2. Academic Validation
  3. Critical assessment of LC3/GABARAP ligands used for degrader development and ligandability of LC3/GABARAP binding pockets

Critical assessment of LC3/GABARAP ligands used for degrader development and ligandability of LC3/GABARAP binding pockets

  • Nat Commun. 2024 Nov 25;15(1):10204. doi: 10.1038/s41467-024-54409-5.
Martin P Schwalm 1 2 3,  Johannes Dopfer 1 2,  Adarsh Kumar 1 2,  Francesco A Greco 1 2,  Nicolas Bauer 1 2,  Frank Löhr 4,  Jan Heering 5,  Sara Cano-Franco 6 7,  Severin Lechner 8,  Thomas Hanke 1 2,  Ivana Jaser 9,  Viktoria Morasch 1 2,  Christopher Lenz 1 2,  Daren Fearon 10,  Peter G Marples 10,  Charles W E Tomlinson 10,  Lorene Brunello 6 7,  Krishna Saxena 1 2,  Nathan B P Adams 9,  Frank von Delft 10,  Susanne Müller 1 2,  Alexandra Stolz 6 7,  Ewgenij Proschak 1 5,  Bernhard Kuster 8,  Stefan Knapp 11 12 13,  Vladimir V Rogov 14 15
Affiliations

Affiliations

  • 1 Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany.
  • 2 Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438, Frankfurt, Germany.
  • 3 German Cancer Consortium (DKTK) / German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120, Heidelberg, Germany.
  • 4 Institute for Biophysical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany.
  • 5 Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596, Frankfurt, Germany.
  • 6 Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
  • 7 Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany.
  • 8 Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
  • 9 NanoTemper Technologies GmbH, Flößergasse 4, 81369, Munich, Germany.
  • 10 Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
  • 11 Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany. knapp@pharmchem.uni-frankfurt.de.
  • 12 Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438, Frankfurt, Germany. knapp@pharmchem.uni-frankfurt.de.
  • 13 German Cancer Consortium (DKTK) / German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120, Heidelberg, Germany. knapp@pharmchem.uni-frankfurt.de.
  • 14 Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany. rogov@pharmchem.uni-frankfurt.de.
  • 15 Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438, Frankfurt, Germany. rogov@pharmchem.uni-frankfurt.de.
PMID: 39587067 DOI: 10.1038/s41467-024-54409-5
Abstract

Recent successes in developing small molecule degraders that act through the ubiquitin system have spurred efforts to extend this technology to Other mechanisms, including the autophagosomal-lysosomal pathway. Therefore, reports of autophagosome tethering compounds (ATTECs) have received considerable attention from the drug development community. ATTECs are based on the recruitment of targets to LC3/GABARAP, a family of ubiquitin-like proteins that presumably bind to the autophagosome membrane and tether cargo-loaded Autophagy receptors into the autophagosome. In this work, we rigorously tested the target engagement of the reported ATTECs to validate the existing LC3/GABARAP ligands. Surprisingly, we were unable to detect interaction with their designated target LC3 using a diversity of biophysical methods. Intrigued by the idea of developing ATTECs, we evaluated the ligandability of LC3/GABARAP by in silico docking and large-scale crystallographic fragment screening. Data based on approximately 1000 crystal structures revealed that most fragments bound to the HP2 but not to the HP1 pocket within the LIR docking site, suggesting a favorable ligandability of HP2. Through this study, we identified diverse validated LC3/GABARAP ligands and fragments as starting points for chemical probe and ATTEC development.

Figures
Products
  • Cat. No.
    Product Name
    Description
    Target
    Research Area
  • HY-168347
    LC3 Ligand