Induced-fit docking of mometasone furoate and further evidence for glucocorticoid receptor 17a pocket flexibility Hongwu Wang a, *, Robert Aslanian b , Vincent S. Madison a a Department of Structural Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA b Department of Chemical Research, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA 1. Introduction Since Hench’s pioneering research in the 1950s using hydro- cortisone for the treatment of rheumatoid arthritis, glucocorticoid (GC) compounds have become the foundation of management of many inflammatory diseases, including those of the lung and upper respiratory tract such as asthma and allergic rhinitis [1–5]. Older oral GCs such as dexamethasone (Dex) and prednisolone are effective at suppressing inflammation, but produce negative side effects such as hyperglycemia and osteoporosis, particularly with long-term administration [6]. The more recent development of GCs administered by inhalation or intranasal application marked a major advance in the management of upper respiratory inflam- matory diseases by providing local drug delivery with minimal systemic absorption. Pharmaceutical research has continued to search for high-affinity GC compounds with minimal toxicity, and the newest GCs for inhalation/intranasal administration (i.e., mometasone furoate [MF], fluticasone furoate [FF], fluticasone propionate [FP] and ciclesonide) have greatly improved benefit- risk ratio. Glucocorticoid pharmacologic activity is mediated through interaction with the glucocorticoid receptor (GR), a member of the nuclear-receptor family of ligand-activated transcription factors that has been shown to suppress the inflammatory response in the context of asthma [7]. Similar to other members of this family, GR is characterized by three major domains: an N-terminal activation function-1 domain (AF-1), a central DNA-binding domain, and a C- terminal ligand-binding domain (LBD) [8]. An accurate under- standing of the structure of the LBD could have tremendous ramifications for glucocorticoid research and pharmaceutical development, but unfortunately this domain is difficult to express in recombinant form and is not easily purified or crystallized [8,9]. To date, three human GR-LBD structures have been documented in the Protein Data Bank (PDB) [8–10]. These structures reveal that GR has a unique side pocket bounded by helices 3, 6, and 7. This pocket can accommodate large substituents at position C17a of GCs that are characteristic of clinically effective compounds. Experimental evidence shows that the GR binding site is extremely flexible and adaptive in its interactions with GCs. Most modeling of ligand–receptor interactions has been done via docking methods that use rigid receptor structures obtained either from crystallography or homology modeling. Ligands that Journal of Molecular Graphics and Modelling 27 (2008) 512–521 ARTICLE INFO Article history: Received 4 April 2008 Received in revised form 22 August 2008 Accepted 2 September 2008 Available online 10 September 2008 Keywords: Induced-fit docking Ligand–protein interaction Protein flexibility Glucocorticoids Glucocorticoid receptor Mometasone furoate ABSTRACT An induced-fit docking method was used to characterize the interactions of the glucocorticoid receptor binding-site with mometasone furoate, a glucocorticoid with a lipophilic ester at the C17a position. Two validation studies demonstrated that the protocol can reproduce crystal structures of nuclear receptors, and is appropriate for modeling ligand binding to the glucocorticoid receptor. Key hydrogen bonding interactions between mometasone furoate and the glucocorticoid receptor, as well as favorable hydrophobic interactions between the furoate group and the 17a pocket, contribute to high affinity and specificity of this ligand for the receptor. Using the glucocorticoid des-ciclesonide, which has an even larger moiety at the 16,17a position, induced-fit docking demonstrates the ability of the 17a pocket of the receptor to expand even further to accommodate the ligand. ß 2008 Elsevier Inc. All rights reserved. * Corresponding author at: Schering-Plough Research Institute, Mailstop K15-L- 0300, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. Tel.: +1 908 740 2924; fax: +1 908 740 4640. E-mail address: hongwu.wang@spcorp.com (H. Wang). Abbreviations: des-CIC, desisobutyryl-ciclesonide; Dex, dexamethasone; FF, fluti- casone furoate; FP, fluticasone propionate; GC, glucocorticoid; GR, glucocorticoid receptor; IFD, induced-fit docking; LBD, ligand-binding domain; MF, mometasone furoate; PDB, Protein Data Bank; PR, progesterone receptor; RBA, relative binding affinity; RMSD, root-mean-square deviation; vdW, van der Waals. Contents lists available at ScienceDirect Journal of Molecular Graphics and Modelling journal homepage: www.elsevier.com/locate/JMGM 1093-3263/$ – see front matter ß 2008 Elsevier Inc. All rights reserved. doi:10.1016/j.jmgm.2008.09.002