Pseudo-Isolated alpha-Helix Platform for the Recognition of Deep and Narrow Targets

Abstract

Although interest in stabilized alpha-helical peptides as next-generation therapeutics for modulating biomolecular inter-faces is increasing, peptides have limited functionality and stability due to their small size. In comparison, alpha-helical ligands based on proteins can make steric clash with targets due to their large size. Here, we report the design of a monomeric pseudo-isolated alpha-helix (mPIH) system in which proteins behave as if they are peptides. The designed proteins contain alpha-helix ligands that do not require any covalent chemical modification, do not have frayed ends, and importantly can make sterically favorable interactions similar to isolated peptides. An optimal mPIH showed a more than 100-fold increase in target selectivity, which might be related to the advantages in conformational selection due to the absence of frayed ends. The alpha-helical ligand in the mPIH displayed high thermal stability well above human body temperature and showed reversible and rapid folding/unfolding transitions. Thus, mPIH can become a promising protein-based platform for developing stabilized alpha-helix pharmaceuticals.