Evaluating the Advantages of Using 3D-Enriched Fragments for Targeting BET Bromodomains

Jorden A. Johnson, Christos A. Nicolaou, Steven E. Kirberger, Anil K. Pandey, Haitao Hu, William C.K. Pomerantz

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Fragment-based ligand discovery has been successful in targeting diverse proteins. Despite drug-like molecules having more 3D character, traditional fragment libraries are largely composed of flat, aromatic fragments. The use of 3D-enriched fragments for enhancing library diversity is underexplored especially against protein-protein interactions. Here, we evaluate using 3D-enriched fragments against bromodomains. Bromodomains are highly ligandable, but selectivity remains challenging, particularly for bromodomain and extraterminal (BET) family bromodomains. We screened a 3D-enriched fragment library against BRD4(D1) via 1H CPMG NMR with a protein-observed 19F NMR secondary assay. The screen led to 29% of the hits that are selective over two related bromodomains, BRDT(D1) and BPTF, and the identification of underrepresented chemical bromodomain inhibitor scaffolds. Initial structure-activity relationship studies guided by X-ray crystallography led to a ligand-efficient thiazepane, with good selectivity and affinity for BET bromodomains. These results suggest that the incorporation of 3D-enriched fragments to increase library diversity can benefit bromodomain screening.

Original languageEnglish (US)
Pages (from-to)1648-1654
Number of pages7
JournalACS Medicinal Chemistry Letters
Issue number12
StatePublished - Dec 12 2019

Bibliographical note

Funding Information:
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsmedchemlett.9b00414 . NMR and FP experimental data; library and screen analyses; general experimental procedures and analytical characterization; BRD4(D1) cocrystal structural analysis of 1 , 18 , and 30 ( PDF ) National Institutes of Health Biotechnology training Grant No. 5T32GM008347–23. Lilly Research Award Program. NIH (GM118047). The authors declare no competing financial interest.

Publisher Copyright:
Copyright © 2019 American Chemical Society.


  • 3D fragment screening
  • CPMG
  • F NMR
  • bromodomains
  • thiazepane

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