Prerequisite Binding Modes Determine the Dynamics of Action of Covalent Agonists of Ion Channel TRPA1

Abstract

Transient receptor potential ankyrin 1 (TRPA1) is a transmembrane protein channeling the influx of calcium ions. As a polymodal nocisensor, TRPA1 can be activated by thermal, mechanical stimuli and a wide range of chemically damaging molecules including small volatile environmental toxicants and endogenous algogenic lipids. After activation by such compounds, the ion channel opens up, its central pore widens allowing calcium influx into the cytosol inducing signal transduction pathways. Afterwards, the calcium influx desensitizes irritant evoked responses and results in an inactive state of the ion channel. Recent experimental determination of structures of apo and holo forms of TRPA1 opened the way towards the design of new agonists, which can activate the ion channel. The present study is aimed at the elucidation of binding dynamics of agonists using experimental structures of TRPA1-agonist complexes at the atomic level applying molecular docking and dynamics methods accounting for covalent and non-covalent interactions. Following a test of docking methods focused on the final, holo structures, prerequisite binding modes were detected involving the apo forms. It was shown how reversible interactions with prerequisite binding sites contribute to structural changes of TRPA1 leading to covalent bonding of agonists. The proposed dynamics of action allowed a mechanism-based forecast of new, druggable binding sites of potent agonists.

Elucidation of the binding mode of organic polysulfides on the human TRPA1 receptor

“…This observation is explained by the overlapping A-loop in the binding site that hinders ligand accessibility in the apo structure, but not in the holo structure. As shown in our previous paper (Zhao et al, 2020;Zsidó et al, 2021), the upward motion of the A-loop after the prerequisite binding of the agonist to P666 and F669 is necessary for the accessibility of the actual binding site.…”

Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design

“…While some techniques for determining binding dynamics have been suggested [64], complete drug mechanisms cannot be produced routinely, and a systematic method for detecting prerequisite binding modes (PMs) has been lacking. Based on the static structures from experiments, theoretical methods have provided the missing binding dynamics, and some PMs of drugs have been found [6,10,12,35] that should be considered "footsteps" on a drug's pathway towards its destination on the target. However, the connections between these PMs have hitherto not been uncovered.…”

“…To date, established experimental methods such as X-ray crystallography [1,2] and cryo-electron microscopy [3][4][5] have been used to capture the atomic resolution structure of a drug bound with its target (called the binding mode). However, these techniques usually do not supply the entire binding mechanism or the intermediate interactions required (the prerequisite binding modes, or PMs), which are often difficult to capture experimentally [6]. Detecting intermediates is especially difficult with targets such as myosin 2 that have long binding cavities.…”

“…Recently, molecular dynamics (MD) has emerged as a suitable approach for identifying PMs of specific drugs binding to specific targets [6,[8][9][10][11][12]. MD can generate appropriate samples of target-ligand complex structures, allowing conformational flexibility and explicit solvent effects [13,14].…”

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

“…The NH 2 end contains 16 anchor protein repetitive sequences (AR1-AR16) that are arranged in tandem to form an elongated ARD. Upon activation of TRPA1 by stimulatory compounds, ion channels open and the central pore expands, allowing calcium to flow into the cytosol to induce signal transduction pathways [ 17 ].…”