Development of DuoMYC: a synthetic cell penetrant miniprotein that efficiently inhibits the oncogenic transcription factor MYC

The master regulator transcription factor MYC is implicated in numerous human cancers, and its targeting is a long-standing challenge in drug development. MYC is a typical ‘undruggable’ target, with no binding pockets on its DNA binding domain and extensive intrinsically disordered regions. Rather than trying to target MYC directly with classical modalities, here we engineer synthetic cell penetrating miniproteins that can bind to MYC’s target DNA, the enhancer box (E-Box), with a high affinity and block MYC-driven transcription. We obtained the miniproteins via structure-based design and a combination of solid phase peptide synthesis and site-specific crosslinking. Our lead variant, DuoMYC, binds to E-Box DNA with high affinity (K _D = 118 nM) and molecular dynamic simulations provide insights into the structural features leading to the high stability of that DNA binding complex. DuoMYC displays an excellent stability in human serum and is able to enter cells and inhibit MYC-driven transcription with submicromolar potency (IC ₅₀ = 464 nM) as shown by reporter gene assay. Notably, DuoMYC surpasses the efficacy of several other recently developed MYC inhibitors. Our results highlight the potential of engineered synthetic protein therapeutics for addressing challenging intracellular targets.