Characterization of interactions and pharmacophore development for DFG-out inhibitors to RET tyrosine kinase

  • Chunxia Gao
  • Morten Grøtli
  • Leif A. Eriksson
Original Paper


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.

Graphical Abstract

Left Ribbon representation of DFG-out RET tyrosine kinase structure showing key residues of RET interacting with inhibitors. Right e-Pharmacophore hypothesis for RET-Abt-348 generated from the complex structure


RET DFG-out inhibitors Molecular dynamics simulation MM-PB(GB)SA e-pharmacophore 



L.A.E. gratefully acknowledges financial support from the Swedish Research Council (VR) and the Faculty of Science at the University of Gothenburg. Grants of computing time at the Chalmers computing center C3SE, within the SNIC framework, are gratefully acknowledged.

Supplementary material

894_2015_2708_MOESM1_ESM.docx (702 kb)
ESM 1 (DOCX 702 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Chunxia Gao
    • 1
  • Morten Grøtli
    • 1
  • Leif A. Eriksson
    • 1
  1. 1.Department of Chemistry and Molecular BiologyUniversity of GothenburgGöteborgSweden

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