Recent advances and method development for drug target identification Janet N.Y. Chan, Corey Nislow and Andrew Emili Department of Molecular Genetics, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada M5S 3E1 Although it is commonly recognized that most drugs cause inhibition or activation of function by physically binding to one or more gene products, the direct inter- actions of bioactive small molecules with specific gene products, or targets, is often not well characterized. From a therapeutic perspective, it is nevertheless essen- tial to know a drug’s binding partner(s) to understand the mechanism of action and anticipate possible side effects to avoid costly clinical failures. This knowledge is increasingly important as the prevalence of polyphar- macy expands to include drugs that engage multiple targets. This review provides a succinct overview of several recent approaches that employ genetics, proteo- mics, expression profiling or bioinformatics procedures for the systematic characterization of the targets of bioactive compounds. The continuous improvement and advancement of existing technologies is critically discussed and we offer a perspective on the future of innovative emerging new generation technologies. The bottleneck in drug research Drug discovery is a challenging process that can take decades and consume over a billion dollars in resources per clinical approval [1,2]. This requisite investment in both cost and infrastructure limits the scope of testing of an increasingly vast diversity of chemical compounds with the potential for development as therapeutic agents [3]. In fact, only a handful of chemical entities are approved by US Food and Drug Administration (FDA) each year, even fewer with full knowledge of their mechanism of action [4]. This lack of mechanistic knowledge can potentially be one reason why most experimental compounds entering clinical trials have failed, because unanticipated biological effects might not be clearly assessed prior to clinical stages. Furthermore, post-approval failures can be equally devas- tating. Therefore, fully understanding the biological activity of potential therapeutics is an essential step of the process to avoid both unnecessary patient morbidity and costly and time-consuming clinical setbacks [1]. Here, we investigate this problem directly by evaluating whether the community can address the current pipeline shortfall by harnessing the enormous potential of existing pharma- ceutical resources with the burgeoning number of possible new targets in a cost-efficient manner. High-throughput phenotypic screening has recently gained both academic and industry-wide adoption with the unified goal of discovering biological pathways that can be modulated by bioactive agents. A systematic approach is increasingly appealing because it places emphasis on the assessment of biological activity early in the discovery process, thus avoiding greater costs later in the pipeline [5,6]. Moreover, by selecting agents that have effective functional outcomes, discovery is not biased towards any single preconceived target. Sophisticated high-content cell or model organism screens that empha- size speed and parallelization have been devised to accel- erate lead compound discovery to generate a myriad of primary molecule ‘‘hits’’ with desired properties [7]. Yet despite the advantages of such approaches, the develop- ment of systematic methods to characterize and validate the molecular interactions of compound hits with complex biological systems is generally difficult. With the rapid maturation and increasing capabilities of diversity-based chemical synthesis [8], a new bottleneck is the identifi- cation of the effector(s) bound by a given compound [9]. Hence, although high-throughput screens offer the poten- tial to accelerate the drug discovery process by selecting a particular phenotype of interest, these assays still criti- cally depend on the development of equally effective methods for target identification [10]. In essence, deconvo- luting the direct target(s) of a compound to explain the biological action of a drug remains an ongoing challenge. To address the bottleneck of target validation, an array of increasingly sophisticated methods have been devised and many have been successfully applied (Table 1), although often in an ad hoc manner, over the past few decades. In the following sections, selected studies describ- ing important developments, variations, improvements and extensions of traditional strategies drawn from the fields of genetics, proteomics, expression profiling and bioinformatics are presented and critically discussed. Genome-wide genetic approaches for drug target identification Existing assays – haploinsufficiency profiling, its variations and overexpression suppressor screens Genetic screening has been recognized as a well-estab- lished strategy for identifying drug targets [11,12]; how- ever, the recent boon in genome sequence availability has fostered innovative systematic approaches for routine Review Corresponding author: Emili, A. (andrew.emili@utoronto.ca) 82 0165-6147/$ – see front matter ß 2009 Elsevier Ltd. All rights reserved. doi:10.1016/j.tips.2009.11.002 Available online 7 December 2009