Original article Discovery of nanomolar phosphoinositide 3-kinase gamma (PI3Kg) inhibitors using ligand-based modeling and virtual screening followed by in vitro analysis Mutasem O. Taha a, * , Mahmoud A. Al-Sha'er b , Mohammad A. Khanfar a , Afaf H. Al-Nadaf c a Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman, Jordan b Faculty of Pharmacy, Zarqa University, Zarqa 13132, Jordan c Department of Pharmaceutical Chemistry, Applied Science University, Amman, Jordan article info Article history: Received 4 May 2014 Received in revised form 3 July 2014 Accepted 17 July 2014 Available online 18 July 2014 Keywords: Phosphoinositide 3-kinase gamma Ligand based analysis Serine peptidase Anticancer Anti-inflammatory abstract Phosphoinositide 3-kinase gamma (PI3Kg) is member of a family of enzymes involved in cancer path- ogenesis. Accordingly, considerable efforts have been carried out to develop new PI3Kg inhibitors. To- wards this end we explored the pharmacophoric space of PI3Kg using three diverse sets of inhibitors. Subsequently, we employed genetic algorithm-based QSAR analysis to select optimal combination of pharmacophoric models and physicochemical descriptors that can explain bioactivity variation within training inhibitors. Interestingly, two successful pharmacophores were selected within two statistically consistent QSAR models. The close similarity among the two binding models prompted us to merge them in a hybrid pharmacophore. The resulting model showed superior receiver operator characteristic curve (ROC) and closely resembled binding interactions seen in crystallographic ligandePI3Kg complexes. The resulting model was employed to screen the national cancer institute (NCI) list of compounds to search for new PI3Kg ligands. After testing captured hits in vitro, 19 compounds showed nanomolar IC 50 values against PI3Kg. The chemical structures and purities of most potent hits were validated using NMR and MS experiments. © 2014 Elsevier Masson SAS. All rights reserved. 1. Introduction Phosphoinositide 3-kinase gamma (PI3Kg) is member of a family of enzymes involved in cellular functions such as cell growth, proliferation, differentiation, motility, survival and intra- cellular trafficking, which are in turn involved in cancer [1]. PI 3 Ks are a family of related intracellular signal transducer en- zymes capable of phosphorylating the 3-OH group of the inositol ring of phosphatidylinositol [2e4]. They generate the secondary messengers phosphatidylinositol-3,4-bisphosphate and phospha- tidylinositol-3,4,5-trisphosphate, which in turn activate down- stream enzymes in a wide-range of signaling pathways involved in cell growth, survival, differentiation, and motility [5]. Activating mutations in the PI 3 K isoform p110a have recently been identified to be of high frequency in several types of cancer [6], while PTEN, the lipid phosphatase that reverses the phosphorylation reaction, has been identified as one of the most commonly inactivated tumor suppressors in cancer genomes [7]. Moreover, the clinical efficacy of recently approved agents that target the epidermal growth factor receptor in breast [8,9] and lung [10,11] cancers has been demonstrated to correlate with the dependence of those cancers on aberrant PI 3 K signaling and the ability of these agents to suppress that pathway. Accordingly, PI 3 K family of kinases has attracted considerable interest as anticancer drug targets [4]. For these reasons, considerable efforts have been directed to- wards the development of selective inhibitors of these enzymes as potential cancer therapeutics [12]. Most recent discovery efforts converge on the development of new PI3Kg inhibitors via structure-based ligand design [13e15] and high throughput screening [16]. To date, several PI3Kg X-ray complexes are docu- mented in the Protein Data Bank with good resolution, e.g., PDB codes: 2WWE, 3APC, 3APD, 3QJZ, 3QK0, 4ANV, 4ANW and 4KZC. However, the reliance of structure-based design methodologies (e.g., docking) on crystallographic structures have limitations related to inadequate resolution [17] and crystallization-related artifacts of the ligandeprotein complex [18e20]. Moreover, * Corresponding author. E-mail address: mutasem@ju.edu.jo (M.O. Taha). Contents lists available at ScienceDirect European Journal of Medicinal Chemistry journal homepage: http://www.elsevier.com/locate/ejmech http://dx.doi.org/10.1016/j.ejmech.2014.07.056 0223-5234/© 2014 Elsevier Masson SAS. All rights reserved. European Journal of Medicinal Chemistry 84 (2014) 454e465