Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor
Biochimica et Biophysica Acta (BBA)-General Subjects, 2020•Elsevier
Background Ensemble docking has proven useful in drug discovery and development. It
increases the hit rate by incorporating receptor flexibility into molecular docking as
demonstrated on important drug targets including G-protein-coupled receptors (GPCRs).
Adenosine A 1 receptor (A 1 AR) is a key GPCR that has been targeted for treating cardiac
ischemia-reperfusion injuries, neuropathic pain and renal diseases. Development of
allosteric modulators, compounds binding to distinct and less conserved GPCR target sites …
increases the hit rate by incorporating receptor flexibility into molecular docking as
demonstrated on important drug targets including G-protein-coupled receptors (GPCRs).
Adenosine A 1 receptor (A 1 AR) is a key GPCR that has been targeted for treating cardiac
ischemia-reperfusion injuries, neuropathic pain and renal diseases. Development of
allosteric modulators, compounds binding to distinct and less conserved GPCR target sites …
Background
Ensemble docking has proven useful in drug discovery and development. It increases the hit rate by incorporating receptor flexibility into molecular docking as demonstrated on important drug targets including G-protein-coupled receptors (GPCRs). Adenosine A1 receptor (A1AR) is a key GPCR that has been targeted for treating cardiac ischemia-reperfusion injuries, neuropathic pain and renal diseases. Development of allosteric modulators, compounds binding to distinct and less conserved GPCR target sites compared with agonists and antagonists, has attracted increasing interest for designing selective drugs of the A1AR. Despite significant advances, more effective approaches are needed to discover potent and selective allosteric modulators of the A1AR.
Methods
Ensemble docking that integrates Gaussian accelerated molecular dynamic (GaMD) simulations and molecular docking using Autodock has been implemented for retrospective docking of known positive allosteric modulators (PAMs) in the A1AR.
Results
Ensemble docking outperforms docking of the receptor cryo-EM structure. The calculated docking enrichment factors (EFs) and the area under the receiver operating characteristic curves (AUC) are significantly increased.
Conclusions
Receptor ensembles generated from GaMD simulations are able to increase the success rate of discovering PAMs of A1AR. It is important to account for receptor flexibility through GaMD simulations and flexible docking.
General significance
Ensemble docking is a promising approach for drug discovery targeting flexible receptors.
Elsevier
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