Drug Metabolism, Interactions and Toxicity: Advances in Metabolomics Approaches

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Pharmacology and Drug Metabolism".

Deadline for manuscript submissions: 15 August 2026 | Viewed by 1957

Special Issue Editors


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Guest Editor
Translational Medicine, Novartis Biomedical Research, Cambridge, MA 02139, USA
Interests: drug metabolism; drug toxicity; ADME; pharmacokinetics; new modalities; MS-based metabolomics
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Guest Editor
Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
Interests: prescription drug negative side effects in the heart, skeletal muscle and bone; associated chemical mechanisms for this toxicity; drug-endogenous substrate interactions; pharmacogenetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Issues related to drug safety remain a major bottleneck in drug discovery and development. Metabolites reflect the integrated readout of various biological processes (gene expression, mRNA transcription, protein expression) and are influenced by environmental factors (microorganism, xenobiotics, dietary and other exogenous components). Recent advancements in analytical technologies and computational methods in metabolomics have enabled researchers to efficiently analyze the alterations in a large number of endogenous and exogenous compounds and identify perturbed biological processes after drug treatment. Additionally, enhancements in advanced in vitro models, such as 3D systems, organoids, and microphysiological systems (MPS), exhibit the potential to recapture organ-specific cellular functionality and the physiological dynamics of human tissues. These new advancements have provided valuable tools in studying the toxicological response to drug treatments. Drug–endobiotic interactions provide a valuable approach to evaluating the toxicological impact of drug treatments, offering insights into how pharmacological agents perturb endogenous biochemical networks and contribute to adverse effects. These interactions can be leveraged for toxicity assessment, the development of safety biomarkers, the prediction of adverse events, and enhancing our mechanistic understanding of the toxicological effects associated with both investigational drug candidates and approved drugs.

This Special Issue is devoted to metabolomics in drug toxicity, with a focus on drug metabolism, drug–drug (food) interactions, and drug–endobiotic interactions. The scope of this Special Issue includes, but is not limited to, studies on targeted and untargeted metabolomic analyses, multi-omics integration, and computational modeling to characterize how investigational drug candidates and approved drugs perturb the endobiotic network; drug–endobiotic interactions; the development of endogenous probes for drug–drug (food) interactions; the development of biomarkers for toxicity assessment and prediction; and the identification of the mechanisms and molecular pathways involved in drug toxicity. Other topics with a similar focus will also be considered.

Dr. Pengcheng Wang
Prof. Dr. Rheem A. Totah
Guest Editors

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Keywords

  • metabolomics
  • drug/xenobiotic metabolism
  • drug–drug interactions
  • drug–endobiotic interactions
  • drug toxicity
  • biomarkers
  • ADME
  • 3D in vitro model

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Published Papers (2 papers)

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Research

17 pages, 1810 KB  
Article
Toxicometabolomics Characterization of Two N1-Sulfonated Dimethyltryptamine Derivatives in Zebrafish Larvae and Human Liver S9 Fractions Using Liquid Chromatography–High-Resolution Mass Spectrometry
by Prajwal Punnamraju, Sascha K. Manier, Selina Hemmer, Matthias Grill, Philip Schippers, Jennifer Herrmann and Markus R. Meyer
Metabolites 2026, 16(2), 134; https://doi.org/10.3390/metabo16020134 - 14 Feb 2026
Viewed by 776
Abstract
Introduction: The availability of toxicokinetic data is critical for detecting and monitoring the intake of psychoactive substances. Timely characterization of novel psychoactive substances (NPS) is particularly important to assess their abuse potential and inform public health responses. Methods: Toxicometabolomics offers a [...] Read more.
Introduction: The availability of toxicokinetic data is critical for detecting and monitoring the intake of psychoactive substances. Timely characterization of novel psychoactive substances (NPS) is particularly important to assess their abuse potential and inform public health responses. Methods: Toxicometabolomics offers a powerful approach to characterize xenobiotic metabolism through high-resolution profiling of biochemical transformations. It thus allows the finding of exogenous biomarkers, such as new drug metabolites, and endogenous biomarkers, which could be indications of acute drug ingestions or sample manipulation, as well as offering information on the mode of action of drugs. In this study, we applied a liquid chromatography–high-resolution mass spectrometry workflow to investigate the toxicometabolomics of two N1-sulfonated N,N-dimethyltryptamine derivatives with potential for both therapeutic use and recreational abuse. Results: Zebrafish (Danio rerio), an increasingly valuable model for preclinical pharmacology and toxicology studies, along with pooled human liver S9 fractions were used to elucidate metabolic pathways and identify key phase I and phase II biotransformations. Furthermore, untargeted metabolomics revealed significant downregulation of L-threonine associated with compound exposure. Conclusions: These findings advance the current understanding of tryptamine metabolism and underscore the utility of toxicometabolomics in the analytical evaluation of NPS. Full article
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25 pages, 6660 KB  
Article
Delivery and Metabolic Fate of Doxorubicin and Betulin Nanoformulations In Vivo: A Metabolomics Approach
by Mihai Adrian Socaciu, Remus Moldovan, Carmen Socaciu, Flaviu Alexandru Tăbăran and Simona Clichici
Metabolites 2025, 15(11), 723; https://doi.org/10.3390/metabo15110723 - 5 Nov 2025
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Abstract
Background: Betulins (betulin, betulinic acid and lupeol) demonstrated antitumor and chemopreventive activity but showed low bioavailability due to their self-aggregation in hydrophilic environments. To overcome these disadvantages, their incorporation into lipid nanoformulations (PEGylated liposomes and Lipid Nanostructured Carriers (NLCs)) has proven to [...] Read more.
Background: Betulins (betulin, betulinic acid and lupeol) demonstrated antitumor and chemopreventive activity but showed low bioavailability due to their self-aggregation in hydrophilic environments. To overcome these disadvantages, their incorporation into lipid nanoformulations (PEGylated liposomes and Lipid Nanostructured Carriers (NLCs)) has proven to represent a viable solution. Objectives: The purpose of this study is to evaluate the size and incorporation rate of these molecules in nanoformulations, as well as their delivery and metabolic fate (pure betulinic acid versus a standardized extract, TT) relative to Doxorubicin using an in vivo protocol. The investigation extended our previous in vitro investigations towards an in vivo evaluation of antitumor activity, metabolic fate and toxicity in Wistar rats bearing Walker 256 carcinoma tumors over 21 days. Since previous studies used oral or intratumor administration, this exploratory study applied intravenous administration via microbubble-assisted sonoporation, considering its higher relevance for translational studies. Methods: The delivery and metabolic fate of the parent molecules, the identification of their fragments and metabolites using UHPLC-QTOF-ESI+MS were investigated, along with the identification of some toxicity biomarkers in rat plasma, tumor tissues and urine. Results: Preferential accumulation of Doxorubicin in tumors was observed compared to betulinic acid and TT components, as well as their persistence in plasma or elimination in urine. Compared to PEGylated liposomes, NLC formulations (especially NLC Doxo) induced a lower survival rate, a decreased bioavailability and increased toxicity by around 20%. Conclusions: These data are a starting point and complement the contrast-enhanced imaging and histology evaluations, which may contribute to the actual knowledge about the in vivo fate of betulins. Full article
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