Molecular modeling studies to characterize N-phenylpyrimidin-2-amine selectivity for CDK2 and CDK4 through 3D-QSAR and molecular dynamics simulations.
@article{Chohan2016MolecularMS,
title={Molecular modeling studies to characterize N-phenylpyrimidin-2-amine selectivity for CDK2 and CDK4 through 3D-QSAR and molecular dynamics simulations.},
author={Tahir A. Chohan and Jiong-jiong Chen and Haiyan Qian and Youlu Pan and Jian-zhong Chen},
journal={Molecular bioSystems},
year={2016},
volume={12 4},
pages={
1250-68
}
}CDK2 is a promising target for the development of anti-cancer agents. It is not an easy task to design CDK2-selective inhibitors which do not exhibit activity for other CDK family members, particularly CDK4, due to a high degree of structural homology among CDK family members. In this study, 4-substituted N-phenylpyrimidin-2-amine derivatives as CDK2 inhibitors were examined to understand the selectivity mechanism against CDK4 using a combined approach of 3D-QSAR, molecular docking, MESP, MD…
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References
SHOWING 1-10 OF 48 REFERENCES
3D-QSAR CoMFA study on indenopyrazole derivatives as cyclin dependent kinase 4 (CDK4) and cyclin dependent kinase 2 (CDK2) inhibitors.
- Biology, ChemistryEuropean journal of medicinal chemistry
- 2006
Insights into the Structural Basis of N2 and O6 Substituted Guanine Derivatives as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors: Prediction of the Binding Modes and Potency of the inhibitors by Docking and ONIOM Calculations
- Chemistry, BiologyJ. Chem. Inf. Model.
- 2009
A good correlation model is obtained between the ONIOM derived quantum chemical descriptor "H-bond interaction energy" and the experimental biological activity, with a correlation coefficient value of R = 0.80 for 75 compounds, which suggests that electrostatic interactions are the principal driving force in this protein-ligand interaction.
Exploring the selectivity of PI3Kα and mTOR inhibitors by 3D-QSAR, molecular dynamics simulations and MM/GBSA binding free energy decomposition
- Chemistry, Biology
- 2013
3D-QSAR CoMFA models on 72 selective inhibitors were established and those residues which can introduce ligand selectivity were discovered and further validated, and the results reveal that the electrostatic field in the hinge region, the steric field and electrostaticField in the solvent accessible region and the affinity subpocket have critical impacts on selectivity.
Molecular Dynamics Simulation, Free Energy Calculation and Structure-Based 3D-QSAR Studies of B-RAF Kinase Inhibitors
- Chemistry, BiologyJ. Chem. Inf. Model.
- 2011
A molecular modeling study combining QM-polarized ligand docking, molecular dynamics, free energy calculation, and three-dimensional quantitative structure-activity relationships (3D-QSAR) was performed to understand the binding mode between the inhibitors and (V600E)B-RAF kinase and the structural requirement for the inhibiting activity.
Computational Study of the Interactions between Guanine Derivatives and Cyclin-Dependent Kinase 2 (CDK2) by CoMFA and QM/MM
- Chemistry, BiologyJ. Chem. Inf. Model.
- 2010
Comparative molecular field analysis (CoMFA) and QM/MM hybrid calculations were performed on 9H-purine derivatives as CDK2 inhibitors, finding the best CoMFA model included steric and electrostatic fields, had a good Q(2) value of 0.845, and adequately predicted the compounds contained in the test set.
Structural determinants of CDK4 inhibition and design of selective ATP competitive inhibitors.
- Biology, ChemistryChemistry & biology
- 2004
2-Anilino-4-(thiazol-5-yl)pyrimidine CDK inhibitors: synthesis, SAR analysis, X-ray crystallography, and biological activity.
- Chemistry, BiologyJournal of medicinal chemistry
- 2004
Results are reported that show, using the most potent CDK2 inhibitor compound from the current series, that the observed antiproliferative and proapoptotic effects are consistent with cellularCDK2 and CDK9 inhibition.
An efficient tool for identifying inhibitors based on 3D-QSAR and docking using feature-shape pharmacophore of biologically active conformation--a case study with CDK2/cyclinA.
- Biology, ChemistryEuropean journal of medicinal chemistry
- 2008
Development of in silico models for pyrazoles and pyrimidine derivatives as cyclin-dependent kinase 2 inhibitors.
- Chemistry, BiologyJournal of molecular graphics & modelling
- 2011
Characterization of molecular recognition of Phosphoinositide-3-kinase α inhibitor through molecular dynamics simulation
- Chemistry, BiologyJournal of Molecular Modeling
- 2011
The predicted binding mode of PIK75 for PI3Kα presented in this study may help design high affinity and selective compounds to target PI3kα.