Novel Structural Features of CDK Inhibition Revealed by an ab Initio Computational Method Combined with Dynamic Simulations

Heady, L. and Fernández-Serra, M. and Mancera, R. L. and Joyce, S. and Venkitaraman, A. R. and Artacho, E. and Skylaris, C. K. and Ciacchi, L. C. and Payne, M. C. (2006) Novel Structural Features of CDK Inhibition Revealed by an ab Initio Computational Method Combined with Dynamic Simulations. Journal of Medicinal Chemistry, 49. pp. 5141-5153. DOI 10.1021/jm060190+

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Abstract

The rational development of specific inhibitors for the 500 protein kinases encoded in the human genome is impeded by a poor understanding of the structural basis for the activity and selectivity of small molecules that compete for ATP binding. Combining classical dynamic simulations with a novel ab initio computational approach linear-scalable to molecular interactions involving thousands of atoms, we have investigated the binding of five distinct inhibitors to the cyclin-dependent kinase CDK2. We report here that polarization and dynamic hydrogen bonding effects, so far undetected by crystallography, affect both their activity and selectivity. The effects arise from the specific solvation patterns of water molecules in the ATP binding pocket or the intermittent formation of hydrogen bonds during the dynamics of CDK/inhibitor interactions and explain the unexpectedly high potency of certain inhibitors such as 3-(3H-imidazol-4-ylmethylene)-5- methoxy-1,3-dihydro-indol-2-one (SU9516). The Lys89 residue in the ATP-binding pocket of CDK2 is observed to form temporary hydrogen bonds with the three most potent inhibitors. This residue is replaced in CDK4 by Thr89, whose shorter side-chain cannot form similar bonds, explaining the relative selectivity of the inhibitors for CDK2. Our results provide a generally applicable computational method for the analysis of biomolecular structures and reveal hitherto unrecognized features of the interaction between protein kinases and their inhibitors.

Item Type: Article
Uncontrolled Keywords: 2006 AREP 2006 P IA52
Subjects: 03 - Mineral Sciences
Divisions: 03 - Mineral Sciences
Journal or Publication Title: Journal of Medicinal Chemistry
Volume: 49
Page Range: pp. 5141-5153
Identification Number: 10.1021/jm060190+
Depositing User: Sarah Humbert
Date Deposited: 16 Feb 2009 13:02
Last Modified: 23 Jul 2013 10:07
URI: http://eprints.esc.cam.ac.uk/id/eprint/369

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