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Tuning Local Hydration Enables a Deeper Understanding of Protein–Ligand Binding: The PP1-Src Kinase Case

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journal contribution
posted on 10.12.2020, 10:43 by Andrea Spitaleri, Syeda R. Zia, Patrizio Di Micco, Bissan Al-Lazikani, Miguel A. Soler, Walter Rocchia
Water plays a key role in biomolecular recognition and binding. Despite the development of several computational and experimental approaches, it is still challenging to comprehensively characterize water-mediated effects on the binding process. Here, we investigate how water affects the binding of Src kinase to one of its inhibitors, PP1. Src kinase is a target for treating several diseases, including cancer. We use biased molecular dynamics simulations, where the hydration of predetermined regions is tuned at will. This computational technique efficiently accelerates the SRC-PP1 binding simulation and allows us to identify several key and yet unexplored aspects of the solvent’s role. This study provides a further perspective on the binding phenomenon, which may advance the current drug design approaches for the development of new kinase inhibitors.