A systematic method for identifying small-molecule modulators of protein-protein interactions

Alexander R. Horswill, Sergey N. Savinov, Stephen J. Benkovic

Research output: Contribution to journalArticlepeer-review

86 Scopus citations

Abstract

Discovering small-molecule modulators of protein-protein interactions is a challenging task because of both the generally noncontiguous, large protein surfaces that form these interfaces and the shortage of high-throughput approaches capable of identifying such rare inhibitors. We describe here a robust and flexible methodology that couples disruption of protein-protein complexes to host cell survival. The feasibility of this approach was demonstrated through monitoring a small-molecule-mediated protein-protein association (FKBP12-rapamycin-FRAP) and two cases of dissociation (homodimeric HIV-1 protease and heterodimeric ribonucleotide reductase). For ribonucleotide reductase, we identified cyclic peptide inhibitors from genetically encoded libraries that dissociated the enzyme subunits. A solid-phase synthetic strategy and peptide ELISAs were developed to characterize these inhibitors, resulting in the discovery of cyclic peptides that operate in an unprecedented manner, thus highlighting the strengths of a functional approach. The ability of this method to process large libraries, coupled with the benefits of a genetic selection, allowed us to identify rare, uniquely active small-molecule modulators of protein-protein interactions at a frequency of less than one in 10 million.

Original languageEnglish (US)
Pages (from-to)15591-15596
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume101
Issue number44
DOIs
StatePublished - Nov 2 2004

All Science Journal Classification (ASJC) codes

  • General

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