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Structural insights into transient receptor potential vanilloid type 1 (TRPV1) from homology modeling, flexible docking, and mutational studies

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Abstract

The transient receptor potential vanilloid subtype 1 (TRPV1) is a non-selective cation channel composed of four monomers with six transmembrane helices (TM1–TM6). TRPV1 is found in the central and peripheral nervous system, and it is an important therapeutic target for pain relief. We describe here the construction of a tetrameric homology model of rat TRPV1 (rTRPV1). We experimentally evaluated by mutational analysis the contribution of residues of rTRPV1 contributing to ligand binding by the prototypical TRPV1 agonists, capsaicin and resiniferatoxin (RTX). We then performed docking analysis using our homology model. The docking results with capsaicin and RTX showed that our homology model was reliable, affording good agreement with our mutation data. Additionally, the binding mode of a simplified RTX (sRTX) ligand as predicted by the modeling agreed well with those of capsaicin and RTX, accounting for the high binding affinity of the sRTX ligand for TRPV1. Through the homology modeling, docking and mutational studies, we obtained important insights into the ligand-receptor interactions at the molecular level which should prove of value in the design of novel TRPV1 ligands.

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Notes

  1. The mutation studies by us and other groups have identified the important residues for the binding of small-molecule agonists including capsaicin and RTX. When we docked the agonists to the monomer model, the results did not match with the mutation data. However, when they were docked into the multimer, they turned out to be bound between the two adjacent monomers and these results were in good agreement with the mutation data. In our tetramer model, the key residues for agonists’ binding locate in TM3/TM4 region, and they are in contact with the neighboring monomer’s TM5, which happens to be part of the pore domain. It could also support the agonistic effect of the ligands.

  2. Our final model worked well to explain the structure–activity relationship of our ligands. Also, our template structure (2R9R.pdb) was released after their tetramer paper, and ours has higher resolution than theirs (2A79.pdb). Moreover, it has the full sequence but theirs has polyalanine residues for TM1 and TM3, which is part of our ligands’ binding site. Considering all these facts and results, we think that our model is unique and more suitable for our research.

  3. The thiourea group in the B-region has planar and rigid conformation, and it restricts the rotation and flexibility of the C-region. Since the higher flexibility would reduce the probability of the active conformation for binding, the rigid thiourea group would be a more energetically favorable linker as long as it fits into the binding site, and it contributed to properly position the C-region to maximize its binding.

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Acknowledgments

This research was supported by Grants R01-2007-000-20052-0 from the Ministry of Education, Science and Technology (MEST) and National Research Foundation of Korea (NRF) (to J. Lee and S. Choi), the National Core Research Center (NCRC) program (R15-2006-020) of MEST and NRF through the Center for Cell Signaling & Drug Discovery Research at Ewha Womans University (to S. Choi), and the Intramural Research Program of the National Institutes of Health, Center for Cancer Research, National Cancer Institute (to P. M. Blumberg).

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Authors and Affiliations

  1. College of Pharmacy, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul, 120-750, Korea

    Jin Hee Lee, Yoonji Lee & Sun Choi

  2. National Core Research Center for Cell Signaling and Drug Discovery Research, Ewha Womans University, Seoul, 120-750, Korea

    Jin Hee Lee, Yoonji Lee & Sun Choi

  3. Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Shinlim-Dong, Kwanak-Ku, Seoul, 151-742, Korea

    HyungChul Ryu, Dong Wook Kang & Jeewoo Lee

  4. Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MA, 20892, USA

    Jozsef Lazar, Larry V. Pearce, Vladimir A. Pavlyukovets & Peter M. Blumberg

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  1. Jin Hee Lee
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  2. Yoonji Lee
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Correspondence to Sun Choi.

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Lee, J.H., Lee, Y., Ryu, H. et al. Structural insights into transient receptor potential vanilloid type 1 (TRPV1) from homology modeling, flexible docking, and mutational studies. J Comput Aided Mol Des 25, 317–327 (2011). https://doi.org/10.1007/s10822-011-9421-5

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