» Articles » PMID: 35793809

Cell Morphological Profiling Enables High-Throughput Screening for PROteolysis TArgeting Chimera (PROTAC) Phenotypic Signature

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.

Citing Articles

Cell Painting: a decade of discovery and innovation in cellular imaging.

Seal S, Trapotsi M, Spjuth O, Singh S, Carreras-Puigvert J, Greene N Nat Methods. 2024; 22(2):254-268.

PMID: 39639168 PMC: 11810604. DOI: 10.1038/s41592-024-02528-8.


Insights into the Identification of iPSC- and Monocyte-Derived Macrophage-Polarizing Compounds by AI-Fueled Cell Painting Analysis Tools.

Bruggenthies J, Dittmer J, Martin E, Zingman I, Tabet I, Bronner H Int J Mol Sci. 2024; 25(22).

PMID: 39596395 PMC: 11595184. DOI: 10.3390/ijms252212330.


SPACe: an open-source, single-cell analysis of Cell Painting data.

Stossi F, Singh P, Marini M, Safari K, Szafran A, Rivera Tostado A Nat Commun. 2024; 15(1):10170.

PMID: 39580445 PMC: 11585637. DOI: 10.1038/s41467-024-54264-4.


LIN28-Targeting Chromenopyrazoles and Tetrahydroquinolines Induced Cellular Morphological Changes and Showed High Biosimilarity with BRD PROTACs.

Jiang M, Giannino N, Goebel G, Sievers S, Wu P ChemMedChem. 2024; 20(1):e202400547.

PMID: 39353851 PMC: 11694606. DOI: 10.1002/cmdc.202400547.


Targeted protein degradation using chimeric human E2 ubiquitin-conjugating enzymes.

Taylor J, Barrett N, Martinez Cuesta S, Cassidy K, Pachl F, Dodgson J Commun Biol. 2024; 7(1):1179.

PMID: 39300128 PMC: 11415077. DOI: 10.1038/s42003-024-06803-4.


References
1.
Trapotsi M, Hosseini-Gerami L, Bender A . Computational analyses of mechanism of action (MoA): data, methods and integration. RSC Chem Biol. 2022; 3(2):170-200. PMC: 8827085. DOI: 10.1039/d1cb00069a. View

2.
Seal S, Yang H, Vollmers L, Bender A . Comparison of Cellular Morphological Descriptors and Molecular Fingerprints for the Prediction of Cytotoxicity- and Proliferation-Related Assays. Chem Res Toxicol. 2021; 34(2):422-437. DOI: 10.1021/acs.chemrestox.0c00303. View

3.
Bray M, Gustafsdottir S, Rohban M, Singh S, Ljosa V, Sokolnicki K . A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay. Gigascience. 2017; 6(12):1-5. PMC: 5721342. DOI: 10.1093/gigascience/giw014. View

4.
Gustafsdottir S, Ljosa V, Sokolnicki K, Wilson J, Walpita D, Kemp M . Multiplex cytological profiling assay to measure diverse cellular states. PLoS One. 2013; 8(12):e80999. PMC: 3847047. DOI: 10.1371/journal.pone.0080999. View

5.
Ermondi G, Garcia-Jimenez D, Caron G . PROTACs and Building Blocks: The 2D Chemical Space in Very Early Drug Discovery. Molecules. 2021; 26(3). PMC: 7865272. DOI: 10.3390/molecules26030672. View