Discovery ofa Novel Selective and Cell-Active N<sup>6</sup>‑MethyladenosineRNA Demethylase ALKBH5 Inhibitor

N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), the most abundant methylation on mRNA, plays pivotal roles in regulating mRNA biological functions, which affect cell functions. ALKBH5, an m<sup>6</sup>A demethylase, was found to be an oncogene in several cancer types, including triple-negative breast cancer (TNBC). Here, we report a novel and selective ALKBH5 covalent inhibitor, <b>W23</b>-<b>1006</b>, through virtual screening and structure optimization. It covalently bonds to the ALKBH5 C200 residue with an IC<sub>50</sub> value of 3.848 μM, representing roughly 30- and 8-fold stronger inhibitory activity than that against FTO and ALKBH3, respectively. Cellular experiments demonstrated that <b>W23-1006</b> could efficiently enhance the m<sup>6</sup>A level on fibronectin 1 (FN1) mRNA, leading to strong suppression of TNBC cell proliferation and migration in vitro as well as tumor growth and metastasis in vivo. Collectively, our study developed a novel, selective, and cell-active ALKBH5 covalent inhibitor, <b>W23-1006</b>, which could be a potential therapeutic option for cancer, such as TNBC treatment.

Publication Details

Journal
Figshare
Published
2025-02-10
DOI
https://doi.org/10.1021/acs.jmedchem.4c01542.s005
Primary Topic
RNA modifications and cancer
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article
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article

Discovery ofa Novel Selective and Cell-Active N6‑MethyladenosineRNA Demethylase ALKBH5 Inhibitor

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RNA modifications and cancer
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Discovery ofa Novel Selective and Cell-Active N6‑MethyladenosineRNA Demethylase ALKBH5 Inhibitor

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Abstract

N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), the most abundant methylation on mRNA, plays pivotal roles in regulating mRNA biological functions, which affect cell functions. ALKBH5, an m<sup>6</sup>A demethylase, was found to be an oncogene in several cancer types, including triple-negative breast cancer (TNBC). Here, we report a novel and selective ALKBH5 covalent inhibitor, <b>W23</b>-<b>1006</b>, through virtual screening and structure optimization. It covalently bonds to the ALKBH5 C200 residue with an IC<sub>50</sub> value of 3.848 μM, representing roughly 30- and 8-fold stronger inhibitory activity than that against FTO and ALKBH3, respectively. Cellular experiments demonstrated that <b>W23-1006</b> could efficiently enhance the m<sup>6</sup>A level on fibronectin 1 (FN1) mRNA, leading to strong suppression of TNBC cell proliferation and migration in vitro as well as tumor growth and metastasis in vivo. Collectively, our study developed a novel, selective, and cell-active ALKBH5 covalent inhibitor, <b>W23-1006</b>, which could be a potential therapeutic option for cancer, such as TNBC treatment.

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