*Result*: Benchmarking In Silico Metabolite Prediction Tools against Human Radiolabeled ADME Data for Small-Molecule Drugs.

Title:
Benchmarking In Silico Metabolite Prediction Tools against Human Radiolabeled ADME Data for Small-Molecule Drugs.
Authors:
Gao L; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.; University of Chinese Academy of Sciences, Beijing 100049, China., Yan S; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China., Feng K; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China., Liu H; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.; Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China., Zhang Z; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China., Diao X; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.; University of Chinese Academy of Sciences, Beijing 100049, China.
Source:
Journal of chemical information and modeling [J Chem Inf Model] 2026 Mar 09; Vol. 66 (5), pp. 2918-2928. Date of Electronic Publication: 2026 Feb 12.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE
Imprint Name(s):
Original Publication: Washington, D.C. : American Chemical Society, c2005-
Substance Nomenclature:
0 (Pharmaceutical Preparations)
0 (Small Molecule Libraries)
Entry Date(s):
Date Created: 20260212 Date Completed: 20260309 Latest Revision: 20260309
Update Code:
20260309
DOI:
10.1021/acs.jcim.5c03045
PMID:
41677243
Database:
MEDLINE

*Further Information*

*Artificial intelligence-based in silico metabolite prediction tools are increasingly used in drug development, but their performance against high-quality human data remains uncertain. We evaluated four open-access models, including SyGMa, GLORYx, BioTransformer 3.0, MetaPredictor, and MetaTrans, using 11 small-molecule drugs with published human radiolabeled ADME data. Predicted metabolites were compared with experimentally identified human metabolites, and model performance was assessed using recall, precision, balanced accuracy, F1, and Jaccard scores. Results indicated a distinct trade-off between coverage and balanced accuracy: SyGMa provided the broadest metabolic coverage but with low precision; GLORYx and BioTransformer achieved a better balance between coverage and relevance, with BioTransformer showing the best overall performance; MetaPredictor produced fewer metabolites, yet yielded competitive scores for several drugs, despite issues with SMILES interpretability. MetaTrans showed moderate overall performance but also generated incorrect metabolite predictions. None of the models captured the mercapturic acid pathway or predicted metabolite abundances. Overall, current artificial intelligence-based tools can partially reproduce human metabolic profiles but remain insufficient to replace experimental studies, serving best as early-stage screening tools. Further advances in molecular representation, pathway completeness, and data quality are needed to improve next-generation metabolite prediction models.*