Location and Character of Volatile General Anesthetics Binding Sites in the Transmembrane Domain of TRPV1

Abstract

It has been proposed that general anesthesia results from direct multisite interactions with multiple and diverse ion channels in the brain. An understanding of the mechanisms by which general anesthetics modulate ion channels is essential to clarify their underlying behavior and their role in reversible immobilization and amnesia. Despite the fact that volatile general anesthetics are drugs that primarily induce insensitivity to pain, they have been reported to sensitize and active the vanilloid-1 receptor, TRPV1, which is known to mediate the response of the nervous system to certain harmful stimuli and which plays a crucial role in the pain pathway. Currently, the mechanism of action of anesthetics is unknown and the precise molecular sites of interaction have not been identified. Here, using ∼2.5 μs of classical molecular dynamics simulations and metadynamics, we explore these enigmas. Binding sites are identified and the strength of the association is further characterized using alchemical free-energy calculations. Anesthetic binding/unbinding proceeds primarily through a membrane-embedded pathway, and subsequently, a complex scenario is established involving multiple binding sites featuring single or multiple occupancy states of two small volatile drugs. One of the five anesthetic binding sites reported was previously identified experimentally, and another one, importantly, is identical to that of capsaicin, one of the chemical stimuli that activate TRPV1. However, in contrast to capsaicin, isoflurane and chloroform binding free-energies render modest to no association compared to capsaicin, suggesting a different activation mechanism. Uncovering chloroform and isoflurane modulatory sites will further our understanding of the TRPV1 molecular machinery and open the possibility of developing site-specific drugs.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

“…Pain medication Paracetamol [283][284][285] Pain medication, opioid receptors Morphine [132], Fentanyl [132], Fentanyl and its analogues [286], Codeine [287] Local anesthetics Benzocaine [288][289][290], KP-23 [147], Dibucaine [291], Lidocaine [289,292,293], Articaine [289], Tetracaine [294,295], Prilocaine [296], Dyclonine, Butamben [290] General anesthetic Xenon [124,125], Chloroform [292,[297][298][299][300][301], Halothane [146,298,302,303], Isoflurane [297,299,304,305], Phenyl-ethanol [306], Desflurane [305,307], Sevoflurane [305,308], Propofol [305,309,310], Diethyl ether [298,308], Enflurane…”

“…In another flooding simulation study, menthol, a small compound extracted from mint that acts as a local anesthetic, bound to the α4β2 nicotinic acetylcholine receptor, to a binding site located at the lipid-protein interface via a membrane-mediated pathway [434]. In other flooding simulations of two anesthetics, chloroform and isoflurane, the molecules first entered the lipid bilayer and then subsequently diffused to the allosteric binding sites of the vanilloid-1 receptor (TRPV1) [297]. These studies identified five binding sites for chloroform and three for isoflurane, in spite of the fact that the overall affinity of the aforementioned drug molecules toward TRPV1 was relatively small.…”

Heat activation mechanism of TRPV1: New insights from molecular dynamics simulation

“…Hanson et al studied the movement of capsaicin through the lipids, and proposed a possible pathway of capsaicin binding [70]. In other simulation studies, the conformational changes induced by PI(4,5)P 2 binding were investigated [71], and the binding sites of general anesthetics were identified [72]. In addition, Feng et al carried out MD simulations of human TRPV1 bound with agonist/antagonist to probe the ligand-binding-induced conformational changes and validate their homology model of human TRPV1 [73,74].…”

High‐resolution structures of transient receptor potential vanilloid channels: Unveiling a functionally diverse group of ion channels

“…Molecular dynamic studies with 40 different versions of common anesthetics revealed multiple binding sites and predicted interactions that can be used in the screening for new drugs. 62 Additional studies have explored peptide-channel interactions (i.e., the sea anemone's peptide toxin HCRG21) as well as binding capacities of synthetic derivatives of various agonists including N-acyl dopamine, capsaicin, RTX, shogaol, and gingerol. [63][64][65] Moreover, potent new antagonists for TRPV2 were generated by systematically elongating the hydrophobic chain of capsaicin based on the TRPV1 vanilloid binding pocket.…”