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Understanding TRPV1 activation by ligands: Insights from the binding modes of capsaicin and resiniferatoxin

  1. Vincenzo Carnevalea,1
  1. aInstitute for Computational Molecular Science, Temple University, Philadelphia, PA 19122;
  2. bDepartment of Chemistry, Temple University, Philadelphia, PA 19122;
  3. cDepartment of Pharmaceutical Chemistry, Tanta University, 31527 Tanta, Egypt;
  4. dDepartment of Pharmacology, Physiology and Neuroscience, Rutgers–New Jersey Medical School, Newark, NJ 07103

  1. Contributed by Michael L. Klein, December 7, 2015 (sent for review November 6, 2015; reviewed by Kenton J. Swartz and Vladimir Yarov-Yarovoy)

Significance

Using computational methodologies, we refined the binding modes of the transient receptor potential cation channel subfamily V member 1 (TRPV1) modulators, capsaicin and resiniferatoxin, provided by the recent experimental cryo-electron microscopy electron density. The resulting insights enable us to predict the binding pose of 96 additional TRPV1 agonists, which we compare with reported mutagenesis studies. Specifically, we characterize the response of five previously unidentified mutants to capsaicin and resiniferatoxin. Analysis of the amino acids engaged in favorable ligand–channel interactions defines the key structural determinants of the TRPV1 vanilloid binding site.

Abstract

The transient receptor potential cation channel subfamily V member 1 (TRPV1) or vanilloid receptor 1 is a nonselective cation channel that is involved in the detection and transduction of nociceptive stimuli. Inflammation and nerve damage result in the up-regulation of TRPV1 transcription, and, therefore, modulators of TRPV1 channels are potentially useful in the treatment of inflammatory and neuropathic pain. Understanding the binding modes of known ligands would significantly contribute to the success of TRPV1 modulator drug design programs. The recent cryo-electron microscopy structure of TRPV1 only provides a coarse characterization of the location of capsaicin (CAPS) and resiniferatoxin (RTX). Herein, we use the information contained in the experimental electron density maps to accurately determine the binding mode of CAPS and RTX and experimentally validate the computational results by mutagenesis. On the basis of these results, we perform a detailed analysis of TRPV1–ligand interactions, characterizing the protein ligand contacts and the role of individual water molecules. Importantly, our results provide a rational explanation and suggestion of TRPV1 ligand modifications that should improve binding affinity.

Footnotes

  • ↵1To whom correspondence may be addressed. Email: mlklein{at}temple.edu or vincenzo.carnevale{at}temple.edu.

  • Author contributions: K.E., L.D., E.P., M.L.K., T.R., and V.C. designed research; K.E. and P.V. performed research; K.E., P.V., L.D., E.P., T.R., and V.C. analyzed data; and K.E., L.D., E.P., M.L.K., T.R., and V.C. wrote the paper.

  • Reviewers: K.J.S., National Institute of Neurological Disorders and Stroke/National Institutes of Health; and V.Y.-Y., University of California.

  • The authors declare no conflict of interest.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1517288113/-/DCSupplemental.

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