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Selectivity Profiling of Bromodomain PROTACs Using Chemical Inducers of Proximity DNA-Encoded Library Screening.
Yuen Ting Chow1,2, Bingqi Tong1,2,3, Zher Yin Tan1,2
1Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.
ACS Chemical Biology
|August 12, 2025
Summary
Chemical Inducers of Proximity DNA-Encoded Library (CIP-DEL) screening identified selective Proteolysis-Targeting Chimera (PROTAC) compounds. This method efficiently profiles compound selectivity across similar protein targets, aiding in the discovery of targeted degraders.
Area of Science:
- Biochemistry
- Chemical Biology
- Drug Discovery
Background:
- Chemical Inducers of Proximity DNA-Encoded Library (CIP-DEL) screening facilitates high-throughput identification of compounds that induce protein-protein interactions, including Proteolysis-Targeting Chimeras (PROTACs).
- Simultaneous screening of protein paralogs using CIP-DEL enables compound selectivity profiling and identification of paralog-selective degraders, a capability not previously reported.
Purpose of the Study:
- To optimize CIP-DEL screening conditions for profiling PROTAC selectivity against closely related protein targets.
- To identify paralog-selective degraders using a von Hippel-Lindau (VHL)-biased CIP-DEL screen against eight Bromodomain and Extra Terminal (BET) bromodomains.
Main Methods:
- Optimized CIP-DEL screening conditions.
- Conducted a VHL-biased CIP-DEL screen using two million DNA-barcoded PROTAC compounds against eight BET bromodomains (BRD2 BD1/BD2, BRD3 BD1/BD2, BRD4 BD1/BD2, BRDT BD1/BD2).
- Analyzed sequencing data and performed in vitro assays to validate compound selectivity.
Main Results:
- Observed a preference for compounds binding the first bromodomain (BD1) over the second bromodomain (BD2) in BET proteins, contrary to existing literature.
- Identified compound 21-1 with promising BRD2 BD1 selectivity, confirmed by sequencing data and in vitro assays.
- Demonstrated that normalized relative enrichment selectivity from sequencing data correlates better with experimentally validated selectivity than unnormalized absolute enrichment.
Conclusions:
- CIP-DEL screening is valuable for profiling PROTAC selectivity against protein families with high sequence homology.
- The developed method facilitates the discovery of selective degraders for challenging protein targets.
- This approach can be broadly applied to other protein families where selective degrader discovery is difficult.
