Data for "Identification of autophagy inhibitors selectively targeting the ATG13-ATG101 protein-protein interaction"

Abstract

The dysregulation of autophagy promotes the development of several diseases like such as neurodegeneration, infection, or cancer. To keep up with their metabolic demand under low nutrient and/or oxygen conditions typically present in the tumor microenvironment, cancer cells can upregulate autophagy autonomously or in surrounding cells. Therefore, the inhibition of autophagy is desired in these settings. However, to date, drugs targeting autophagy selectively remain rare. The autophagy-inducing ULK1 complex comprises ULK1/2, FIP200, and a heterodimer consisting of ATG13 and ATG101. We previously showed that the ATG13-ATG101 protein-protein interaction is crucial for the assembly of the ULK1 complex and initiation of autophagic activity. Thus, targeting the ATG13-ATG101 protein-protein interaction with small molecules promises to yield new tools for the study of autophagy as well as to deliver new therapeutic starting points. By screening a diversity set of 15k compounds in a biochemical setup, followed by extensive cell-based validation studies, we identified the compounds AFS30 and AFS32. Both compounds inhibited the ATG13-ATG101 PPI in the low micromolar range and led to reduced autophagic activity in different cell lines, with IC50 values of 3-4 µM in the LC3 HiBiT reporter assay. Spectral shift assays, molecular dynamics simulations, and STD-NMR suggested that the compounds bind allosterically to ATG13. AFS30 and AFS32 also promoted apoptosis in different cancer cell lines exposed to nutrient stress. We propose that AFS30 and AFS32 are promising lead compounds for the development of PPI inhibitors that selectively inhibiting the ATG13-ATG101 interaction and thus autophagy.