The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery

• Published in: Journal of medicinal chemistry Vol. 60; no. 16; pp. 6781 - 6827
• Main Authors: Spyrakis, Francesca, Ahmed, Mostafa H, Bayden, Alexander S, Cozzini, Pietro, Mozzarelli, Andrea, Kellogg, Glen E
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 24.08.2017
• Subjects: Binding Sites; Catalysis; Crystallography, X-Ray; Drug Design; Drug Discovery; Ligands; Models, Molecular; Pharmaceutical Preparations - chemistry; Protein Folding; Proteins - chemistry; Thermodynamics; Water - chemistry
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/acs.jmedchem.7b00057

The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being “hot” and “cold”, which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective’s summary features guidelines for exploiting water molecules in drug discovery.