Inhibitors of protein-protein interactions (PPIs): an analysis of scaffold choices and buried surface area

Curr Opin Chem Biol. 2018 Jun;44:75-86. doi: 10.1016/j.cbpa.2018.06.004. Epub 2018 Jun 13.


Protein-protein interactions (PPI) were once considered 'undruggable', but clinical successes, driven by advanced methods in drug discovery, have challenged that notion. Here, we review the last three years of literature on PPI inhibitors to understand what is working and why. From the 66 recently reported PPI inhibitors, we found that the average molecular weight was significantly greater than 500Da, but that this trend was driven, in large part, by the contribution of peptide-based compounds. Despite differences in average molecular weight, we found that compounds based on small molecules or peptides were almost equally likely to be potent inhibitors (KD<1μM). Finally, we found PPIs with buried surface area (BSA) less than 2000Å2 were more likely to be inhibited by small molecules, while PPIs with larger BSA values were typically inhibited by peptides. PPIs with BSA values over 4000Å2 seemed to create a particular challenge, especially for orthosteric small molecules. Thus, it seems important to choose the inhibitor scaffold based on the properties of the target interaction. Moreover, this survey suggests a (more nuanced) conclusion to the question of whether PPIs are good drug targets; namely, that some PPIs are readily 'druggable' given the right choice of scaffold, while others still seem to deserve the 'undruggable' moniker.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Animals
  • Drug Discovery / methods*
  • Humans
  • Peptides / chemistry
  • Peptides / pharmacology*
  • Protein Binding / drug effects
  • Protein Interaction Maps / drug effects*
  • Proteins / chemistry
  • Proteins / metabolism*
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology*


  • Peptides
  • Proteins
  • Small Molecule Libraries