Cell-based high-throughput screening using a target–NanoLuc fusion construct to identify molecular glue degraders of c-Myc oncoprotein

Abstract

Oncoprotein c-Myc (Myc) plays a critical role in regulating cellular gene expression. Although Myc dysregulation is found in more than 70% of cancers and can facilitate tumor initiation and progression, it is still considered to be an “undruggable” oncotarget years after its first discovery. Recent advances in the field of targeted protein degradation provide alternative Myc-targeting strategies. Here, we develop the first Myc-NanoLuc fusion plasmid transfected cell-based high-throughput screening assay to identify Myc-downregulating small molecules. We verified the effectiveness of our assay by demonstrating that previously known Myc-downregulating compounds (G9 and SY-1365) were successfully identified from a library of bioactive compounds with established biological function. Next, we screened another 108 800 compounds from the diverse ChemDiv library collection, and 14 novel Myc-downregulating compounds were identified after cherry-pick triplicate confirmation, counter-screening, dose–response and western blotting experiments. A cellular thermal shift assay further demonstrated that five out of the 14 Myc-downregulating compounds bound to endogenous Myc protein in crude 293T whole-cell lysate. Subsequently, compound C1 was shown to selectively degrade Myc protein at a DC₅₀ value of around 5 μM. Further characterization showed that C1 killed cancer cells with high Myc expression at a lower dose than it killed cancer cells with low Myc expression. Moreover, C1 selectively reduced the expression of various Myc-target genes. Intriguingly, co-immunoprecipitation showed that C1 functionally acted like a molecular glue to aggregate Myc proteins and block Myc/Max interaction. The self-aggregation of Myc and the dissociation of the Myc/Max dimer by C1 promoted Myc degradation. Using a target–NanoLuc fusion strategy in our novel cell-based high-throughput screening system, we identified a molecular glue-like small molecule degrader of Myc.