Downsizing Electrophilic MAX-Derived Helical Zipper Peptides to Covalently Bind and Degrade Oncogenic MYC

MYC is an intrinsically disordered oncoprotein that drives cancer progression via widespread transcriptional dysregulation. Upon binding partner protein MAX, their basic-helix1-loop-helix2-Zip (bHLH-Zip) domains assemble into an ordered heterodimer that binds E-box DNA to promote cellular proliferation. This interface has been undruggable by small molecules. Here, we report a novel covalent downsizing strategy to inhibit MYC-MAX interaction by targeting the C-terminal Cys438 present in MYC, but absent in MAX and related proteins. Incorporating a mild acrylamide electrophile to covalently bond specifically with Cys438 enabled truncation of MAX to shorter peptides with high affinity for MYC. Using intracellular protein-fragment complementation, MAX-derived sequences were optimized for interaction with MYC. Further downsizing, inserting a helix-inducing constraint, and optimal electrophile positioning produced a serum-stable 24-residue covalent inhibitor that captured endogenous MYC from cell lysates. Esterifying six Glu/Asp residues enhanced membrane permeability, while intracellular esterolysis achieved robust cytosolic and nuclear accumulation of the MYC inhibitor. Microscopy confirmed nuclear delivery correlating directly with progressive loss of nuclear MYC. The esterified compound exhibited antiproliferative activity across MYC-dependent cancer cell lines, inhibited migration, and triggered ubiquitin-proteasome mediated MYC degradation, downregulating key target genes downstream of MYC. This covalent downsizing approach is a generalizable chemical strategy for targeting recalcitrant transcription factors.