title: Perturbation of fluid dynamics properties of water molecules during G protein-coupled receptor-ligand recognition: the human A2A adenosine receptor as a key study.
abstract: Recent advances in structural biology revealed that water molecules play a crucial structural role in the protein architecture and ligand binding of G protein-coupled receptors. In this work, we present an alternative approach to monitor the time-dependent organization of water molecules during the final stage of the ligand-receptor recognition process by means of membrane molecular dynamics simulations. We inspect the variation of fluid dynamics properties of water molecules upon ligand binding with the aim to correlate the results with the binding affinities. The outcomes of this analysis are transferred into a bidimensional graph called water fluid dynamics maps, that allow a fast graphical identification of protein "hot-spots" characterized by peculiar shape and electrostatic properties that can play a critical role in ligand binding. We hopefully believe that the proposed approach might represent a valuable tool for structure-based drug discovery that can be extended to cases where crystal structures are not yet available, or have not been solved at high resolution.
authors.affiliation: Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Sabbadin
authors.forename: Antonella
authors.initials: A
authors.lastname: Ciancetta
authors.forename: Stefano
authors.initials: S
authors.lastname: Moro
mesh_terms: D058917:Adenosine A2 Receptor Antagonists / Q000737:chemistry*; D000465:Algorithms; D001665:Binding Sites; D018360:Crystallography, X-Ray; D006801:Humans; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D043705:Receptor, Adenosine A2A / Q000737:chemistry*; D040681:Structural Homology, Protein; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014227:Triazines / Q000737:chemistry*; D014584:User-Computer Interface; D014867:Water / Q000737:chemistry*
chemical_list: D058917:Adenosine A2 Receptor Antagonists; D008024:Ligands; D043705:Receptor, Adenosine A2A; D014227:Triazines; D014867:Water