Targeted Transcriptional Repression by Induced Proximity

Abstract

Most cancer-driving proteins remain "undruggable" due to the absence of ligandable pockets and their reliance on intrinsically disordered or protein-DNA/protein-protein interactions. Transcription factors, which orchestrate oncogenic gene expression programs, are particularly challenging: they turn over rapidly, evade durable pharmacological inhibition, and resist even emerging targeted protein degradation strategies. Here, we describe a new induced-proximity therapeutic modality, Transcriptional Regulation via Active Control of Epigenetic Reprogramming (TRACER), that enforces locus-specific transcriptional silencing by recruiting endogenous corepressor complexes to transcription factor binding sites. We developed small-molecule TRACERs that tether methyl-CpG binding domain protein 2 (MBD2) and the Nucleosome Remodeling and Deacetylase (NuRD) complex to transcription factor-directed ligands. An estrogen receptor (ER) TRACER potently suppressed ER transcriptional activity in breast cancer cells, downregulated canonical ER target genes, and required MBD2 and histone deacetylase (HDAC1/2) for activity, confirming on-target epigenetic repression. Extending this approach to prostate cancer, an androgen receptor (AR) TRACER transcriptionally repressed both full-length AR and the drug-resistant truncation variant AR-V7, achieving >90% inhibition of AR transcriptional activity in androgen-independent prostate cancer cells with locus-specific gene repression. We further show that TRACERs can be modularly reprogrammed to recruit alternative repressors, including PRC2. Collectively, these findings establish TRACERs as a generalizable modality to pharmacologically silence undruggable transcription factors through targeted epigenetic reprogramming, offering a powerful new strategy for treating cancers refractory to existing therapies.