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Int. J. Mol. Sci. 2012, 13(7), 8958-8969; doi:10.3390/ijms13078958
Article

Binding Mode Prediction of Evodiamine within Vanilloid Receptor TRPV1

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Received: 30 April 2012; in revised form: 18 June 2012 / Accepted: 26 June 2012 / Published: 18 July 2012
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Abstract: Accurate assessment of the potential binding mode of drugs is crucial to computer-aided drug design paradigms. It has been reported that evodiamine acts as an agonist of the vanilloid receptor Transient receptor potential vanilloid-1 (TRPV1). However, the precise interaction between evodiamine and TRPV1 was still not fully understood. In this perspective, the homology models of TRPV1 were generated using the crystal structure of the voltage-dependent shaker family K+ channel as a template. We then performed docking and molecular dynamics simulation to gain a better understanding of the probable binding modes of evodiamine within the TRPV1 binding pocket. There are no significant interspecies differences in evodiamine binding in rat, human and rabbit TRPV1 models. Pharmacophore modeling further provided confidence for the validity of the docking studies. This study is the first to shed light on the structural determinants required for the interaction between TRPV1 and evodiamine, and gives new suggestions for the rational design of novel TRPV1 ligands.
Keywords: transient receptor potential vanilloid type 1; homology modeling; molecular docking; molecular dynamics; capsaicin; evodiamine transient receptor potential vanilloid type 1; homology modeling; molecular docking; molecular dynamics; capsaicin; evodiamine
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Wang, Z.; Sun, L.; Yu, H.; Zhang, Y.; Gong, W.; Jin, H.; Zhang, L.; Liang, H. Binding Mode Prediction of Evodiamine within Vanilloid Receptor TRPV1. Int. J. Mol. Sci. 2012, 13, 8958-8969.

AMA Style

Wang Z, Sun L, Yu H, Zhang Y, Gong W, Jin H, Zhang L, Liang H. Binding Mode Prediction of Evodiamine within Vanilloid Receptor TRPV1. International Journal of Molecular Sciences. 2012; 13(7):8958-8969.

Chicago/Turabian Style

Wang, Zhanli; Sun, Lidan; Yu, Hui; Zhang, Yanhui; Gong, Wuzhuang; Jin, Hongwei; Zhang, Liangren; Liang, Huaping. 2012. "Binding Mode Prediction of Evodiamine within Vanilloid Receptor TRPV1." Int. J. Mol. Sci. 13, no. 7: 8958-8969.



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