Target deconvolution strategies in drug discovery

In this postgenomic era, the perceived 'failure' of target-based drug discovery (in part owing to the complexities of biological systems and disease pathophysiology) has recently led to the renaissance of a more holistic approach that involves screening small organic molecules to determine whether they elicit any phenotypic changes in mammalian cells and model organisms.The retrospective identification of the molecular targets that underlie observed phenotypic responses — termed target deconvolution — is important for elucidating biological mechanisms of disease and will also greatly aid rational drug design and enable efficient structure–activity relationship studies to be carried out in a chemical optimization programme by configuration of target-specific assays.A wide range of experimental strategies can in principle be applied to the identification of targets that mediate phenotypic effects. The choice will often mainly be influenced by the properties of the small molecule.Methods that lead to the direct identification of targets typically exploit the affinity between the small organic molecule and its target protein. These methods include affinity chromatography, three-hybrid systems, phage and mRNA display, protein and 'reverse-transfected' cell microarrays, and biochemical suppression.Methods that are based on comprehensive DNA microarray or proteomics analyses can aid target deconvolution because they investigate the mode of action of an active small molecule. In a more indirect way, these technologies can also lead to the identification of molecular targets.The final aim of target deconvolution is not only the identification of biological targets that directly interact with the small molecule, but also the demonstration that the target's modulation is associated with functional effects that are detectable in the phenotypic assay. The 'authenticity' of targets can be confirmed by functional studies that employ a variety of methods, such as RNA interference and protein overexpression.Since phenotype-based drug discovery regained momentum, target deconvolution has become an important aspect of current drug discovery.