Cell Morphological Profiling Enables High-Throughput Screening for PROteolysis TArgeting Chimera (PROTAC) Phenotypic Signature
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Abstract
PROteolysis TArgeting Chimeras (PROTACs) use the ubiquitin-proteasome system to degrade a protein of interest for therapeutic benefit. Advances made in targeted protein degradation technology have been remarkable, with several molecules having moved into clinical studies. However, robust routes to assess and better understand the safety risks of PROTACs need to be identified, which is an essential step toward delivering efficacious and safe compounds to patients. In this work, we used Cell Painting, an unbiased high-content imaging method, to identify phenotypic signatures of PROTACs. Chemical clustering and model prediction allowed the identification of a mitotoxicity signature that could not be expected by screening the individual PROTAC components. The data highlighted the benefit of unbiased phenotypic methods for identifying toxic signatures and the potential to impact drug design.
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PROTAC phenotypic signatures have already been identified through cell morphological profiling.
“Indeed, PROTAC phenotypic signatures have already been identified through cell morphological profiling.186”
From Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence (2023) · cites this paper as [186]
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Self-citationSeal, S., Yang, H., Trapotsi, M.-A., Singh, S., Puigvert, J. C., Spjuth, O., & Bender, A. (2024) · Figshare · doi:10.6084/m9.figshare.26593601
Self-citationSeal, S., Yang, H., Trapotsi, M.-A., Singh, S., Puigvert, J. C., Spjuth, O., & Bender, A. (2024) · Figshare · doi:10.6084/m9.figshare.26593592
Self-citationSeal, S., Yang, H., Trapotsi, M.-A., Singh, S., Puigvert, J. C., Spjuth, O., & Bender, A. (2024) · Figshare · doi:10.6084/m9.figshare.26593604
Self-citationPredicting DNA damage response using synthetic cell painting profiles and experimental analysis
Seo, C., Lim, H., Piao, Z., Koh, Y. J., & Lee, S. J. (2026) · iScience · doi:10.1016/j.isci.2026.115000
Disrupting linearity of PROTAC scaffolds prevents off-target complex I inhibitionPreprint
Richert, N., Nůsková, H., Samarin, J., Ivanov, B. S., Saoud, M., Deis, F. H., de Vries, N., Sievers, S., Poschet, G., Ziegler, S., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.13.702718
Cell painting and thermal proteome profiling for inference of drug targets and mechanism of action
Johansson, C., Johansson, M., Kasi, P. B., Larsson, M., Jakobsson, P., Göransson, U., Puigvert, J. C., Spjuth, O., & Jansson, E. T. (2026) · Molecular Systems Biology · doi:10.1038/s44320-026-00214-9
High-Throughput Screen for Candidate PROTAC Identification
Chen, X., & Zhu, C. (2026) · Handbook of experimental pharmacology · doi:10.1007/164_2026_841
Silva, J., Costa, P., & Beatriz, A. (2025) · International Journal of Pharmaceutical and Phytopharmacological Research · doi:10.51847/ibkm6kdcw1
Cellular Morphological Profiling of PROTAC Degraders of the m6A RNA Methyltransferase METTL3
Jiang, M., Chukwudi Thomas, U. G. W. U., Wortmann, L., Schloßhauer, J. L., Begemann, C., Sievers, S., Kliza, K. W., & Wu, P. (2026) · ACS Bio & Med Chem Au · doi:10.1021/acsbiomedchemau.6c00136
High-content morphological profiling by Cell Painting in 3D spheroids
Ringers, C., Holmberg, D., Larsson, A., Jung, B., Jarvius, M., Łuchniak, A., Rosén, D., Johansson, M., Georgiev, P., Seashore-Ludlow, B. A., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-78596-5 · Cited by 5 · see citing works
- Authors
- Trapotsi, M.-A., Mouchet, E., Williams, G., Monteverde, T., Juhani, K., Turkki, R., Miljković, F., Martinsson, A., Mervin, L., Pryde, K. R., Müllers, E., Barrett, I., Engkvist, O., Bender, A., & Moreau, K.
- Affiliations
- AstraZeneca (United Kingdom) (GB)
- AstraZeneca (Sweden) (SE)
- University of Cambridge (GB)
- Safety Innovation, Clinical Pharmacology and Safety Sciences R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
- ORCID
- Venue
- ACS Chemical Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2022-07-06
- Volume
- 17
- Issue
- 7
- Pages
- 1733-1744
- ISSN
- 1554-8929 (ISSN-L)
- 1554-8937
- PMC
- PMC9295119
- OpenAlex
- W4284671611
- Cited by
- 51
- References
- 40
- Citations by year
- 2026: 8 · 2025: 8 · 2024: 16 · 2023: 16 · 2022: 3
- FWCI
- 3.83
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- ACS Chemical Biology (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by-nc-nd)
- Apollo
- Funders
- AstraZeneca
- Biotechnology and Biological Sciences Research Council (BB/M011194/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- PROTACs, targeted protein degradation, Cell Painting, phenotypic profiling, mitochondrial toxicity, drug safety, chemical clustering, model prediction, high-content imaging, ubiquitin-proteasome system
- MeSH terms
- Humans, Ubiquitin-Protein Ligases, Proteasome Endopeptidase Complex, High-Throughput Screening Assays, Proteolysis
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