RAPID is a next-generation chemoproteomics technology for identifying small molecules that bind reversibly to a pre-specified target of interest in a living cell. We will introduce the RAPID assay technology and describe its application towards the discovery of first-in-class inhibitors of SLC6A19, a genetically validated target for the treatment of PKU, as well as the first described ligands for the transcription factor IRF3 for the treatment of interferon-driven autoimmune disease.