Development of CDK-targeted scoring functions for prediction of binding affinity

• Published in: Biophysical chemistry Vol. 235; pp. 1 - 8
• Main Authors: Levin, Nayara Maria Bernhardt, Pintro, Val Oliveira, Bitencourt-Ferreira, Gabriela, de Mattos, Bruna Boldrini, de Castro Silvério, Ariadne, de Azevedo, Walter Filgueira
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.04.2018
• Subjects: Binding Sites; Bioinformatics; CDK; Cyclin-Dependent Kinases; Docking; Drug design; Ligands; Machine Learning; Protein; Docking; Drug design; CDK; Bioinformatics; Protein; Machine learning
• ISSN: 0301-4622; 1873-4200
• DOI: 10.1016/j.bpc.2018.01.004

Cyclin-dependent kinase (CDK) is an interesting biological macromolecule due to its role in cell cycle progression, transcription control, and neuronal development, to mention the most studied biological activities. Furthermore, the availability of hundreds of structural studies focused on the intermolecular interactions of CDK with competitive inhibitors makes possible to develop computational models to predict binding affinity, where the atomic coordinates of binary complexes involving CDK and ligands can be used to train a machine learning model. The present work is focused on the development of new machine learning models to predict binding affinity for CDK. The CDK-targeted machine learning models were compared with classical scoring functions such as MolDock, AutoDock 4, and Vina Scores. The overall performance of our CDK-targeted scoring function was higher than the previously mentioned scoring functions, which opens the possibility of increasing the reliability of virtual screening studies focused on CDK. •Development of a novel CDK-targeted machine learning model to predict log(IC50)•The use of a dataset composed of 176 CDK crystallographic structures•Improved predictive power of the CDK-targeted model to predict log(IC50) for CDK, when compared with classical scoring