Identification of Xenobiotic Biotransformation Products Using Mass Spectrometry-Based Metabolomics Integrated with a Structural Elucidation Strategy by Assembling Fragment Signatures

Overview

Journal Anal Chem

Specialty Chemistry

Date 2023 Sep 15

PMID 37713273

Authors

Yuan-Chih Chen

Hsin-Yi Wu

Wei-Sheng Wu

Jen-Yi Hsu

Chih-Wei Chang

Yuan-Han Lee

Pao-Chi Liao

Affiliations

Soon will be listed here.

Abstract

The identification of xenobiotic biotransformation products is crucial for delineating toxicity and carcinogenicity that might be caused by xenobiotic exposures and for establishing monitoring systems for public health. However, the lack of available reference standards and spectral data leads to the generation of multiple candidate structures during identification and reduces the confidence in identification. Here, a UHPLC-HRMS-based metabolomics strategy integrated with a metabolite structure elucidation approach, namely, FragAssembler, was proposed to reduce the number of false-positive structure candidates. biotransformation product candidates were filtered by mass defect filtering (MDF) and multiple-group comparison. FragAssembler assembled fragment signatures from the MS/MS spectra and generated the modified moieties corresponding to the identified biotransformation products. The feasibility of this approach was demonstrated by the three biotransformation products of di(2-ethylhexyl)phthalate (DEHP). Comprehensive identification was carried out, and 24 and 13 biotransformation products of two xenobiotics, DEHP and 4'-Methoxy-α-pyrrolidinopentiophenone (4-MeO-α-PVP), were annotated, respectively. The number of 4-MeO-α-PVP biotransformation product candidates in the FragAssembler calculation results was approximately 2.1 times lower than that generated by BioTransformer 3.0. Our study indicates that the proposed approach has great potential for efficiently and reliably identifying xenobiotic biotransformation products, which is attributed to the fact that FragAssembler eliminates false-positive reactions and chemical structures and distinguishes modified moieties on isomeric biotransformation products. The FragAssembler software and associated tutorial are freely available at https://cosbi.ee.ncku.edu.tw/FragAssembler/ and the source code can be found at https://github.com/YuanChihChen/FragAssembler.

Citing Articles

Mass Spectrometry Rearrangement Ions and Metabolic Pathway-Based Discovery of Indole Derivatives during the Aging Process in 'Chachi'.

Li T, Chen K, Wang X, Wang Y, Su Y, Guo Y Foods. 2024; 13(1).

PMID: 38201037 PMC: 10778486. DOI: 10.3390/foods13010008.

References

Tsugawa H, Kind T, Nakabayashi R, Yukihira D, Tanaka W, cajka T . Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software. Anal Chem. 2016; 88(16):7946-58. PMC: 7063832. DOI: 10.1021/acs.analchem.6b00770. View

Hsu J, Tien C, Shih C, Liao P, Wong H, Liao P . Using a high-resolution mass spectrometry-based metabolomics strategy for comprehensively screening and identifying biomarkers of phthalate exposure: Method development and application. Environ Int. 2019; 128:261-270. DOI: 10.1016/j.envint.2019.04.041. View

Wang Y, Backman T, Horan K, Girke T . fmcsR: mismatch tolerant maximum common substructure searching in R. Bioinformatics. 2013; 29(21):2792-4. DOI: 10.1093/bioinformatics/btt475. View

Shanu-Wilson J, Evans L, Wrigley S, Steele J, Atherton J, Boer J . Biotransformation: Impact and Application of Metabolism in Drug Discovery. ACS Med Chem Lett. 2020; 11(11):2087-2107. PMC: 7667663. DOI: 10.1021/acsmedchemlett.0c00202. View

Blazenovic I, Kind T, Ji J, Fiehn O . Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics. Metabolites. 2018; 8(2). PMC: 6027441. DOI: 10.3390/metabo8020031. View

Ellefsen K, Wohlfarth A, Swortwood M, Diao X, Concheiro M, Huestis M . 4-Methoxy-α-PVP: in silico prediction, metabolic stability, and metabolite identification by human hepatocyte incubation and high-resolution mass spectrometry. Forensic Toxicol. 2016; 34:61-75. PMC: 4705136. DOI: 10.1007/s11419-015-0287-4. View

Takahashi M, Izumi Y, Iwahashi F, Nakayama Y, Iwakoshi M, Nakao M . Highly Accurate Detection and Identification Methodology of Xenobiotic Metabolites Using Stable Isotope Labeling, Data Mining Techniques, and Time-Dependent Profiling Based on LC/HRMS/MS. Anal Chem. 2018; 90(15):9068-9076. DOI: 10.1021/acs.analchem.8b01388. View

Fenner K, Gao J, Kramer S, Ellis L, Wackett L . Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction. Bioinformatics. 2008; 24(18):2079-85. DOI: 10.1093/bioinformatics/btn378. View

Liu K, Lee C, Singer G, Bais P, Castellanos F, Woodworth M . Large scale enzyme based xenobiotic identification for exposomics. Nat Commun. 2021; 12(1):5418. PMC: 8440538. DOI: 10.1038/s41467-021-25698-x. View

10.

Huber C, Muller E, Schulze T, Brack W, Krauss M . Improving the Screening Analysis of Pesticide Metabolites in Human Biomonitoring by Combining High-Throughput Incubation and Automated LC-HRMS Data Processing. Anal Chem. 2021; 93(26):9149-9157. DOI: 10.1021/acs.analchem.1c00972. View

11.

Bort R, Ponsoda X, Jover R, Gomez-Lechon M, Castell J . Diclofenac toxicity to hepatocytes: a role for drug metabolism in cell toxicity. J Pharmacol Exp Ther. 1998; 288(1):65-72. View

12.

Cao Y, Charisi A, Cheng L, Jiang T, Girke T . ChemmineR: a compound mining framework for R. Bioinformatics. 2008; 24(15):1733-4. PMC: 2638865. DOI: 10.1093/bioinformatics/btn307. View

13.

Zhang H, Zhang D, Ray K . A software filter to remove interference ions from drug metabolites in accurate mass liquid chromatography/mass spectrometric analyses. J Mass Spectrom. 2003; 38(10):1110-2. DOI: 10.1002/jms.521. View

14.

Kirchmair J, Goller A, Lang D, Kunze J, Testa B, Wilson I . Predicting drug metabolism: experiment and/or computation?. Nat Rev Drug Discov. 2015; 14(6):387-404. DOI: 10.1038/nrd4581. View

15.

Zhang H, Zhang D, Ray K, Zhu M . Mass defect filter technique and its applications to drug metabolite identification by high-resolution mass spectrometry. J Mass Spectrom. 2009; 44(7):999-1016. DOI: 10.1002/jms.1610. View

16.

Duhrkop K, Fleischauer M, Ludwig M, Aksenov A, Melnik A, Meusel M . SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nat Methods. 2019; 16(4):299-302. DOI: 10.1038/s41592-019-0344-8. View

17.

Stading R, Gastelum G, Chu C, Jiang W, Moorthy B . Molecular mechanisms of pulmonary carcinogenesis by polycyclic aromatic hydrocarbons (PAHs): Implications for human lung cancer. Semin Cancer Biol. 2021; 76:3-16. PMC: 8728691. DOI: 10.1016/j.semcancer.2021.07.001. View

18.

Koch H, Preuss R, Angerer J . Di(2-ethylhexyl)phthalate (DEHP): human metabolism and internal exposure-- an update and latest results. Int J Androl. 2006; 29(1):155-65. DOI: 10.1111/j.1365-2605.2005.00607.x. View

19.

Montesano C, Vannutelli G, Fanti F, Vincenti F, Gregori A, Togna A . Identification of MT-45 Metabolites: In Silico Prediction, In Vitro Incubation with Rat Hepatocytes and In Vivo Confirmation. J Anal Toxicol. 2017; 41(8):688-697. DOI: 10.1093/jat/bkx058. View

20.

Wu H, Chen Y, Hsu J, Lu H, Pan Y, Ma M . Untargeted metabolomics analysis assisted by signal selection for comprehensively identifying metabolites of new psychoactive substances: 4-MeO-α-PVP as an example. J Food Drug Anal. 2023; 31(1):137-151. PMC: 10208664. DOI: 10.38212/2224-6614.3447. View