Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4
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The Bromo- and Extra-Terminal (BET) proteins BRD2, BRD3, and BRD4 play important roles in transcriptional regulation, epigenetics, and cancer and are the targets of pan-BET selective bromodomain inhibitor JQ1. However, the lack of intra-BET selectivity limits the scope of current inhibitors as probes for target validation and could lead to unwanted side effects or toxicity in a therapeutic setting. We designed Proteolysis Targeted Chimeras (PROTACs) that tether JQ1 to a ligand for the E3 ubiquitin ligase VHL, aimed at triggering the intracellular destruction of BET proteins. Compound MZ1 potently and rapidly induces reversible, long-lasting, and unexpectedly selective removal of BRD4 over BRD2 and BRD3. The activity of MZ1 is dependent on binding to VHL but is achieved at a sufficiently low concentration not to induce stabilization of HIF-1α. Gene expression profiles of selected cancer-related genes responsive to JQ1 reveal distinct and more limited transcriptional responses induced by MZ1, consistent with selective suppression of BRD4. Our discovery opens up new opportunities to elucidate the cellular phenotypes and therapeutic implications associated with selective targeting of BRD4.
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The pan-bromodomain and extra-terminal (BET) inhibitor JQ1, which binds and inhibits the BET proteins BRD2, BRD3, and BRD4, could be converted into a selective BRD4 PROTAC.
“For example, the pan-bromodomain and extra-terminal (BET) inhibitor JQ1, which binds and inhibits the BET proteins BRD2, BRD3, and BRD4, could be converted into a selective BRD4 PROTAC44.”
From Using proteolysis-targeting chimera technology to reduce navitoclax platelet toxicity and improve its senolytic activity (2020) · cites this paper as [44]
Several mechanisms contribute to increased selectivity of PROTACs, including steric incapability of some targets to form a productive ternary complex, or lack of a suitably positioned lysine residue for ubiquitination.
“Several mechanisms have been shown to contribute to this increase in selectivity. This includes steric incapability of some targets to form a productive ternary complex, or lack of a suitably positioned lysine residue for ubiquitination.62−69”
From Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence (2023) · cites this paper as [62]
Differences in proteome response could be attributed to distinct recruitment ligases used by MZ1 (VHL) or dBET6 (CRBN), as well as established differences in selectivity for BBDs, where MZ1 preferentially degrades BRD4, whereas dBET6 degrades BRD2, BRD3 and BRD4 equivalently.
“These differences could be attributed to the distinct recruitment ligases used by MZ1 (VHL) or dBET6 (CRBN), as well as the established differences in selectivity for the BBDs, where MZ1 preferentially degrades BRD4 (17), whereas dBET6 degrades BRD2, BRD3 and BRD4, equivalently (16).”
From The drug efflux pump MDR1 promotes intrinsic and acquired resistance to PROTACs in cancer cells (2022) · cites this paper as [17]
The discovery of small-molecule mimetics of the HIF1α peptide opened the door to the rational design of PROTACs based wholly on small molecular structures - for example, the first PROTACs based on the bromodomain protein inhibitor JQ1 that recruited VHL to degrade bromodomain-containing protein 4 (BRD4).
“The discovery of small-molecule mimetics of the HIF1α peptide20,21 opened the door to the rational design of PROTACs based wholly on small molecular structures — for example, the first PROTACs based on the bromodomain protein inhibitor JQ1 that recruited VHL to degrade bromodomain-containing protein 4 (BRD4)22,23.”
From PROTAC targeted protein degraders: the past is prologue (2022) · cites this paper as [23]
MZ1, a VHL-based BRD4 PROTAC utilizing JQ1, became a selective BRD4 degrader even though JQ1 inhibits BRD2, 3 and 4.
“The VHL-based BRD4 PROTAC, named MZ1, developed by Ciulli’s group utilized JQ1 as BRD4 ligand. Though JQ1 inhibits BRD2, 3 and 4, after being converted to a PROTAC, MZ1 became a selective BRD4 degrader [23].”
From PROteolysis TArgeting Chimeras (PROTACs) as emerging anticancer therapeutics (2020) · cites this paper as [23]
A VHL-recruiting BRD4 PROTAC exhibited a clear preference for BRD4, but BRD2 and 3 were also degraded at either high concentrations or prolonged treatments.
“While the PROTAC exhibited a clear preference for BRD4, BRD2 and 3 were also degraded at either high concentrations or prolonged treatments [94].”
From Advances in targeted degradation of endogenous proteins (2019) · cites this paper as [94]
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Targeted Protein Degradation by Small Molecules
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Discovery of SHP2-D26 as a First, Potent, and Effective PROTAC Degrader of SHP2 Protein
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Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta
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Amide-to-Ester Substitution as a Strategy for Optimizing PROTAC Permeability and Cellular Activity
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Self-citationLigandability of E3 Ligases for Targeted Protein Degradation Applications
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The drug efflux pump MDR1 promotes intrinsic and acquired resistance to PROTACs in cancer cells
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Integrative Modeling of PROTAC-Mediated Ternary Complexes
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PROTAC-mediated degradation of class I histone deacetylase enzymes in corepressor complexes
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A Nimbolide-Based Kinase Degrader Preferentially Degrades Oncogenic BCR-ABL
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Bifunctional chemical probes inducing protein–protein interactions
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Advances in targeted degradation of endogenous proteins
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UBE2G1 governs the destruction of cereblon neomorphic substrates
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- Authors
- Zengerle, M., Chan, K.-H., & Ciulli, A.
- Affiliations
- University of Dundee (GB)
- Corresponding author
- Ciulli, Alessio
- Venue
- ACS Chemical Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-06-02
- Volume
- 10
- Issue
- 8
- Pages
- 1770-1777
- ISSN
- 1554-8929 (ISSN-L)
- 1554-8937
- PMC
- PMC4548256
- OpenAlex
- W2227431445
- Cited by
- 1,056
- References
- 37
- Citations by year
- 2026: 85 · 2025: 124 · 2024: 115 · 2023: 114 · 2022: 116 · 2021: 127 · 2020: 127 · 2019: 93 · 2018: 57 · 2017: 57 · 2016: 31 · 2015: 9
- FWCI
- 22.57
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- ACS Chemical Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (acceptedVersion, cc-by-nc-nd)
- Funders
- European Research Council (311460)
- Biotechnology and Biological Sciences Research Council (BB/G023123/2, BB/J001201/2)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- BRD4, BET proteins, PROTACs, JQ1, VHL E3 ubiquitin ligase, MZ1, bromodomain inhibitors, HIF-1α, transcriptional regulation, selective protein degradation
- MeSH terms
- Bromodomain Containing Proteins, Dipeptides, HeLa Cells, Heterocyclic Compounds, 3-Ring, Humans, Neoplasms, Nuclear Proteins, Transcription Factors, Drug Design, Gene Expression Regulation, Neoplastic, Cell Cycle Proteins, Ubiquitin-Protein Ligases, Von Hippel-Lindau Tumor Suppressor Protein, Small Molecule Libraries, Proteolysis
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