Structural Modeling of TRPA1 Ion Channel—Determination of the Binding Site for Antagonists

Abstract

TRPA1 is a transmembrane cation channel, one of the most promising targets in the context of respiratory diseases. Its general structure has already been experimentally resolved, but the binding site of TRPA1 antagonists such as HC-030031, a model methylxanthine derivative, remains unknown. The present study aimed to determine the potential binding site of xanthine antagonists and to describe their binding mode, using a molecular modeling approach. This study represents the first attempt to bring together site-directed mutagenesis reports and the latest cryo-EM structure of an antagonist bound to TRPA1. Our research suggests that the core moiety of HC-030031 binds to a pocket formed by the TRP-like domain and the pre-S1, S4, S5 helices of one subunit. The structure, determined by cryo-EM, shows interactions of a core hypoxanthine moiety in the same area of the binding site, sharing the interaction of xanthine/hypoxanthine with Trp-711. Moreover, the predicted binding mode of HC-030031 assumes interaction with Asn-855, a residue demonstrated to be important for HC-030031 recognition in site-directed mutagenesis studies. Our model proved to be advantageous in a retrospective virtual screening benchmark; therefore, it will be useful in research on new TRPA1 antagonists among xanthine derivatives and their bioisosteres.

TRPA1 Inhibition Effects by 3-Phenylcoumarin Derivatives

“…We observed a new putative binding site of phenylcoumarins located in TRPA1's ankyrin repeat domain. This ARD binding site has also been reported by Gawalska et al 17 ARD consists of a short, typically 33 amino acid long residue and it forms an antiparallel helix-turn-helix structure followed by a β-hairpin loop. 11 It has shown that ankyrin domain can have interactions with small molecules leading to the activation of the ion channel.…”

Visual analysis of global research on the transient receptor potential ankyrin 1 channel: A literature review from 2002 to 2022

“…Allyl isothiocyanate [ 110 ], 15-deoxy-delta(12,14)-prostaglandin J(2) [ 77 ], and other electrophilic agonists activate TRPA1 by covalently modifying cysteine residues [ 111 ]. Three of these cysteine residues, C621, C641, and C665, are critical for the activation of electrophilic stimuli [ 112 ], which are all located in the region containing the ankyrin repeats, linker, and pre-S1-helix [ 11 ]. It has been found that C621 is located in the first helix-turn-helix, C641 is in the first strand of the putative β-sheet, and C665 is in the flexible loop connecting the β-strands to the second helix-turn-helix, further clarifying the spatial distribution of cysteine residues [ 16 ].…”

“…TRPA1 is mainly involved in the expression of primary sensory neurons and the dorsal root ganglion (DRG) [ 10 ]. As such, TRPA1 has promising research potential in pain-related and respiratory diseases [ 11 ] and is currently being investigated as a therapeutic target because of its anti-oxidant, anti-apoptotic, and anti-inflammatory mechanisms. Emerging disciplines such as chemical optogenetics [ 12 ] and sequence analysis [ 13 ] are now being carried out, further enriching the research field of TRPA1.…”

Application of automated machine learning in the identification of multi‐target‐directed ligands blocking PDE4B, PDE8A, and TRPA1 with potential use in the treatment of asthma and COPD

“…The structural model of the TRPA1 ion channel was previously described, and was characterized in retrospective virtual screening by the following parameters: EF 1 % reached 33, BEDROC 0.785 (α = 20) and AUAC 0.96 [32]. On its basis, a grid file for docking containing hydrogen bond constraint on Asn-855 (a hydrogen bond donor) was prepared.…”

“…ZINC306137810, in the TRPA1 binding pocket, showed hydrogen bonding with Asn-855 as well as a π-π stacking interaction with Trp-711. Both of these amino acids are essential for the inhibitory activity of reference compound HC-030031 [32,38], therefore the potential activity of ZINC306137810 on this ion channel can be assumed. Additionally, the position of the selected MTDL is stabilized by hydrogen bonds with Glu-854 and Arg-1011.…”