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Cited by 5RNA modifications and cancerEpigenetics and DNA MethylationDNA and Nucleic Acid Chemistry

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DNA-encoded library screening uncovers potent DNMT2 inhibitors targeting a cryptic allosteric binding site

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Frey, Ariane F., Schwan, Merlin, Weldert, Annabelle C., Kadenbach, Valerie, Kopp, Jürgen, Nidoieva, Zarina, Zimmermann, Robert A., Gleue, Lukas, Zimmer, Collin, Jörg, Marko, Friedland, Kristina, Helm, Mark, Sinning, Irmgard, Barthels, Fabian·2025·iScience
DOI 10.1016/j.isci.2025.113300PMC PMC12396291

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Abstract

ABSTRACT The human RNA methyltransferase DNMT2 is thought to be involved in various pathophysiological processes, yet, a major challenge in drug targeting DNMT2 is given by the fact that current SAH-derived inhibitors have poor target selectivity and limited cellular permeability. In this study, we have performed a DNA-encoded library (DEL) screening on DNMT2 yielding five non-SAH-like hit structures, three of which feature a peptidomimetic scaffold. All DEL hits could be validated by orthogonal biophysical and biochemical assays for DNMT2 binding. At the same time, the lead structure did not interact with related methyltransferases from the DNMT and NSUN families highlighting an unmatched DNMT2-targeting selectivity profile. Subsequent crystallographic studies revealed the unique ligand binding mode including an active site loop rearrangement and the formation of a cryptic allosteric binding pocket able to modulate the enzymatic activity by non-covalent DNMT2 dimerization. Based on the crystallographic results, we performed a structure-activity relationship study around the inhibitor lead structure resulting in an optimized DNMT2 inhibitor ( K D =3.04 µM), which was able to reduce m 5 C levels in MOLM-13 tRNA. GRAPHICAL ABSTRACT

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Metadata

Authors
Frey, A. F., Schwan, M., Weldert, A. C., Kadenbach, V., Kopp, J., Nidoieva, Z., Zimmermann, R. A., Gleue, L., Zimmer, C., Jörg, M., Friedland, K., Helm, M., Sinning, I., & Barthels, F.
Affiliations
  • Johannes Gutenberg University Mainz (DE)
  • Heidelberg University (DE)
Corresponding author
Barthels, Fabian
ORCID
Venue
iScience
Publisher
Elsevier BV
Published
2025-09
Volume
28
Issue
9
Pages
113300
ISSN
2589-0042 (ISSN-L)
DOI
10.1016/j.isci.2025.113300
PMC
PMC12396291
OpenAlex
W4412999305
Cited by
5
References
3
Citations by year
2026: 4 · 2025: 1
FWCI
1.50
Type
journal article
Language
en
Open access
Licence
Locations
  • iScience (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Gutenberg Open Science (cc-by)
Funders
  • Deutsche Forschungsgemeinschaft (INST 35/1314-1 FUGG, INST 35/1503-1 FUGG, 439669440)
  • Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Keywords
DNMT2, allosteric site, DNA methyltransferases, tRNA methyltransferase, MOLM-13, doxorubicin synergy, allosteric modulation, protein structural plasticity

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