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@ARTICLE{Mileti:298895,
      author       = {N. Miletić and J. Weckesser and T. Mosler and R. Rathore
                      and M. E. Hoffmann and P. Gehrtz and S. Schlesiger and I. V.
                      Hartung and N. Berner$^*$ and S. Wilhelm and J. Müller and
                      B. Adhikari and V. Němec and S. A. Sivashanmugam and L.
                      Elson and H. Holzmann and M. P. Schwalm and L. Hoffmann and
                      K. R. Abdul Azeez and S. Müller and B. Kuster$^*$ and E.
                      Wolf and I. Đikić and S. Knapp$^*$},
      title        = {{W}orkflow for {E}3 {L}igase {L}igand {V}alidation for
                      {PROTAC} {D}evelopment.},
      journal      = {ACS chemical biology},
      volume       = {20},
      number       = {2},
      issn         = {1554-8929},
      address      = {Washington, DC},
      publisher    = {Soc.},
      reportid     = {DKFZ-2025-00338},
      pages        = {507-521},
      year         = {2025},
      note         = {2025 Feb 21;20(2):507-521},
      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.},
      cin          = {FM01 / MU01},
      ddc          = {540},
      cid          = {I:(DE-He78)FM01-20160331 / I:(DE-He78)MU01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:39932098},
      doi          = {10.1021/acschembio.4c00812},
      url          = {https://inrepo02.dkfz.de/record/298895},
}