A yeast two-hybrid system for the screening and characterization of small-molecule inhibitors of protein–protein interactions identifies a novel putative Mdm2-binding site in p53
Open accessAbstract
BACKGROUND: Protein-protein interactions (PPIs) are fundamental to the growth and survival of cells and serve as excellent targets to develop inhibitors of biological processes such as host-pathogen interactions and cancer cell proliferation. However, isolation of PPI inhibitors is extremely challenging. While several in vitro assays to screen for PPI inhibitors are available, they are often expensive, cumbersome, and require large amounts of purified protein. In contrast, limited in vivo assays are available to screen for small-molecule inhibitors of PPI. METHODS: We have engineered a yeast strain that is suitable for screening of small-molecule inhibitors of protein-protein interaction using the Yeast 2-hybrid Assay. We have optimised and validated the assay using inhibitors of the p53-Mdm2 interaction and identified a hitherto unreported putative Mdm2-binding domain in p53. RESULTS: We report a significantly improved and thoroughly validated yeast two-hybrid (Y2H) assay that can be used in a high throughput manner to screen for small-molecule PPI inhibitors. Using the p53-Mdm2 interaction to optimize the assay, we show that the p53-Mdm2 inhibitor nutlin-3 is a substrate for the yeast ATP-binding cassette (ABC) transporter Pdr5. By deleting nine ABC transporter-related genes, we generated a ABC9Δ yeast strain that is highly permeable to small molecules. In the ABC9Δ strain, p53-Mdm2 interaction inhibitors, like AMG232 and MI-773, completely inhibited the p53-Mdm2 interaction at nanomolar concentrations in the Y2H assay. In addition, we identified a conserved segment in the core DNA-binding domain of p53 that facilitates stable interaction with Mdm2 in yeast cells and in vitro. CONCLUSION: The Y2H assay can be utilized for high-throughput screening of small-molecule inhibitors of PPIs and to identify domains that stabilize PPIs.
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The aforementioned screening assays, as well as scalable methods to discover drug-induced PPIs such as Y2H-based/related assays, may generate the necessary data to include QSAR modeling in the loop of design.
“In this line, the aforementioned screening assays, as well as scalable methods to discover drug-induced PPIs such as Y2H-based/related assays,268 may generate the necessary data to include QSAR modeling in the loop of design.”
From Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence (2023) · cites this paper as [268]
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- Authors
- Wong, J. H., Alfatah, M., Sin, M. F., Sim, H. M., Verma, C. S., Lane, D. P., & Arumugam, P.
- Affiliations
- Bioinformatics Institute (SG)
- National University of Singapore (SG)
- Corresponding author
- Arumugam, Prakash
- Venue
- BMC Biology
- Published
- 2017-11-09
- Volume
- 15
- Issue
- 1
- Pages
- 108-108
- ISSN
- 1741-7007 (ISSN-L)
- PMC
- PMC5680816
- OpenAlex
- W2767626798
- Cited by
- 45
- References
- 38
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 3 · 2023: 5 · 2022: 5 · 2021: 3 · 2020: 5 · 2019: 9 · 2018: 5 · 2016: 1
- FWCI
- 2.29
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- National University of Singapore (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DR-NTU (Nanyang Technological University) (submittedVersion, cc-by)
- Funders
- Bioinformatics Institute
- A-STAR (IAF311013)
- Topics
- Health Sciences › Medicine › Oncology › Cancer-related Molecular Pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
- Keywords
- protein-protein interaction inhibitors, small molecule inhibitors, yeast two-hybrid, p53-MDM2 interaction, p53 DNA-binding domain, Nutlin-3, high-throughput screening, MDM2
- MeSH terms
- Binding Sites, Protein Binding, Saccharomyces cerevisiae, Tumor Suppressor Protein p53, Two-Hybrid System Techniques, Saccharomyces cerevisiae Proteins, Proto-Oncogene Proteins c-mdm2, Protein Interaction Domains and Motifs, Small Molecule Libraries
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Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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