Structural mimicry of UM171 and neomorphic cancer mutants co-opts E3 ligase KBTBD4 for HDAC1/2 recruitment

• Published in: Nature communications Vol. 16; no. 1; pp. 3144 - 16
• Main Authors: Chen, Zhuoyao, Chi, Gamma, Balo, Timea, Chen, Xiangrong, Montes, Beatriz Ralsi, Clifford, Steven C., D’Angiolella, Vincenzo, Szabo, Timea, Kiss, Arpad, Novak, Tibor, Herner, András, Kotschy, András, Bullock, Alex N.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 02.04.2025; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 13/1; 13/106; 13/109; 13/44; 14/1; 631/45/474/2073; 631/45/535/1258/1259; 631/67/395; 631/80/304; 631/92/613; 82/16; 82/29; 82/58; 82/80; 9/10; Cancer; Co-Repressor Proteins - genetics; Co-Repressor Proteins - metabolism; Cryoelectron Microscopy; Epigenetics; HDAC2 protein; Hematopoietic stem cells; Histone deacetylase; Histone Deacetylase 1 - chemistry; Histone Deacetylase 1 - genetics; Histone Deacetylase 1 - metabolism; Histone Deacetylase 2 - chemistry; Histone Deacetylase 2 - genetics; Histone Deacetylase 2 - metabolism; Humanities and Social Sciences; Humans; Immunosuppressive agents; Medulloblastoma; Mimicry; Mode of action; multidisciplinary; Mutants; Mutation; Protein Binding; Science; Science (multidisciplinary); Stem cell transplantation; Stem cells; Ubiquitin-protein ligase; Ubiquitin-Protein Ligases - chemistry; Ubiquitin-Protein Ligases - genetics; Ubiquitin-Protein Ligases - metabolism; Ubiquitination
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-025-58350-z

Neomorphic mutations and drugs can elicit unanticipated effects that require mechanistic understanding to inform clinical practice. Recurrent indel mutations in the Kelch domain of the KBTBD4 E3 ligase rewire epigenetic programs for stemness in medulloblastoma by recruiting LSD1-CoREST-HDAC1/2 complexes as neo-substrates for ubiquitination and degradation. UM171, an investigational drug for haematopoietic stem cell transplantation, was found to degrade LSD1-CoREST-HDAC1/2 complexes in a wild-type KBTBD4-dependent manner, suggesting a potential common mode of action. Here, we identify that these neomorphic interactions are mediated by the HDAC deacetylase domain. Cryo-EM studies of both wild-type and mutant KBTBD4 capture 2:1 and 2:2 KBTBD4-HDAC2 complexes, as well as a 2:1:1 KBTBD4-HDAC2-CoREST1 complex, at resolutions spanning 2.7 to 3.3 Å. The mutant and drug-induced complexes adopt similar structural assemblies requiring both Kelch domains in the KBTBD4 dimer for each HDAC2 interaction. UM171 is identified as a bona fide molecular glue binding across the ternary interface. Most strikingly, the indel mutation reshapes the same surface of KBTBD4 providing an example of a natural mimic of a molecular glue. Together, the structures provide mechanistic understanding of neomorphic KBTBD4, while structure-activity relationship (SAR) analysis of UM171 reveals analog S234984 as a more potent molecular glue for future studies. LSD1-CoREST-HDAC1/2 complexes are degraded by both the drug UM171 and cancer-associated mutations in the E3 ligase KBTBD4. Here, the authors use cryo-EM to demonstrate how these mutations and UM171 similarly alter KBTBD4 to recruit HDAC1/2, illustrating a natural example of a molecular glue.