Cyclin-dependent kinases 5 template: Useful for virtual screening Siripit Pitchuanchom a , Chantana Boonyarat b , Stefano Forli c , Arthur J. Olson c , Chavi Yenjai a,n a Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand b Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand c Department of Molecular Biology, The Scripps Research Institute, CA 92037, USA article info Article history: Received 21 September 2010 Accepted 27 October 2011 Keywords: Cyclin-dependent kinases 5 Docking Virtual screening Active site Drug design Cancer Template abstract The present study reports the development of a template for the active binding site of Cdk5 for structure-based drug design. The developed template of Cdk5 was validated by redocking with ligands I (PBD code 1UNG), II (PBD code 1UNL) and III (PBD code 1UNH). The results demonstrate a good match of the docked and the crystallographic binding orientations with RMSD less than 2.0 ˚ A. The validation results show that the constructed Cdk5 template is a good model system for predicting ligand binding orientations and binding affinities. Furthermore, the developed template was applied to predict binding mode and binding affinity of thirty-six known Cdk5 inhibitors. The results showed that the binding energy of almost Cdk5 inhibitors related to their biological evaluation. & 2011 Elsevier Ltd. All rights reserved. 1. Introduction Cyclin-dependent kinase5 (Cdk5) is a serine/threonine kinase that is expressed in most tissues including proliferating cells [1]. Similar to other Cdks, monomeric Cdk5 shows no enzymatic activity and requires regulatory proteins for activation. The non- cyclin proteins, p35, p39 and p25, a proteolytic fragment of p35, have been identified as Cdk5 activators that are localized to the cell membrane [2]. Although the enzymatic activity of Cdk5 is highest in the central nervous system, where it is critical for neuronal migration and secretion [3], recent reports indicate that it also has important functions in non-neuronal cells. For example, Cdk5 activity promotes glucose-dependent insu- lin secretion in pancreatic beta cells [4] and regulates GTP- dependent secretion from neutrophils [5]. Cdk5 blockade not only inhibited pancreatic cancer migration in vitro and metastases in vivo but also downregulated anchorage-independent growth and primary tumor engraftment in xenograft models, suggesting a more pervasive requirement for sustained Cdk5 signaling on pancreatic tumorigenesis [6]. Until now, little is known about its functional role in cell cycle regulation or in cancer, though recently the expression and activity of Cdk5 has been reported in prostate [2], breast [7], and medullary thyroid carcinoma cells [8]. All these studies collectively indicate that in addition to the role of Cdk5 in central nervous system, it seems to have some extra-neural function(s) particularly in cancer cells. It has been reported that Cdk5 plays a role in the proliferation of prostate, pancreatic cancer, thyroid carcinoma, MCF-7 and MDA MB-231 cells. Therefore, Cdk5 has been implicated as a target of cancer therapy. Cdk5 belongs to a large family of heterodimeric serine/threo- nine protein kinases comprising a catalytic Cdk subunit and an activating subunit. This kinase has 60% homology to human Cdk 2 [9]. The kinases are folded into a typical bilobal conformation. It has an N-terminal domain of approximately 85 residues in a mainly b-sheet structure, a predominantly helix C-terminal domain of about 170 amino acids, and a deep ATP-binding cleft between the two lobes. Studies on binding modes are necessary to understand key structural features and interactions to provide valuable information for the design of efficient inhibitors. To date, a few Cdk5 inhibitors have been reported. Their initial binding is competitive with sub- strate by interacting with the kinase ATP-binding pocket of the Cdk5. Several compound classes have been identified as Cdk5 inhibitors such as the meridianins [10], indirubins [11], flavinols [12], pyrazolo- quinoxalines [13], purines [14], andthiazoles [15], pyrrolo[3,2-b]pyr- azines {s(1)}and 3,4-dihydro-1H-quinazolin-2-ones [16]. Recent studies have been devoted to the binding sites of Cdk5 at the kinase ATP-binding pocket by homology modeling using Cdk2 crystallographic data [17] or the X-ray methods [18,19]. As a result, the ATP-binding domain is the primary target for Cdk5 inhibitors. Recently, X-ray crystal structures of Cdk5 were reported in the Protein Data Bank [18,19]. This finding provides an opportunity for the development of Cdk5 inhibitors. Virtual screening, a recently developed approach to drug design, has been widely used in the process of lead generation. Successful virtual Contents lists available at SciVerse ScienceDirect journal homepage: www.elsevier.com/locate/cbm Computers in Biology and Medicine 0010-4825/$ - see front matter & 2011 Elsevier Ltd. All rights reserved. doi:10.1016/j.compbiomed.2011.10.014 n Corresponding author. Tel.: þ66 43 202222 41x12243; fax: þ66 43 202373. E-mail address: chayen@kku.ac.th (C. Yenjai). Computers in Biology and Medicine 42 (2012) 106–111