In-solution enrichment identifies peptide inhibitors of protein-protein interactions

  • Nat Chem Biol. 2019 Apr;15(4):410-418. doi: 10.1038/s41589-019-0245-2.
Fayçal Touti  1 ,  Zachary P Gates  2 ,  Anupam Bandyopadhyay  2 ,  Guillaume Lautrette  2 ,  Bradley L Pentelute  3  4
Affiliations
  • 1. Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
  • 2. Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • 3. Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
  • 4. Koch Institute, Broad Institute of Harvard and MIT, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
PMID: 30886434 DOI: 10.1038/s41589-019-0245-2
Abstract

The use of competitive inhibitors to disrupt protein-protein interactions (PPIs) holds great promise for the treatment of disease. However, the discovery of high-affinity inhibitors can be a challenge. Here we report a platform for improving the affinity of peptide-based PPI inhibitors using non-canonical Amino acids. The platform utilizes size exclusion-based enrichment from pools of synthetic peptides (1.5-4 kDa) and liquid chromatography-tandem mass spectrometry-based peptide Sequencing to identify high-affinity Binders to protein targets, without the need for 'reporter' or 'encoding' tags. Using this approach-which is inherently selective for high-affinity binders-we realized gains in affinity of up to ~100- or ~30-fold for Binders to the oncogenic ubiquitin Ligase MDM2 or HIV capsid protein C-terminal domain, which inhibit MDM2-p53 interaction or HIV capsid protein C-terminal domain dimerization, respectively. Subsequent macrocyclization of select MDM2 inhibitors rendered them cell permeable and cytotoxic toward Cancer cells, demonstrating the utility of the identified compounds as functional PPI inhibitors.

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