Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering Daniel Muthas, Yogesh A. Sabnis, Magnus Lundborg, Anders Karle ´n * Department of Medicinal Chemistry, Division of Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden Received 20 June 2007; received in revised form 16 November 2007; accepted 21 November 2007 Available online 18 January 2008 Abstract We have investigated the influence of post-filtering virtual screening results, with pharmacophoric features generated from an X-ray structure, on enrichment rates. This was performed using three docking softwares, zdock+, Surflex and FRED, as virtual screening tools and pharmacophores generated in UNITY from co-crystallized complexes. Sets of known actives along with 9997 pharmaceutically relevant decoy compounds were docked against six chemically diverse protein targets namely CDK2, COX2, ERa, fXa, MMP3, and NA. To try to overcome the inherent limitations of the well-known docking problem, we generated multiple poses for each compound. The compounds were first ranked according to their scores alone and enrichment rates were calculated using only the top scoring pose of each compound. Subsequently, all poses for each compound were passed through the different pharmacophores generated from co-crystallized complexes and the enrichment factors were re-calculated based on the top-scoring passing pose of each compound. Post-filtering with a pharmacophore generated from only one X-ray complex was shown to increase enrichment rates in all investigated targets compared to docking alone. This indicates that this is a general method, which works for diverse targets and different docking softwares. # 2007 Elsevier Inc. All rights reserved. Keywords: Flo+; Surflex; FRED; Enrichment factor; Docking performance; Structure-based virtual screening; Pharmacophore filtering 1. Introduction It is estimated that bringing a drug from idea to market takes approximately 12 years and costs as much as US$ 802 millions [1]. To cope with this high cost, more cost-efficient methods are required and various experimental and theoretical approaches have been developed. Virtual screening (VS) has arisen as an efficient method for rapidly identifying hits in terms of cost and time [2]. When the 3D-structure of the target is known, either by experimental or computational techniques, virtual screening is often performed by using structure-based docking [3]. With the advent of novel algorithms and faster computers it is now possible to screen millions of compounds in a matter of days. Virtual screening methods have been validated for their performance in several different studies (see for example Refs. [4–16]) and although these methods have been successfully used, they have some inherent limitations. The so-called docking problem consists of correctly identifying the binding mode of a compound, i.e. finding the correct conformation and placement within the active site. The success of a docking is often compromised by the fact that the associated scoring functions often cannot resolve the most likely binding mode [17]. This highlights the importance of inspecting multiple conformations for the docked compounds and not only the highest scoring one. However, one can only visually inspect a much smaller number of compounds than the number of compounds usually contained in a screening library [18]. Database searching based on pharmacophore constraints is an alternative VS strategy [19–23]. One advantage of using pharmacophores is that they focus on specific key interactions for protein ligand binding. However, this approach does not perform optimally when used alone since little or no consideration of the shape of the binding site is taken into www.elsevier.com/locate/JMGM Available online at www.sciencedirect.com Journal of Molecular Graphics and Modelling 26 (2008) 1237–1251 * Corresponding author at: Department of Medicinal Chemistry, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden. Tel.: +46 18 471 4293; fax: +46 18 471 4474. E-mail address: anders.karlen@orgfarm.uu.se (A. Karle ´n). 1093-3263/$ – see front matter # 2007 Elsevier Inc. All rights reserved. doi:10.1016/j.jmgm.2007.11.005