Validation of the use of intermolecular NOE constraints for obtaining docked structures of protein-ligand complexes

The use of intermolecular NOEs for docking a small ligand molecule into its target protein has been investigated with the aim of determining the effectiveness and methodology of this type of NOE docking calculation. A high-resolution X-ray structure of a protein-ligand complex has been used to simulate loose distance constraints of varying degrees of quality, typical of those estimated from experimental NOE intensities. These simulated data were used to examine the effect of the number, distribution and representation of the experimental constraints on the precision and accuracy of the calculated structures. A standard simulated annealing protocol was used, as well as a more novel method based on rigid-body dynamics. The results showed some analogies with those from similar studies on complete protein NMR structure determinations, but it was found that more constraints per torsion angle are required to define docked structures of similar quality. The effectiveness of different NOE-constraint averaging methods was explored and the benefits of using 'R-6 averaging' rather than 'centre averaging' with small sets of NOE constraints were shown. The starting protein structure used in docking calculations was obtained from previous X-ray or NMR structure studies on a related complex. The effects on the calculated conformations of introducing structural differences into the binding site of the initial protein structure were also considered.