Project summary Eukaryotic bHLH/PAS (basic helix-loop-helix/Per-ARNT-Sim) transcription factors play a critical role in regulating cellular responses to hypoxia, xenobiotic compounds, and several other environmental conditions. Deregulation of these pathways is highly correlated with several forms of cancer, including solid tumor onset and progression, as best exhibited by links between overexpression of HIF (Hypoxia Inducible Factor) isoforms and predisposition to kidney cancers. The PAS domains within these transcription factors are attractive targets for small molecule regulation given the role that these domains play as cofactor-regulated protein/protein interaction domains in a wide range of sensory proteins throughout biology. Here we propose to combine the complementary strengths of the Gardner lab (CCNY) and Tan lab (MSK) for a multi-pronged attack on studying the structure and artificial regulation of interactions between ARNT (aryl hydrocarbon nuclear receptor translocator), a common element of several bHLH/PAS heterodimeric complexes, and several coactivator proteins that are essential for ARNT function. Preliminary data strongly support the feasibility of this project, including cryoEM and other biophysical data on several ARNT complexes and moderate potency small-molecule inhibitors of ARNT/CCC interactions. Coupled with the expertise of the two groups with the requisite assays and methods, plus their past experience in comparable projects, there is substantial confidence in this project catalyzing interactions between the two labs and developing novel routes for small molecule regulation of cancer-driving transcription factors using an integrated strategy of structural, chemical, and cellular research approaches. Relevance We propose to combine the expertise in the Gardner and Tan labs in structural biology, biochemistry, and synthetic organic chemistry to characterize and inhibit interactions between the ARNT transcriptional regulator and a series of coactivator proteins. Misregulation of ARNT-containing complexes are correlated with a variety of cancers; results from our work will both guide understanding of how such complexes are assembled and guide development of small molecule tool compounds to control their formation.