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Published on: June 30, 2023
Small Molecule Inhibition of the Autophagy Kinase ULK1 and Identification of ULK1 Substrates
Daniel F Egan1, Matthew G H Chun1, Mitchell Vamos2
1Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Abstract:
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.
Insights
Researchers identified a key protein motif for autophagy regulation and developed a novel ULK1 inhibitor, SBI-0206965. This compound effectively targets cancer cell survival and shows promise when combined with mTOR inhibitors for cancer therapy.
Area of Science:
- Biochemistry
- Molecular Biology
- Cancer Research
Background:
- Autophagy is crucial for tumor cell survival, making its inhibition a promising cancer therapy strategy.
- ULK1 (unc-51 like autophagy activating kinase 1) is a central serine/threonine kinase in autophagy, representing a key drug target.
- Understanding ULK1's precise role in promoting autophagy is essential for developing effective inhibitors.
Purpose of the Study:
- To identify the optimal substrate motif for ULK1 kinase activity.
- To discover and characterize novel small molecule inhibitors of ULK1.
- To evaluate the therapeutic potential of ULK1 inhibition in cancer treatment.
Main Methods:
- Screening of degenerate peptide libraries to determine the ULK1 substrate motif.
- Verification of in vivo ULK1 phosphorylation sites in core autophagy proteins.
- Cell-based screening to identify ULK1 small molecule inhibitors, including SBI-0206965.
- In vitro kinase assays and cellular assays to assess inhibitor selectivity and efficacy.
Main Results:
- Identified the optimal ULK1 substrate motif and 15 novel in vivo ULK1 phosphorylation sites.
- Discovered and characterized SBI-0206965, a potent and selective ULK1 kinase inhibitor.
- SBI-0206965 effectively suppressed ULK1 activity in cells, impacting autophagy and cell survival.
- SBI-0206965 demonstrated significant synergy with mTOR inhibitors in killing tumor cells.
Conclusions:
- ULK1 plays a critical role in autophagy-dependent cancer cell survival.
- SBI-0206965 is a promising ULK1 inhibitor with potential for cancer therapy.
- Combination therapy with ULK1 and mTOR inhibitors offers a strong rationale for clinical application in oncology.
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