A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes

Huarui Cui, Anand Divakaran, Zachariah J. Hoell, Mikael O. Ellingson, Cole R. Scholtz, Huda Zahid, Jorden A. Johnson, Elizabeth C. Griffith, Clifford T. Gee, Amani L. Lee, Shalil Khanal, Ke Shi, Hideki Aihara, Vijay H. Shah, Richard E. Lee, Daniel A. Harki, William C.K. Pomerantz

Research output: Contribution to journalArticlepeer-review


Chemical probes for epigenetic proteins are essential tools for dissecting the molecular mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small molecule inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compounds 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concentration in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were observed. These results provide new design rules for selective inhibitors of an individual BET bromodomain.

Original languageEnglish (US)
Pages (from-to)2342-2360
Number of pages19
JournalJournal of Medicinal Chemistry
Issue number3
StatePublished - Feb 10 2022

ASJC Scopus subject areas

  • Molecular Medicine
  • Drug Discovery


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