Τίτλος:
Insights to the Binding of a Selective Adenosine A3 Receptor Antagonist Using Molecular Dynamic Simulations, MM-PBSA and MM-GBSA Free Energy Calculations, and Mutagenesis
Γλώσσες Τεκμηρίου:
Αγγλικά
Περίληψη:
Adenosine A3 receptor (A3R) is a promising drug target cancer and for a number of other conditions like inflammatory diseases, including asthma and rheumatoid arthritis, glaucoma, chronic obstructive pulmonary disease, and ischemic injury. Currently, there is no experimentally determined structure of A3R. We explored the binding profile of O4-[3-(2,6-dichlorophenyl)-5-methylisoxazol-4-yl]carbonyl-2-methyl-1,3-thiazole-4-carbohydroximamide (K18), which is a new specific and competitive antagonist at the orthosteric binding site of A3R. MD simulations and MM-GBSA calculations of the WT A3R in complex with K18 combined with in vitro mutagenic studies show that the most plausible binding conformation for the dichlorophenyl group of K18 is oriented toward trans-membrane helices (TM) 5, 6 and reveal important residues for binding. Further, MM-GBSA calculations distinguish mutations that reduce or maintain or increase antagonistic activity. Our studies show that selectivity of K18 toward A3R is defined not only by direct interactions with residues within the orthosteric binding area but also by remote residues playing a significant role. Although V1695.30 is considered to be a selectivity filter for A3R binders, when it was mutated to glutamic acid, K18 maintained antagonistic potency, in agreement with our previous results obtained for agonists binding profile investigation. Mutation of the direct interacting residue L903.32 in the low region and the remote L2647.35 in the middle/upper region to alanine increases antagonistic potency, suggesting an empty space in the orthosteric area available for increasing antagonist potency. These results approve the computational model for the description of K18 binding at A3R, which we previously performed for agonists binding to A3R, and the design of more effective antagonists based on K18. Copyright © 2019 American Chemical Society.
Συγγραφείς:
Lagarias, P.
Barkan, K.
Tzortzini, E.
Stampelou, M.
Vrontaki, E.
Ladds, G.
Kolocouris, A.
Περιοδικό:
Journal of Chemical Information and Computer Sciences (now called Journal of Chemical Information and Modeling)
Εκδότης:
American Chemical Society
Λέξεις-κλειδιά:
Amino acids; Binders; Free energy; Molecular dynamics; Pulmonary diseases, Antagonistic activity; Binding conformations; Chronic obstructive pulmonary disease; Computational model; Free-energy calculations; Inflammatory disease; Receptor antagonists; Rheumatoid arthritis, Binding energy, adenosine A3 receptor; adenosine A3 receptor antagonist; amide; immunoglobulin; K-18 conjugate; melphalan; protein binding, chemistry; enzyme specificity; genetics; metabolism; molecular docking; molecular dynamics; mutagenesis; Poisson distribution; protein conformation; thermodynamics, Adenosine A3 Receptor Antagonists; Amides; gamma-Globulins; Melphalan; Molecular Docking Simulation; Molecular Dynamics Simulation; Mutagenesis; Poisson Distribution; Protein Binding; Protein Conformation; Receptor, Adenosine A3; Substrate Specificity; Thermodynamics
DOI:
10.1021/acs.jcim.9b00751
