Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor

Journal Article · · Biochimica et Biophysica Acta - General Subjects
Not Available
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1693791
Journal Information:
Biochimica et Biophysica Acta - General Subjects, Journal Name: Biochimica et Biophysica Acta - General Subjects Journal Issue: 8 Vol. 1864; ISSN 0304-4165
Publisher:
ElsevierCopyright Statement
Country of Publication:
Netherlands
Language:
English

References (62)

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function journal November 1998
Scalable molecular dynamics with NAMD journal January 2005
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility journal December 2009
G‐Protein‐Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State journal October 2019
GPCR6A Is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea journal April 2018
The calculation of the potential of mean force using computer simulations journal September 1995
VMD: Visual molecular dynamics journal February 1996
Synthesis and biological effects of a new series of 2-amino-3-benzoylthiophenes as allosteric enhancers of A1-adenosine receptor journal September 2000
Structure-based drug design: the discovery of novel nonpeptide orally active inhibitors of human renin journal July 2000
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design journal May 2015
New paradigms in GPCR drug discovery journal December 2015
3- and 6-Substituted 2-amino-4,5,6,7-tetrahydrothieno[2,3-c]pyridines as A1 adenosine receptor allosteric modulators and antagonists journal October 2009
Ensemble-based docking: From hit discovery to metabolism and toxicity predictions journal October 2016
The synthesis and biological evaluation of 2-amino-4,5,6,7,8,9-hexahydrocycloocta[b]thiophenes as allosteric modulators of the A1 adenosine receptor journal June 2011
Ensemble Docking in Drug Discovery journal May 2018
Structure of the Adenosine A1 Receptor Reveals the Basis for Subtype Selectivity journal February 2017
Allosteric modulation of A1-adenosine receptor: a review journal June 2013
TRR469, a potent A1 adenosine receptor allosteric modulator, exhibits anti-nociceptive properties in acute and neuropathic pain models in mice journal June 2014
Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor journal July 2015
Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex journal February 2016
Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation journal July 2015
Gaussian Accelerated Molecular Dynamics in NAMD journal December 2016
Identification and Structure–Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli journal July 2017
Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations are Needed To Reproduce Known Ligand Binding? journal January 2019
Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors journal July 2019
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data journal June 2013
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation journal May 2014
Computational Drug Design Accommodating Receptor Flexibility:  The Relaxed Complex Scheme journal May 2002
Improved Scoring of Ligand−Protein Interactions Using OWFEG Free Energy Grids journal February 2001
2-Amino-3-aroyl-4,5-alkylthiophenes:  Agonist Allosteric Enhancers at Human A 1 Adenosine Receptors journal January 2002
2-Amino-3-benzoylthiophene Allosteric Enhancers of A 1 Adenosine Agonist Binding:  New 3, 4-, and 5-Modifications journal May 2003
Discovery of a Novel Binding Trench in HIV Integrase journal April 2004
Synthesis and Characterization of Novel 2-Amino-3-benzoylthiophene Derivatives as Biased Allosteric Agonists and Modulators of the Adenosine A 1 Receptor journal February 2012
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking journal July 2012
Synthesis and Biological Evaluation of Novel Allosteric Enhancers of the A 1 Adenosine Receptor Based on 2-Amino-3-(4′-Chlorobenzoyl)-4-Substituted-5-Arylethynyl Thiophene journal September 2014
Allosteric Modulators of the Adenosine A 1 Receptor: Synthesis and Pharmacological Evaluation of 4-Substituted 2-Amino-3-benzoylthiophenes journal July 2009
Viracept (Nelfinavir Mesylate, AG1343):  A Potent, Orally Bioavailable Inhibitor of HIV-1 Protease journal November 1997
Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design journal December 1999
Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65 journal November 2015
Computational protein–ligand docking and virtual drug screening with the AutoDock suite journal April 2016
Adenosine receptors as therapeutic targets journal March 2006
G protein-coupled receptors: novel targets for drug discovery in cancer journal December 2010
The druggable genome journal September 2002
Structure of the adenosine-bound human adenosine A1 receptor–Gi complex journal June 2018
Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor journal November 2018
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules journal June 2004
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics journal October 2007
A statistical analysis of the precision of reweighting-based simulations journal July 2008
Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics journal August 2018
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei journal November 2008
Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor journal September 2016
Allosteric interactions at adenosine A 1 and A 3 receptors: new insights into the role of small molecules and receptor dimerization : Allosterism at adenosine A journal February 2014
Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23 journal November 2017
Allosteric modulation of adenosine A1 receptor coupling to G-proteins in brain journal May 2005
Allosteric Adenosine Receptor Modulation Reduces Hypersensitivity Following Peripheral Inflammation by a Central Mechanism journal February 2003
Extracellular Loop 2 of the Adenosine A 1 Receptor Has a Key Role in Orthosteric Ligand Affinity and Agonist Efficacy journal September 2016
Role of the Second Extracellular Loop of the Adenosine A 1 Receptor on Allosteric Modulator Binding, Signaling, and Cooperativity journal September 2016
Allosteric Enhancers of A 1 Adenosine Receptors Increase Receptor-G Protein Coupling and Counteract Guanine Nucleotide Effects on Agonist Binding journal November 2003
AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility journal December 2015
The quinic acid derivative KZ-41 prevents glucose-induced caspase-3 activation in retinal endothelial cells through an IGF-1 receptor dependent mechanism journal August 2017
Flexible receptor docking for drug discovery journal August 2015
Allosteric Enhancers of A1 Adenosine Receptors: State of the Art and New Horizons for Drug Development journal October 2010

Similar Records

On the G protein-coupling selectivity of the native A2B adenosine receptor
Journal Article · Tue May 01 00:00:00 EDT 2018 · Biochemical Pharmacology · OSTI ID:1702085

Selective Photoswitchable Allosteric Agonist of a G Protein-Coupled Receptor
Journal Article · Fri Jun 11 00:00:00 EDT 2021 · Journal of the American Chemical Society · OSTI ID:1816033

Photomodulation of G Protein-Coupled Adenosine Receptors by a Novel Light-Switchable Ligand
Journal Article · Thu Oct 02 00:00:00 EDT 2014 · Bioconjugate Chemistry · OSTI ID:1159759

Related Subjects