Deceased on August 31, 2008.
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Research Article
Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: The role of water molecules examined
Article first published online: 3 DEC 2010
DOI: 10.1002/prot.22890
Copyright © 2010 Wiley-Liss, Inc.
Issue
Proteins: Structure, Function, and Bioinformatics
Volume 79, Issue 3, pages 703–719, March 2011
Additional Information
How to Cite
Hayes, J. M., Skamnaki, V. T., Archontis, G., Lamprakis, C., Sarrou, J., Bischler, N., Skaltsounis, A.-L., Zographos, S. E. and Oikonomakos, N. G. (2011), Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: The role of water molecules examined. Proteins: Structure, Function, and Bioinformatics, 79: 703–719. doi: 10.1002/prot.22890
Publication History
- Issue published online: 1 FEB 2011
- Article first published online: 3 DEC 2010
- Accepted manuscript online: 7 OCT 2010 08:51AM EST
- Manuscript Accepted: 16 SEP 2010
- Manuscript Revised: 15 SEP 2010
- Manuscript Received: 16 JUL 2010
Funded by
- EU Marie Curie Host Fellowship for the Transfer of Knowledge. Grant Number: MTKD-CT-2006-042776
- EU FP7 “SP4-Capacities Coordination and Support Action, Support Actions” EUROSTRUCT Project. Grant Number: CSA-SA_FP7-REGPOT-2008-1 Grant Agreement No. 230146
Keywords:
- type 2 diabetes;
- protein kinase inhibitors;
- induced-fit docking;
- Desmond molecular dynamics;
- receptor flexibility
Abstract
With an aim toward glycogenolysis control in Type 2 diabetes, we have investigated via kinetic experiments and computation the potential of indirubin (IC50 > 50 μM), indirubin-3′-oxime (IC50 = 144 nM), KT5720 (Ki = 18.4 nM) and staurosporine (Ki = 0.37 nM) as phosphorylase kinase (PhKγtrnc) ATP-binding site inhibitors, with the latter two revealed as potent inhibitors in the low nM range. Because of lack of structural information, we have exploited information from homologous kinase complexes to direct in silico calculations (docking, molecular dynamics, and MM-GBSA) to predict the binding characteristics of the four ligands. All inhibitors are predicted to bind in the same active site area as the ATP adenine ring, with binding dominated by hinge region hydrogen bonds to Asp104:O and Met106:O (all four ligands) and also Met106:NH (for the indirubins). The PhKγtrnc-staurosporine complex has the greatest number of receptor-ligand hydrogen bonds, while for the indirubin-3′-oxime and KT5720 complexes there is an important network of interchanging water molecules bridging inhibitor-enzyme contacts. The MM-GBSA results revealed the source of staurosporine's low nM potency to be favorable electrostatic interactions, while KT5720 has strong van der Waals contributions. KT5720 interacts with the greatest number of protein residues either by direct or 1-water bridged hydrogen bond interactions, and the potential for more selective PhK inhibition based on a KT5720 analogue has been established. Including receptor flexibility in Schrödinger induced-fit docking calculations in most cases correctly predicted the binding modes as compared with the molecular dynamics structures; the algorithm was less effective when there were key structural waters bridging receptor-ligand contacts. Proteins 2011. © 2010 Wiley-Liss, Inc.