Abstract
Purpose
The clearance pathways of drugs are critical elements for understanding the pharmacokinetics of drugs. We previously developed in silico systems to predict the five clearance pathway using a rectangular method and a support vector machine (SVM). In this study, we improved our classification system by increasing the number of clearance pathways available for our prediction (CYP1A2, CYP2C8, CYP2C19, and UDP-glucuronosyl transferases (UGTs)) and by accepting multiple major pathways.
Methods
Using the four default descriptors (charge, molecular weight, logD at pH 7.0, and unbound fraction in plasma), three kinds of SVM-based predictors based on traditional single-step approach or two-step focusing approaches with subset or partition clustering were developed. The two-step approach with subset clustering resulted in the highest prediction performance. The feature-selection of additional descriptors based on a greedy algorithm was employed to further improve the predictability.
Results
The prediction accuracy for each pathway was increased to more than 0.83 with the exception of CYP2C19 and UGTs pathways, whose accuracies were below 0.7. Prediction performance of CYP1A2, CYP3A4 and renal excretion pathways were found to be acceptable using external dataset.
Conclusions
We successfully constructed a novel SVM-based predictor for the multiple major clearance pathways based on chemical structures.
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Abbreviations
- CYP:
-
Cytochrome P450
- fup :
-
Protein unbound fraction in plasma
- logD:
-
Octanol-water distribution coefficient
- MW:
-
Molecular weight
- OATP:
-
Organic anion transporting polypeptide
- SVM:
-
Support vector machine
- UGT:
-
UDP-glucuronosyltransferase
- VDW:
-
Van der Waals
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Wakayama, N., Toshimoto, K., Maeda, K. et al. In Silico Prediction of Major Clearance Pathways of Drugs among 9 Routes with Two-Step Support Vector Machines. Pharm Res 35, 197 (2018). https://doi.org/10.1007/s11095-018-2479-1
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DOI: https://doi.org/10.1007/s11095-018-2479-1