First-in-class stabilizing inhibitor of CHD4 that traps and disassembles the NuRD complex

CHD4, the catalytic core of the NuRD complex, regulates chromatin remodeling, transcriptional repression, and DNA repair. Its overexpression in glioblastoma correlates with poor prognosis, yet CHD4 has remained undruggable. Employing a novel cell target engagement strategy, we identified CH41, a first-in-class small molecule that covalently engages cystine residues in the CHD4 chromodomain. The compound stabilizes CHD4 on chromatin, blocks its remodeling activity, and induces NuRD complex dissociation and proteasomal degradation. MICRO-TAG® cellular target engagement assay system applied in both discovery and validation stages, confirms direct CHD4 binding and real-time intracellular stabilization consistent with mechanistic trapping. CH41 disrupts CHD4 interaction with ZMYND8 and RBBP4/7, represses RAD51 expression, and impairs homologous-recombination repair, leading to reduced RAD51 foci and increased gammaH2AX and 53BP1 accumulation. Functionally, CH41 disables CHD4-dependent DNA repair and transcriptional control, re-sensitizing temozolomide-resistant glioblastoma cells. The data establishes CH41 as the first selective CHD4 inhibitor and illustrates how advances in cellular biophysics and cellular target engagement profiling are transforming the discovery of small molecule modulators of challenging transcription factor targets, such as chromatin remodelers.