Structure-Based Design of Non-natural Macrocyclic Peptides That Inhibit Protein–Protein Interactions

Macrocyclic
peptides can interfere with challenging biomolecular
targets including protein–protein interactions. Whereas there
are various approaches that facilitate the identification of peptide-derived
ligands, their evolution into higher affinity binders remains a major
hurdle. We report a virtual screen based on molecular docking that
allows the affinity maturation of macrocyclic peptides taking non-natural
amino acids into consideration. These macrocycles bear large and flexible
substituents that usually complicate the use of docking approaches.
A virtual library containing more than 1400 structures was screened
against the target focusing on docking poses with the core structure
resembling a known bioactive conformation. Based on this screen, a
macrocyclic peptide 22 involving two non-natural amino
acids was evolved showing increased target affinity and biological
activity. Predicted binding modes were verified by X-ray crystallography.
The presented workflow allows the screening of large macrocyclic peptides
with diverse modifications thereby expanding the accessible chemical
space and reducing synthetic efforts.