Covalent targeting of the vacuolar H+-ATPase activates autophagy via mTORC1 inhibition

  • Nat Chem Biol. 2019 Aug;15(8):776-785. doi: 10.1038/s41589-019-0308-4.
Clive Yik-Sham Chung  1  2 ,  Hijai R Shin  3  4 ,  Charles A Berdan  5 ,  Breanna Ford  5 ,  Carl C Ward  2  3 ,  James A Olzmann  5 ,  Roberto Zoncu  6  7 ,  Daniel K Nomura  8  9  10  11
Affiliations
  • 1. Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
  • 2. Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
  • 3. Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
  • 4. The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA.
  • 5. Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA.
  • 6. Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. [email protected].
  • 7. The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA. [email protected].
  • 8. Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. [email protected].
  • 9. Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA. [email protected].
  • 10. Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. [email protected].
  • 11. Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA. [email protected].
PMID: 31285595 DOI: 10.1038/s41589-019-0308-4
Abstract

Autophagy is a lysosomal degradation pathway that eliminates aggregated proteins and damaged organelles to maintain cellular homeostasis. A major route for activating Autophagy involves inhibition of the mTORC1 kinase, but current mTORC1-targeting compounds do not allow complete and selective mTORC1 blockade. Here, we have coupled screening of a covalent ligand library with activity-based protein profiling to discover EN6, a small-molecule in vivo activator of Autophagy that covalently targets cysteine 277 in the ATP6V1A subunit of the lysosomal v-ATPase, which activates mTORC1 via the Rag guanosine triphosphatases. EN6-mediated ATP6V1A modification decouples the v-ATPase from the Rags, leading to inhibition of mTORC1 signaling, increased lysosomal acidification and activation of Autophagy. Consistently, EN6 clears TDP-43 aggregates, a causative agent in frontotemporal dementia, in a lysosome-dependent manner. Our results provide insight into how the v-ATPase regulates mTORC1, and reveal a unique approach for enhancing cellular clearance based on covalent inhibition of lysosomal mTORC1 signaling.

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