期刊
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
卷 1864, 期 8, 页码 -出版社
ELSEVIER
DOI: 10.1016/j.bbagen.2020.129615
关键词
Adenosine A(1) receptor; Allosteric modulators; Gaussian accelerated molecular dynamics; Ensemble docking; G-protein-coupled receptors
资金
- National Science Foundation, USA [ACI-1548562, TG-MCB180049]
- National Energy Research Scientific Computing Center (NERSC) [M2874, DE-AC02-05CH11231]
- American Heart Association [17SDG33370094]
- National Institutes of Health, USA [R01GM132572]
- College of Liberal Arts and Sciences at the University of Kansas, USA
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 compared with agonists and antagonists, has attracted increasing interest for designing selective drugs of the A(1)AR. Despite significant advances, more effective approaches are needed to discover potent and selective allosteric modulators of the A(1)AR. 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 A(1)AR. 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 A(1)AR. 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.
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