Download MendeleyDNA-encoded library screening uncovers potent DNMT2 inhibitors targeting a cryptic allosteric binding site.
Frey, A.F., Schwan, M., Weldert, A.C., Kadenbach, V., Kopp, J., Nidoieva, Z., Zimmermann, R.A., Gleue, L., Zimmer, C., Jorg, M., Friedland, K., Helm, M., Sinning, I., Barthels, F.(2025) iScience 28: 113300-113300
- PubMed: 40894903
- DOI: https://doi.org/10.1016/j.isci.2025.113300
- Primary Citation of Related Structures:
9HGM - PubMed Abstract:
DNMT2 (TRDMT1) is a human RNA methyltransferase implicated in various disease processes. However, small-molecule targeting of DNMT2 remains challenging due to poor selectivity and low cellular availability of known S -adenosylhomocysteine (SAH)-derived ligands. In this study, a DNA-encoded library (DEL) screen identified five non-SAH-like chemotypes that selectively bind DNMT2, including three peptidomimetics. Orthogonal assays confirmed target engagement, and X-ray crystallography revealed a previously unknown allosteric binding pocket formed via active site loop rearrangement. Guided by structural insights, the authors optimized a lead compound with a K D of 3.04 μM that reduces m 5 C levels in MOLM-13 tRNA and synergizes with doxorubicin to impair cell viability. These inhibitors exhibit unprecedented selectivity over other methyltransferases, offering a promising scaffold for future DNMT2-targeting therapeutics. Beyond pharmacological implications, the study provides conceptual advances in understanding allosteric modulation and structural plasticity of DNMT2.
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), 55128 Mainz, Germany.
Organizational Affiliation:
