Induced-fit docking studies of the active and inactive states of protein tyrosine kinases Haizhen Zhong *, Ly M. Tran, Jenna L. Stang Department of Chemistry, The University of Nebraska at Omaha, DSC362, 6001 Dodge Street, Omaha, NE 68182, USA 1. Introduction Uncontrolled proliferation of tumor cells is a hallmark of cancer. Tyrosine kinase activity is tightly regulated under normal physiological conditions. Dysregulation of tyrosine kinase activity in cancer patients results in enhanced proliferation of cancer cells. Tyrosine kinases can be classified into two classes: receptor tyrosine kinases and nonreceptor tyrosine kinases. The epidermal growth factor receptor (EGFR) is the receptor tyrosine kinase and is a validated target for the therapy of non-small-cell lung cancer (NSCLC) and the gastrointestinal stromal tumor (GIST). Binding of the endogenous epidermal growth factor (EGF) to EGFR in cancer cells leads to a cascade of signal transduction events, triggering cell proliferation and differentiation. Family members of human EGFR and its homologs are frequently overexpressed in many solid tumors [1]. Therefore, extensive research has been focused on the inhibition of EGFR for anticancer drug design. One working strategy for EGFR-targeted anticancer drug design is to inhibit the intracellular tyrosine kinase domain of the receptor by a small molecule. Gefitinib (Iressa 1 , Fig. 1, 1) and erlotinib (Tarceca 1 , Fig. 1, 2) are small molecule tyrosine kinase inhibitors (TKIs) that inhibit the EGFR for the treatment of NSCLC. Gefitinib was the first commercially available EGFR tyrosine kinase inhibitor for the treatment of the NSCLC. However, gefitinib was removed from the market in the US and the European Union due to the failure of prolonging survival in patients with advanced NSCLC in the Iressa Survival Evaluation in Lung Cancer (ISEL) study [2]. Erlotinib, on the other hand, showed a survival benefit for advanced NSCLC patients even in subsets in which gefitinib was inactive [3]. The mechanism of sensitivity between EGFR/erlotinib and EGFR/ gefitinib is yet to be known. The ABL (Abelson leukemia virus) protein kinase belongs to the nonreceptor tyrosine kinases. The chronic myelogenous leukemia (CML) is associated with the BCR (breakpoint cluster region)-ABL gene rearrangement (the BCR-ABL protein, short as ABL hereafter) [4]. Imatinib (Gleevec 1 , Fig. 1, 3) was initially developed to treat the chronic myelogenous leukemia [5]. Imatinib binds to the ABL kinase domain and induces complete remission in most CML patients in the early stage of the disease. However, resistance to imatinib becomes an increasing problem. To date, more than seventeen mutations have been observed within the ABL kinase domain. Imatinib was shown to inhibit the epidermal growth factor receptor (EGFR) as well [6]. Therefore, imatinib is also prescribed for the treatment of the gastrointestinal stromal tumor Journal of Molecular Graphics and Modelling 28 (2009) 336–346 ARTICLE INFO Article history: Received 25 February 2009 Received in revised form 21 August 2009 Accepted 25 August 2009 Available online 31 August 2009 Keywords: Protein kinase Imatinib Erlotinib Inhibitor design Loop movement ABSTRACT Inhibition of tyrosine kinases (such as the epidermal growth factor receptor, EGFR, and/or Abelson leukemia virus protein kinase, ABL) represents a major advancement in the treatment of solid tumors, supported by the clinical administration of gefitinib, erlotinib, imatinib, and dasatinib. The identification of the binding interactions in the EGFR/ligands and the ABL/ligands complexes can facilitate the structure-based design of new tyrosine kinase inhibitors. We carried out induced-fit docking studies of 18 structurally diverse kinase inhibitors against the EGFR, the active and inactive states of the ABL protein. Our docking data show that the induced-fit docking (IFD) protocol can successfully reproduce the native poses of ligands from different sources. The binding interactions and the docked poses are consistent with the available experimental data. Our results indicate that imatinib is a weak binder to the active state of ABL but a strong binder to EGFR. The increased sensitivity of erlotinib to EGFR might be attributed to Cys797 of EGFR. In addition to Cys797, other important residues for kinase inhibitor design include Thr790, Met793, Lys745 and Asp855 of EGFR; and Thr315, Met318, Asp381 and Glu286 of the ABL. The minimum number of H-bonds required for the ligand binding provides a reasonable explanation to the effectiveness of nilotinib against most imatinib resistant mutants. ß 2009 Elsevier Inc. All rights reserved. * Corresponding author. Tel.: +1 402 554 3145; fax: +1 402 554 3888. E-mail address: hzhong@mail.unomaha.edu (H. Zhong). Contents lists available at ScienceDirect Journal of Molecular Graphics and Modelling journal homepage: www.elsevier.com/locate/JMGM 1093-3263/$ – see front matter ß 2009 Elsevier Inc. All rights reserved. doi:10.1016/j.jmgm.2009.08.012