Prediction of Protein−compound Binding Energies from Known Activity Data: Docking‐score‐based Method and its Applications

• Published in: Molecular informatics 2018-07, Vol.37 (6-7), p.e1700120-n/a
• Main Authors: Fukunishi, Yoshifumi, Yamashita, Yasunobu, Mashimo, Tadaaki, Nakamura, Haruki
• Format: Article
• Language: English
• Subjects: Binding free energy; ChEMBL; Computer simulation; Docking; Docking score; Free energy; Humans; Kinases; Ligands; Mathematical models; Matrix metalloproteinase; Matrix Metalloproteinases - chemistry; Matrix Metalloproteinases - metabolism; Metalloproteinase; Metals; Molecular Docking Simulation - methods; Pharmacology; Prediction models; Protein Kinases - chemistry; Protein Kinases - metabolism; Proteins; Protein−compound docking; Quantitative Structure-Activity Relationship; Regularization; Structure-activity relationships
• ISSN: 1868-1743; 1868-1751
• DOI: 10.1002/minf.201700120

We used protein−compound docking simulations to develop a structure‐based quantitative structure−activity relationship (QSAR) model. The prediction model used docking scores as descriptors. The binding free energy was approximated by a weighted average of docking scores for multiple proteins. This approximation was based on a pharmacophore model of receptor pockets and compounds. The weights of the docking scores were restricted to small values to avoid unrealistic weights by a regularization term. Additional outlier elimination improved the results. We applied this method to two groups of targets. The first target was the kinase family. The cross‐validation results of 107 kinase proteins showed that the RMSE of predicted binding free energies was 1.1 kcal/mol. The second target was the matrix metalloproteinase (MMP) family, which has been difficult for docking programs. MMPs require metal‐binding groups in their inhibitor structures in many cases. A quantum effect contributes to the metal−ligand interaction. Despite this difficulty, the present method worked well for the MMPs. This method showed that the RMSE of predicted binding free energies was 1.1 kcal/mol. In comparison, with the original docking method the RMSE was 1.7 kcal/mol. The results suggest that the present QSAR model should be applied to general target proteins.