HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors

The HADDOCK score, a scoring function for both protein–protein and protein-nucleic acid modeling, has been successful in selecting near-native docking poses in a variety of cases, including those of the CAPRI blind prediction experiment. However, it has yet to be optimized for small molecules, and in particular inhibitors of protein–protein interactions, that constitute an “unmined gold reserve” for drug design ventures. We describe here HADDOCK2P2I, a biophysical model capable of predicting the binding affinity of protein–protein complex inhibitors close to experimental error (∼2-fold larger). The algorithm was trained and 4-fold cross-validated against experimental data for 27 inhibitors targeting 7 protein–protein complexes of various functions and tested on an independent set of 24 different inhibitors for which Kd/IC50 data are available. In addition, two popular ligand topology generation and parametrization methods (ACPYPE and PRODRG) were assessed. The resulting HADDOCK2P2I model, derived from the original HADDOCK score, provides insights into inhibition determinants: while the role of electrostatics and desolvation energies is case-dependent, the interface area plays a more critical role compared to protein–protein interactions.