Thermodynamics of Water Displacement from Binding Sites and its Contributions to Supramolecular and Biomolecular Affinity

The role of water displacement in noncovalent binding has been debated in the fields of supramolecular chemistry and drug design. We use molecular dynamics simulations of idealized host-guest systems to address the long-standing controversy of whether water is merely a bystander or an actual driver of noncovalent binding in aqueous solution. To isolate hydration effects, we consider a pseudo-hard-sphere guest binding to a series of cucurbit[8]uril-based macrocyclic host models whose energetic interactions with water vary widely. The computed free energy cost of displacing water from binding sites ranges from 0 to +37 kcal mol$^{−1}$, strongly influencing binding affinities. However, neither water density nor excess chemical potential reliably indicates the thermodynamic favorability of cavity water. These results support the concept that “unfavorable” binding site water contributes to high-affinity binding and resolve the paradox of stable but thermodynamically unfavorable cavity water. This work provides insights into the nature of the hydrophobic effect in molecular recognition and offers a framework for understanding the role of water in binding across various host-guest and protein-ligand systems.