Insight into the structural mechanism for PKBα allosteric inhibition by molecular dynamics simulations and free energy calculations

• Published in: Journal of molecular graphics & modelling 2014-03, Vol.48, p.36-46
• Main Authors: Chen, Shi-Feng, Cao, Yang, Han, Shuang, Chen, Jian-Zhong
• Format: Article
• Language: English
• Subjects: Allosteric inhibitor; Allosteric Regulation; Allosteric Site; Binding free energy; Binding mechanism; Catalytic Domain; Heterocyclic Compounds, 3-Ring - chemistry; Humans; Hydrogen Bonding; Molecular Dynamics Simulation; Protein Binding; Protein kinase B/PKB; Protein Kinase Inhibitors - chemistry; Protein Structure, Secondary; Proto-Oncogene Proteins c-akt - chemistry; Pyrimidines - chemistry; Pyrroles - chemistry; Thermodynamics
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2013.12.002

•MDs were done to simulate the binding modes of 3 allosteric inhibitors with PKBα.•The structure requirements were analyzed for allosteric inhibitor binding to PKBα.•The free energy calculations mirrored the allosteric inhibitors’ bioactivities.•The possible structural mechanism of PKBα inhibition was explored theoretically. Protein kinase B (PKB/Akt) is an attractive target for the treatment of tumor. Unlike PKB's ATP-competitive inhibitors, its allosteric inhibitors can maintain PKB's inactive state via its binding in a pocket between PH domain and kinase domain, which specifically inhibit PKB by preventing the phosphorylations of Thr308 and Ser473. In the present studies, MD simulations were performed on three allosteric inhibitors with different inhibitory potencies (IC50) to investigate the interaction modes between the inhibitors and PKBα. MM/GB(PB)SA were further applied to calculate the binding free energies of these inhibitors binding to PKBα. The computed binding free energies were consistent with the ranking of their experimental bioactivities. The key residues of PKBα interacting with the allosteric inhibitor were further discussed by analyzing the different interaction modes of these three inhibitors binding to PKBα and by calculating binding free energy contributions of corresponding residues around the binding pocket. The structural requirements were then summarized for the allosteric inhibitor binding to PKBα. A possible structural mechanism of PKBα inhibition induced by the binding of allosteric inhibitor was formulated. The current studies indicate that there should be an optimum balance between the van der Waals and total electrostatic interactions for further designing of PKBα allosteric inhibitors.