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Borisevich SS, Aksinina TE, Ilyina MG, Shender VO, Anufrieva KS, Arapidi GP, Antipova NV, Anizon F, Esvan YJ, Giraud F, Tatarskiy VV, Moreau P, Shakhparonov MI, Pavlyukov MS, Shtil AA. The Nitro Group Reshapes the Effects of Pyrido[3,4- g]quinazoline Derivatives on DYRK/CLK Activity and RNA Splicing in Glioblastoma Cells. Cancers (Basel) 2024; 16:834. [PMID: 38398225 PMCID: PMC10886777 DOI: 10.3390/cancers16040834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/10/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Serine-threonine protein kinases of the DYRK and CLK families regulate a variety of vital cellular functions. In particular, these enzymes phosphorylate proteins involved in pre-mRNA splicing. Targeting splicing with pharmacological DYRK/CLK inhibitors emerged as a promising anticancer strategy. Investigation of the pyrido[3,4-g]quinazoline scaffold led to the discovery of DYRK/CLK binders with differential potency against individual enzyme isoforms. Exploring the structure-activity relationship within this chemotype, we demonstrated that two structurally close compounds, pyrido[3,4-g]quinazoline-2,10-diamine 1 and 10-nitro pyrido[3,4-g]quinazoline-2-amine 2, differentially inhibited DYRK1-4 and CLK1-3 protein kinases in vitro. Unlike compound 1, compound 2 efficiently inhibited DYRK3 and CLK4 isoenzymes at nanomolar concentrations. Quantum chemical calculations, docking and molecular dynamic simulations of complexes of 1 and 2 with DYRK3 and CLK4 identified a dramatic difference in electron donor-acceptor properties critical for preferential interaction of 2 with these targets. Subsequent transcriptome and proteome analyses of patient-derived glioblastoma (GBM) neurospheres treated with 2 revealed that this compound impaired CLK4 interactions with spliceosomal proteins, thereby altering RNA splicing. Importantly, 2 affected the genes that perform critical functions for cancer cells including DNA damage response, p53 signaling and transcription. Altogether, these results provide a mechanistic basis for the therapeutic efficacy of 2 previously demonstrated in in vivo GBM models.
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Affiliation(s)
- Sophia S Borisevich
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, Ufa 450054, Russia
- Institute of Cyber Intelligence Systems, National Research Nuclear University MEPhI, Moscow 115409, Russia
| | - Tatiana E Aksinina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Margarita G Ilyina
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, Ufa 450054, Russia
- Institute of Cyber Intelligence Systems, National Research Nuclear University MEPhI, Moscow 115409, Russia
| | - Victoria O Shender
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia
| | - Ksenia S Anufrieva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia
| | - Georgij P Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia
| | - Nadezhda V Antipova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Fabrice Anizon
- Université Clermont Auvergne, Centre National de la Recherche Scientifique, Clermont Auvergne Institut National Polytechnique, Institute of Chemistry of Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Yannick J Esvan
- Université Clermont Auvergne, Centre National de la Recherche Scientifique, Clermont Auvergne Institut National Polytechnique, Institute of Chemistry of Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Francis Giraud
- Université Clermont Auvergne, Centre National de la Recherche Scientifique, Clermont Auvergne Institut National Polytechnique, Institute of Chemistry of Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Pascale Moreau
- Université Clermont Auvergne, Centre National de la Recherche Scientifique, Clermont Auvergne Institut National Polytechnique, Institute of Chemistry of Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Mikhail I Shakhparonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Marat S Pavlyukov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander A Shtil
- Blokhin National Medical Research Center of Oncology, Moscow 115522, Russia
- Department of Chemistry, Moscow State University, Moscow 119234, Russia
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