Structural Insight into Tetrameric hTRPV1 from Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Virtual Screening, and Bioassay Validations

Abstract

The transient receptor potential vanilloid type 1 (TRPV1) is a heat-activated cation channel protein, which contributes to inflammation, acute and persistent pain. Antagonists of human TRPV1 (hTRPV1) represent a novel therapeutic approach for the treatment of pain. Developing various antagonists of hTRPV1, however, has been hindered by the unavailability of a 3D structure of hTRPV1. Recently, the 3D structures of rat TRPV1 (rTRPV1) in the presence and absence of ligand have been reported as determined by cryo-EM. rTRPV1 shares 85.7% sequence identity with hTRPV1. In the present work, we constructed and reported the 3D homology tetramer model of hTRPV1 based on the cryo-EM structures of rTRPV1. Molecular dynamics (MD) simulations, energy minimizations, and prescreen were applied to select and validate the best model of hTRPV1. The predicted binding pocket of hTRPV1 consists of two adjacent monomers subunits, which were congruent with the experimental rTRPV1 data and the cyro-EM structures of rTRPV1. The detailed interactions between hTRPV1 and its antagonists or agonists were characterized by molecular docking, which helped us to identify the important residues. Conformational changes of hTRPV1 upon antagonist/agonist binding were also explored by MD simulation. The different movements of compounds led to the different conformational changes of monomers in hTRPV1, indicating that TRPV1 works in a concerted way, resembling some other channel proteins such as aquaporins. We observed that the selective filter was open when hTRPV1 bound with an agonist during MD simulation. For the lower gate of hTRPV1, we observed large similarities between hTRPV1 bound with antagonist and with agonist. A five-point pharmacophore model based on several antagonists was established, and the structural model was used to screen in silico for new antagonists for hTRPV1. By using the 3D TRPV1 structural model above, the pilot in silico screening has begun to yield promising hits with activity as hTRPV1 antagonists, several of which showed substantial potency.

Structural basis of TRPV5 channel inhibition by econazole revealed by cryo-EM

“…9a,c). As also seen in simulations of TRPV1 bound to antagonists or agonists 33 , the four monomers in the TRPV5 tetramer show different dynamic behavior, as evident from comparison of their Cα r.m.s. fluctuations (Supplementary Fig.…”

Multi-Functional Diarylurea Small Molecule Inhibitors of TRPV1 with Therapeutic Potential for Neuroinflammation

“…Briefly, this model was constructed according to the cryo-EM-derived structure [23] of R. norvegicus TRPV1 (rTRPV1)-capsaicin (PDB entry: 3J5R, EM resolution: 4.2 Å). The 3D TRPV1 structural model has been previously validated by our MD simulations and bioassay data [24]. …”

Role of computer-aided drug design in modern drug discovery

“…Initially, they generated a pharmacophore model from known TRPV1 antagonists and used it to filter the NCI database before performing docking experiments against the hTRPV1 homology model. From the docking results, they selected the top-scoring compounds for further experimental testing, yielding novel antagonists for hTRPV1 (Feng et al 2015). In addition to assisting in the selection of potential leads for a given target, computational tools can also provide viable interaction hypotheses for experimentally validated inhibitors of a target disease.…”