Dual Inhibition of ULK1 and mTOR Enhances Tumor Cell Apoptosis

Unc-51–like autophagy activating kinase 1 (ULK1) is a serine/threonine kinase that initiates one of the first steps of autophagy, a cell survival mechanism for many tumors, particularly in response to nutrient deprivation or inhibition of mTOR, which negatively regulates ULK1. To provide insight into the role of ULK1 in autophagy and its potential as a therapeutic target, Egan, Chun, and colleagues identified an optimal ULK1 consensus phosphorylation motif using arrayed degenerate peptide libraries. Mass spectrometry analysis revealed that ULK1 phosphorylates several components of the autophagy cascade, including autophagy-related 101 (ATG101), Beclin1, and VPS34. A cell-based screen of pyrimidine analogs identified the small-molecule SBI-0206965 as a potent and selective ULK1 kinase inhibitor. SBI-0206965 blocked the phosphorylation of ULK1 substrate proteins and strongly suppressed the induction of autophagy following pharmacologic mTOR inhibition in cancer cell lines, similar to the phenotype observed with ULK1 knockdown. Immunoblot analysis revealed that under nutrient-depleted, but not nutrient-replete, conditions, SBI-0206965 resulted in the degradation of ULK1 and its interaction partner ATG13 and induced apoptosis in mouse embryonic fibroblasts, as well as in human glioblastoma cells and murine lung cancer cells. Furthermore, similar to the effects observed under nutrient starvation, SBI-0206965 synergized with multiple catalytic mTOR inhibitors to trigger enhanced apoptosis in human lung cancer cells, suggesting that ULK1 blockade converts the cytostatic response of mTOR inhibition to a cytotoxic response. Of note, this small-molecule ULK1 inhibitor was more effective at inducing apoptosis than the general autophagy inhibitor chloroquine. Overall, these findings identify the small molecule SBI-0206965 as a selective ULK1 kinase inhibitor and demonstrate its synergy with mTOR inhibition to induce cancer cell death, suggesting the potential for this combination therapy to enhance the efficacy of mTOR inhibitors in cancer.

Egan DF, Chun MG, Vamos M, Zou H, Rong J, Miller CJ, et al. Small molecule inhibition of the autophagy kinase ULK1 and identification of ULK1 substrates. Mol Cell 2015 Jun 25 [Epub ahead of print].