Identifying small-molecule modulators of protein-protein interactions

Curr Protoc Protein Sci. 2006 Dec;Chapter 19:Unit 19.15. doi: 10.1002/0471140864.ps1915s46.


This unit outlines methods for identifying cyclic peptides that inhibit protein-protein interactions. Proteins of interest are cloned into a two-hybrid system engineered to operate in reverse, allowing the disruption of a protein complex to be coupled to cell growth. Cyclic peptide libraries are generated using an intein-based plasmid construct, and the cyclized sequence is randomized using a PCR procedure. By transforming plasmid libraries into host cells containing the two-hybrid fusions, cyclic peptide inhibitors can be identified by growing the cells under the appropriate selective conditions. A detailed procedure for performing the genetic selection and identifying false positives is provided. Methods for building the two-hybrid protein fusions and optimizing media conditions, as well as an additional protocol for constructing cyclic peptide libraries are also provided.

MeSH terms

  • Base Sequence
  • DNA Primers
  • Genetic Vectors
  • Peptide Library
  • Peptides, Cyclic / drug effects
  • Peptides, Cyclic / metabolism
  • Plasmids
  • Polymerase Chain Reaction
  • Protein Binding
  • Proteins / drug effects
  • Proteins / metabolism*


  • DNA Primers
  • Peptide Library
  • Peptides, Cyclic
  • Proteins