Development of a large-scale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action

Successful drug discovery requires accurate decision making in order to advance the best candidates from initial lead identification to final approval. Chemogenomics, the use of genomic tools in pharmacology and toxicology, offers a promising enhancement to traditional methods of target identification/validation, lead identification, efficacy evaluation, and toxicity assessment. To realize the value of chemogenomics information, a contextual database is needed to relate the physiological outcomes induced by diverse compounds to the gene expression patterns measured in the same animals. Massively parallel gene expression characterization coupled with traditional assessments of drug candidates provides additional, important mechanistic information, and therefore a means to increase the accuracy of critical decisions. A large-scale chemogenomics database developed from in vivo treated rats provides the context and supporting data to enhance and accelerate accurate interpretation of mechanisms of toxicity and pharmacology of chemicals and drugs. To date, approximately 600 different compounds, including more than 400 FDA approved drugs, 60 drugs approved in Europe and Japan, 25 withdrawn drugs, and 100 toxicants, have been profiled in up to 7 different tissues of rats (representing over 3200 different drug-dose-time-tissue combinations). Accomplishing this task required evaluating and improving a number of in vivo and microarray protocols, including over 80 rigorous quality control steps. The utility of pairing clinical pathology assessments with gene expression data is illustrated using three anti-neoplastic drugs: carmustine, methotrexate, and thioguanine, which had similar effects on the blood compartment, but diverse effects on hepatotoxicity. We will demonstrate that gene expression events monitored in the liver can be used to predict pathological events occurring in that tissue as well as in hematopoietic tissues.

Analysis of gene and protein expression for drug mode of toxicity

The rapid sequencing of the genomes of a number of organisms, including humans, has led to major changes in the drug industry. The abundance of genome data, and the reagents generated from these genomes, have enabled the study of changes in large numbers of genes and proteins in parallel, using methods such as DNA microarrays to examine gene expression changes, or 2D polyacrylamide electrophoresis (2D-PAGE) to observe changes in the expression of proteins. While these techniques have been in use for several years, their application has primarily focused on the target discovery phase, with some early work carried out on drug- or toxin-induced changes in proteins using 2D-PAGE. In the last two years, a slew of publications have appeared on the application of array technologies to the study of toxicology, and the aim of this review is to highlight some recent examples of these applications.

Expression databases--resources for pharmacogenomic R&D

This review aims to outline the primary biological databases that are being generated to understand fundamental biology, identify new drug targets, and to look at compound profiling in a new light. We will give a brief overview of four of the main areas being studied in molecular biology: genomics, pharmacogenomics, pharmacogenetics and proteomics. Looking initially at each data set and some of its potential applications, we will go on to describe some of the potentially enormous advantages gained by fully integrating these data sets.

The pharmacology of apoptosis

Apoptosis is an area of intense scientific interest, which encompasses the study of and triggers mechanisms involved in mediating the cell biology of programmed cell death. A number of low molecular weight compounds have been used to inhibit or enhance this fundamental cellular process and so apoptosis has now become amenable to pharmacological manipulation. In this review Ross Kinloch, Mark Treherne, Mike Furness and Iradj Hajimohamadreza will focus on the current literature describing the pharmacology of apoptosis, with particular reference to the therapeutic potential that could arise from the development of pro- and anti-apoptotic drugs. The pivotal role of apoptosis in such diverse pathological processes as tumour growth, the immune response and neurodegeneration suggests that an understanding of how apoptosis can be regulated by drugs will become increasingly important to the pharmaceutical industry.

Pharmacogenomics - it's not just pharmacogenetics

New technologies in both combinatorial chemistry and combinatorial biology promise to unlock new opportunities for drug discovery and lead optimisation. Using such genome-based technologies to measure the dynamic properties of pharmacological systems, pharmacogenomics can now provide an objective measure of a drug's biological efficacy, including its potential adverse effects.

Cloning and pharmacological characterization of human alpha-1 adrenergic receptors: sequence corrections and direct comparison with other species homologues

We have cloned cDNAs encoding three human alpha-1 adrenergic receptor (AR) subtypes and characterized pharmacological properties of the expressed receptor protein. A number of significant sequence corrections have been identified and compared with previously published data, at both nucleotide and amino acid levels; the most major differences occur for the human alpha-1a/dAR. Pharmacological characterization was performed simultaneously using six cloned alpha-1AR subtypes (human and rat alpha-1a/d, human and hamster alpha-1b, human and bovine alpha-1c) stably expressed in rat-1 fibroblasts at approximately equal receptor concentrations (1-2 pmol/mg of total protein). In general, human alpha-1AR subtypes have similar pharmacology compared to their rat, hamster and bovine homologs, although a few minor species differences important for alpha-1AR classification are noted. In addition, much lower inactivation (approximately 20%) by the alkylating agent chloroethylclonidine is noted in this study compared to previous reports for both human and bovine alpha-1cAR membrane preparations. All six alpha-1AR subtypes couple to phosphoinositide hydrolysis in a pertussis toxin-insensitive manner, including the cloned human alpha-1a/dAR which had not been expressed previously. In spite of significant sequence differences between human alpha-1ARs and their other species counterparts, previously established ligand selectivity remains fairly comparable. In summary, these data represent the first side-by-side comparison of pharmacological properties between species homologs of alpha-1AR subtypes and should facilitate the development of alpha-1AR subtype selective drugs for clinical use.