized gelatin as a non-viral gene carrier

The objective of this study was to prepare cationized gelatins grafted with poly(ethylene glycol) (PEG) (PEG-cationized gelatin) and evaluate the in vivo efficiency as a non-viral gene carrier. Cationized gelatin was prepared by chemical introduction of ethylenediamine to the carboxyl groups of gelatin. PEG with one terminal of active ester group was coupled to the amino groups of cationized gelatin to prepare PEG-cationized gelatins. Electrophoretic experiments revealed that the PEG-cationized gelatin with low PEGylation degrees was complexed with a plasmid DNA of luciferase, in remarked contrast to that with high PEGylation degrees. When the plasmid DNA complexed with the cationized gelatin or PEG-cationized gelatin was mixed with deoxyribonuclease I (DNase I) in solution to evaluate the resistance to enzymatic degradation, stronger protection effect of the PEG-cationized gelatin was observed than that of the cationized gelatin. The complex of plasmid DNA and PEG-cationized gelatin had an apparent molecular size of about 300 nm and almost zero surface charge. These findings indicate that the PEG-cationized gelatin-plasmid DNA complex has a nano-order structure where the plasmid DNA is covered with PEG molecules. When the PEG-cationized gelatin-plasmid DNA complex was intramuscularly injected, the level of gene expression was significantly increased compared with the injection of plasmid DNA solution. It is concluded that the PEG-cationized gelatin was a promising non-viral gene carrier to enhance gene expression in vivo.

Rapid development of glomerular injury and renal failure in mice lacking p53R2

The Rrm2b gene encodes p53R2, a catalytic subunit of ribonucleotide reductase that is required for DNA repair. Embryonic stem (ES) cells containing a retroviral insertion in the Rrm2b locus were used to generate mutant mice. Analysis of kidney RNA from Rrm2b (-/-) mice showed that the retroviral insertion disrupted expression of Rrm2b transcripts. Rrm2b (-/-) pups were represented at the expected Mendelian ratios at 10-12 days of age and grew normally past weaning. Mice failed to thrive after 6 weeks of age and began to die by 8 weeks of age. Phenotyping revealed that Rrm2b (-/-) mice died from a severe glomerular lesion that led to nephrotic syndrome and chronic renal failure. In kidneys of Rrm2b (-/-) mice, podocytes were enlarged and there was evidence of foot process effacement by 6 weeks of age. By 8 weeks of age, progressive podocyte hypertrophy and loss of foot processes was accompanied by hypertrophy of glomerular capillary endothelial cells that was extensive enough to restrict capillary blood flow. Collapsing glomerulopathy with avascular glomeruli was widespread in mice surviving beyond 9 weeks of age. Additional abnormalities in other organ systems were minor or consistent with secondary effects of renal failure. These findings suggest that lack of p53R2, the protein encoded by Rrm2b, has early and relatively selective detrimental effects on the kidney glomerulus that lead to rapid death from progressive renal failure.

Transgenic plant-derived pharmaceuticals – the practical approach?

Production of biopharmaceuticals in transgenic plants would involve the creation of a new industry. Those transgenic plants, including staple food crops, could provide many benefits to people all over the world. However, the new industry might require a strict regulation system. It is probable that such a strict system would not be acceptable to Japan or to most developing countries. Many countries should use non-food crops for production of biopharmaceuticals and take on more simple systems. The new industry must develop strategies for promoting the benefits of transgenic plant-derived biopharmaceuticals on both the domestic and worldwide scales.

Setting sights on the treatment of ocular angiogenesis using antisense oligonucleotides

The application of antisense technology to study physiological and disease processes continues to mature. Antisense approaches are among the most direct means to use genomic sequence information. When developing therapeutics, applications range from early target validation in discovery to the therapeutic product. In this review, we describe the application of antisense oligonucleotides (ASOs) to identify genes that are important in controlling angiogenesis. High-throughput assays in vitro have been used to evaluate many gene targets. Genes that appear to be important in angiogenesis are then evaluated further in animal models of ocular angiogenesis. The ability of ASOs to reduce target-gene expression in the appropriate cells in the eye raises the possibility that this class of compounds could be used for target validation in vivo, and also be developed as a novel class of therapeutics in their own right.

Identification and validation of PDGF transcriptional targets by microarray-coupled gene-trap mutagenesis

We developed a versatile, high-throughput genetic screening strategy by coupling gene mutagenesis and expression profiling technologies. Using a retroviral gene-trap vector optimized for efficient mutagenesis and cloning, we randomly disrupted genes in mouse embryonic stem (ES) cells and amplified them to construct a cDNA microarray. With this gene-trap array, we show that transcriptional target genes of platelet-derived growth factor (PDGF) can be efficiently and reliably identified in physiologically relevant cells and are immediately accessible to genetic studies to determine their in vivo roles and relative contributions to PDGF-regulated developmental processes. The same platform can be used to search for genes of specific biological relevance in a broad array of experimental settings, providing a fast track from gene identification to functional validation.

Target discovery

Target discovery, which involves the identification and early validation of disease-modifying targets, is an essential first step in the drug discovery pipeline. Indeed, the drive to determine protein function has been stimulated, both in industry and academia, by the completion of the human genome project. In this article, we critically examine the strategies and methodologies used for both the identification and validation of disease-relevant proteins. In particular, we will examine the likely impact of recent technological advances, including genomics, proteomics, small interfering RNA and mouse knockout models, and conclude by speculating on future trends.

Validation and calibration of DEXA body composition in mice

Validated methods of determining murine body composition are required for studies of obesity in mice. Dual-energy X-ray absorptiometry (DEXA) provides a noninvasive approach to assess body fat and lean tissue contents. Similar to DEXA analyses in other species, body fat measurements in mice show acceptable precision but suffer from poor accuracy. Because fat and lean tissues each contain various components, these inaccuracies likely result from selection of inappropriate calibration standards. Analysis of solvents showed that the PIXImus2 DEXA gave results consistent with theoretical calculations. Male mice weighing 26-60 g and having body fat percentages ranging from 3 to 49% were analyzed by both PIXImus2 DEXA and chemical carcass analysis. DEXA overestimated mouse fat content by an average of 3.3 g, and algorithms were generated to calculate body fat from both measured body fat values and the measured ratio of high- to low-energy X-ray attenuations. With calibration to mouse body fat content measured by carcass analysis, the PIXImus2 DEXA gives accurate body composition values in mice.

Maximizing the value of genomics in the drug discovery and development process

Genomics and all the associated technologies it has spawned have fundamentally changed the way research and development organizations carry out the work they do in the early stages of discovery. However, successful organizations must move from product concept through to registration as efficiently as possible. In order to achieve this, the early "basic" science must be combined with the clinical perspective from the start. Furthermore, since the genomics industry was first established in the early 1990s it has evolved from tool and data suppliers to drug development companies. It is therefore likely that we will see technology advances in genomics become more limited in the years ahead.

Knockouts model the 100 best-selling drugs--will they model the next 100?

The biopharmaceutical industry is currently faced with a tremendous number of potential drug targets identified through the sequencing of the human genome. The challenge ahead is to delineate those targets with the greatest value for therapeutic intervention. Here, we critically evaluate mouse-knockout technology for target discovery and validation. A retrospective evaluation of the knockout phenotypes for the targets of the 100 best-selling drugs indicates that these phenotypes correlate well with known drug efficacy, illuminating a productive path forward for discovering future drug targets. Prospective mining of the druggable genome is being catalysed by large-scale mouse knockout programs combined with phenotypic screens focused on identifying targets that modulate mammalian physiology in a therapeutically relevant manner.

Genomics versus orphan nuclear receptors--a half-time report

Following the successful cloning of the orphan nuclear receptors during the 1990s we entered the 21st century with knowledge of the full complement of human nuclear receptors. Many of these proteins are ligand-activated transcription factors that act as the cognate receptors for steroid, retinoid, and thyroid hormones. In addition to these well characterized endocrine hormone receptors, there are a large number of orphan receptors of which less is known about the nature and function of their ligands. The task of deciphering the physiological function of these orphan receptors has been aided by a new generation of genomic technologies. Through application of chemical, structural, and functional genomics, several orphan nuclear receptors have emerged as pharmaceutical drug targets for the treatment of important human diseases. The significant progress that has been made in the functional analysis of more than half of the nuclear receptor gene family provides an opportunity to review the impact of genomics in this endeavor.