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

J Med Chem. 2017 Nov 9;60(21):8982-8988. doi: 10.1021/acs.jmedchem.7b01221. Epub 2017 Oct 27.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids
  • Animals
  • Binding Sites
  • Crystallography, X-Ray
  • Drug Design*
  • Humans
  • Molecular Docking Simulation
  • Peptide Library
  • Peptides, Cyclic / chemistry
  • Peptides, Cyclic / pharmacology*
  • Protein Binding / drug effects
  • Protein Interaction Domains and Motifs / drug effects*
  • Structure-Activity Relationship


  • Amino Acids
  • Peptide Library
  • Peptides, Cyclic