A development of chimeric VEGFR2 TK inhibitor based on two ligand conformers from PDB: 1Y6A complex – Medicinal chemistry consequences of a TKs analysis

•We developed TK inhibitor 22SYM possessing IC50 = 15.1 nM VEGFR2 activity.•We screened 22SYM in different in vitro and in vivo assays.•We analysed all 34 VEGFR2 TKs and other tyrosine kinase structures from PDB.•A-loop in DFG-out TKs with Type I inhibitor can adopt different conformations.•A flexible A-loop can disturb Type I inhibitor activity in DFG-out TKs.

VEGFR2 is an important mediator of angiogenesis and influences fate of some cancer stem cells. Here we analysed all 34 structures of VEGFR2 TK available from PDB database. From them a complex PDB: 1Y6A has an exceptional AAZ ligand bound to TK in form of two conformers (U- and S-shaped). This observation inspired us to develop three chimeric bispyridyl VEGFR2 inhibitors by combining structural features of both AAZ conformers and/or their relative ligand AAX (PDB: 1Y6B).Our most interesting inhibitor 22SYM has an enzymatic VEGFR2 TK activity (IC50: 15.1 nM) comparable or better to the active compounds from clinical drugs Nexavar and Sutent. 22SYM inhibits growth, migration and tube formation of endothelial cells (EC) and selectively induces EC apoptosis. 22SYM also inhibits in vivo angiogenesis in Zebrafish embryo assay.Additionally to the above results, we proved here that tyrosine kinases in an inactive form possessing Type I inhibitors can adopt both a closed or an opened conformation of kinase A-loop independently on their DFG-out arrangement. We proposed here that an activity of certain Type I inhibitors (e.g. 22SYM-like) in complex with DFG-out TK can be negatively influenced by collisions with a dynamically moving TK A-loop.

Graphical abstractAAZ conformers (U- and S-shaped) found in PDB: 1Y6A. Develloped chimeric 22SYM inhibitor possessing U-like/S-like pyridine rings with predicted intermolecular interactions, determined enzymatic activity and its proposed pose in VEGFR2 TK. Inactive (DFG-out) tyrosine kinases possessing Type I inhibitor can adopt from a closed to an opened conformation of their activation loop. The flexible A-loop can influencestability of such complex and activity of Type I inhibitor.Figure optionsDownload full-size imageDownload as PowerPoint slide