Development of quantitative structure-binding affinity relationship models based on novel geometrical chemical descriptors of the protein-ligand interfaces

Novel geometrical chemical descriptors have been derived on the basis of the computational geometry of protein-ligand interfaces and Pauling atomic electronegativities (EN). Delaunay tessellation has been applied to a diverse set of 517 X-ray characterized protein-ligand complexes yielding a unique collection of interfacial nearest neighbor atomic quadruplets for each complex. Each quadruplet composition was characterized by a single descriptor calculated as the sum of the EN values for the four participating atom types. We termed these simple descriptors generated from atomic EN values and derived with the Delaunay Tessellation the ENTess descriptors and used them in the variable selection k-nearest neighbor quantitative structure-binding affinity relationship (QSBR) studies of 264 diverse protein-ligand complexes with known binding constants. Twenty-four complexes with chemically dissimilar ligands were set aside as an independent validation set, and the remaining dataset of 240 complexes was divided into multiple training and test sets. The best models were characterized by the leave-one-out cross-validated correlation coefficient q² as high as 0.66 for the training set and the correlation coefficient R² as high as 0.83 for the test set. The high predictive power of these models was confirmed independently by applying them to the validation set of 24 complexes yielding R² as high as 0.85. We conclude that QSBR models built with the ENTess descriptors can be instrumental for predicting the binding affinity of receptor-ligand complexes.