Changes in protein-protein interactions that occur in response to environmental cues are difficult to uncover and have been poorly characterized to date. Here we describe a yeast-based assay that allows many binary protein interactions to be assessed in parallel and under various conditions. This method combines molecular barcoding and tag array technology with the murine dihydrofolate reductase-based protein-fragment complementation assay. A total of 238 protein-fragment complementation assay strains, each representing a unique binary protein complex, were tagged with molecular barcodes, pooled, and then interrogated against a panel of 80 diverse small molecules. Our method successfully identified specific disruption of the Hom3:Fpr1 interaction by the immunosuppressant FK506, illustrating the assay's capacity to identify chemical inhibitors of protein-protein interactions. Among the additional findings was specific cellular depletion of the Dst1:Rbp9 complex by the anthracycline drug doxorubicin, but not by the related drug idarubicin. The assay also revealed chemical-induced accumulation of several binary multidrug transporter complexes that largely paralleled increases in transcript levels. Further assessment of two such interactions (Tpo1: Pdr5 and Snq2:Pdr5) in the presence of 1,246 unique chemical compounds revealed a positive correlation between drug lipophilicity and the drug response in yeast.protein network | cell-based assay | drug screening | chemogenomics P rotein-protein interactions (PPIs) are of fundamental importance to virtually all cellular processes, including signal transduction and regulation of gene expression. Emergent highthroughput technologies that identify protein complexes and/or binary interactions have produced a wealth of information and have further underscored the ubiquitous role that PPIs play in cell biology (1-8). Although changes in protein complexes can occur from routine biochemical signaling events (i.e., posttranslational modification, protein degradation, or relocalization), the aforementioned studies were performed under standard growth conditions, and thus network connectivity changes that occur in response to different environmental cues remain ill-defined. Measuring such changes-for example, in response to chemical (i.e., small molecule) perturbations-is valuable in understanding both cellular systems and the biological effects of the chemical in question (9).The cell's "interactome" also represents a tremendous opportunity for unique therapeutic strategies. Small-molecule drugs that directly inhibit specific PPIs could be used to modulate the activity of certain cellular processes while minimally interfering with others. PPIs are perceived to be among the most challenging targets for small molecules because of the sheer size of the interaction interface and the lack of small, deep cavities amenable to small-molecule binding (reviewed in ref. 10). Thus, despite an ever-increasing commitment by drug developers to pursue PPIs, and a growing list of small molecules th...