Micromap (µMap) Photoproximity Labeling for Integrated Phenotypic Screening and Accelerated Prioritization of Targeted Protein Degrader Compounds

Phenotypic screening is a powerful tool for discovering first-in-class medicines, but its potential is limited by the significant challenge of triaging hit compounds and deconvoluting their mechanisms. Similarly, targeted protein degradation (TPD) represents a powerful new therapeutic strategy but is constrained by its reliance on a small number of E3 ligases with limited capability to discover new degradation mechanisms within validated platforms. Here, we present an integrated platform that bridges phenotype and mechanism, enabling rapid prioritization and characterization of small molecule hits from high throughput screening with sequential proximity labeling technologies. First, immunophotoproximity labeling (µMapX) is used to profile drug-induced interactome changes of an endogenous protein target to rapidly triage hits displaying discrete or promising mechanisms. Second, photocatalytic µMap target identification (µMap TargetID) is used to characterize protein engagement for candidate compounds and provide orthogonal mechanistic insight. As a test case, we applied this platform to discover degraders of BTB and CNC Homolog 2 (BACH2), a key immunoregulatory transcription factor. This approach rapidly prioritized a lead compound scaffold that inhibits GSK3β to induce proximity between β-catenin and BACH2, leading to its degradation through a LON peptidase-dependent mechanism. Together, this integrated platform provides a generalizable strategy to accelerate drug discovery by de-risking and prioritizing phenotypic hits, discovering degraders with novel mechanisms, and uncovering therapeutically targetable biology.