An evaluation of indirubin analogues as phosphorylase kinase inhibitors.

Abstract

Phosphorylase kinase (PhK) has been linked with a number of conditions such as glycogen storage diseases, psoriasis, type 2 diabetes and more recently, cancer (Camus et al., 2012 [6]). However, with few reported structural studies on PhK inhibitors, this hinders a structure based drug design approach. In this study, the inhibitory potential of 38 indirubin analogues have been investigated. 11 of these ligands had IC50 values in the range 0.170-0.360μM, with indirubin-3'-acetoxime (1c) the most potent. 7-Bromoindirubin-3'-oxime (13b), an antitumor compound which induces caspase-independent cell-death (Ribas et al., 2006 [20]) is revealed as a specific inhibitor of PhK (IC50=1.8μM). Binding assay experiments performed using both PhK-holo and PhK-γtrnc confirmed the inhibitory effects to arise from binding at the kinase domain (γ subunit). High level computations using QM/MM-PBSA binding free energy calculations were in good agreement with experimental binding data, as determined using statistical analysis, and support binding at the ATP-binding site. The value of a QM description for the binding of halogenated ligands exhibiting σ-hole effects is highlighted. A new statistical metric, the 'sum of the modified logarithm of ranks' (SMLR), has been defined which measures performance of a model for both the "early recognition" (ranking earlier/higher) of active compounds and their relative ordering by potency. Through a detailed structure activity relationship analysis considering other kinases (CDK2, CDK5 and GSK-3α/β), 6'(Z) and 7(L) indirubin substitutions have been identified to achieve selective PhK inhibition. The key PhK binding site residues involved can also be targeted using other ligand scaffolds in future work.

• Authors: Jaida Begum, Vassiliki T Skamnaki, Colin Moffatt, Nicolas Bischler, Josephine Sarrou, Alexios-Leandros Skaltsounis, Demetres D Leonidas, Nikos G Oikonomakos, Joseph M Hayes
• Journal: Journal of molecular graphics & modelling (J Mol Graph Model) Vol. 61 Pg. 231-42 (Sep 2015) ISSN: 1873-4243 [Electronic] United States
• PMID: 26364215 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: Copyright © 2015 Elsevier Inc. All rights reserved.

Chemical References

• 7-bromoindirubin-3'-oxime
• Hypoglycemic Agents
• Indoles
• Ligands
• Oximes
• Protein Kinase Inhibitors
• Phosphorylase Kinase
• Cyclin-Dependent Kinase 5
• Glycogen Synthase Kinase 3 beta
• CDK2 protein, human
• CDK5 protein, human
• Cyclin-Dependent Kinase 2
• Glycogen Synthase Kinase 3
• glycogen synthase kinase 3 alpha
• indirubin

Topics

• Amino Acid Motifs
• Binding Sites
• Cyclin-Dependent Kinase 2 (chemistry)
• Cyclin-Dependent Kinase 5 (chemistry)
• Glycogen Synthase Kinase 3 (chemistry)
• Glycogen Synthase Kinase 3 beta
• High-Throughput Screening Assays
• Humans
• Hypoglycemic Agents (chemistry)
• Indoles (chemistry)
• Ligands
• Molecular Docking Simulation
• Molecular Sequence Data
• Oximes (chemistry)
• Phosphorylase Kinase (antagonists & inhibitors, chemistry)
• Protein Binding
• Protein Kinase Inhibitors (chemistry)
• Protein Structure, Secondary
• Protein Structure, Tertiary
• Structure-Activity Relationship
• Thermodynamics
• User-Computer Interface