Discovery of Potent Inhibitors of Cyclin-Dependent Kinases 7 and 9: Design, Synthesis, Structure-Activity Relationship Analysis and Biological Evaluation

Graphical Abstract

Two targets: 4-(Imidazo[1,2-a]pyrimidin-3-yl)-N-pyridinylpyrimidin-2-amines were found to be not only potent inhibitors of cyclin-dependent kinases (CDKs) 7 and 9 but also effective anti-proliferative agents against a range of human cancer cell lines. The findings from cellular mechanistic studies support that the observed anti-proliferative effect could originate from the inhibition of both CDKs.A previous version of this manuscript has been deposited on a preprint server (https://doi.org/10.2139/ssrn.4210989).

Abstract

Cyclin-dependent kinases (CDKs) 7 and 9 are deregulated in various types of human cancer and are thus viewed as therapeutic targets. Accordingly, small-molecule inhibitors of both CDKs are highly sought-after. Capitalising on our previous discovery of CDKI-73, a potent CDK9 inhibitor, medicinal chemistry optimisation was pursued. A number of N-pyridinylpyrimidin-2-amines were rationally designed, chemically synthesised and biologically assessed. Among them, N-(6-(4-cyclopentylpiperazin-1-yl)pyridin-3-yl)-4-(imidazo[1,2-a]pyrimidin-3-yl)pyrimidin-2-amine was found to be one of the most potent inhibitors of CDKs 7 and 9 as well as the most effective anti-proliferative agent towards multiple human cancer cell lines. The cellular mode of action of this compound was investigated in MV4-11 acute myeloid leukaemia cells, revealing that the compound dampened the kinase activity of cellular CDKs 7 and 9, arrested the cell cycle at sub-G1 phase and induced apoptosis.