AMPA Receptor Noncompetitive Inhibitors Occupy a Promiscuous Binding Site

Abstract

Noncompetitive inhibitors of AMPA receptors have attracted interest in recent years as antiepileptic drugs. However, their development is hindered by a lack of detailed understanding of the protein–inhibitor interaction mechanisms. Recently, structures of AMPA receptor complexes with the structurally dissimilar, noncompetitive, small-molecule inhibitors pyridone perampanel (PMP), GYKI 53655 (GYKI), and CP 465022 (CP) were resolved, revealing that all three share a common binding site. However, due to the low resolution of the ligands, their exact binding modes and protein–ligand interactions remain ambiguous and insufficiently detailed. We carried out molecular dynamics (MD) simulations on X-ray-resolved and docked AMPA receptor complexes, including thermodynamic integration (TI) to compute ligand binding constants, in order to investigate the inhibitor binding modes in detail and identify key protein–ligand interaction mechanisms. Our analysis and simulations show that the ligand binding pocket at the interface of the receptor’s transmembrane domain exhibits features also found in the binding pockets of the multidrug-resistance proteins. The inhibitors bind to such promiscuous pockets by forming multiple weak contacts, while the large, flexible pocket undergoes adjustments to accommodate structurally different ligands in different orientations. TI was able to identify a specific more favorable binding mode for GYKI, while PMP, which has a symmetric ring structure, produced several comparable poses indicating that it may bind in several orientations.

Structure, Function, and Pharmacology of Glutamate Receptor Ion Channels

“…Residues that directly interact with the noncompetitive inhibitors are located within the S1-M1 and S2-M4 linkers and the extracellular segments of the M3 and M4 domains (Yelshanskaya et al, 2016b). Molecular dynamic simulations of NAM binding and further mutagenesis of putative interacting residues suggest that the NAM binding pocket in AMPA receptors is flexible enough to allow for interaction of diverse chemical structures that assume distinct poses within the pocket (Narangoda et al, 2019;Stenum-Berg et al, 2019). The mechanism of negative allosteric modulation was envisioned as constraining conformational changes required for channel opening by stabilizing the closed state of the receptor (Balannik et al, 2005;Yelshanskaya et al, 2016b).…”

Structural basis of AMPA receptor inhibition by trans‐4‐butylcyclohexane carboxylic acid

“…The protein model was embedded into a POPC lipid bilayer surrounded by water and ions (Figure 3a). The entire model system was equilibrated using the previously developed protocol (Narangoda, Sakipov, & Kurnikova, 2019). Parameters for 4‐BCCA model molecule were specifically developed for this study.…”

“…The first approved drug treatment for epilepsy based upon AMPA receptor inhibition was perampanel (Fycompa; PMP), a noncompetitive AMPA receptor antagonist that is used as an adjunctive treatment for partial-onset and primary generalised tonic-clonic seizures (Frampton, 2015). The binding site for PMP on AMPA receptors has been well characterised, providing insight to how it inhibits receptor function (Chang et al, 2016;Narangoda, Sakipov & Kurnikova, 2019;Yelshanskaya, Singh, Sampson, Narangoda, Kurnikova & Sobolevsky, 2016;Yuan, Shi, Srinivasan, Ptak, Oswald & Nowak, 2019). However, PMP has dose-dependent behavioural side-effects, limiting its use in some patients (Rugg-Gunn, 2014).…”

α-Lipoic Acid Derivatives as Allosteric Modulators for Targeting AMPA-Type Glutamate Receptors’ Gating Modules

“…Residues in the pre-M1 (Ser 516, Phe 517, Asp 519, Pro 520), M3 (Ser 615, Tyr 616, Leu 620, Phe 623), and M4 (Asn 791) helices of the receptor, as well as one residue in the S2-M4 (Ser 788) linker, are among those targeted. The S2-M4 linker, in particular, demonstrates remarkable adaptability since two neighboring pockets may share it, allowing them to interact with two ligands simultaneously [ 41 , 42 ].…”