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Theoretical studies on the selectivity mechanisms of PI3Kδ inhibition with marketed idelalisib and its derivatives by 3D-QSAR, molecular docking, and molecular dynamics simulation

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Abstract

Phosphoinositide 3-kinases (PI3Ks) are crucial for cell proliferation, metabolism, motility, and cancer progression. Since the selective PI3Kδ inhibitor, idelalisib, was firstly approved by the FDA in 2014, large numbers of selective PI3Kδ inhibitors have been reported, but the detailed mechanisms of selective inhibition to PI3Kδ for idelalisib or its derivatives have not been well addressed. In this study, 3D-QSAR with COMFA, molecular docking, and molecular dynamic (MD) simulations was used to explore the binding modes between PI3Kδ and idelalisib derivatives. Firstly, a reliable COMFA model (q2 = 0.59, ONC = 8, r2 = 0.966) was built and the contour maps showed that the electrostatic field had more significant contribution to the bioactivities of inhibitors. Secondly, two molecular docking methods including rigid receptor docking (RRD) and induced fit docking (IFD) were employed to predict the docking poses of all the studied inhibitors and revealed the selective binding mechanisms. And then, the results of the MD simulation and the binding free energy decomposition verified that the binding of PI3Kδ/inhibitors was mainly contributed from hydrogen bonding and hydrophobic interactions and some key residues for selective binding were highlighted. Finally, based on the models developed, 14 novel inhibitors were optimized and some showed satisfactory predicted bioactivity. Taken together, the results provided by this study may facilitate the rational design of novel and selective PI3Kδ inhibitors.

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Funding

The study was financially supported by the National Natural Science Foundation of China (No. 21807049, 81803430) and the Fundamental Research Funds for the Central Universities (JUSRP11892).

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  1. Jingyu Zhu and Ke Ke contributed equally to this work.

Authors and Affiliations

  1. School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, Jiangsu, China

    Jingyu Zhu, Ke Ke & Jian Jin

  2. Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China

    Lei Xu

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  1. Jingyu Zhu
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Correspondence to Jingyu Zhu or Jian Jin.

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Zhu, J., Ke, K., Xu, L. et al. Theoretical studies on the selectivity mechanisms of PI3Kδ inhibition with marketed idelalisib and its derivatives by 3D-QSAR, molecular docking, and molecular dynamics simulation. J Mol Model 25, 242 (2019). https://doi.org/10.1007/s00894-019-4129-x

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