Assessing the Cell Permeability of Bivalent Chemical Degraders Using the Chloroalkane Penetration Assay
Open accessAbstract
Bivalent chemical degraders provide a catalytic route to selectively degrade disease-associated proteins. By linking target-specific ligands with E3 ubiquitin ligase recruiting ligands, these compounds facilitate targeted protein ubiquitination and degradation by the proteasome. Due to the complexity of this multistep mechanism, the development of effective degrader molecules remains a difficult, lengthy, and unpredictable process. Since degraders are large heterobifunctional molecules, the efficacy of these compounds may be limited by poor cell permeability, and an efficient and reliable method to quantify the cell permeability of these compounds is lacking. Herein, we demonstrate that by the addition of a chloroalkane tag on the BRD4 specific degrader, MZ1, cell permeability can be quantified via the chloroalkane penetration assay. By extending this analysis to individual components of the degrader molecule, we have obtained structure–permeability relationships that will be informative for future degrader development, particularly as degraders move into the clinic as potential therapeutics.
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Cell permeability was found to be extremely low for the complete JQ1-based degrader, below the concentration needed for effective degradation of BRD4, implying that this PROTAC must rely heavily on turnover to achieve depletion of its target protein.
“Cell permeability was measured for chloroalkane-tagged components of a JQ1-based degrader, and was found to be extremely low for the complete PROTAC: below even the concentration needed for effective degradation of BRD4, implying that this PROTAC must rely heavily on turnover to achieve depletion of its target protein 67.”
From Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta (2021) · cites this paper as [67]
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- Authors
- Foley, C. A., Potjewyd, F., Lamb, K. N., James, L. I., & Frye, S. V.
- Affiliations
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Frye, Stephen V.
- Venue
- ACS Chemical Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2019-12-17
- Volume
- 15
- Issue
- 1
- Pages
- 290-295
- ISSN
- 1554-8929 (ISSN-L)
- 1554-8937
- PMC
- PMC7010361
- OpenAlex
- W2996636067
- Cited by
- 89
- References
- 44
- Citations by year
- 2026: 8 · 2025: 7 · 2024: 11 · 2023: 11 · 2022: 17 · 2021: 16 · 2020: 17 · 2019: 1 · 2018: 1
- FWCI
- 4.30
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- ACS Chemical Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Center for Strategic Scientific Initiatives, National Cancer Institute (R01CA218392)
- National Institute on Drug Abuse (R61DA047023-01)
- National Institute of General Medical Sciences (R01GM100919)
- 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 › Ubiquitin and proteasome pathways
- Keywords
- membrane permeability, targeted protein degradation, BRD4, MZ1, structure-permeability relationship, heterobifunctional molecules, proteasomal degradation
- MeSH terms
- Bromodomain Containing Proteins, Cell Line, Cell Membrane Permeability, Dipeptides, Drug Evaluation, Preclinical, Heterocyclic Compounds, 3-Ring, Humans, Hydrocarbons, Ligands, Structure-Activity Relationship, Transcription Factors, Biosensing Techniques, Molecular Structure, Cell Cycle Proteins, Ubiquitin-Protein Ligases, Small Molecule Libraries, Ubiquitination, Proteolysis
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