Developmental biology is now both a molecular and systems-level science. Forward- and reverse-genetic technologies have identified individual genes that regulate tissue formation and contribute to their oncogenic transformation later in life. High-throughput sequencing has revealed the “omic” features that differentiate cellular states. Translating this knowledge into mechanistic understanding will require new scientific approaches, and chemistry can help bridge this gap. Chemical synthesis and protein engineering can empower us to interrogate tissue biology in new ways, and the resulting technologies and insights can lead to innovative treatments for human disease. With these goals in mind, our research group has explored the interface of chemistry and developmental biology. Over the past four years, we have developed an optogenetic system for targeted cell ablation, identified novel small-molecule inhibitors of Gli transcription factor function, and discovered the first specific inhibitors of aldehyde dehydrogenase 1B1 (ALDH1B1), a mitochondrial enzyme that is expressed in multipotent cells of the adult intestine and pancreas and promotes colorectal and pancreatic cancer. We have also used high-throughput and systems-level approaches to establish a regulatory model for ARHGAP36, a non- canonical Gli activator that controls motor neuron specification and can induce medulloblastoma. We now seek to build upon these accomplishments and explore new scientific directions. One focus of our research program will be the creation of new optogenetic tools that act through inducible allostery rather than proximity. To facilitate the discovery of such constructs, we have established a transposon-based platform that recapitulates the evolution of natural photoreceptors. Using this approach, we will develop optogenetic regulators of the Hedgehog pathway, focusing on light-oxygen-voltage (LOV) domain-functionalized forms of Smoothened and GLI1. We will elucidate the mechanistic basis of their light-dependent activities, optimize their functionality, and apply these reagents to study Hedgehog pathway-dependent patterning in zebrafish models. We will also extend this platform to other developmental pathways such as bone morphogenetic protein signaling. Our second research focus will be ALDH1 isoforms that are highly expressed in normal stem cells and integral to tumor initiation and progression. We will investigate the roles of ALDH1B1 in pancreatic cancer and develop specific inhibitors of ALDH1A3, a cytoplasmic enzyme that promotes breast cancer, melanoma, and glioblastoma, and other malignancies. In addition, we will pursue small molecules that target ALDH1A1 and/or ALDH1A2, motivated by the roles of these enzymes in spermatogenesis and their potential as non-hormonal male contraceptive targets. Collectively, our studies will open new windows into developmental biology and new doors to clinical therapies.