Targeted protein degradation reveals BET bromodomains as the cellular target of Hedgehog pathway inhibitor-1

  • Nat Commun. 2023 Jul 1;14(1):3893. doi: 10.1038/s41467-023-39657-1.
Meropi Bagka  1 ,  Hyeonyi Choi  1 ,  Margaux Héritier  2  3 ,  Hanna Schwaemmle  4 ,  Quentin T L Pasquer  1 ,  Simon M G Braun  4 ,  Leonardo Scapozza  2  3 ,  Yibo Wu  5 ,  Sascha Hoogendoorn  6
Affiliations
  • 1. Department of Organic Chemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland.
  • 2. School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
  • 3. Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.
  • 4. Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
  • 5. Chemical Biology Mass Spectrometry Platform (CHEMBIOMS), Faculty of Sciences, University of Geneva, Geneva, Switzerland.
  • 6. Department of Organic Chemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland. [email protected].
PMID: 37393376 DOI: 10.1038/s41467-023-39657-1
Abstract

Target deconvolution of small molecule hits from phenotypic screens presents a major challenge. Many screens have been conducted to find inhibitors for the Hedgehog signaling pathway - a developmental pathway with many implications in health and disease - yielding many hits but only few identified cellular targets. We here present a strategy for target identification based on Proteolysis-Targeting Chimeras (PROTACs), combined with label-free quantitative proteomics. We develop a PROTAC based on Hedgehog Pathway Inhibitor-1 (HPI-1), a phenotypic screen hit with unknown cellular target. Using this Hedgehog Pathway PROTAC (HPP) we identify and validate BET bromodomains as the cellular targets of HPI-1. Furthermore, we find that HPP-9 is a long-acting Hedgehog pathway inhibitor through prolonged BET bromodomain degradation. Collectively, we provide a powerful PROTAC-based approach for target deconvolution, that answers the longstanding question of the cellular target of HPI-1 and yields a PROTAC that acts on the Hedgehog pathway.

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