MolSHAP: Interpreting Quantitative Structure–Activity Relationships Using Shapley Values of R‑Groups

• Published in: Journal of chemical information and modeling Vol. 64; no. 7; pp. 2236 - 2249
• Main Authors: Tian, Tingzhong, Li, Shuya, Fang, Meng, Zhao, Dan, Zeng, Jianyang
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 08.04.2024
• Subjects: Algorithms; Drug Discovery - methods; Lead compounds; Machine Learning; Machine Learning and Deep Learning; Optimization; Quantitative Structure-Activity Relationship; Regression models; Reproducibility of Results
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/acs.jcim.3c00465

Optimizing the activities and properties of lead compounds is an essential step in the drug discovery process. Despite recent advances in machine learning-aided drug discovery, most of the existing methods focus on making predictions for the desired objectives directly while ignoring the explanations for predictions. Although several techniques can provide interpretations for machine learning-based methods such as feature attribution, there are still gaps between these interpretations and the principles commonly adopted by medicinal chemists when designing and optimizing molecules. Here, we propose an interpretation framework, named MolSHAP, for quantitative structure–activity relationship analysis by estimating the contributions of R-groups. Instead of attributing the activities to individual input features, MolSHAP regards the R-group fragments as the basic units of interpretation, which is in accordance with the fragment-based modifications in molecule optimization. MolSHAP is a model-agnostic method that can interpret activity regression models with arbitrary input formats and model architectures. Based on the evaluations of numerous representative activity regression models on a specially designed R-group ranking task, MolSHAP achieved significantly better interpretation power compared with other methods. In addition, we developed a compound optimization algorithm based on MolSHAP and illustrated the reliability of the optimized compounds using an independent case study. These results demonstrated that MolSHAP can provide a useful tool for accurately interpreting the quantitative structure–activity relationships and rationally optimizing the compound activities in drug discovery.