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

  • Eur J Med Chem. 2019 Sep 1;177:316-337. doi: 10.1016/j.ejmech.2019.05.041.
Yann-Vaï Le Bihan  1 ,  Rachel M Lanigan  1 ,  Butrus Atrash  1 ,  Mark G McLaughlin  1 ,  Srikannathasan Velupillai  2 ,  Andrew G Malcolm  1 ,  Katherine S England  3 ,  Gian Filippo Ruda  2 ,  N Yi Mok  1 ,  Anthony Tumber  3 ,  Kathy Tomlin  1 ,  Harry Saville  1 ,  Erald Shehu  1 ,  Craig McAndrew  1 ,  LeAnne Carmichael  1 ,  James M Bennett  3 ,  Fiona Jeganathan  1 ,  Paul Eve  1 ,  Adam Donovan  1 ,  Angela Hayes  1 ,  Francesca Wood  1 ,  Florence I Raynaud  1 ,  Oleg Fedorov  3 ,  Paul E Brennan  3 ,  Rosemary Burke  1 ,  Rob L M van Montfort  1 ,  Olivia W Rossanese  1 ,  Julian Blagg  4 ,  Vassilios Bavetsias  5
Affiliations
  • 1. Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
  • 2. Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK.
  • 3. Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK.
  • 4. Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK. Electronic address: [email protected].
  • 5. Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK. Electronic address: [email protected].
PMID: 31158747 DOI: 10.1016/j.ejmech.2019.05.041
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.

Keywords
Histone demethylases; KDM inhibitors; KDM4 subfamily; KDM5 subfamily; Pyridopyrimidinones.
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