AlphaFold2 ‐Guided Cyclic Peptide Stabilizer Design to Target Protein–Protein Interactions

ABSTRACT The control and modulation of protein–protein interactions (PPIs) is of central importance for the majority of biological processes and most biomedical applications. Stabilization of PPIs, besides inhibition, is of growing pharmaceutical interest. Due to their small size, drug‐like organic molecules may not provide sufficient interaction surfaces to allow for high‐affinity dual binding to both partners of a protein–protein complex. Cyclic peptides offer larger interaction surfaces, making them a promising class of stabilizers of PPIs. We have developed a computational protocol to rapidly and systematically design cyclic peptides that optimize not only the interaction with one target protein but simultaneously optimize the dual binding to two protein partners. The cyclic peptide generation is based on a modified AlphaFold2‐based peptide design approach and combines confidence scoring with force field‐based scoring using Molecular Dynamics simulations. The performance of the method is tested on protein–protein complexes with known cyclic peptide binders and stabilizers. In addition, the approach is used to design cyclic peptides that can act as bifunctional molecules, recruiting the cellular protein degradation system to a target protein. The designed cyclic peptides achieve similar or better calculated interaction scores than known binders and exhibit well‐balanced interactions with both protein partners. The design protocol is generally applicable to cyclic peptide design for modulating or inducing protein–protein association and could be useful for many biomedical design efforts.