Pharmacometabolomics in Drug Mechanism, Efficacy and Toxicity

A Special Issue of Metabolites (ISSN 2218-1989) belonging to the section "Pharmacology and Drug Metabolism".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 1054

Editors


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Guest Editor
1 Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
2 INBB—Biostructures and Biosystems National Institute, 00136 Roma, Italy
Interests: endocrine disruptors toxicity and mode of action; probiotic as mitigation strategy; metabolomics; proteomics; transcript analysis; histology and immunohistochemistry; cell culture; 3D in vitro models; organoids; spheroids

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Guest Editor
Department of Life Sciences, Health, and Health Professions, Link Campus University, 00165 Rome, Italy
Interests: bioactive compounds; oxidative stress; inflammation; human nutrition; lipoproteins; paraoxonase 2
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Special Issue Information

Dear Colleagues, 

Pharmacometabolomics is rapidly emerging as a powerful systems-level approach to elucidate how drugs interact with the complexity of human metabolism. By integrating advanced metabolite profiling, computational analytics and mechanistic interpretation, pharmacometabolomics offers unprecedented opportunities to characterize drug actions, predict therapeutic responses and identify pathways underlying adverse effects. This Special Issue, Pharmacometabolomics in Drug Mechanism, Efficacy and Toxicity, aims to gather cutting-edge contributions that advance our understanding of how metabolic networks shape and are shaped by pharmacological interventions.

The focus of this Special Issue is to highlight methodological and conceptual innovations that leverage metabolomics, lipidomics, cheminformatics, metabolic flux analysis and computational modelling to unravel drug‐related biochemical processes. Studies exploring novel workflows for biological sample preparation, improvements in low-molecular-weight metabolite detection and curation and integrated multi-omics approaches are particularly welcome.

The scope encompasses experimental, translational and computational research across diverse biological systems, from cell models to animal models and human studies. We invite submissions addressing metabolic signatures of drug efficacy, resistance and toxicity; downstream metabolic consequences of genetic or environmental perturbations; and biomarker discovery for personalized medicine. Contributions that demonstrate the clinical and industrial relevance of pharmacometabolomics, including applications in toxicology, metabolic disease and environmental exposure assessment, are also encouraged.

The purpose of this Special Issue is to provide a comprehensive platform for researchers working at the interface of metabolism and pharmacology, promoting novel insights into metabolic pathways that define drug behavior. By consolidating emerging trends and innovative approaches, this issue aims to foster progress toward more effective, safer and personalized therapeutic strategies.

Dr. Christian Giommi
Dr. Camilla Morresi
Guest Editors

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • pharmacometabolomics
  • drug mechanisms
  • metabolic biomarkers
  • drug efficacy
  • drug toxicity
  • metabolic flux analysis
  • lipidomics and metabolomics profiling
  • computational metabolomics
  • systems pharmacology
  • precision medicine

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Published Papers (1 paper)

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Research

18 pages, 2269 KB  
Article
Untargeted Metabolomics Analysis Reveals Potential Metabolic Targets in Gemcitabine-Treated Pancreatic Cancer Cells
by Arjun Prasad Tiwari, Blake R. Rushing, Larissa Silva, Susan J. Sumner and Pinku Mukherjee
Metabolites 2026, 16(7), 471; https://doi.org/10.3390/metabo16070471 - 6 Jul 2026
Viewed by 547
Abstract
Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by limited treatment options and poor prognosis. Gemcitabine is a commonly used chemotherapy; however, gemcitabine resistance in PDAC poses a critical barrier to effective treatment, as the underlying mechanisms are not yet [...] Read more.
Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by limited treatment options and poor prognosis. Gemcitabine is a commonly used chemotherapy; however, gemcitabine resistance in PDAC poses a critical barrier to effective treatment, as the underlying mechanisms are not yet fully understood. Methods: This study employs an exploratory untargeted metabolomics approach to investigate metabolic differences in PDAC cells in the presence and absence of gemcitabine treatment. HPAF-II, MIA PaCa-2, and BxPC-3 cell lines were used as models for gemcitabine-resistant, moderately responsive, and permissive PDAC cells, respectively. Results: MTT assay results revealed that BxPC-3 cells are highly sensitive to gemcitabine treatment, HPAF-II cells are the most resistant, and MIA PaCa-2 cells exhibit moderate sensitivity. Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) of the metabolomics data demonstrated clear differentiation of gemcitabine-treated and untreated (control) cells. When comparing the treated vs. control conditions, 170 metabolites matched to an in-house library of standards were significant (p < 0.05 or fold change ≥ 2 or VIP ≥ 1) differentiators in HPAF-II cells, whereas MIA PaCa-2 and BxPC-3 cells had 178 and 218 differentiating metabolites, respectively. HPAF-II cells treated with gemcitabine had significantly higher levels of N-acetylneuraminic acid and 7-dehydrocholesterol compared with the control group. In contrast, these metabolites were significantly lower or non-significant in BxPC-3 treated cells. Pathway analysis revealed that the steroid biosynthesis pathway was significantly perturbed in HPAF-II cells, whereas amino sugar and nucleotide sugar metabolism was predominantly altered in BxPC-3 cells. Conclusions: Overall, this exploratory study reveals metabolic differences between treated and untreated cells to derive targeted therapeutic strategies that could be used in the future to improve treatment outcomes for PDAC patients. Full article
(This article belongs to the Special Issue Pharmacometabolomics in Drug Mechanism, Efficacy and Toxicity)
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