BioSystems 138 (2015) 39–52 Contents lists available at ScienceDirect BioSystems jo ur nal home p age: www.elsevier.com/locate/biosystems Pharmacophore modeling, virtual screening, molecular docking studies and density functional theory approaches to identify novel ketohexokinase (KHK) inhibitors Rengarajan Kavitha a , Subramanian Karunagaran b , Subramaniam Subhash Chandrabose c , Keun Woo Lee d , Chandrasekaran Meganathan b,∗ a Sri Ramanujar Engineering College, Kolapakkam, Vandalur 600 048, Tamil Nadu, India b G.K.M College of Engineering and Technology, Alapakkam, Mappedu Road, Perungalathur, 600 063 Chennai, Tamil Nadu, India c Centre for Research and Development, PRIST University, Trichy-Thanjavur Road, Vallam 621 316, Tamil Nadu, India d Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Gazha-dong, Jinju 660-701, Republic of Korea a r t i c l e i n f o Article history: Received 17 January 2015 Received in revised form 7 September 2015 Accepted 25 October 2015 Available online 11 November 2015 Keywords: Ketohexokinase Pharmacophore modeling Virtual screening Molecular docking a b s t r a c t Fructose catabolism starts with phosphorylation of d-fructose to fructose 1-phosphate, which is per- formed by ketohexokinase (KHK). Fructose metabolism may be the key to understand the long-term consumption of fructose in human’s obesity, diabetes and metabolic states in western populations. The inhibition of KHK has medicinally potential roles in fructose metabolism and the metabolic syndrome. To identify the essential chemical features for KHK inhibition, a three-dimensional (3D) chemical-feature- based QSAR pharmacophore model was developed for the first time by using Discovery Studio v2.5 (DS). The best pharmacophore hypothesis (Hypo1) consisting two hydrogen bond donor, two hydrophobic features and has exhibited high correlation co-efficient (0.97), cost difference (76.1) and low RMS (0.66) value. The robustness and predictability of Hypo1 was validated by fisher’s randomization method, test set, and the decoy set. Subsequently, chemical databases like NCI, Chembridge and Maybridge were screened for validated Hypo1. The screened compounds were further analyzed by applying drug-like fil- ters such as Lipinski’s rule of five, ADME properties, and molecular docking studies. Further, the highest occupied molecular orbital, lowest unoccupied molecular orbital and energy gap values were calculated for the hits compounds using density functional theory. Finally, 3 hit compounds were selected based on their good molecular interactions with key amino acids in the KHK active site, GOLD fitness score, and lowest energy gaps. © 2015 Elsevier Ireland Ltd. All rights reserved. 1. Introduction Fructose is a kind of monosaccharide and it is present in honey, fruits and vegetables. Fructose is transported into the liver with the help of GLUT5 and/or GLUT2 transporters. The ketohexokinase (KHK) is the first enzyme in the degradation of fructose and it is Abbreviations: KHK, ketohexokinase; DS, Discovery Studio v2.5; HBA, hydro- gen bond acceptor; HBD, hydrogen bond donor; HY, hydrophobic; RMS, root mean square; EF, enrichment factor; GH, goodness of hit; ADME, absorption, distribution, metabolism, and excretion; BBB, blood–brain barrier; ADT, AutoDock tool; DFT, den- sity functional theory; HOMO, highest occupied molecular orbital; LUMO, lowest unoccupied molecular orbital. ∗ Corresponding author. Tel.: +91 9840774537. E-mail address: megac2005@gmail.com (C. Meganathan). phosphorylated as fructose 1-phosphate by KHK in the liver and in kidney (Arooj et al., 2013; Cirillo et al., 2009). When fructose is phosphorylated by KHK, adenosine triphosphate (ATP) is consumed with the formation of adenosine monophosphate (AMP). The high level of KHK was also found in the renal cortex, small intestine, and pancreas (Kasim-Karakas et al., 1996; Koo et al., 2008). The elevated fructose ingestion promotes various metabolic disturbances in ani- mal models, including weight gain, hyperlipidemia, hypertension, and insulin resistance (Hwang et al., 1987; Kasim-Karakas et al., 1996; Martinez et al., 1994; Reiser and Hallfrisch, 1977; Zavaroni et al., 1980). The consumption of fructose in humans increases energy intake, fat mass, body weight, blood pressure, and plasma triglycerides (Raben et al., 2002; Teff et al., 2004). The metabolism of fructose results in brain exerts an orexi- genic effect. Due to fructose metabolism the level of Malonyl-CoA http://dx.doi.org/10.1016/j.biosystems.2015.10.005 0303-2647/© 2015 Elsevier Ireland Ltd. All rights reserved.