Summary The stress hormone, cortisol, coordinates the body’s chronic metabolism, but also coordinates acute responses to stress by regulating stem cell differentiation in different tissues, restraining inflammatory and immune responses from being hyperactive, and coordinates acute metabolic responses to nutrient composition and feeding or fasting. Cortisol is also known as a glucocorticoid because it controls glucose metabolism. Synthetic glucocorticoids (GCs) are wide used for reducing pain and inflammation across many diseases, but can cause insulin resistance, muscle atrophy, and osteoporosis. We have developed an approach to studying GCs that enables us to understand how the glucocorticoid receptor coordinates these activities by binding to specific genes and changing the proteins made by those genes to control tissue-selective activity. This occurs as the GCs bind to the receptor and change its shape, enabling it to interact with different enzymes that control transcription. Previous efforts to understand these processes have been hampered by the fact that most of the existing GCs that we study are very similar. We instead make GCs that have a full range of desirable and undesirable activities, which gives us the statistical variance to understand them, a technique we call ligand class analysis, as we identify different classes of GC ligands that interact with different transcriptional regulatory enzymes to control expression of specific genes. Another major barrier has been the very wide expertise needed to understand the links between the GC chemical structure, receptor structure, the interacting coregulators, the regulated genes, and the tissue selective activities. We have assembled the required expertise and approaches to overcome these barriers by studying GC action on skeletal muscle, stem cell differentiation into bone, inflammation, and immune responses to colitis. We will use a chemical systems biology approach with novel GCs along with an integrative structural biology platform to define the signaling code for the glucocorticoid receptor in these aims: Aim 1 Biology: Identify which GC effects are correlated and which can be separated using physiologically relevant biology for the study of skeletal muscle, T cell differentiation, inflammation, and colitis, and osteoblast mineralization and effects on bone. Aim 2 Chemistry: Development of GCs to perturb GR structure and function in novel ways. We will enlarge three classes of compounds based on specific structural hypotheses to enlarge the chemical-structural space and test a novel steroidal scaffold to access new chemical space. Chemistry will focus on creating a diversity of effects on bone versus skeletal muscle while maintaining anti-inflammatory effects of the compounds. Aim 3 Structure: identify the structural underpinnings of selective GC signaling. We will apply machine learning and regression approaches to our structural and biological data to build and test models defining...