Predicting drug metabolism and pharmacokinetics features of in-house compounds by a hybrid machine-learning model

• Published in: Drug metabolism and pharmacokinetics Vol. 39; p. 100395
• Main Authors: Sasahara, Katsunori, Shibata, Masakazu, Sasabe, Hiroyuki, Suzuki, Tomoki, Takeuchi, Kenji, Umehara, Ken, Kashiyama, Eiji
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.08.2021
• Subjects: Artificial intelligence (AI); Computer Simulation; Cytochrome P-450 Enzyme System - metabolism; Drug Discovery - methods; Humans; In silico tools; Inactivation, Metabolic; Lead optimization; Machine Learning; Machine learning (ML); Metabolic Clearance Rate - physiology; Pharmaceutical Preparations - analysis; Pharmaceutical Preparations - chemistry; Pharmaceutical Preparations - metabolism; Pharmacokinetics; Physicochemical parameters; Prediction; Predictive Value of Tests; Quantitative Structure-Activity Relationship; Reproducibility of Results; Screening; Screening; In silico tools; Artificial intelligence (AI); Prediction; Lead optimization; Machine learning (ML); Physicochemical parameters
• ISSN: 1347-4367; 1880-0920
• DOI: 10.1016/j.dmpk.2021.100395

We constructed machine learning-based pharmacokinetic prediction models with very high performance. The models were trained on 26138 and 16613 compounds involved in metabolic stability and cytochrome P450 inhibition, respectively. Because the compound features largely differed between the publicly available and in-house compounds, the models learned on the public data could not predict the in-house compounds, suggesting that outside of a certain applicability domain (AD), the prediction results are unreliable and can mislead the design of novel compounds. To exclude the uncertain prediction results, we constructed another machine learning model that determines whether the newly designed compound is inside or outside the AD. The AD was evaluated multi-dimensionally with some explanatory variables: The structural similarities and the probability obtained from the pharmacokinetic prediction model. The accuracy of predicting metabolic stability was 79.9% on the test set, increasing significantly to 93.6% after excluding the low-reliability compounds. The model properly classified the reliability of the compounds. After learning on the in-house compounds, the reliability model classified almost all (90%) of the public compounds as low reliability, indicating that the AD was properly determined by the model. [Display omitted]