Discovery and Design of YTHDF2-Selective and Pan-YTHDF Inhibitors for m6A Binding by the YTH Aromatic Cage
6 affiliations
- 1University of Helsinki , , Haartmaninkatu 8 , ,
- 2Helsinki University Hospital , , Haartmaninkatu 4 , ,
- 3University of Tartu , , Ravila tn 14a , ,
- 4Chemestmed, Ltd , Soola tn 8 , ,
- 5HiLIFE, University of Helsinki , , Viikinkaari 5d , ,
- 6University of Jyväskylä , , Survontie 9 C , ,
Abstract
Recognition of N6-methyl-adenosine (m6A) in the RNA sequences by the YT521-B homology domain-containing protein family paralogs 1–3 (YTHDF1–3) is a dominant layer of myriad cellular regulation. Dysregulated YTHDF paralog expression and activities have been reported in cancer, including glioblastoma multiforme (GBM) in which YTHDF2 has been identified as a druggable dependency. Guided by structure-based in silico screening, we identified structurally related small-molecule compound families of promising YTHDF inhibitor compounds. Following in vitro screening, two hits, DT11 and DT15, emerged and were further examined. We identified DT11 as a YTHDF2-selective inhibitor of the YTH domain using proximity-based bead assays, microscale thermophoresis, molecular dynamics, and nuclear magnetic resonance spectroscopy. DT11 demonstrated 10–100-fold YTHDF2-selectivity (IC50: YTHDF2 16.6 μM; YTHDF1 185 μM; YTHDF3 1300 μM) in inhibiting m6A-RNA binding, whereas the pan-inhibitor DT15 effectively inhibited all the paralogs (IC50: YTHDF2 12.6 μM; YTHDF1 18.8 μM; YTHDF3 31 μM). In LN229 glioblastoma cells, DT11 reduced cell viability and showed relevant additive efficacy with the gold standard Temozolomide. DT15 blocked GBM cell invasion and scratch wound closure. Similar effects were observed after inhibition of the m6A writer METTL3 activity by STM2457. No such effects were observed with DT11. A minutely modified DT11 derivative, DT11-1, showed 10-fold increases in YTHDF2-selective m6A binding and LN229 cell viability inhibitory potencies. All the compounds produced high GBM preference over primary neurons and HEK293 cells in their effects. Our results further define pharmacological molecular comprehensions for paralog-dependent engagement of m6A in RNA by the aromatic cage for the selective modulation of YTHDF functions.
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BibTeX
@article{sikorski2026discovery,
title = {{Discovery and Design of YTHDF2-Selective and Pan-YTHDF Inhibitors for m6A Binding by the YTH Aromatic Cage}},
author = {Vilbert Sikorski and Joni Salo and Simona Selberg and Diogo Costa Sa and Brunaldo Renzi and Indrek Teino and Daria Blokhina and Salla Virtanen and Lina Antenucci and Mart Saarma and Perttu Permi and Mati Karelson and Esko Kankuri},
journal = {ACS Omega},
year = {2026},
month = oct,
doi = {10.1021/acsomega.6c05268},
url = {https://pubs.acs.org/acsodf/article/11/42/64760/5451005/Discovery-and-Design-of-YTHDF2-Selective-and-Pan},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Discovery and Design of YTHDF2-Selective and Pan-YTHDF Inhibitors for m6A Binding by the YTH Aromatic Cage
AU - Vilbert Sikorski
AU - Joni Salo
AU - Simona Selberg
AU - Diogo Costa Sa
AU - Brunaldo Renzi
AU - Indrek Teino
AU - Daria Blokhina
AU - Salla Virtanen
AU - Lina Antenucci
AU - Mart Saarma
AU - Perttu Permi
AU - Mati Karelson
AU - Esko Kankuri
PY - 2026
DA - 2026/10/14
JO - ACS Omega
DO - 10.1021/acsomega.6c05268
UR - https://pubs.acs.org/acsodf/article/11/42/64760/5451005/Discovery-and-Design-of-YTHDF2-Selective-and-Pan
AB - Recognition of N6-methyl-adenosine (m6A) in the RNA sequences by the YT521-B homology domain-containing protein family paralogs 1–3 (YTHDF1–3) is a dominant layer of myriad cellular regulation. Dysregulated YTHDF paralog expression and activities have been reported in cancer, including glioblastoma multiforme (GBM) in which YTHDF2 has been identified as a druggable dependency. Guided by structure-based in silico screening, we identified structurally related small-molecule compound families of promising YTHDF inhibitor compounds. Following in vitro screening, two hits, DT11 and DT15, emerged and were further examined. We identified DT11 as a YTHDF2-selective inhibitor of the YTH domain using proximity-based bead assays, microscale thermophoresis, molecular dynamics, and nuclear magnetic resonance spectroscopy. DT11 demonstrated 10–100-fold YTHDF2-selectivity (IC50: YTHDF2 16.6 μM; YTHDF1 185 μM; YTHDF3 1300 μM) in inhibiting m6A-RNA binding, whereas the pan-inhibitor DT15 effectively inhibited all the paralogs (IC50: YTHDF2 12.6 μM; YTHDF1 18.8 μM; YTHDF3 31 μM). In LN229 glioblastoma cells, DT11 reduced cell viability and showed relevant additive efficacy with the gold standard Temozolomide. DT15 blocked GBM cell invasion and scratch wound closure. Similar effects were observed after inhibition of the m6A writer METTL3 activity by STM2457. No such effects were observed with DT11. A minutely modified DT11 derivative, DT11-1, showed 10-fold increases in YTHDF2-selective m6A binding and LN229 cell viability inhibitory potencies. All the compounds produced high GBM preference over primary neurons and HEK293 cells in their effects. Our results further define pharmacological molecular comprehensions for paralog-dependent engagement of m6A in RNA by the aromatic cage for the selective modulation of YTHDF functions.
SN - 2470-1343
ER -