Thermodynamics of 'hydrophobic' versus 'hydrophilic' binding in ligand-protein complexes

Complex biological processes involve the binding of one molecule by another. In some cases this involves the binding of one protein by another, whereas in others the protein binds a small organic molecule ('ligand'). In certain instances, for example in a disease state, there is a need to discover a novel small molecule that binds more tightly (ie has higher affinity) than the natural ligand. Ideally, this novel molecule or 'lead', can be further developed as a drug molecule effective against the particular disease state. The binding process can be thought of as a 'shape' problem, whereby the strength of binding depends critically on shape complementarity between the ligand and the binding pocket on the protein. However, the binding process is more complicated than this, since it is also determined by the extent of dynamics ('floppiness') of the interacting partners. To complicate matters further, there is a third partner in the interaction, namely molecules of solvent water in which all biological interactions take place. The discovery of new drug molecules on the basis of structural information (structure-based drug design) is currently hampered by the lack of information on these additional component parts. For this reason many drugs are discovered by screening large numbers of discrete compounds, which can be very time-consuming. This proposal aims to quantify the contributions to binding affinity from the various components described above. Ultimately, this may enable us to predict binding affinities from protein structures using high-speed computers, thereby inproving the efficiency of the drug discovery process.

Complex biological systems depend critically on highly specific recognition between molecules with carefully tuned affinities. Biological molecules have a combination of hydrophobic and hydrophilic components, and intermolecular interactions take place in water, further complicating the energetics of recognition and binding. In current BBSRC-funded work, we have examined the thermodynamics of binding of a series of small hydrophobic ligands to the major urinary protein (MUP), a promiscuous binder of such molecules. We have made significant progress towards decomposing the standard free energy of binding into enthalpic and entropic contributions from the ligand, protein and solvent. On the strength of this work we propose a comparative investigation of the principles of binding thermodynamics in a protein with a similar fold but with a 'hydrophilic' binding pocket, namely the histamine binding protein from R. appendiculatus. This will be achieved via a multidisciplinary programme of research involving protein crystallography, isothermal titration calorimetry, nuclear magnetic resonance and molecular modelling methods. It is our hope that a detailed comparison of the various enthalpic and entropic contributions to binding in a 'hydrophobic' and a 'hydrophilic' binder will offer more general fundamental insights into the thermodynamics of biomolecular associations involving species that fall between these two extremes. In this manner we hope to gain a better understanding of the factors that govern ligand binding affinity. Such information is urgently required in order to enhance structure-based drug design as a general lead discovery tool for the pharmaceutical industry.