Structure-Guided Computational Methods Predict Multiple Distinct Binding Modes for Pyrazoloquinolinones in GABAA Receptors

Abstract

Pyrazoloquinolinones (PQs) are a versatile class of GABAA receptor ligands. It has been demonstrated that high functional selectivity for certain receptor subtypes can be obtained by specific substitution patterns, but so far, no clear SAR rules emerge from the studies. As is the case for many GABAA receptor targeting chemotypes, PQs can interact with distinct binding sites on a given receptor pentamer. In pentamers of αβγ composition, such as the most abundant α1β2γ2 subtype, many PQs are high affinity binders of the benzodiazepine binding site at the extracellular α+/γ2− interfaces. There they display a functionally near silent, flumazenil-like allosteric activity. More recently, interactions with extracellular α+/β− interfaces have been investigated, where strong positive modulation can be steered toward interesting subtype preferences. The most prominent examples are functionally α6-selective PQs. Similar to benzodiazepines, PQs also seem to interact with sites in the transmembrane domain, mainly the sites used by etomidate and barbiturates. This promiscuity leads to potential contributions from multiple sites to net modulation. Developing ligands that interact exclusively with the extracellular α+/β− interfaces would be desired. Correlating functional profiles with binding sites usage is hampered by scarce and heterogeneous experimental data, as shown in our meta-analysis of aggregated published data. In the absence of experimental structures, bound states can be predicted with pharmacophore matching methods and with computational docking. We thus performed pharmacophore matching studies for the unwanted sites, and computational docking for the extracellular α1,6+/β3− interfaces. The results suggest that PQs interact with their binding sites with diverse binding modes. As such, rational design of improved ligands needs to take a complex structure-activity landscape with branches between sub-series of derivatives into account. We present a workflow, which is suitable to identify and explore potential branching points on the structure-activity landscape of any small molecule chemotype.

GABAA Receptor Modulators with a Pyrazolo[1,5-a]quinazoline Core: Synthesis, Molecular Modelling Studies and Electrophysiological Assays

“…However, other combinations of GABA A R containing different isoforms are distributed in the CNS and even located extrasynaptically (GABA A receptors with α4, α6 and δ subunits) [ 1 ]. The neurotransmitter binds the two orthosteric sites at the interface of the α−/β+ subunits, while the benzodiazepine binding site is between α-/γ+ subunits; moreover, recently, the presence of another ‘benzodiazepine binding site’ at the α+/β− interface (the so-called low-affinity diazepam binding site) [ 2 ] has been confirmed [ 3 ] and defined as the “pyrazoloquinolinones binding site” [ 4 ].…”

Investigation of 1, 3, 4 Oxadiazole Derivative in PTZ-Induced Neurodegeneration: A Simulation and Molecular Approach

“…GABA with PDB-ID: 6D6T is also used in previous research in computational studies by many researchers. 33 Based on literature study and evidences about GABA for its involvement in seizures we also select it in our study. In…”

What has scripting ever done for us? The CSD Python application programming interface (API)

“…In another example, a workflow for writing a docking protocol to target GABA-A receptors has been developed (Fabjan et al, 2021). One benefit of using a script for such endeavours is that it naturally leads to a degree of repeatability if the workflow code is published along with the input configuration files.…”