Small Molecule Inhibition of the Autophagy Kinase ULK1 and Identification of ULK1 Substrates
Open accessAbstract
Many tumors become addicted to autophagy for survival, suggesting inhibition of autophagy as a potential broadly applicable cancer therapy. ULK1/Atg1 is the only serine/threonine kinase in the core autophagy pathway and thus represents an excellent drug target. Despite recent advances in the understanding of ULK1 activation by nutrient deprivation, how ULK1 promotes autophagy remains poorly understood. Here, we screened degenerate peptide libraries to deduce the optimal ULK1 substrate motif and discovered 15 phosphorylation sites in core autophagy proteins that were verified as in vivo ULK1 targets. We utilized these ULK1 substrates to perform a cell-based screen to identify and characterize a potent ULK1 small molecule inhibitor. The compound SBI-0206965 is a highly selective ULK1 kinase inhibitor in vitro and suppressed ULK1-mediated phosphorylation events in cells, regulating autophagy and cell survival. SBI-0206965 greatly synergized with mechanistic target of rapamycin (mTOR) inhibitors to kill tumor cells, providing a strong rationale for their combined use in the clinic.
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Successful transfection in the screen was confirmed by a killer siRNA that reduced cell count by 85%-90%.
“Successful transfection was confirmed by a killer siRNA [23] which reduced the cell count by 85%–90%.”
From miRNA family miR-29 inhibits PINK1-PRKN signaling via ATG9A (2026) · cites this paper as [23]
The Results section on ULK1 siRNA describes a focused RNAi screen and control-siRNA-transfected cells, but does not describe a killer siRNA used to confirm transfection. Searches for “killer siRNA,” “cell count,” and “85%–90%” found no passage supporting the reported reduction. (LLM, conf=0.73)
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- Authors
- Egan, D. F., Chun, M. G. H., Vamos, M., Zou, H., Rong, J., Miller, C. J., Lou, H. J., Raveendra-Panickar, D., Yang, C.-C., Sheffler, D. J., Teriete, P., Asara, J. M., Turk, B. E., Cosford, N. D. P., & Shaw, R. J.
- Affiliations
- Salk Institute for Biological Studies (US)
- Sanford Burnham Prebys Medical Discovery Institute (US)
- Yale University (US)
- Beth Israel Deaconess Medical Center (US)
- Corresponding author
- Cosford, Nicholas D.P.
- Shaw, Reuben J.
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2015-07
- Volume
- 59
- Issue
- 2
- Pages
- 285-297
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC4530630
- OpenAlex
- W1864635191
- Cited by
- 715
- References
- 4
- Citations by year
- 2026: 41 · 2025: 56 · 2024: 55 · 2023: 66 · 2022: 75 · 2021: 97 · 2020: 83 · 2019: 76 · 2018: 63 · 2017: 51 · 2016: 38 · 2015: 12
- FWCI
- 42.89
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Defense
- Howard Hughes Medical Institute
- American Cancer Society
- National Institutes of Health
- University of California, San Diego
- National Cancer Institute (R01CA172229, R01CA188694, P01CA120964, P30CA030199, P30CA014195)
- National Institute of General Medical Sciences (T32GM007240, T32GM007324, R01GM104047)
- Topics
- Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › PI3K/AKT/mTOR signaling in cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Keywords
- ULK1, autophagy, small-molecule kinase inhibitors, SBI-0206965, phosphorylation sites, cancer therapy, mTOR inhibitors, combination therapy, nutrient deprivation, peptide library screening
- MeSH terms
- Autophagy-Related Protein-1 Homolog, Amino Acid Sequence, Animals, Autophagy, Benzamides, Cell Survival, Cells, Cultured, Humans, Molecular Sequence Data, Phosphorylation, Pyrimidines, Recombinant Proteins, Substrate Specificity, Consensus Sequence, Protein Serine-Threonine Kinases, Catalytic Domain, RNA, Small Interfering, Protein Kinase Inhibitors, Intracellular Signaling Peptides and Proteins, Mice, Gene Knockout Techniques, HEK293 Cells
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