C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays

Journal article

Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences between the histone substrate binding sites in order to improve affinity for the KDM4-subfamily over KDM5-subfamily enzymes. In particular, residues E169 and V313 (KDM4A numbering) were targeted. Additionally, conformational restriction of the flexible pyridopyrimidinone C8-substituent was investigated. These approaches yielded potent and cell-penetrant dual KDM4/5-subfamily inhibitors including 19a (KDM4A and KDM5B Ki = 0.004 and 0.007 μM, respectively). Compound cellular profiling in two orthogonal target engagement assays revealed a significant reduction from biochemical to cell-based activity across multiple analogues; this decrease was shown to be consistent with 2OG competition, and suggests that sub-nanomolar biochemical potency will be required with C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one compounds to achieve sub-micromolar target inhibition in cells.

Authors: Le Bihan, Y-V; Lanigan, RM; Atrash, B; McLaughlin, MG; Velupillai, S

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Elsevier
• Journal: European Journal of Medicinal Chemistry
• Volume: 177
• Pages: 316-337
• Publication date: 2019-05-17
• Acceptance date: 2019-05-14
• DOI: 10.1016/j.ejmech.2019.05.041
• EISSN: 1768-3254
• ISSN: 0223-5234
• Pmid: 31158747
• Language: English
• Keywords: drug screening assays; antitumor; cell line; tumor; crystallography; X-Ray; humans; enzyme inhibitors; pyridines; molecular structure; hydrophobic and hydrophilic interactions; jumonji domain-containing histone demethylases; pyrimidinones; FFR; protein binding; structure-activity relationship