Correlation between ligand solubility and formation of protein-ligand complexes in X-ray crystallography

Structure determination of ligands bound to their target proteins using X-ray crystallography is an important part in the drug discovery process. However, this is not always easy to achieve, especially in cases where the affinity is poor and the solubility of the ligand in the crystallization condition is low. The aim of this project was to investigate a possible correlation between the solubility of a ligand in a soaking condition and the possibility to form protein-ligand complexes by using different cosolvents. Further conclusions were drawn by comparing the results obtained with properties of the ligands. Two protein systems were used of which protein A was combined with seven different ligands and two isoforms of protein B were combined with one poorly soluble ligand. Two different temperatures, 20°C and 30°C, were used. The solubilities of the ligands in the soaking condition were determined with nuclear magnetic resonance (NMR) spectroscopy and structure determination was performed with X-ray crystallography. The results showed that the choice of cosolvent affects the solubility in the soaking condition and also that the distribution coefficient, logD, of the ligand could help in deciding with solvent to use. A 10°C difference in temperature did not affect the solubility or the complex formation, based on the results obtained. A tendency could be seen that a higher solubility in the soaking condition increases the possibility to obtain ligand-protein complexes. Further experiments in the future could help confirm the results from this project and draw new conclusions. Other proteins, ligands and solvents could be used and other parameters could be investigated like pH or a wider difference in temperature.