title: Sampling protein motion and solvent effect during ligand binding.
abstract: An exhaustive description of the molecular recognition mechanism between a ligand and its biological target is of great value because it provides the opportunity for an exogenous control of the related process. Very often this aim can be pursued using high resolution structures of the complex in combination with inexpensive computational protocols such as docking algorithms. Unfortunately, in many other cases a number of factors, like protein flexibility or solvent effects, increase the degree of complexity of ligand/protein interaction and these standard techniques are no longer sufficient to describe the binding event. We have experienced and tested these limits in the present study in which we have developed and revealed the mechanism of binding of a new series of potent inhibitors of Adenosine Deaminase. We have first performed a large number of docking calculations, which unfortunately failed to yield reliable results due to the dynamical character of the enzyme and the complex role of the solvent. Thus, we have stepped up the computational strategy using a protocol based on metadynamics. Our approach has allowed dealing with protein motion and solvation during ligand binding and finally identifying the lowest energy binding modes of the most potent compound of the series, 4-decyl-pyrazolo[1,5-a]pyrimidin-7-one.
authors.affiliation: Department of Chemistry and Applied Biosciences, Computational Science, Eidgenössiche Technische Hochschule, ETH, Zürich, Switzerland.
authors.forename: Vittorio
authors.initials: V
authors.lastname: Limongelli
authors.forename: Luciana
authors.initials: L
authors.lastname: Marinelli
authors.forename: Sandro
authors.initials: S
authors.lastname: Cosconati
authors.forename: Concettina
authors.initials: C
authors.lastname: La Motta
authors.forename: Stefania
authors.initials: S
authors.lastname: Sartini
authors.forename: Laura
authors.initials: L
authors.lastname: Mugnaini
authors.forename: Federico
authors.initials: F
authors.lastname: Da Settimo
authors.forename: Ettore
authors.initials: E
authors.lastname: Novellino
authors.forename: Michele
authors.initials: M
authors.lastname: Parrinello
mesh_terms: D000465:Algorithms; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012997:Solvents / Q000737:chemistry*
chemical_list: D008024:Ligands; D011506:Proteins; D012997:Solvents