Proteomic discovery and characterization of chemical tools that degrade the NuRD chromatin regulatory complex

Project Summary As virtually all aspects of cell behavior and identity converge upon programmed responses in gene expression, transcriptional control features centrally in both normal homeostasis and progression to disease. Accordingly, pharmacologic perturbation of gene regulatory machinery is an attractive approach for understanding and

modulating complex cellular disease states. Transcriptionally targeted drugs must overcome key hurdles, however, including the limited accessibility of DNA binding factors and multi-component complexes to traditional drug design approaches, as well as the indiscriminate activity caused by disruption of transcriptional processes

shared across distinct cell types and states. In this proposal, we present and build on a novel discovery of an immunosuppressive electrophilic chemical probe termed "L4" that avoids these pitfalls through its remarkable ability to cause selective degradation of multiple NuRD (Nucleosome Remodeling Deacetylase) complex

subunits in a T-cell-restricted manner. Empowered by our laboratory’s recent development of chemical proteomic strategies to globally map small molecule-protein interactions in native biological systems, we propose a research strategy to study the mechanism of the unprecedented pharmacological features of L4 and their

implications for broader drug design approaches to target transcriptional complexes. In addition, we will investigate the relationship between L4-mediated degradation of the NuRD complex and the compound’s blockade of T-cell activation. In Specific Aim 1, we will apply our group’s chemical proteomic expertise to

characterize NuRD degradation by L4 and map relevant protein targets in human T-cells using a suite of L4- related compounds and NuRD complex-directed enrichment approaches. In Specific Aim 2, we will evaluate the role of candidate L4 targets underpinning NuRD degradation using genetic and biochemical approaches and

examine how the identified mechanisms result in the striking features of multi-subunit degradation and state- dependent (cell type-restricted) activity. In Specific Aim 3, we extend to examine the relationship of L4’s action on NuRD to its ability to block T-cell activation, and assess and apply this compound as a tool for further study

of T-cell biology. By providing in-depth understanding of the unique pharmacological activity of L4, the proposed research will contribute to the overarching goals of exploring both novel mechanisms in targeted protein degradation and state-dependent control of gene regulatory proteins. Together, these broader ambitions

represent promising avenues to overcome challenges in the development of transcriptionally targeted chemical probes and medicines.