Structure-based discovery of the first allosteric inhibitors of cyclin-dependent kinase 2

摘要: Allosteric targeting of protein kinases via displacement the structural αC helix with type III allosteric inhibitors is currently gaining a foothold in drug discovery. Recently, first crystal structure CDK2 an open pocket adjacent to has been described, prospecting new opportunities design more selective inhibitors, but not yet exploited for structure-based inhibitors. In this work we report results virtual screening campaign that resulted discovery first-in-class ligands CDK2. Using combination docking and post-docking analyses made our tool BEAR, 7 (hit rate 20%) micromolar affinity were identified, some them inhibiting growth breast cancer cell lines range. Competition experiments performed presence ATP-competitive inhibitor staurosporine confirmed are truly allosteric, agreement their design. Of these, compound 2 bound EC50 value 3 μM inhibited proliferation MDA-MB231 ZR-75–1 cells IC50 values approximately 20 μM, while 4 had 71 around μM. Remarkably, most potent was able selectively inhibit CDK2-mediated Retinoblastoma phosphorylation, confirming its mechanism action fully compatible inhibition phosphorylation cells. Finally, hit expansion through analog search revealed additional ligand 4g similar vitro potency on