title: Characterization of interactions and pharmacophore development for DFG-out inhibitors to RET tyrosine kinase.
abstract: RET (rearranged during transfection) tyrosine kinase is a promising target for several human cancers. Abt-348, Birb-796, Motesanib and Sorafenib are DFG-out multi-kinase inhibitors that have been reported to inhibit RET activity with good IC50 values. Although the DFG-out conformation has attracted great interest in the design of type II inhibitors, the structural requirements for binding to the RET DFG-out conformation remains unclear. Herein, the DFG-out conformation of RET was determined by homology modelling, the four inhibitors were docked, and the binding modes investigated by molecular dynamics simulation. Binding free energies were calculated using the molecular mechanics/Poisson-Bolzmann surface area (MM/PBSA) method. The trends in predicted binding free affinities correlated well with experimental data and were used to explain the activity difference of the studied inhibitors. Per-residue energy decomposition analyses provided further information on specific interaction properties. Finally, we also conducted a detailed e-pharmacophore modelling of the different RET-inhibitor complexes, explaining the common and specific pharmacophore features of the different complexes. The results reported herein will be useful in future rational design of novel DFG-out RET inhibitors.
authors.affiliation: Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden.
authors.forename: Chunxia
authors.initials: C
authors.lastname: Gao
authors.forename: Morten
authors.initials: M
authors.lastname: Grøtli
authors.forename: Leif A
authors.initials: LA
authors.lastname: Eriksson
mesh_terms: D000631:Aminopyridines / Q000737:chemistry*; D001665:Binding Sites; D006801:Humans; D007211:Indoles / Q000737:chemistry*; D007700:Kinetics; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009281:Naphthalenes / Q000737:chemistry*; D009536:Niacinamide / Q000031:analogs & derivatives* / Q000737:chemistry; D009841:Oligonucleotides; D010671:Phenylurea Compounds / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000737:chemistry*; D051096:Proto-Oncogene Proteins c-ret / Q000037:antagonists & inhibitors / Q000737:chemistry*; D011720:Pyrazoles / Q000737:chemistry*; D000077157:Sorafenib; D040681:Structural Homology, Protein; D013816:Thermodynamics; D040301:Vascular Endothelial Growth Factor Receptor-2 / Q000737:chemistry
chemical_list: D000631:Aminopyridines; D007211:Indoles; D009281:Naphthalenes; D009841:Oligonucleotides; D010671:Phenylurea Compounds; D047428:Protein Kinase Inhibitors; D011720:Pyrazoles; D009536:Niacinamide; C577638:ilorasertib; D000077157:Sorafenib; C000588866:KDR protein, human; D051096:Proto-Oncogene Proteins c-ret; C099282:RET protein, human; D040301:Vascular Endothelial Growth Factor Receptor-2; C519562:imetelstat; C452139:doramapimod