Reaction-driven de novo design, synthesis and testing of potential type II kinase inhibitors

Background: De novo design of drug-like compounds with a desired pharmacological activity profile has become feasible through innovative computer algorithms. Fragment-based design and simulated chemical reactions allow for the rapid generation of candidate compounds as blueprints for organic synthesis. Methods: We used a combination of complementary virtual-screening tools for the analysis of de novo designed compounds that were generated with the aim to inhibit inactive polo-like kinase I (PlkI), a target for the development of cancer therapeutics. A homology model of the inactive state of PlkI was constructed and the nucleotide binding pocket conformations in the DFG-in and DFG-out state were compared. The de novo-designed compounds were analyzed using pharmacophore matching, structure activity landscape analysis, and automated ligand docking. One compound was synthesized and tested in vitro. Results: The majority of the designed compounds possess a generic architecture present in known kinase inhibitors. Predictions favor kinases as targets of these compounds but also suggest potential off-target effects. Several bioisosteric replacements were suggested, and de novo designed compounds were assessed by automated docking for potential binding preference toward the inactive (type II inhibitors) over the active conformation (type I inhibitors) of the kinase ATP binding site. One selected compound was successfully synthesized as suggested by the software. The de novo-designed compound exhibited inhibitory activity against inactive PlkI in vitro, but did not show significant inhibition of active PlkI and 38 other kinases tested. Conclusions: Computer-based de novo design of screening candidates in combination with ligand- and receptor-based virtual screening generates motivated suggestions for focused library design in hit and lead discovery. Attractive, synthetically accessible compounds can be obtained together with predicted on- and off-target profiles and desired activities.