CRISPR Screen Reveals BRD2/4 Molecular Glue-like Degrader via Recruitment of DCAF16

Authors:
Andrea G. Shergalis, Violeta L. Marin, David Y. Rhee, Sameera Senaweera, Rebecca L. McCloud,Judith A. Ronau, Charles W. Hutchins, Shaun McLoughlin, Kevin R. Woller, Scott E. Warder,Anil Vasudevan, and Justin M. Reitsma*
In:
Source: ACS Nano
Publication Date: (2023)
Issue: 18 (2): 331-339
Research Area:
Cancer Research/Cell Biology
Immunotherapy / Hematology
Basic Research
Drug Discovery
Cells used in publication:
293
Species: human
Tissue Origin: kidney
Platform:
384-well HT Nucleofector® System
Experiment

Arrayed CRISPR/Cas9-Based Dependency Screen.

HEK293 BRD4-HiBiT cells were cultured to be 30-50% confluent at the time of nucleofection. To prepare the RNP (ribonucleoprotein) complexes, Alt-R S.p. Cas9 Nuclease V3 (30 pmol, Integrated DNA Technologies, Newark, NJ), 30 pmol of Electroporation Enhancer (Integrated DNA Technologies), and 60 pmol of sgRNA (Synthego, Redwood City, CA) were mixed and incubated at room temperature. The cells were dispensed into RNP mixture, and the mixture was transferred to 384- well nucleocuvette plates at 30,000 cells/well (Lonza Bioscience, Morrisville, NC). The 384-well Nucleofector System was used to transfect the cells (Nucleofection condition: CM-130, SF Buffer, Lonza Bioscience). Post-nucleofection, the cells were incubated at room temperature and transferred to 384-well tissue culture plates using an automated liquid handling system.

Abstract

Molecular glues (MGs) are monovalent small molecules that induce an interaction between proteins (native or non-native partners) by altering the protein- protein interaction (PPI) interface toward a higher-affinity state. Enhancing the PPI between a protein and E3 ubiquitin ligase can lead to degradation of the partnering protein. Over the past decade, retrospective studies of clinical drugs identified that immunomodulatory drugs (e.g., thalidomide and analogues) and indisulam exhibit a molecular glue effect by driving the interaction between non-native substrates to CRBN and DCAF15 ligases, respectively. Ensuing reports of phenotypic screens focused on MG discovery have suggested that these molecules may be more common than initially anticipated. However, prospective discovery of MGs remains challenging. Thus, expanding the repertoire of MGs will enhance our understanding of principles for prospective design. Herein, we report the results of a CRISPR/Cas9 knockout screen of over 1000 ligases and ubiquitin proteasome system components in a BRD4 degradation assay with a JQ1-based monovalent degrader, compound 1a. We identified DCAF16, a substrate recognition component of the Cul4 ligase complex, as essential for compound activity, and we demonstrate that compound 1a drives the interaction between DCAF16 and BRD2/4 to promote target degradation. Taken together, our data suggest that compound 1a functions as an MG degrader between BRD2/4 and DCAF16 and provides a foundation for further mechanistic dissection to advance prospective MG discovery