Membrane‐Facilitated Allosteric Modulation of GABA A Receptor by Farnesol: An In Silico Modeling and Simulation Study

Objective GABA A receptors (GABA A Rs) 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 GABA A Rs, our team demonstrated positive allosteric receptor modulation (PAM) by farnesol, an endogenous isoprenol. Furthermore, farnesol attenuated seizures in vivo using mouse models of GABA A R‐dependent seizures. Here, we present a computational study that provides a structural basis for the observed farnesol‐mediated allosteric modulation of GABA A Rs 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 α 1 β 3 γ 2 GABA A R 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 GABA A R 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 GABA A R by farnesol in atomistic details consistent with both in vitro and in vivo data. This structural and dynamic model for the PAM of GABA A R may benefit the design of novel therapeutics targeting transmembrane allosteric sites of the GABA A R 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 .