Discovery of a potent CDK2 inhibitor with a novel binding mode, using virtual screening and initial, structure-guided lead scoping Christine M. Richardson, * Claire L. Nunns, Douglas S. Williamson, Martin J. Parratt, Pawel Dokurno, Rob Howes, Jenifer Borgognoni, Martin J. Drysdale, Harry Finch, Roderick E. Hubbard, Philip S. Jackson, Peter Kierstan, Georg Lentzen, Jonathan D. Moore, James B. Murray, Heather Simmonite, Allan E. Surgenor and Christopher J. Torrance Vernalis (R&D) Ltd, Granta Park, Cambridge CB21 6GB, UK Received 28 March 2007; revised 30 April 2007; accepted 30 April 2007 Available online 6 May 2007 Abstract—Virtual screening against a pCDK2/cyclin A crystal structure led to the identification of a potent and novel CDK2 inhib- itor, which exhibited an unusual mode of interaction with the kinase binding motif. With the aid of X-ray crystallography and mod- elling, a medicinal chemistry strategy was implemented to probe the interactions seen in the crystal structure and to establish SAR. A fragment-based approach was also considered but a different, more conventional, binding mode was observed. Compound selec- tivity against GSK-3b was improved using a rational design strategy, with crystallographic verification of the CDK2 binding mode. Ó 2007 Elsevier Ltd. All rights reserved. Virtual screening is now recognized as an important tool in the armoury of methods which can be applied to hit identification in the industrial environment. 1–4 One pop- ular approach involves the use of high throughput dock- ing methods to screen catalogues of compound structures, in order to select a subset of molecules for acquisition and assay. A number of successful applica- tions have been reported, including the discovery of li- gands targeting the Chk1 kinase 5 and Hsp90. 6 Whilst virtual screening methods can be applied to homology models, 7–10 they are more typically used in conjunction with experimental structural data, particularly X-ray crystallographic data. The availability of crystal struc- tures greatly aids the virtual screening process and also provides important insights into the kinds of changes in protein conformation, which may be significant in determining both likely hit rates, and also the kinds of ligands which may be identified as hits. 11,12 Kinases comprise one of the most important families of drug targets, accounting for 20–30% of the drug discov- ery programmes of many companies, second only to GPCRs. 13 They are of particular interest in oncology, as a number of them are involved in the regulation of cell growth and survival. In addition, the CDK2 protein is highly amenable to crystallography, with a large num- ber of crystal structures, both of the monomeric form of the protein and the activated pCDK2/cyclin A complex, being available. In common with some earlier studies, 14–16 this report documents the use of the activated, and possibly more physiologically relevant, complex in a protein structure-guided drug discovery strategy. How- ever, it should be noted that where the same ligand has been crystallized with both the monomeric and acti- vated complexes (unpublished data), there is generally good agreement between the observed binding modes in our hands. Differential packing interactions may af- fect some ligands, however, as can be seen in the struc- tures with pdb codes 2C6M and 2C6T. 17,18 CDK2, along with other cyclin dependent kinase (CDK) family homologues, is known to be important in regulat- ing entry into, and progression through, the cell cycle. 0960-894X/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved. doi:10.1016/j.bmcl.2007.04.110 Keywords: Virtual screening; Docking; CDK2; Cyclin dependent kin- ase; X-ray crystallography; Structure-guided drug design; Fragment based. * Corresponding author. Tel.: +44 1223 895434; fax: +44 1223 895556; e-mail: c.richardson@vernalis.com Bioorganic & Medicinal Chemistry Letters 17 (2007) 3880–3885