Entwicklung von MYC G-Quadruplex bindenden Wirkstoffen durch virtuelles Screening dynamischer Ensembles
Zusammenfassung der Projektergebnisse
The aim of this project was to find novel anticancer drug candidates by virtual screening of newly generated dynamic ensembles of DNA G-quadruplexes. As a first step, we performed the first evaluation of the most popular software for molecular docking of G-quadruplexes, which is crucial for virtual screening. Unfortunately, none of the available software works reliably enough for a meaningful virtual screening because the scoring algorithms have not yet been trained for G-quadruplexes. As the dynamic G-quadruplex ensembles have lost their relevance for this project, since virtual screening cannot be performed, the project was modified to contribute in a different way to the development of G-quadruplex targeting anti-cancer drugs. High-resolution structures can show how small molecule ligands recognize G-quadruplexes with atomic resolution and this guides the structure-based rational design of improved compounds. Moreover, a large number of these structures is needed for the future training of docking algorithms. Thus, we determined the high-resolutions structures for the PEQ and berberine ligand bound to G- quadruplexes that control the transcription of the MYC oncogene. PEQ is a newly discovered ligand with more drug-like properties that most reported G-quadruplex binders. Berberine is a well-known natural product with anti-cancer activity. Our results provided insights into the recognition of G- quadruplexes by small molecules, the underlying driving forces, and suggestions how to modify PEQ and berberine to increase binding affinity and selectivity. Moreover, our results showed that the berberine binding under physiologically relevant solution conditions differs notably from a previous reported berberine-quadruplex crystal structure. Another part of the modified project focused on the unusual vacancy G-quadruplexes whose central core lacks a guanosine. This vacancy can be filled-in by guanine metabolites as shown in our NMR high-resolutions structure for a vacancy G-quadruplex from the PDGFR-b promoter region bound to a dGMP metabolite. Binding and stabilization of vacancy G-quadruplexes by guanine derivatives may be a new way how cell control gene expression based on metabolite concentrations. In addition, we showed how berberine binds the vacancy G-quadruplex-dGMP complex and further stabilizes the dGMP fill-in. Conjugates of quadruplex ligands and guanine derivatives may provide an opportunity to selectively target vacancy G-quadruplexes, for example, in cancer therapy.
Projektbezogene Publikationen (Auswahl)
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PDGFR-β Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs. Journal of the American Chemical Society, 142(11), 5204-5211.
Wang, Kai-Bo; Dickerhoff, Jonathan; Wu, Guanhui & Yang, Danzhou
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Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution. Journal of Medicinal Chemistry, 64(21), 16205-16212.
Dickerhoff, Jonathan; Brundridge, Nicole; McLuckey, Scott A. & Yang, Danzhou
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Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNA. International Journal of Molecular Sciences, 22(19), 10801.
Dickerhoff, Jonathan; Warnecke, Kassandra R.; Wang, Kaibo; Deng, Nanjie & Yang, Danzhou
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Solution Structure of Ternary Complex of Berberine Bound to a dGMP–Fill-In Vacancy G-Quadruplex Formed in the PDGFR-β Promoter. Journal of the American Chemical Society, 143(40), 16549-16555.
Wang, Kai-Bo; Dickerhoff, Jonathan & Yang, Danzhou
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Structural recognition of the MYC promoter G-quadruplex by a quinoline derivative: insights into molecular targeting of parallel G-quadruplexes. Nucleic Acids Research, 49(10), 5905-5915.
Dickerhoff, Jonathan; Dai, Jixun & Yang, Danzhou
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Oxidative Damage Induces a Vacancy G-Quadruplex That Binds Guanine Metabolites: Solution Structure of a cGMP Fill-in Vacancy G-Quadruplex in the Oxidized BLM Gene Promoter. Journal of the American Chemical Society, 144(14), 6361-6372.
Wang, Kai-Bo; Liu, Yushuang; Li, Yipu; Dickerhoff, Jonathan; Li, Jinzhu; Yang, Ming-Hua; Yang, Danzhou & Kong, Ling-Yi
