Targeting Unoccupied Surfaces on Protein-Protein Interfaces

J Am Chem Soc. 2017 Nov 8;139(44):15560-15563. doi: 10.1021/jacs.7b05960. Epub 2017 Aug 4.

Abstract

The use of peptidomimetic scaffolds to target protein-protein interfaces is a promising strategy for inhibitor design. The strategy relies on mimicry of protein motifs that exhibit a concentration of native hot spot residues. To address this constraint, we present a pocket-centric computational design strategy guided by AlphaSpace to identify high-quality pockets near the peptidomimetic motif that are both targetable and unoccupied. Alpha-clusters serve as a spatial representation of pocket space and are used to guide the selection of natural and non-natural amino acid mutations to design inhibitors that optimize pocket occupation across the interface. We tested the strategy against a challenging protein-protein interaction target, KIX/MLL, by optimizing a single helical motif within MLL to compete against the full-length wild-type MLL sequence. Molecular dynamics simulation and experimental fluorescence polarization assays are used to verify the efficacy of the optimized peptide sequence.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding Sites / genetics
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Binding / genetics
  • Protein Domains
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / metabolism*

Substances

  • Proteins