2. Academic Validation
  3. A development of chimeric VEGFR2 TK inhibitor based on two ligand conformers from PDB: 1Y6A complex--medicinal chemistry consequences of a TKs analysis

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

  • Eur J Med Chem. 2014 Jan 24:72:146-59. doi: 10.1016/j.ejmech.2013.11.023.
Lucia Lintnerová 1,  Melissa García-Caballero 2,  Fridrich Gregáň 3,  Milan Melicherčík 4,  Ana R Quesada 5,  Juraj Dobiaš 1,  Ján Lác 6,  Marta Sališová 1,  Andrej Boháč 7
Affiliations

Affiliations

  • 1 Comenius University, Faculty of Natural Sciences, Department of Organic Chemistry, Mlynská dolina, 842 15 Bratislava, Slovakia.
  • 2 Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain.
  • 3 Matej Bel University, Faculty of Natural Sciences, Department of Chemistry Tajovského 40, 974 01 Banská Bystrica, Slovakia. Electronic address: fridrich.gregan@umb.sk.
  • 4 Matej Bel University, Faculty of Natural Sciences, Department of Chemistry Tajovského 40, 974 01 Banská Bystrica, Slovakia. Electronic address: milan.melichercik@umb.sk.
  • 5 Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain. Electronic address: quesada@uma.es.
  • 6 Biomagi, Inc., Mamateyova 26, 851 04 Bratislava, Slovakia.
  • 7 Comenius University, Faculty of Natural Sciences, Department of Organic Chemistry, Mlynská dolina, 842 15 Bratislava, Slovakia; Biomagi, Inc., Mamateyova 26, 851 04 Bratislava, Slovakia. Electronic address: andrej.bohac@fns.uniba.sk.
PMID: 24368209 DOI: 10.1016/j.ejmech.2013.11.023
Abstract

VEGFR2/KDR/Flk-1 is an important mediator of angiogenesis and influences fate of some Cancer Stem Cells. Here we analysed all 34 structures of VEGFR2/KDR/Flk-1 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/KDR/Flk-1 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/KDR/Flk-1 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.

Keywords

Angiogenesis sorafenib Nexavar sunitinib Sutent oxazole; Flexible tyrosine kinase activation loop; HTPMEGBLXVAKBQ-UHFFFAOYSA-N; JQHYGGAREUQSFO-UHFFFAOYSA-N; Medicinal chemistry consequences; NACPZCJMBBHZEB-UHFFFAOYSA-N; Properties of VEGFR-2 tyrosine kinase variants; SELRMMCYEMBVON-UHFFFAOYSA-N; SPZMRCAVVHLMHS-UHFFFAOYSA-N; Type I inhibitor DFG-out A-loop/ligand collision.

Figures