ULK1/2 Inhibitors that Degrade ATG13 Effectively Target KRAS-Mutant Cancers

KRAS mutations drive tumorigenesis in multiple cancer types, including lung and pancreatic cancer. Autophagy is a cell survival pathway that supports tumor growth under metabolic stress and has been proposed to be a potential therapeutic avenue specifically in KRAS mutant cancers. The Unc-51-like ATG-activating kinases 1 and 2 (ULK) initiate the earliest regulated steps of autophagy and are the only protein kinases in the canonical autophagy pathway, thus making them attractive therapeutic targets for KRAS mutant tumors. We show here that genetic depletion of ULK1 or ATG13, core components of the ULK1 complex, in KRAS mutant lung and pancreatic cancer cell lines results in growth inhibition. Previously, we developed small molecule ULK1 inhibitors that not only inhibit ULK kinase activity but also induced the degradation of other core members of the ULK complex including ATG101 and ATG13. Therefore, we developed a high-throughput screening (HTS) assay in which ATG13 was HiBiT-tagged in KRAS mutant lung cancer cells to evaluate ULK inhibitors for ATG13 degradation. Using this approach, we discovered a lead ULK inhibitor, SBP-1750, that potently inhibited ULK activity, promoted robust ATG13 degradation, impaired ATG, and induced KRAS mutant cancer cell death. Studies in a KRAS-mutant orthotopic syngeneic pancreatic cancer model show that oral treatment with SBP-1750 significantly reduced tumor growth. Pharmacokinetic analysis of SBP-1750 indicates favorable drug exposure and pharmacodynamic analysis confirms ATG13 degradation in vivo, mirroring in vitro results. Finally, immunohistochemical staining of orthotopic pancreatic tumors reveals a significant increase in CD4 and CD8 T cell infiltration upon treatment, suggesting that SBP-1750 enhances anti-tumor immunity. These findings support further development of SBP-1750 as a novel ATG-targeting cancer therapy.