Journal of Molecular Graphics and Modelling 29 (2010) 309–320 Contents lists available at ScienceDirect Journal of Molecular Graphics and Modelling journal homepage: www.elsevier.com/locate/JMGM DFG-in and DFG-out homology models of TrkB kinase receptor: Induced-fit and ensemble docking ˇ Crtomir Podlipnik a,b,∗ , Federico Tutino b , Anna Bernardi c , Pierfausto Seneci b,c a University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aˇ skerˇ ceva 5, 1000 Ljubljana, Slovenia b Universitá degli Studi di Milano, Center for Biomolecular Interdisciplinary Studies and Industrial Applications (CISI), Via Fantoli 16/15, 20138 Milano, Italy c Universitá degli Studi di Milano, Dipartimento di Chimica Organica e Industriale, via Venezian 21, 20133 Milano, Italy article info Article history: Received 1 June 2010 Received in revised form 14 September 2010 Accepted 16 September 2010 Available online 7 October 2010 Keywords: Kinase inhibitors DFG-in and DFG-out TrkB abstract Kinases from the Trk family are important for the regulation of development and for the correct func- tioning of the neural system. Deregulation (over-expression) of Trks leads to survival and proliferation of different human cancers. Therefore, development of inhibitors for Trks that can disrupt the signal path- way of Trks could lead to cure against cancer as well as to nociception. Homology models built by YASARA have been used as targets for docking various libraries of known Trk inhibitors. The receptor plasticity was compensated with induced fit docking and/or ensemble docking. It was determined that DFG-in and DFG-out conformational states of TrkB kinase must be taken into account in order to get more reason- able relationships between the docking score and the activity measured by pIC 50 for the corresponding ligands. © 2010 Elsevier Inc. All rights reserved. 1. Introduction Trk (tropomyosin related kinase) receptors are transmembrane proteins belonging to the family of receptor tyrosine kinases (RTKs). Trk receptors exist in three different homologous isoforms: TrkA, TrkB and TrkC. Different growth factors called neurotrophines (NT) are required for the activation of each of those three Trk receptors: namely, TrkA is activated by nerve growth factor (NGF), TrkB is pref- erentially activated by brain derived neurotrophic factor (BDNF) and neurotrophin NT-4/5, and TrkC is normally activated by neu- rotrophin NT-3. The structure of each Trk receptor is divided into three regions: an extracellular domain (NT ligand binding), a trans- membrane region, and an intracellular kinase domain. The binding of neurotrophic factor to the extracellular domain of Trks causes their autophosphorylation, and consequently triggers downstream signal transduction pathways. An example of such transduction pathway is coupling Trk/BDNF with translational control in den- drites as shown in Fig. 1 [1]. Trks are important for maintenance and survival of neuronal tissue cells during their development in the embryonic phase. There is some reported evidence that Trks are necessary also in the postembryonic phase for the correct func- tioning of the nervous system, as well as for nociception [2,3]. Several studies have also indicated association of TrkB receptor ∗ Corresponding author at: University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aˇ skerˇ ceva 5, 1000 Ljubljana, Slovenia. Tel.: +386 1 2419 434. E-mail address: crtomir.podlipnik@fkkt.uni-lj.si ( ˇ C. Podlipnik). with Alzheimer’s disease [4,5]. Numerous studies have reported some connection between over-expression of Trks outside the central neural system and various types of cancer [6]. Normally, Trks are expressed at low levels outside the central neural sys- tem in adults, while pathological over-expression, activation and amplification of Trks are typical for numerous cancers including neuroblastoma [6–9], ovarian [10,11], prostate [12] and colorec- tal cancer [13]. Thus the interest of the pharmaceutical industry for the discovery and the development of selective inhibitors of Trk receptor kinases that might provide targeted treatments for cancer and pain is not surprising. An excellent review on small- molecule inhibitors of Trk receptor was recently written by Wang et al. [14], reporting many inhibitors that possess excellent in vitro potencies and, in some cases, have progressed into clinical tri- als. Up to date no high resolution crystallographic structure of the kinase domain of any Trk family member has been deposited in RCSB Protein Data Bank (PDB) [15]. Therefore, researchers are lim- ited to using homology models or surrogate crystal structures for structure-based design of Trk kinase receptor inhibitors. All kinases have a conserved activation loop, which is important in regulating their activity and is marked by a conserved DFG motif. The activation loop can assume both a conformation that is catalyt- ically competent (DFG-in), and an ‘inactive’ conformation DFG-out in which the activation loop blocks the substrate binding site. Type-I kinase inhibitors recognize the active, DFG-in conformer, but type-II inhibitors recognize the inactive (DFG-out) conforma- tion, hence both conformer are relevant for drug design purposes. 1093-3263/$ – see front matter © 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.jmgm.2010.09.008