Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites

Sinisa Vukovic,David J Huggins,Paul E Brennan

doi:10.1088/0953-8984/28/34/344007

Abstract

The interaction between any two biological molecules must compete with their interaction with water molecules. This makes water the most important molecule in medicine, as it controls the interactions of every therapeutic with its target. A small molecule binding to a protein is able to recognize a unique binding site on a protein by displacing bound water molecules from specific hydration sites. Quantifying the interactions of these water molecules allows us to estimate the potential of the protein to bind a small molecule. This is referred to as ligandability. In the study, we describe a method to predict ligandability by performing a search of all possible combinations of hydration sites on protein surfaces. We predict ligandability as the summed binding free energy for each of the constituent hydration sites, computed using inhomogeneous fluid solvation theory. We compared the predicted ligandability with the maximum observed binding affinity for 20 proteins in the human bromodomain family. Based on this comparison, it was determined that effective inhibitors have been developed for the majority of bromodomains, in the range from 10 to 100 nM. However, we predict that more potent inhibitors can be developed for the bromodomains BPTF and BRD7 with relative ease, but that further efforts to develop inhibitors for ATAD2 will be extremely challenging. We have also made predictions for the 14 bromodomains with no reported small molecule Kd values by isothermal titration calorimetry. The calculations predict that PBRM1(1) will be a challenging target, while others such as TAF1L(2), PBRM1(4) and TAF1(2), should be highly ligandable. As an outcome of this work, we assembled a database of experimental maximal Kd that can serve as a community resource assisting medicinal chemistry efforts focused on BRDs. Effective prediction of ligandability would be a very useful tool in the drug discovery process.

Highlights

Water molecules at protein surfaces can be weakly or strongly bound
We have presented a new method capable of generating and evaluating all possible combinations of hydration sites on the surface of a protein
The majority of BRDs are predicted to have similar ligandability. This is in line with the maximal observed Kd values determined by isothermal calorimetry (ITC) for BRDs, which are mostly in the 10–100 nM range

Summary

Introduction

Water molecules at protein surfaces can be weakly or strongly bound. the binding of a small molecule to a particular region of the surface is affected by the existing network of hydration sites in the absence of the small molecule. There are a number of computational methods to predict ligandability including MAPPOD [9], SiteMap [10], fpocket [11], DLID [12], DrugFEATURE [13], LIGSITE [14], Q-SiteFinder [15], i-SITE [16], DrugPred [17], JEDI [18]. All of these methods apply large-scale data analysis to structural, and physicochemical data that is empirically derived using a training sets for ligands, proteins, and protein–ligand complexes

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Discussion

Conclusion