Design, synthesis and biological evaluation of novel G9a inhibitors with improved brain permeability from a scaffold hopping approach

The lysine methyltransferase G9a (also known as EHMT2) catalyses the addition two methyl groups to lysine 9 of histone H3. Due to its central role in epigenetic control, the aberrant activity of this enzyme is associated to several diseases including cancer. In particular, recent evidences revealed G9a involvement in the progression of REST-expressing (repressor element (RE)-1 silencing transcription factor) medulloblastomas. Only a few among the selective inhibitors of G9a reported to date are useful chemical probes for cell-based and animal studies. Starting from the inhibitor UNC0638, (3) we applied a scaffold hopping approach to develop novel chemical entities endowed with high affinity towards G9a. In particular, we replaced the quinazoline core, common to most of the reported inhibitors, with 1,4-benzodiazepine nucleus, known to be a privileged structure. We chose the 3,4-dihydro-5H-benzo[e][1,4]diazepin-5-one scaffold, that can be obtained through an efficient and gram-scale continuous-flow protocol, previously optimized by our group. (4) Moreover, this scaffold could be easily decorated to provide a number of highly functionalized potential ligands (Figure 1). To validate our approach, we designed and synthesized a small library of UNC0638 analogues. The UNC0638 benzodiazepine analogue (EML741) showed a good activity in a peptide-based AlphaLISA, together with a promising membrane permeability profile (PAMPA-BBB).