Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site

J Comput Aided Mol Des (2009) 23:571582 DOI 10.1007/s10822-009-9286-z

Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site

Ksenia Oguievetskaia Laetitia Martin-Chanas Artem Vorotyntsev Olivia Doppelt-Azeroual Xavier Brotel Stewart A. Adcock Alexandre G. de Brevern Francois Delfaud Fabrice Moriaud

Received: 16 February 2009 / Accepted: 19 May 2009 / Published online: 17 June 2009 Springer Science+Business Media B.V. 2009

Abstract Eg5, a mitotic kinesin exclusively involved in the formation and function of the mitotic spindle has attracted interest as an anticancer drug target. Eg5 is co-crystallized with several inhibitors bound to its allosteric binding pocket. Each of these occupies a pocket formed by loop 5/helix a2 (L5/a2). Recently designed inhibitors additionally occupy a hydrophobic pocket of this site. The goal of the present study was to explore this hydrophobic pocket with our MED-SuMo fragment-based protocol, and thus discover novel chemical structures that might bind as inhibitors. The MED-SuMo software is able to compare and superimpose similar interaction surfaces upon the whole protein data bank (PDB). In a fragment-based protocol, MED-SuMo retrieves MED-Portions that encode protein-fragment binding sites and are derived from cross-mining protein-ligand structures with libraries of small molecules. Furthermore we have excluded intra-family MED-Portions derived from Eg5 ligands that occupy the hydrophobic pocket and predicted new potential ligands by hybridization that would ll simultaneously both pockets. Some of the

latter having original scaffolds and substituents in the hydrophobic pocket are identied in libraries of synthetically accessible molecules by the MED-Search software.

Keywords Fragment-based Drug design PDB

Anti-mitotic Kinesin Allosteric pocket

AbbreviationsSCF Surface Chemical Feature PDB Protein Data BankKSP Kinesin Spindle Protein HYD HydrophobicL5/a2 loop 5/helix a2

AngstrmDu MED-Portion dummy atomROC Receiver Operating Characteristic

Introduction

During metaphase, the mitotic spindle maintains a constant shape and size though their principal constituent, the microtubules are continuously being polymerized, depolymerized and transported towards the two spindle poles [13]. Motor proteins from the kinesin family are involved in the mitotic spindle assembly, as well as an important number of cellular processes such as intracellular vesicles transport, chromosome segregation, cell division and motility in a tight collaboration with proteins of the cyto-skeleton tubulin and actin [4, 5].

Inhibition of the mitotic spindle formation is an interesting target in cancer chemotherapy. Anti-mitotic agents...