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Molecular dynamic simulations reveal the mechanism of binding between xanthine inhibitors and DPP-4

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Abstract

We apply molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation to investigate and reveal the binding mechanism between five xanthine inhibitors and DPP-4. The electrostatic and van der Waals interactions of the five inhibitors with DPP-4 are analyzed and discussed. The computed binding free energies using MM-PBSA method are in qualitatively agreement with experimental inhibitory potency of five inhibitors. The hydrogen bonds of inhibitors with Ser630 and Asp663 can stabilize the inhibitors in binding sites. The van der Waals interactions, especially the key contacts with His740, Asn710, Trp629, and Tyr666 have larger contributions to the binding free energy and play important roles in distinguishing the variant bioactivity of five inhibitors.

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Acknowledgments

This work is supported by grants from the National Science Foundation of China (Nos. 21276122, 21136001, and 20876073) and State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology of China (No. ZK201212).

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  1. State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing, 210009, China

    Yongliang Gu, Wei Wang, Xiaolei Zhu & Keke Dong

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  1. Yongliang Gu
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  2. Wei Wang
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Correspondence to Xiaolei Zhu.

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Gu, Y., Wang, W., Zhu, X. et al. Molecular dynamic simulations reveal the mechanism of binding between xanthine inhibitors and DPP-4. J Mol Model 20, 2075 (2014). https://doi.org/10.1007/s00894-014-2075-1

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