We have developed an allosteric kinase inhibitory and modulatory library based on published allosteric kinase inhibitors and allosteric modulatory compounds. The allosteric kinase inhibitory library contains more than 2000 compounds. Recently X-ray diffraction experiments with co-crystallized inhibitors like Gleevec (inhibitor of Bcr-Abl) and BIRB-796 (inhibitor of p38 MAP kinase) proved allosteric-type binding mode or DFG-out binding for these drugs. Several published kinase inhibitors with allosteric binding mode are now known: Gleevec for Bcr-Abl, BIRB-796 for p38, BMS345541 for IKK, Lapatinib for EGFR/Her2, Nilotinib for Gleevec-resistant Bcr-Abl and Sorafenib for Raf.
DFG-out binders have an elevated residence time on the targetkinase, and are therefore ‘better’ drugs, since they can cope physiochemical deficiencies. In addition to the DFG-out binders, there are other allosteric inhibitors known, like the Erk1/2 inhibitors, PD98059, PD184352, some Akt inhibitors, Vichem’s PDGFR inhibitory HDL series and some tyrphostins developed earlier for SUGEN Inc.
Applying Vichem’s special ‘theoretical interactive surface’ pharmacophore modeling on pre-filtered ‘non-ATP-like’ kinase inhibitors, we were able to identify the main structural features needed for allosteric binding. Appropriate molecular shape, size and electronic properties in suitable positions can afford selective and high affinity binding at allosteric binding sites of kinases. We developed a few hundred allosteric inhibitor analogues around proven allosteric-type core structures, which are available for testing. These structures have been tested active on several kinases in the low micromolar and nanomolar concentrations.
Type II inhibitors occupy the nucleotide pocket, extend into an adjacent “allosteric pocket” and induce DFG-out configuration. Type III inhibitors exclusively bind to this “allosteric pocket” and blocks kinase activity without displacing ATP. Type IV inhibitors bind to sites several Angstroms (A) away from the nucleotide binding pocket.
Determination of binding type: Reporter Displacement Binding Assay (with Proteros), Environmental sensitive fluorophore assay for Type II and III inhibitors.