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PubMed2007

Ribozyme technology for cancer gene target identification and validation.

Ribozymes are naturally occurring RNAs with catalytic activities including cis- or trans- cleavage of RNA at predefined sequence sites. This activity has been exploited for specific gene inactivation in cells during the last two decades, and ribozymes have been important functional genomics tools, especially in the pre-RNAi era. It has also been broadly applied in drug target identification and validation in pharmaceutical R&D. This chapter covers many application principles and case studies of ribozyme technology in the areas of cancer research. We also described RNAi applications in some of the same studies for comparison. Although RNAi may be more effective than ribozymes in many respects, they are nonetheless built on many of the same principles.

Animals↗
PubMed2007

Protein arrays: a versatile toolbox for target identification and monitoring of patient immune responses.

Functional proteomics is a promising technique for the rational identification of novel therapeutic targets and biological markers. The studies of protein-protein interactions have been gained from the development of high-throughput technologies such as the yeast two-hybrid system, protein arrays, phage display, and systematic analysis of interaction maps for the prediction of protein functions. Because antibodies are used extensively as diagnostic and clinical tools, the characterization of their antigen specificity is of prime importance. Indeed, screening protein arrays with sera from patients with either cancer or autoimmune diseases would facilitate the identification of autoantibody signatures that can be used for diagnosis and/or prognosis of patients. The usefulness of multiplexed measurements lies not only in the ability to screen many individual marker candidates but also in evaluating the use of multiple markers in combination. Here, we review the advantage of protein and serum screening of peptides and cDNA repertoires displayed on phages as well as the fabrication of protein microarrays for probing immune responses in patients.

Autoantibodies↗
PubMed2007

Chemical genetics: an evolving toolbox for target identification and lead optimization.

Chemical genetics combines chemistry with biology as a means of exploring the function of unknown proteins or identifying the proteins responsible for a particular phenotype. Chemical genetics is thus a valuable tool in the identification of novel drug targets. This chapter describes the application of chemical genetics in traditional and systems-based approaches to drug target discovery and the tools/approaches that appear most promising for guiding future pharmaceutical development.

Combinatorial Chemistry Techniques↗
PubMed2005

FMRP RNA targets: identification and validation.

The Fragile X Syndrome is caused by the loss of function of the FMR1 gene (Pieretti et al. 1991. Cell 66, 817-822; O'Donnell & Warren 2002. Annu Rev Neurosci 25, 315-338]. Identification of the RNA targets to which FMRP binds is a key step in understanding the function of the protein and the cellular defects caused by its absence (Darnell et al. 2004 Ment Retard Dev Disabil Res Rev 10, 49-52). Here we discuss the current understanding of FMRP as an RNA-binding protein, the different approaches that have been taken to identify FMRP RNA targets and the relevance of some of these approaches to FMRP biology. In addition, we present evidence that point mutations in the K-homology (KH)1 or KH2 domains of FMRP abrogate its polyribosome association in transfected neuroblastoma cells but that the deletion of the RGG box does not. This suggests that RNA binding by the RGG box of FMRP may mediate other aspects of cellular mRNA metabolism such as mRNA localization or that it may have a role downstream of polyribosome association.

Animals↗
PubMed2004

Recent developments in target identification against hepatitis C virus.

Chronic hepatitis C is a leading cause of liver cirrhosis and hepatocellular carcinoma worldwide. Recent progress in the understanding of the molecular virology of hepatitis C has allowed the identification of novel antiviral targets. Moreover, in vitro and in vivo model systems have been developed that allow the systematic evaluation of new therapeutic strategies. Exciting results from proof-of-concept clinical studies have now been reported for a specific hepatitis C virus serine protease inhibitor. These and other novel antiviral strategies may complement existing therapeutic modalities in the future.

Animals↗
PubMed2006

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.

Animals↗
PubMed1987

Spatial frequency filtering and target identification.

Twenty subjects identified filtered pictures of previously learned target stimuli. Five filters were utilized: 3 two-octave wide band-pass and 2 complementary (same cutoff) high- and low-pass. Response times and per cent errors were used to assess performance. The filtered pictures were presented at two sizes: to ten subjects at twice the size presented to the other ten. The results indicated that higher spatial frequencies contribute more to the identification task than do the low spatial frequencies, but also that neither low nor very high frequencies are redundant for identification. It was also seen that both the proximal (c/deg) and the distal (c/picture) scales of spatial frequency measurement are involved in the identification process.

Adolescent↗
PubMed2005

Using bioinformatics for drug target identification from the genome.

Genomics and proteomics technologies have created a paradigm shift in the drug discovery process, with bioinformatics having a key role in the exploitation of genomic, transcriptomic, and proteomic data to gain insights into the molecular mechanisms that underlie disease and to identify potential drug targets. We discuss the current state of the art for some of the bioinformatic approaches to identifying drug targets, including identifying new members of successful target classes and their functions, predicting disease relevant genes, and constructing gene networks and protein interaction networks. In addition, we introduce drug target discovery using the strategy of systems biology, and discuss some of the data resources for the identification of drug targets. Although bioinformatics tools and resources can be used to identify putative drug targets, validating targets is still a process that requires an understanding of the role of the gene or protein in the disease process and is heavily dependent on laboratory-based work.

Alzheimer Disease↗
PubMed2002

PCR-based ordered genomic libraries: a new approach to drug target identification for Streptococcus pneumoniae.

Described here are the development and validation of a novel approach to identify genes encoding drug targets in Streptococcus pneumoniae. The method relies on the use of an ordered genomic library composed of PCR amplicons that were generated under error-prone conditions so as to introduce random mutations into the DNA. Since some of the mutations occur in drug target-encoding genes and subsequently affect the binding of the drug to its respective cellular target, amplicons containing drug targets can be identified as those producing drug-resistant colonies when transformed into S. pneumoniae. Examination of the genetic content of the amplicon giving resistance coupled with bioinformatics and additional genetic approaches could be used to rapidly identify candidate drug target genes. The utility of this approach was verified by using a number of known antibiotics. For drugs with single protein targets, amplicons were identified that rendered S. pneumoniae drug resistant. Assessment of amplicon composition revealed that each of the relevant amplicons contained the gene encoding the known target for the particular drug tested. Fusidic acid-resistant mutants that resulted from the transformation of S. pneumoniae with amplicons containing fusA were further characterized by sequence analysis. A single mutation was found to occur in a region of the S. pneumoniae elongation factor G protein that is analogous to that already implicated in other bacteria as being associated with fusidic acid resistance. Thus, in addition to facilitating the identification of genes encoding drug targets, this method could provide strains that aid future mechanistic studies.

Anti-Bacterial Agents↗
PubMed2005

A proteomic approach to tumour target identification using phage display, affinity purification and mass spectrometry.

Tumour-associated cell surface markers are potential targets for antibody-based therapies. We have obtained a panel of myeloid cell binding single chain variable fragments (scFv) by applying phage display selection on myeloid cell lines followed by a selection round on freshly isolated acute myeloid leukaemia (AML) blasts using flow cytometry. To identify the target antigens, the scFv were recloned and expressed in an IgG(1) format and tested for their ability to immunoprecipitate cell surface proteins. The IgGs that reacted with distinct cell membrane extractable proteins were used in large-scale affinity purification of the target antigen followed by mass-spectrometry-based identification. Well-characterised cell surface antigens, such as leukocyte antigen-related receptor protein tyrosine phosphatase (LAR PTP) and activated leukocyte adhesion molecule (ALCAM) in addition to several unknown proteins, like ATAD3A, were identified. These experiments demonstrate that phage antibody selection in combination with affinity chromatography and mass spectrometry can be exploited successfully to identify novel antibody target molecules on malignant cells.

Activated-Leukocyte Cell Adhesion Molecule↗
PubMed2003

Sequence-based design of kinase inhibitors applicable for therapeutics and target identification.

A platform for specifically modulating kinase-dependent signaling using peptides derived from the catalytic domain of the kinase is presented. This technology, termed KinAce, utilizes the canonical structure of protein kinases. The targeted regions (subdomain V and subdomains IX and X) are analyzed and their sequence, three-dimensional structure, and involvement in protein-protein interaction are highlighted. Short myristoylated peptides were derived from the target regions of the tyrosine kinases c-Kit and Lyn and the serine/threonine kinases 3-phosphoinositide-dependent kinase-1 (PDK1) and Akt/protein kinase B (PKB). For each kinase an active designer peptide is shown to selectively inhibit the signaling of the kinase from which it is derived, and to inhibit cancer cell proliferation in the micromolar range. This technology emerges as an applicable tool for deriving sequence-based selective inhibitors for a broad range of protein kinases as hits that may be further developed into drugs. Moreover, it enables identification of novel kinase targets for selected therapeutic indications as demonstrated in the KinScreen application.

3-Phosphoinositide-Dependent Protein Kinases↗
PubMed2003

Dual target identification and the attentional blink in Parkinson's disease.

In healthy adults, deficits in identifying a second target following a previously attended target in Rapid Serial Visual Presentation (RSVP) occur between intertarget intervals of approximately 100-500 ms. This Attentional Blink (AB) is investigated in nondemented medicated Parkinson's patients using a modification of the standard paradigm that required the identification of two red letters embedded in a black letter distractor stream. Parkinson's patients and controls produced an equivalent AB, although with a different pattern of errors. Thus, the processing and clearance of information was largely preserved in nondemented Parkinson's patients, without evidence of bradyphrenia. However, perseveration of earlier RSVP items in short-term memory was thought to explain the different pattern of errors.

Aged↗
PubMed1998

Obesity genes: molecular genetic approaches to drug target identification.

The environment for developing novel therapeutic agents has undergone dramatic change over the past decade. Innovative strategies for identifying and utilizing molecular targets linked to particular human diseases are replacing the classic approach of screening chemical compounds for potential therapeutic action on unknown targets. Since genetic components are involved in many known diseases, mouse and human genetics, positional cloning and other molecular biology-based approaches are now used to identify genes that are associated with these diseases. It is thought that identification of these disease-linked genes may lead to the discovery and understanding of the physiologically relevant biochemical pathways underlying the disease processes. Clearly, a knowledge of these biochemical pathways will provide future molecular targets, enzymes or receptors, that will offer opportunities to apply modern methods of high throughput screening, medicinal chemistry, parallel synthesis and combinatorial chemistry for drug discovery. In this manuscript, we illustrate how mouse genetics and molecular biology-based approaches have led to the identification of all five known single gene mutations that cause obesity in mice. Additionally, we describe how identification of these genes has helped unravel underlying biochemical pathways that regulate behavioral, metabolic and neuroendocrine responses in rodents.

Animals↗
PubMed1991

Natural products as probes for new drug target identification.

One traditional aspect of natural products in medical research has been their use in the identification and investigation of the physiological/pathological role of receptors and enzymes as possible targets for drug design programmes. Classical examples of this function of natural products in drug research can be seen in the investigation of the cholinergic system. For example, the importance of alkaloids such as nicotine, physostigmine and curare for research into the nicotine receptor and muscarine, pilocarpine and the tropane alkaloids on the muscarinic receptor. On binding of a ligand to its cell surface membrane receptor and prior to a physiological/pharmacological response two mechanisms are currently known to be involved in membrane signal transductance. In the minority of cases signal transductance involves the direct opening of an ion channel, for example sodium ion influx, but in the majority of cases involves stimulation of a family of G-proteins and subsequent activation of second messenger systems. For example, the cyclic-AMP/adenylate cyclase system and the phosphoinositol cycle. In this communication, the part played currently by the tumour-promoting and pro-inflammatory phorbol esters from the plant family Euphorbiaceae in furthering our understanding of the role of a group of related kinases from one arm of the phosphoinositol cycle as a signal transduction pathway will be illustrated. The possibilities of using these new receptors as targets for future drug development will also be described.

Animals↗
PubMed1987

Age differences in target identification as a function of retinal location and noise level: examination of the useful field of view.

Foveal and peripheral target detection were compared in young adults (M age = 22 years) and older adults (M age = 66 years) who were optically corrected for the viewing distance. In a two-alternative, forced-choice task, target letters were presented at 0 degree to 10.5 degrees from fixation. Targets were presented alone, flanked on each side by one noise element (i.e., nontarget letter), or embedded in a horizontal row of 19 noise elements. An Age X Noise Level X Location interaction was obtained, wherein age differences were largest for peripheral targets presented in noise. Slope analyses of latency data showed that the performance of young adults in the high-noise condition was most similar to that of older adults in the low-noise condition. At the functional level, results indicated that aging is associated with a restricted useful field of view. In addition, the data suggest that age differences in search can be described by a model in which older adults take smaller perceptual samples from the visual scene and scan these samples more slowly than do the young adults.

Adult↗
PubMed2005

Laboratory models of alcoholism: treatment target identification and insight into mechanisms.

Laboratory models, including animal tissues and live animals, have proven useful for discovery of molecular targets of alcohol action as well as for characterization of genetic and environmental factors that influence alcohol's neural actions. Here we consider strengths and weaknesses of laboratory models used in alcohol research and analyze the limitations of using animals to model a complex human disease. We describe targets for the neural actions of alcohol, and we review studies in which animal models were used to examine excessive alcohol drinking and to discover genes that may contribute to risk for alcoholism. Despite some limitations of the laboratory models used in alcohol research, these experimental approaches are likely to contribute to the development of new therapies for alcohol abuse and alcoholism.

Alcoholism↗
PubMed2005

RNAi and high-content screening in target identification and validation.

The development of effective novel therapeutic agents faces many significant challenges, such as demonstrating that a candidate target plays a critical role in disease progression. RNA interference (RNAi) has proven to be a robust and highly scalable technology, and as such, has become an essential method for studying targets in many disease models. High-content screening (HCS) is a platform for quantitatively measuring cellular features such as transcription factor localization. This is a more powerful method of measuring signal transduction than reporter assays because the image-based data of HCS can eliminate many sources of assay artifacts, and the associated statistical tools are highly effective. While it appears obvious that convergence of technologies is required to establish RNAi screening assays in HCS formats, some challenges arise when combining the approaches. However, combining RNAi and HCS provides significant and unique advantages to a target validation program.

Animals↗