Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach

We tested different approaches to including the effect of binding-site water molecules for ligand-binding affinities within the MM/GBSA approach (molecular mechanics combined with generalised Born and surface-area solvation). As a test case, we studied the binding of nine phenol analogues to ferritin. The effect of water molecules mediating the interaction between the receptor and the ligand can be studied by considering a few water molecules as a part of the receptor. We extended previous methods by allowing for a variable number of water molecules in the binding site. The effect of displaced water molecules can also be considered within the MM/GBSA philosophy by calculating the affinities of binding-site water molecules, both before and after binding of the ligand. To obtain proper energies, both the water molecules and the ligand need then to be converted to non-interacting ghost molecules and a single-average approach (i.e., the same structures are used for bound and unbound states) based on the simulations of both the complex and the free receptor can be used to improve the precision. The only problem is to estimate the free energy of an unbound water molecule. With an experimental estimate of this parameter, promising results were obtained for our test case.