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Binding Mode Prediction of Evodiamine within Vanilloid Receptor TRPV1
State Key Laboratory of Trauma, Burns, and Combined Injury, Department 1, Research Institute of Surgery, Daping Hospital, The Third Military Medical University, Chongqing 400042, China
The First Affiliated Hospital, Baotou Medical College, Baotou 014010, China
State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
The Second Affiliated Hospital, Baotou Medical College, Baotou 014010, China
* Authors to whom correspondence should be addressed.
Received: 30 April 2012; in revised form: 18 June 2012 / Accepted: 26 June 2012 / Published: 18 July 2012
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
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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.
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.
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.