DyScore: A Boosting Scoring Method with Dynamic Properties for Identifying True Binders and Non-binders in Structure-based Drug Discovery

Abstract

The accurate prediction of protein-ligand binding affinity is critical for the success of computer-aided drug discovery. However, the accuracy of current scoring functions is usually unsatisfactory due to their rough approximation or sometimes even omittance of many factors involved in protein-ligand binding. For instance, the intrinsic dynamic of the protein-ligand binding state is usually disregarded in scoring function because these rapid binding affinity prediction approaches are only based on a representative complex structure of the protein and ligand in the binding state. That is, the dynamic protein-ligand binding complex ensembles are simplified as a static snapshot in calculation. In this study, two novel features were proposed for characterizing the dynamic properties of protein-ligand binding based on the static structure of the complex, which is expected to be a valuable complement to the current scoring functions. The two features demonstrate the geometry-shape matching between a protein and a ligand as well as the dynamic stability of protein-ligand binding. We further combined these two novel features with several classical scoring functions to develop a binary classification model called DyScore that uses the Extreme Gradient Boosting algorithm to classify compound poses as binders or non-binders. We have found that DyScore achieves state-of-the-art performance in distinguishing active and decoy ligands on both enhanced DUD dataset and external test sets with both proposed novel features showing significant contributions to the improved performance. Especially, DyScore exhibits superior performance on early recognition, a crucial requirement for success in virtual screening and de novo drug design. The standalone version of DyScore and Dyscore-MF are freely available to all at: https://github.com/YanjunLi-CS/dyscore Key PointsO_LITwo novel binding features were proposed for characterizing the dynamic properties of protein-ligand binding only based on a static snapshot of complex. C_LIO_LIBased on the XGBoost machine learning method, the DyScore recognition model was proposed to accurately classify compound binding poses as binders or non-binders. DyScore consistently outperforms all the state-of-the-art published models on three different metrics by a large margin. C_LIO_LIDyScore showed superior performance in early recognition with an average of 73.3% success rate for the top three ranked compounds for each protein target. C_LIO_LIThe standalone version of DyScore and DyScore-MF are freely available to all at: https://github.com/YanjunLi-CS/dyscore C_LI TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/465921v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1e96bborg.highwire.dtl.DTLVardef@3a0a8corg.highwire.dtl.DTLVardef@8a6f7eorg.highwire.dtl.DTLVardef@9dfa19_HPS_FORMAT_FIGEXP M_FIG C_FIG