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

Le Bihan, Yann-Vaï and Lanigan, Rachel M and Atrash, Butrus and McLaughlin, Mark G and Velupillai, Srikannathasan and Malcolm, Andrew G and England, Katherine S and Ruda, Gian Filippo and Mok, N Yi and Tumber, Anthony and Tomlin, Kathy and Saville, Harry and Shehu, Erald and McAndrew, Craig and Carmichael, LeAnne and Bennett, James M and Jeganathan, Fiona and Eve, Paul and Donovan, Adam and Hayes, Angela and Wood, Francesca and Raynaud, Florence I and Fedorov, Oleg and Brennan, Paul E and Burke, Rosemary and van Montfort, RobL M and Rossanese, Olivia W and Blagg, Julian and Bavetsias, Vassilios (2019) 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. European Journal of Medicinal Chemistry, 177. pp. 316-337. ISSN 1768-3254

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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, the 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 suggest 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.