@Article{macau_mods_00005818, author = {Mileti{\'{c}}, Neboj{\v{s}}a and Weckesser, Janik and Mosler, Thorsten and Rathore, Rajeshwari and Hoffmann, Marina E. and Gehrtz, Paul and Schlesiger, Sarah and Hartung, Ingo V. and Berner, Nicola and Wilhelm, Stephanie and M{\"u}ller, Juliane and Adhikari, Bikash and N{\v{e}}mec, V{\'a}clav and Sivashanmugam, Saran Aswathaman and Elson, Lewis and Holzmann, Hanna and Schwalm, Martin P. and Hoffmann, Lasse and Abdul Azeez, Kamal Rayees and M{\"u}ller, Susanne and Kuster, Bernhard and Wolf, Elmar and {\DJ}iki{\'{c}}, Ivan and Knapp, Stefan}, title = {Workflow for E3 Ligase Ligand Validation for PROTAC Development}, journal = {ACS chemical biology / American Chemical Society}, year = {2025}, publisher = {American Chemical Society (ACS)}, address = {Washington, DC}, volume = {20}, number = {2}, pages = {507--521}, keywords = {Humans; Ubiquitin-Protein Ligases; Adaptor Proteins, Signal Transducing; Protein Kinase Inhibitors; Ligands; Von Hippel-Lindau Tumor Suppressor Protein; Drug Discovery; Workflow; Proteolysis}, abstract = {Proteolysis targeting chimeras (PROTACs) have gained considerable attention as a new modality in drug discovery. The development of PROTACs has been mainly focused on using CRBN (Cereblon) and VHL (Von Hippel-Lindau ligase) E3 ligase ligands. However, the considerable size of the human E3 ligase family, newly developed E3 ligase ligands, and the favorable druggability of some E3 ligase families hold the promise that novel degraders with unique pharmacological properties will be designed in the future using this large E3 ligase space. Here, we developed a workflow aiming to improve and streamline the evaluation of E3 ligase ligand efficiency for PROTAC development and the assessment of the corresponding "degradable" target space using broad-spectrum kinase inhibitors and the well-established VHL ligand VH032 as a validation system. Our study revealed VH032 linker attachment points that are highly efficient for kinase degradation as well as some of the pitfalls when using protein degradation as a readout. For instance, cytotoxicity was identified as a major mechanism leading to PROTAC- and VHL-independent kinase degradation. The combination of E3 ligase ligand negative controls, competition by kinase parent compounds, and neddylation and proteasome inhibitors was essential to distinguish between VHL-dependent and -independent kinase degradation events. We share here the findings and limitations of our study and hope that this study will provide guidance for future evaluations of new E3 ligase ligand systems for degrader development.}, issn = {1554-8929}, doi = {10.1021/acschembio.4c00812}, url = {https://macau.uni-kiel.de/receive/macau_mods_00005818}, url = {https://doi.org/10.1021/acschembio.4c00812}, url = {http://www.ncbi.nlm.nih.gov/pubmed/39932098}, file = {:https://macau.uni-kiel.de/servlets/MCRFileNodeServlet/macau_derivate_00007278/miletic-et-al-2025-workflow-for-e3-ligase-ligand-validation-for-protac-development.pdf:PDF}, language = {en} }