Chemical proteomics and its application to drug discovery

The completion of the human genome sequencing project has provided a flood of new information that is likely to change the way scientists approach the study of complex biological systems. A major challenge lies in translating this information into new and better ways to treat human disease. The multidisciplinary science of chemical proteomics can be used to distill this flood of new information. This approach makes use of synthetic small molecules that can be used to covalently modify a set of related enzymes and subsequently allow their purification and/or identification as valid drug targets. Furthermore, such methods enable rapid biochemical analysis and small-molecule screening of targets thereby accelerating the often difficult process of target validation and drug discovery.     

转人APP基因小鼠视网膜视神经细胞超微结构改变

目的观察转人APP基因AD模型小鼠视网膜各层细胞超微结构的改变。方法实验采用C57BL/6J转人APP基因小鼠6只,采用同背景10个月龄的C57 BL/6J正常小鼠6只做为对照。灌注处死小鼠,完整取出右眼球分离视网膜,制作电镜标本观察视网膜各层细胞超微结构改变。结果与对照组相比,模型组视网膜各层细胞异常明显:膜盘排列结构模糊,局部间隙溶解、甚至消失;外核层细胞体干枯变形,染色质聚集浓缩;内核层可见固缩细胞;神经节细胞胞膜不完整,线粒体水肿,并可见染色质聚集。结论转人APP基因AD模型小鼠视网膜各层神经细胞超微结构存在明显病理改变。     

Novel computational biology methods and their applications to drug discovery

Computational biology methods are now firmly entrenched in the drug discovery process. These methods focus on modeling and simulations of biological systems to complement and direct conventional experimental approaches. Two important branches of computational biology include protein homology modeling and the computational biophysics method of molecular dynamics. Protein modeling methods attempt to accurately predict three-dimensional (3D) structures of uncrystallized proteins for subsequent structure-based drug design applications. Molecular dynamics methods aim to elucidate the molecular motions of the static representations of crystallized protein structures. In this review we highlight recent novel methodologies in the field of homology modeling and molecular dynamics. Selected drug discovery applications using these methods conclude the review.     

Luteinizing hormone modulates cognition and amyloid-beta deposition in Alzheimer APP transgenic mice

Until recently, the study of hormonal influences in Alzheimer disease was limited to the role of sex steroids. Despite numerous epidemiological studies supporting a protective role for estrogen in Alzheimer disease, recent studies show that estrogen administration in elderly women increases the risk of disease. Reconciling these contradictory reports, we previously hypothesized that other hormones of the hypothalamic-pituitary-gonadal axis, such as luteinizing hormone, may be involved in the onset and development of the disease. In this regard, luteinizing hormone is elevated in Alzheimer disease and is known to modulate amyloidogenic processing of amyloid-beta protein precursor. Therefore, in this study, to evaluate the therapeutic potential of luteinizing hormone ablation, we administered a gonadotropin-releasing hormone analogue, leuprolide acetate, to an aged transgenic mouse model of Alzheimer disease (Tg 2576) and measured cognitive Y-maze performance and amyloid-beta deposition after 3 months of treatment. Our data indicate that luteinizing hormone ablation significantly attenuated cognitive decline and decreased amyloid-beta deposition as compared to placebo-treated animals. Importantly, leuprolide acetate-mediated reduction of amyloid-beta correlated with improved cognition. Since both cognitive loss and amyloid-beta deposition are features of Alzheimer disease, leuprolide acetate treatment may prove to be a useful therapeutic strategy for this disease.     

SOD-1 inhibits FAS expression in cortex of APP transgenic mice

Peptides derived from proteolytic processing of the amyloid precursor protein (APP) are important for the pathogenesis of Alzheimers disease (AD). In the present study, we found that transgenic mice overexpressing wild-type human APP gene (hAPP/+) displayed a much higher expression of FAS, one of the death receptor subfamily. This FAS overexpression was significantly reduced in the cortex of mice overexpressing both wild-type hAPP gene and wild-type human superoxide dismutase-1 gene (hSOD-1). Moreover hSOD-1 transgenic expression was associated with an increase of Glial fibrillary acidic protein (GFAP) production. This study indicates that SOD-1 overexpression can inhibit FAS expression, which may be beneficial in AD.     

Integrated expressional analysis: application to the drug discovery process

Microarray technology enables high-throughput testing of gene expression to investigate various neuroscience related questions. This in turn creates a demand for scalable methods to confirm microarray results and the opportunity to use this information to discover and test novel pathways and therapeutic applications. Discovery of new central nervous system (CNS) treatments requires a comprehensive understanding of multiple aspects including the biology of a target, the pathophysiology of a disease/disorder, and the selection of successful lead compounds as well as efficient biomarker and drug disposition strategies such as absorption (how a drug is absorbed), distribution (how a drug spreads through an organism), metabolism (chemical conversion of a drug, if any, and into which substances), and elimination (how is a drug eliminated) (ADME). Understanding of the toxicity is also of paramount importance. These approaches, in turn, require novel high-content integrative assay technologies that provide thorough information about changes in cell biology. To increase efficiency of profiling, characterization, and validation, we established a new screening strategy that combines high-content image-based testing on Array Scan (Cellomics) with a confocal system and the multiplexed TaqMan RT-PCR method for quantitative mRNA expression analysis. This approach could serve as an interface between high-throughput microarray testing and specific application of markers discovered in the course of a microarray experiment. Markers could pinpoint activation or inhibition of a molecular pathway related, for instance, to neuronal viability. We demonstrate the successful testing of the same cell population in an image-based translocational assay followed by poly(A) mRNA capture and multiplexed single tube RT-PCR. In addition, Ciphergen ProteinChip analysis can be performed on the supernatant, thus allowing significant complementarity in the data output and interpretation by also including the capture and initial analysis of proteins in the integrative approach presented. We have determined various conditions including the number of cells, RT and PCR optimization, which are necessary for successful detection and consequent assay integration. We also show the successful convergence of various different approaches and multiplexing of different targets within a single real-time PCR tube. This novel integrative technological approach has utility for CNS drug discovery, target and biomarker identification, selection and characterization as well as for the study of toxicity- and adverse event-associated molecular mechanisms.     

Luteinizing hormone modulates cognition and amyloid-β deposition in Alzheimer APP transgenic mice

Until recently, the study of hormonal influences in Alzheimer disease was limited to the role of sex steroids. Despite numerous epidemiological studies supporting a protective role for estrogen in Alzheimer disease, recent studies show that estrogen administration in elderly women increases the risk of disease. Reconciling these contradictory reports, we previously hypothesized that other hormones of the hypothalamic–pituitary–gonadal axis, such as luteinizing hormone, may be involved in the onset and development of the disease. In this regard, luteinizing hormone is elevated in Alzheimer disease and is known to modulate amyloidogenic processing of amyloid-β protein precursor. Therefore, in this study, to evaluate the therapeutic potential of luteinizing hormone ablation, we administered a gonadotropin-releasing hormone analogue, leuprolide acetate, to an aged transgenic mouse model of Alzheimer disease (Tg 2576) and measured cognitive Y-maze performance and amyloid-β deposition after 3 months of treatment. Our data indicate that luteinizing hormone ablation significantly attenuated cognitive decline and decreased amyloid-β deposition as compared to placebo-treated animals. Importantly, leuprolide acetate-mediated reduction of amyloid-β correlated with improved cognition. Since both cognitive loss and amyloid-β deposition are features of Alzheimer disease, leuprolide acetate treatment may prove to be a useful therapeutic strategy for this disease.     

APP/PS1双转基因小鼠的繁育、鉴定及评价

目的：评价APP/PS1双转基因小鼠基因表达及认知行为能力的变化,为AD的相关研究提供有效的动物模型。方法：采用雄、雌鼠1：1合笼配对的方式,令APP/PS1双转基因小鼠自然交配进行繁育。PCR鉴定APP/PS1双转基因鼠仔鼠的基因型后,选择APP/PS1阳性小鼠作为模型（AD）组,同批APP/PS1阴性为对照（CT）组,每组8只小鼠。以Morris水迷宫实验检测仔鼠的空间学习记忆能力,以HE染色、刚果红染色观察仔鼠脑片组织病理学改变。结果：①APP/PS1双转基因鼠仔鼠基因经PCR扩增,出现约360 bp的目的基因条带,表明成功繁育出转入APP/PS1基因的仔鼠;②Morris水迷宫实验结果显示,与7月龄阴性小鼠（CT组）比较,同月龄的双转基因AD组小鼠的空间学习记忆能力明显降低（P<0.05）;③HE染色结果显示,AD组小鼠海马结构及细胞形态出现明显异常;刚果红染色结果显示,AD组小鼠脑片组织出现β淀粉样蛋白斑块沉积。结论：APP/PS1双转基因小鼠较好地模拟了AD的病理变化及行为学特征,可作为研究AD发病机制及开发AD防治药物的实验工具。     

APP mRNA splicing is upregulated in the brain of biglycan transgenic mice

Many of the risk factors for cerebrovascular disease and atherosclerosis also increase the risk of Alzheimer's disease, characterized by the cerebral deposition of beta-amyloid plaques resulting from the abnormal processing of the transmembrane amyloid precursor protein (APP). The initiating event of cholesterol-induced atherosclerosis is the retention and accumulation of atherogenic apolipoprotein B (apoB) together with low-density lipoproteins in the vascular intima. Biglycan, a member of the small leucine-rich protein family, was suspected of contributing to this process. The individual and combined overexpressions of biglycan and apoB-100 were therefore examined on the cortical APP mRNA levels of transgenic mice by means of semiquantitative PCR. As compared with the control littermates, transgenic biglycan mice had significantly increased cortical APP695 (122%) and APP770 (157%) mRNA levels, while the double transgenic (apoB(+/-)xbiglycan(+/-)) mice did not exhibit any changes. These results provide the first experimental evidence that the atherogenic risk factor biglycan alters APP splicing and may participate in the pathogenesis of both Alzheimer and vascular dementias.     

Contribution of genetic and dietary insulin resistance to Alzheimer phenotype in APP/PS1 transgenic mice

According to epidemiological studies, type‐2 diabetes increases the risk of Alzheimer’s disease. Here, we induced hyperglycaemia in mice overexpressing mutant amyloid precursor protein and presenilin‐1 (APdE9) either by cross‐breeding them with pancreatic insulin‐like growth factor 2 (IGF‐2) overexpressing mice or by feeding them with high‐fat diet. Glucose and insulin tolerance tests revealed significant hyperglycaemia in mice overexpressing IGF‐2, which was exacerbated by high‐fat diet. However, sustained hyperinsulinaemia and insulin resistance were observed only in mice co‐expressing IGF‐2 and APdE9 without correlation to insulin levels in brain. In behavioural tests in aged mice, APdE9 was associated with poor spatial learning and the combination of IGF‐2 and high‐fat diet further impaired learning. Neither high‐fat diet nor IGF‐2 increased β‐amyloid burden in the brain. In male mice, IGF‐2 increased β‐amyloid 42/40 ratio, which correlated with poor spatial learning. In contrast, inhibitory phosphorylation of glycogen synthase kinase 3β, which correlated with good spatial learning, was increased in APdE9 and IGF‐2 female mice on standard diet, but not on high‐fat diet. Interestingly, high‐fat diet altered τ isoform expression and increased phosphorylation of τ at Ser202 site in female mice regardless of genotype. These findings provide evidence for new regulatory mechanisms that link type‐2 diabetes and Alzheimer pathology.     

Development and application of physiologically based pharmacokinetic-modeling tools to support drug discovery

Physiologically based pharmacokinetic (PBPK) modeling integrates physicochemical (PC) and in vitro pharmacokinetic (PK) data using a mechanistic framework of principal ADME (absorption, distribution, metabolism, and excretion) processes into a physiologically based whole-body model. Absorption, distribution, and clearance are modeled by combining compound-specific PC and PK properties with physiological processes. Thereby, isolated in vitro data can be upgraded by means of predicting full concentration-time profiles prior to animal experiments. The integrative process of PBPK modeling leads to a better understanding of the specific ADME processes driving the PK behavior in vivo, and has the power to rationally select experiments for a more focussed PK project support. This article presents a generic disposition model based on tissue-composition-based distribution and directly scaled hepatic clearance. This model can be used in drug discovery to identify the critical PK issues of compound classes and to rationally guide the optimization path of the compounds toward a viable development candidate. Starting with a generic PBPK model, which is empirically based on the most common PK processes, the model will be gradually tailored to the specifics of drug candidates as more and more experimental data become available. This will lead to a growing understanding of the 'drug in the making', allowing a range of predictions to be made for various purposes and conditions. The stage is set for a wide penetration of PK modeling and simulations to form an intrinsic part of a project starting from lead discovery, to lead optimization and candidate selection, to preclinical profiling and clinical trials.     

Genome-wide application of RNAi to the discovery of potential drug targets

Progress is being made in the development of RNA interference-based (RNAi-based) strategies for the control of gene expression. It has been demonstrated that small interfering RNAs (siRNAs) can silence the expression of target genes in a sequence-specific manner in mammalian cells. Various groups, including our own, have developed systems for vector-mediated specific RNAi. Vector-based siRNA- (or shRNA) expression libraries directed against the entire human genome and siRNA libraries based on chemically synthesized oligonucleotides now allow the rapid identification of functional genes and potential drug targets. Use of such libraries will enhance our understanding of numerous biological phenomena and contribute to the rational design of drugs against heritable, infectious and malignant diseases.     

Integrated pathway-genome databases and their role in drug discovery.

Integrated pathway-genome databases describe the genes and genome of an organism, as well as its predicted pathways, reactions, enzymes and metabolites. In conjunction with visualization and analysis software, these databases provide a framework for improved understanding of microbial physiology and for antimicrobial drug discovery. We describe pathway-based analyses of the genomes of a number of medically relevant microorganisms and a novel software tool that visualizes gene-expression data on a diagram showing the whole metabolic network of the microorganism.     

Genomic approaches to drug discovery

Considerable progress has been made in exploiting the enormous amount of genomic and genetic information for the identification of potential targets for drug discovery and development. New tools that incorporate pathway information have been developed for gene expression data mining to reflect differences in pathways in normal and disease states. In addition, forward and reverse genetics used in a high-throughput mode with full-length cDNA and RNAi libraries enable the direct identification of components of signaling pathways. The discovery of the regulatory function of microRNAs highlights the importance of continuing the investigation of the genome with sophisticated tools. Furthermore, epigenetic information including DNA methylation and histone modifications that mediate important biological processes add to the possibilities to identify novel drug targets and patient populations that will benefit from new therapies.     

Antibody discovery: the use of transgenic mice to generate human monoclonal antibodies for therapeutics

Technical advances made in the 1980s and early 1990s resulted in monoclonal antibodies that are now approved for human therapy. Novel transgenic mouse strains provide a powerful technology platform for creating fully human monoclonal antibodies as therapeutics; ten such antibodies have entered clinical trials since 1998 and more are in preclinical testing. Improved transgenic mouse strains provide a powerful technology platform for creating human therapeutics in the future.     

The application of cell-based label-free technology in drug discovery

Cell-based assays are an important part of the drug discovery process allowing for interrogation of targets and pathways in a more physiological setting compared to biochemical assays. One of the main hurdles in the cell-based assay field is to design sufficiently robust assays with adequate signal to noise parameters while maintaining the inherent physiology of the pathway or target being investigated. Conventional label and reporter-based cell assays may be more prone to artifacts due to considerable manipulation of the cell either by the label or over-expression of targets or reporter proteins. Cell-based label-free technologies preclude the need for cellular labeling or over-expression of reporter proteins, utilizing the inherent morphological and adhesive characteristics of the cell as a physiologically relevant and quantitative readout for various cellular assays. Furthermore, these technologies utilize non-invasive measurements allowing for time resolution and kinetics in the assay. In this article, we have reviewed the various label-free technologies that are being used in drug discovery settings and have focused our discussion on impedance-based label-free technologies and its main applications in drug discovery.