A systematic method for identifying small-molecule modulators of protein–protein interactions
Open accessAbstract
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.
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Modulators of Protein–Protein Interactions
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- Authors
- Horswill, A. R., Savinov, S. N., & Benkovic, S. J.
- Affiliations
- Pennsylvania State University (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2004-10-21
- Volume
- 101
- Issue
- 44
- Pages
- 15591-15596
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC524857
- OpenAlex
- W2039063799
- Cited by
- 110
- References
- 31
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 6 · 2023: 2 · 2022: 4 · 2021: 2 · 2020: 4 · 2019: 5 · 2018: 4 · 2017: 8 · 2016: 6 · 2015: 4 · 2014: 12 · 2013: 9 · 2012: 6
- FWCI
- 1.89
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Damon Runyon Cancer Research Foundation
- GlaxoSmithKline
- Purdue University
- University of Pennsylvania
- University of Oklahoma
- Iowa State University
- National Institutes of Health
- National Institute of General Medical Sciences (GM24129, R01GM024129, R37GM024129)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein-protein interaction, small molecule modulators, host cell survival, HIV-1 protease, ribonucleotide reductase, cyclic peptide inhibitors, solid-phase synthesis, peptide ELISA, genetic selection
- MeSH terms
- Carrier Proteins, Enzyme Inhibitors, Enzyme-Linked Immunosorbent Assay, Peptides, Cyclic, Protein Binding, Proteins, Recombinant Proteins, Ribonucleotide Reductases, HIV Protease, Phosphotransferases (Alcohol Group Acceptor), Peptide Library, Sirolimus, Two-Hybrid System Techniques, Tacrolimus Binding Protein 1A, TOR Serine-Threonine Kinases, In Vitro Techniques
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