AMPA Receptor Noncompetitive Inhibitors Occupy a Promiscuous Binding Site

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.