Sampling protein motion and solvent effect during ligand binding

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 109; no. 5; pp. 1467 - 1472
• Main Authors: Limongelli, Vittorio, Marinelli, Luciana, Cosconati, Sandro, La Motta, Concettina, Sartini, Stefania, Mugnaini, Laura, Da Settimo, Federico, Novellino, Ettore, Parrinello, Michele
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 31.01.2012; National Acad Sciences
• Subjects: Active sites; Algorithms; Atoms; Binding sites; Biological Sciences; Enzymes; Free energy; Hemic system; Lead; Ligands; Mathematical minima; Models, Molecular; Molecules; Physical Sciences; Protein Binding; Proteins; Proteins - chemistry; Proteins - metabolism; Solvents; Solvents - chemistry
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1112181108

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.