Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy
Recently, the <sup>1</sup>H-detected in-cell NMR spectroscopy has emerged as a unique tool allowing the characterization of interactions between nucleic acid-based targets and drug-like molecules in living human cells. Here, we assess the application potential of <sup>1</sup>...
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| Format: | Article |
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MDPI AG
2021-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/11/6042 |
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| author | Daniel Krafčík Eva Ištvánková Šimon Džatko Pavlína Víšková Silvie Foldynová-Trantírková Lukáš Trantírek |
| author_facet | Daniel Krafčík Eva Ištvánková Šimon Džatko Pavlína Víšková Silvie Foldynová-Trantírková Lukáš Trantírek |
| author_sort | Daniel Krafčík |
| collection | DOAJ |
| description | Recently, the <sup>1</sup>H-detected in-cell NMR spectroscopy has emerged as a unique tool allowing the characterization of interactions between nucleic acid-based targets and drug-like molecules in living human cells. Here, we assess the application potential of <sup>1</sup>H and <sup>19</sup>F-detected in-cell NMR spectroscopy to profile drugs/ligands targeting DNA G-quadruplexes, arguably the most studied class of anti-cancer drugs targeting nucleic acids. We show that the extension of the original in-cell NMR approach is not straightforward. The severe signal broadening and overlap of <sup>1</sup>H in-cell NMR spectra of polymorphic G-quadruplexes and their complexes complicate their quantitative interpretation. Nevertheless, the <sup>1</sup>H in-cell NMR can be used to identify drugs that, despite strong interaction in vitro, lose their ability to bind G-quadruplexes in the native environment. The in-cell NMR approach is adjusted to a recently developed 3,5-bis(trifluoromethyl)phenyl probe to monitor the intracellular interaction with ligands using <sup>19</sup>F-detected in-cell NMR. The probe allows dissecting polymorphic mixture in terms of number and relative populations of individual G-quadruplex species, including ligand-bound and unbound forms in vitro and in cellulo. Despite the probe’s discussed limitations, the <sup>19</sup>F-detected in-cell NMR appears to be a promising strategy to profile G-quadruplex–ligand interactions in the complex environment of living cells. |
| first_indexed | 2024-03-10T10:44:53Z |
| format | Article |
| id | doaj.art-7079282477f74255ab7a83ef84c2a20e |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T10:44:53Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-7079282477f74255ab7a83ef84c2a20e2023-11-21T22:39:31ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-06-012211604210.3390/ijms22116042Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR SpectroscopyDaniel Krafčík0Eva Ištvánková1Šimon Džatko2Pavlína Víšková3Silvie Foldynová-Trantírková4Lukáš Trantírek5Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicCentral European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicCentral European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicCentral European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicInstitute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech RepublicCentral European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech RepublicRecently, the <sup>1</sup>H-detected in-cell NMR spectroscopy has emerged as a unique tool allowing the characterization of interactions between nucleic acid-based targets and drug-like molecules in living human cells. Here, we assess the application potential of <sup>1</sup>H and <sup>19</sup>F-detected in-cell NMR spectroscopy to profile drugs/ligands targeting DNA G-quadruplexes, arguably the most studied class of anti-cancer drugs targeting nucleic acids. We show that the extension of the original in-cell NMR approach is not straightforward. The severe signal broadening and overlap of <sup>1</sup>H in-cell NMR spectra of polymorphic G-quadruplexes and their complexes complicate their quantitative interpretation. Nevertheless, the <sup>1</sup>H in-cell NMR can be used to identify drugs that, despite strong interaction in vitro, lose their ability to bind G-quadruplexes in the native environment. The in-cell NMR approach is adjusted to a recently developed 3,5-bis(trifluoromethyl)phenyl probe to monitor the intracellular interaction with ligands using <sup>19</sup>F-detected in-cell NMR. The probe allows dissecting polymorphic mixture in terms of number and relative populations of individual G-quadruplex species, including ligand-bound and unbound forms in vitro and in cellulo. Despite the probe’s discussed limitations, the <sup>19</sup>F-detected in-cell NMR appears to be a promising strategy to profile G-quadruplex–ligand interactions in the complex environment of living cells.https://www.mdpi.com/1422-0067/22/11/6042in-cell NMRG-quadruplexliganddrugBcl2telomeric DNA |
| spellingShingle | Daniel Krafčík Eva Ištvánková Šimon Džatko Pavlína Víšková Silvie Foldynová-Trantírková Lukáš Trantírek Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy International Journal of Molecular Sciences in-cell NMR G-quadruplex ligand drug Bcl2 telomeric DNA |
| title | Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy |
| title_full | Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy |
| title_fullStr | Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy |
| title_full_unstemmed | Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy |
| title_short | Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy |
| title_sort | towards profiling of the g quadruplex targeting drugs in the living human cells using nmr spectroscopy |
| topic | in-cell NMR G-quadruplex ligand drug Bcl2 telomeric DNA |
| url | https://www.mdpi.com/1422-0067/22/11/6042 |
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