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

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.

Access this article

Log in via an institution

Subscribe and save

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

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.

References

  1. Alawi K, Keeble J (2010) The paradoxical role of the transient receptor potential vanilloid 1 receptor in inflammation. Pharmacol Ther 125:181–195
    Article CAS Google Scholar
  2. Szallasi A, Blumberg PM (1999) Vanilloid (Capsaicin) receptors and mechanisms. Pharmacol Rev 51:159–212
    CAS Google Scholar
  3. Wong GY, Gavva NR (2009) Therapeutic potential of vanilloid receptor TRPV1 agonists and antagonists as analgesics: recent advances and setbacks. Brain Res Rev 60:267–277
    Article CAS Google Scholar
  4. Szallasi A, Cortright DN, Blum CA, Eid SR (2007) The vanilloid receptor TRPV1: 10 years from channel cloning to antagonist proof-of-concept. Nat Rev Drug Discov 6:357–372
    Article CAS Google Scholar
  5. Lazar J, Gharat L, Khairathkar-Joshi N, Blumberg PM, Szallasi A (2009) Screening TRPV1 antagonists for the treatment of pain: lessons learned over a decade. Expert Opinion Drug Discov 4:159–180
    Article CAS Google Scholar
  6. Gunthorpe MJ, Chizh BA (2009) Clinical development of TRPV1 antagonists: targeting a pivotal point in the pain pathway. Drug Discov Today 14:56–67
    Article CAS Google Scholar
  7. Appendino G, Szallasi A (1997) Euphorbium: modern research on its active principle, resiniferatoxin, revives an ancient medicine. Life Sci 60:681–696
    Article CAS Google Scholar
  8. Szallasi AB, Blumberg PM (1989) Resiniferatoxin, a phorbol-related diterpene, acts as an ultrapotent analog of capsaicin, the irritant constituent in red pepper. Neuroscience 30:515–520
    Article CAS Google Scholar
  9. Lee J, Kang M, Shin M, Kim JM, Kang SU, Lim JO, Choi HK, Suh YG, Park HG, Oh U, Kim HD, Park YH, Ha HJ, Kim YH, Toth A, Wang Y, Tran R, Pearce LV, Lundberg DJ, Blumberg PM (2003) _N_-(3-acyloxy-2-benzylpropyl)-_N_′-[4-(methylsulfonylamino)benzyl]thiourea analogues: novel potent and high affinity antagonists and partial antagonists of the vanilloid receptor. J Med Chem 46:3116–3126
    Article CAS Google Scholar
  10. Lee J, Kim J, Kim SY, Chun MW, Cho H, Hwang SW, Oh U, Park YH, Marquez VE, Beheshti M, Szabo T, Blumberg PM (2001) _N_-(3-Acyloxy-2-benzylpropyl)-_N_′-(4-hydroxy-3-methoxybenzyl) thiourea derivatives as potent vanilloid receptor agonists and analgesics. Bioorg Med Chem 9:19–32
    Article CAS Google Scholar
  11. Kedei N, Szabo T, Lile JD, Treanor JJ, Olah Z, Iadarola MJ, Blumberg PM (2001) Analysis of the native quaternary structure of vanilloid receptor 1. J Biol Chem 276:28613–28619
    Article CAS Google Scholar
  12. Harteneck C, Plant TD, Schultz G (2000) From worm to man: three subfamilies of TRP channels. Trends Neurosci 23:159–166
    Article CAS Google Scholar
  13. Moiseenkova-Bell VY, Stanciu LA, Serysheva II, Tobe BJ, Wensel TG (2008) Structure of TRPV1 channel revealed by electron cryomicroscopy. Proc Natl Acad Sci USA 105:7451–7455
    Article CAS Google Scholar
  14. Jordt SE, Julius D (2002) Molecular basis for species-specific sensitivity to “hot” chili peppers. Cell 108:421–430
    Article CAS Google Scholar
  15. Gavva NR, Klionsky L, Qu Y, Shi L, Tamir R, Edenson S, Zhang TJ, Viswanadhan VN, Toth A, Pearce LV, Vanderah TW, Porreca F, Blumberg PM, Lile J, Sun Y, Wild K, Louis JC, Treanor JJ (2004) Molecular determinants of vanilloid sensitivity in TRPV1. J Biol Chem 279:20283–20295
    Article CAS Google Scholar
  16. Chou MZ, Mtui T, Gao YD, Kohler M, Middleton RE (2004) Resiniferatoxin binds to the capsaicin receptor (TRPV1) near the extracellular side of the S4 transmembrane domain. Biochemistry 43:2501–2511
    Article CAS Google Scholar
  17. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
    Article CAS Google Scholar
  18. ExPASy Proteomics Server. http://www.expasy.org/tools/
  19. Feig M, Brooks CL III (2004) Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Opin Struct Biol 14:217–224
    Article CAS Google Scholar
  20. SAVES. http://nihserver.mbi.ucla.edu/SAVS/
  21. Brauchi S, Orta G, Mascayano C, Salazar M, Raddatz N, Urbina H, Rosenmann E, Gonzalez-Nilo F, Latorre R (2007) Dissection of the components for PIP2 activation and thermosensation in TRP channels. Proc Natl Acad Sci USA 104:10246–10251
    Article CAS Google Scholar
  22. Accelrys Software Inc (2009) Discovery studio modeling environment, release 2.5. Accelrys Software Inc., San Diego
    Google Scholar
  23. Long SB, Tao X, Campbell EB, MacKinnon R (2007) Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature 450:376–382
    Article CAS Google Scholar
  24. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477–486
    Article CAS Google Scholar
  25. Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511–1519
    Article CAS Google Scholar
  26. Tominaga M, Tominaga T (2005) Structure and function of TRPV1. Pflugers Arch 451:143–150
    Article CAS Google Scholar
  27. Christopher SJ, Walpole RW, Stuart B, Elizabeth AC, Andy D, Iain FJ, Kay JM, Martin NP, Janet W (1993) Analogues of capsaicin with agonist activity as novel analgesic agents; structure-activity studies. 3. The hydrophobic side-chain “C-region”. J Med Chem 36:2381–2389
    Article Google Scholar

Download references

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).

Author information

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

Authors

  1. Jin Hee Lee
    You can also search for this author inPubMed Google Scholar
  2. Yoonji Lee
    You can also search for this author inPubMed Google Scholar
  3. HyungChul Ryu
    You can also search for this author inPubMed Google Scholar
  4. Dong Wook Kang
    You can also search for this author inPubMed Google Scholar
  5. Jeewoo Lee
    You can also search for this author inPubMed Google Scholar
  6. Jozsef Lazar
    You can also search for this author inPubMed Google Scholar
  7. Larry V. Pearce
    You can also search for this author inPubMed Google Scholar
  8. Vladimir A. Pavlyukovets
    You can also search for this author inPubMed Google Scholar
  9. Peter M. Blumberg
    You can also search for this author inPubMed Google Scholar
  10. Sun Choi
    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence toSun Choi.

Electronic supplementary material

Rights and permissions

About this article

Cite this article

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

Download citation

Keywords