Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex
Open accessAbstract
G-quadruplexes (G4s) are noncanonical DNA structures that frequently occur in the promoter regions of oncogenes, such as MYC , and regulate gene expression. Although G4s are attractive therapeutic targets, ligands capable of discriminating between different G4 structures are rare. Here, we describe DC-34, a small molecule that potently downregulates MYC transcription in cancer cells by a G4-dependent mechanism. Inhibition by DC-34 is significantly greater for MYC than other G4-driven genes. We use chemical, biophysical, biological, and structural studies to demonstrate a molecular rationale for the recognition of the MYC G4. We solve the structure of the MYC G4 in complex with DC-34 by NMR spectroscopy and illustrate specific contacts responsible for affinity and selectivity. Modification of DC-34 reveals features required for G4 affinity, biological activity, and validates the derived NMR structure. This work advances the design of quadruplex-interacting small molecules to control gene expression in therapeutic areas such as cancer.
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Walters, Mock and Schneekloth Jr's group reported DC-34, which showed inhibitory activity on Myc at the transcriptional level only when a G4 is present in the promoter.
“In 2018, Walters, Mock and Schneekloth Jr’s group synthesized a library of drug-like compounds and reported a small molecule, named DC-34 (249), which showed impressive inhibitory activity on Myc at the transcriptional level only when a G4 is present in the promoter.584”
From Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials (2023) · cites this paper as [584]
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A Rationally Designed Azobenzene Photoswitch for DNA G‐Quadruplex Regulation in Live Cells
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- Authors
- Calabrese, D. R., Chen, X., Leon, E. C., Gaikwad, S. M., Phyo, Z., Hewitt, W. M., Alden, S., Hilimire, T. A., He, F., Michalowski, A. M., Simmons, J. K., Saunders, L. B., Zhang, S., Connors, D., Walters, K. J., Mock, B. A., & Schneekloth, J. S.
- Affiliations
- National Cancer Institute (US)
- National Institutes of Health (US)
- Corresponding author
- Walters, Kylie J.
- Mock, Beverly A.
- Schneekloth, John S.
- ORCID
- Venue
- Nature Communications
- Published
- 2018-10-12
- Volume
- 9
- Issue
- 1
- Pages
- 4229-4229
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6185959
- OpenAlex
- W2896637864
- Cited by
- 172
- References
- 72
- Citations by year
- 2026: 8 · 2025: 17 · 2024: 23 · 2023: 23 · 2022: 20 · 2021: 36 · 2020: 25 · 2019: 17 · 2018: 2
- FWCI
- 7.11
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (1 ZIA BC011065, 1 ZIA BC011490)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Health Sciences › Medicine › Oncology › Metal complexes synthesis and properties
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Keywords
- c-Myc, G-quadruplex, small-molecule ligands, oncogene promoters, ligand selectivity, structure-activity relationship
- MeSH terms
- Binding Sites, Cell Line, Cell Survival, Humans, Hydrogen Bonding, Magnetic Resonance Spectroscopy, Promoter Regions, Genetic, Protein Binding, Structure-Activity Relationship, Blotting, Western, Molecular Structure, Proto-Oncogene Proteins c-myc, Protein Structure, Secondary, Surface Plasmon Resonance, Cell Line, Tumor, G-Quadruplexes
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