Rational Design of Proteolytically Stable, Cell-Permeable Peptide-Based Selective Mcl-1 Inhibitors

Direct chemical modifications of helical peptides have provided a simple and effective means to ‘translate’ the bioactive helical peptides into potential therapeutics targeting intracellular protein-protein interactions. Previously, we have shown that the distance-matching bisaryl cross-linkers can reinforce peptide helices containing two cysteines at the i.i+7 positions and confer cell permeability to the cross-linked peptides. In this work, we report the first crystal structure of a biphenyl cross-linked Noxa peptide in complex with its target Mcl-1 at a 2.0 Å resolution. Guided by this structure, we remodeled the surface of this cross-linked peptide through side chain substitution and N-methylation, and obtained a pair of cross-linked peptides with substantially increased helicity, cell permeability, proteolytic stability, and cell-killing activity in Mcl-1-overexpressing U937 cells. The success of this structure-based design of Mcl-1 inhibitors underscores the value of synergistic use of multifaceted modifications in developing peptide-based therapeutics.