Abstract
Small molecules are important not only as therapeutics to treat disease but also as chemical tools to probe complex biological processes. The discovery of novel bioactive small molecules has largely been catalyzed by screening diverse chemical libraries for alterations in specific activities in pure proteins assays or in generating cell-based phenotypes. New approaches are needed to close the vast gap between the ability to study either single proteins or whole cellular processes. This Review focuses on the growing number of studies aimed at understanding in more detail how small molecules perturb particular signaling pathways and larger networks to yield distinct cellular phenotypes. This type of pathway-level analysis and phenotypic profiling provides valuable insight into mechanistic action of small molecules and can reveal off-target effects and improve our understanding of how proteins within a pathway regulate signaling.