Membrane‐Facilitated Allosteric Modulation of GABAA Receptor by Farnesol: An In Silico Modeling and Simulation Study
Authors: Jeevan B GC , Szlenk Christopher T. , Gibson K. Michael , Roullet Jean‐Baptiste , Natesan Senthil 
Published: June 2021

Objective

GABAA receptors (GABAARs) are ligand‐gated ion channels that can be activated by γ‐aminobutyric acid (GABA) and allosterically modulated by several antiepileptic drugs and endogenous neurosteroids. Using electrophysiology (patch‐clamp) and HEK cells expressing human α1β3γ2 GABAARs, our team demonstrated positive allosteric receptor modulation (PAM) by farnesol, an endogenous isoprenol. Furthermore, farnesol attenuated seizures in vivo using mouse models of GABAAR‐dependent seizures. Here, we present a computational study that provides a structural basis for the observed farnesol‐mediated allosteric modulation of GABAARs and illustrates the plausible role of membrane in facilitating access and binding of the ligand.

Methods

The membrane partitioning of farnesol were investigated in dimyristoyl phosphatidylcholine model membrane system by steered molecular dynamics (MD) and Umbrella Sampling simulations using NAMD2.12 software. To investigate farnesol's PAM mechanism, we initially constructed a computerized heteropentameric model of the human α1β3γ2 GABAAR in which two GABA molecules were sequentially docked to the extracellular orthosteric sites at the β+α‐interfaces. Subsequently, we used this GABA‐docked model to build two additional models: 1) farnesol docked at the transmembrane lipid‐facing neurosteroid‐binding site, and 2) 10 mol% farnesol molecules placed randomly in the bulk membrane around the receptor. The energetically favorable location and orientation of farnesol within the bilayer suggested the neurosteroid binding site as a potential allosteric site. Each model was subjected to 1 μs all‐atom MD simulations totaling 3 μs.

Results

The mechanism of channel activation by farnesol was characterized by examining dynamic structural variables including global twisting of the channel, tilting of the extracellular domain, and configuration of the ion pore including pore radius, hydration status, and electrostatic potential. We observed the channel pore opening associated with an increased flux of water molecules and pore hydration that supports the conductance (or open state) of GABAAR with farnesol docked to the neurosteroid‐binding site. Remarkably, in the bulk simulation with multiple ligand molecules around the receptor, one of the farnesol molecules reached the neurosteroid binding site via lateral diffusion followed by binding in a configuration identical to the docking simulation. The membrane interactions of farnesol seemed to play an apparent role in its access and binding.

Conclusions

This study provides a structural basis for the positive allosteric modulation of the GABAAR by farnesol in atomistic details consistent with both in vitro and in vivo data. This structural and dynamic model for the PAM of GABAAR may benefit the design of novel therapeutics targeting transmembrane allosteric sites of the GABAAR in both health and disease.

Support or Funding Information

National Institutes of Health – R15GM13129

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.