1. 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
- Author
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Le Bihan, Y-V, Lanigan, RM, Atrash, B, McLaughlin, MG, Velupillai, S, Malcolm, AG, England, KS, Ruda, GF, Mok, NY, Tumber, A, Tomlin, K, Saville, H, Shehu, E, McAndrew, C, Carmichael, L, Bennett, JM, Jeganathan, F, Eve, P, Donovan, A, Hayes, A, Wood, F, Raynaud, FI, Fedorov, O, Brennan, PE, Burke, R, Van Montfort, RLM, Rossanese, OW, Blagg, J, and Bavetsias, V
- Subjects
KDM4 subfamily ,Jumonji Domain-Containing Histone Demethylases ,Molecular Structure ,Pyridines ,Pyrimidinones ,Crystallography, X-Ray ,Article ,Pyridopyrimidinones ,Structure-Activity Relationship ,Cell Line, Tumor ,Humans ,KDM inhibitors ,Drug Screening Assays, Antitumor ,Enzyme Inhibitors ,KDM5 subfamily ,Hydrophobic and Hydrophilic Interactions ,Histone demethylases ,Protein Binding - Abstract
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., Graphical abstract Image 1, Highlights • Targeting of KDM4A residues E169 and V313 to improve affinity for the KDM4-subfamily. • Potent and cell-penetrant KDM4/5-subfamily inhibitors such as 19a were identified. • Significant drop from biochemical to cell-based activity was observed. • Lower potency in cells is linked to competition with the 2OG co-substrate.
- Published
- 2019