Demystifying The Molecular Basis Of Pyrazoloquinolinones Recognition At The Extracellular Alpha 1+/Beta 3-Interface Of The Gaba(A)Receptor By Molecular Modeling

GABA(A)receptors are pentameric ligand-gated ion channels that serve as major inhibitory neurotransmitter receptors in the mammalian brain and the target of numerous clinically relevant drugs interacting with different ligand binding sites. Here, we report an in silico approach to investigate the binding of pyrazoloquinolinones (PQs) that mediate allosteric effects through the extracellular alpha+/beta- interface of GABA(A)receptors. First, we docked a potent prototype of PQs into the alpha 1+/beta 3- site of a homology model of the human alpha 1 beta 3 gamma 2 subtype of the GABA(A)receptor. Next, for each docking pose, we computationally derived protein-ligand complexes for 18 PQ analogs with known experimental potency. Subsequently, binding energy was calculated for all complexes using the molecular mechanics-generalized Born surface area method. Finally, docking poses were quantitatively assessed in the light of experimental data to derive a binding hypothesis. Collectively, the results indicate that PQs at the alpha 1+/beta 3- site likely exhibit a common binding mode that can be characterized by a hydrogen bond interaction with beta 3Q64 and hydrophobic interactions involving residues alpha 1F99, beta 3Y62, beta 3M115, alpha 1Y159, and alpha 1Y209. Importantly, our results are in good agreement with the recently resolved cryo-Electron Microscopy structures of the human alpha 1 beta 3 gamma 2 and alpha 1 beta 2 gamma 2 subtypes of GABA(A)receptors.