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Updated: Jul 5, 2026

Protein Target Prediction and Validation of Small Molecule Compound
Published on: February 23, 2024
Identifying small-molecule modulators of protein-protein interactions
Alexander R Horswill1, Stephen J Benkovic2
1University of Iowa, Iowa City, Iowa.
Abstract:
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.
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