The Endo-GeneScreen platform identifies drug-like probes that regulate endogenous protein levels within physiological...

Traditional phenotypic drug discovery platforms suffer from poor scalability and/or a lack of mechanistic understanding of discovered probes. We address this by creating Endo-GeneScreen (EGS), a high-throughput platform that identifies small molecules that regulate endogenous protein levels encoded by a preselected target gene within disease-modeling contexts. Two initial screens identify >40 validated small molecules that boost endogenous neuronal Syngap1 levels, a gene that causes a neurodevelopmental disorder when haploinsufficient. EGS assays also accelerate preclinical development of drug candidates and facilitate mode-of-action deconvolution studies of orphaned probes. SR-1815 represents a fully validated proof-of-concept candidate from the platform. It is a previously unknown drug-like small molecule multikinase inhibitor that regulates splicing of Syngap1 transcripts. It restores SynGAP protein abundance to wildtype levels and mitigates major cellular consequences of Syngap1 loss-of-function. Thus, the EGS platform promotes identification and development of small molecules that alter the abundance of disease-linked proteins in a translationally-relevant context.