Data for "Early-stage autophagy inhibitors targeting the ATG101-ATG13 subunit of the ULK1 complex"

Autophagy is commonly up- or down-regulated in cancer cells due to the unique metabolic needs of these cells, and small molecules modulating the autophagy pathway are already in clinical trials. However, specific autophagy-targeting compounds remain rare. A new potential mechanism for effective early-stage autophagy inhibition was described by us and others recently, involving the inhibition of the interaction between ATG101 and ATG13 subunits of the autophagy-initiating ULK1 complex. Here, we describe the discovery of two small molecules inhibiting the ATG101-ATG13 interaction, one by binding to ATG101 with micromolar affinity (EC50 = 151 µM) and the other by binding to both ATG101 and ATG13 with micromolar affinity (EC50 = 135 µM and EC50 = 107 µM, respectively). In two independent assays, both compounds inhibit autophagy. Scrutinizing the binding mechanism by molecular dynamics simulations and STD-NMR spectroscopy indicates that the compounds bind to ATG101 in an orthosteric fashion, at the interface of the protein-protein interaction, while the binding to ATG13 is allosteric. Both compounds have a favorable predicted ADME-Tox profile. The compounds can serve as tool compounds to inhibit autophagy or as candidates for further optimization toward lead structures.