Advances in Computational Methods of Studying Exposure to Chemicals

A special issue of Toxics (ISSN 2305-6304). This special issue belongs to the section "Novel Methods in Toxicology Research".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 4448

Special Issue Editors


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Guest Editor
Office of Innovation and Analytics, Agency for Toxic Substances and Disease Registry (ATSDR), Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA
Interests: computational toxicology; machine learning methods; PBPK; QSAR; risk assessment; chemical mixtures; computational systems biology; NAMs; fate and transport modeling; statistics
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Guest Editor
Department of Environmental Sciences, College of Natural & Agricultural Sciences, University of California, Riverside, CA 92521, USA
Interests: computational toxicology; environmental health; artificial intelligence and machine learning

Special Issue Information

Dear Colleagues,

The use of computational approaches has changed our understanding of toxicology by revealing important information about chemical exposure. The potential risks and effects of diverse chemical substances on human health and the environment are predicted with these methods using cutting-edge algorithms, scientific methods, technologies, and mathematical models. In this Special Issue, we explore some of the noteworthy developments and applications in computational approaches and new alternative methods that have aided our understanding of chemical exposure and risk. It will include case studies and examples of models and approaches in environmental and human health; the integration of several data streams and approaches; chemical-exposure–gene interactions; the application of NAMs for risk assessment; emerging chemicals; in silico and mixture frameworks; and research that highlights and illustrates advances in computer modeling, exposures, and chemical risk assessments.

The current information on databases, chemicals, toxicity, and multiple data streams remains insufficient to address exposure, the biomarkers of their effect, and their risks. Therefore, the aim of this Special Issue is to further contribute to the collection of information, innovative approaches, and research related to advancements in computational modeling as well as new approaches and methods that address chemical exposures and risks.

This Special Issue welcomes original articles as well as systematic reviews on these relevant topics, including but not limited to the following:

  • Computational toxicology
  • Machine learning
  • Quantitative Structure-Activity Relationship (QSAR)
  • In silico modeling
  • Molecular Docking and Molecular Dynamics Simulations
  • PBPK and PK modeling
  • Fate and transport modeling
  • High-Throughput Screening (HTS)
  • Integrated Testing Strategies (ITS) Artificial intelligence
  • Risk assessment and modeling
  • Adverse outcome pathway (AOP)
  • New approach methodologies (NAMs)
  • Chemical mixtures

Dr. Patricia Ruiz
Dr. Wei-Chun Chou
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Toxics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 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

  • computational toxicology
  • machine learning
  • quantitative structure-activity relationship (QSAR)
  • in silico modeling
  • molecular docking and molecular dynamics simulations
  • PBPK and PK modeling
  • fate and transport modeling
  • high-throughput screening (HTS)
  • integrated testing strategies (ITS)
  • artificial intelligence
  • risk assessment
  • adverse outcome pathway (AOP)
  • new approach methodologies (NAMs)
  • chemical mixtures

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Published Papers (3 papers)

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Research

14 pages, 1117 KB  
Article
Dimethyl Sulfoxide as a Biocompatible Extractant for Enzymatic Bioluminescent Toxicity Assays: Experimental Validation and Molecular Dynamics Insights
by Oleg S. Sutormin, Victoria I. Lonshakova-Mukina, Anna A. Deeva, Alena A. Gromova, Ruslan Ya. Bajbulatov and Valentina A. Kratasyuk
Toxics 2025, 13(12), 1038; https://doi.org/10.3390/toxics13121038 - 30 Nov 2025
Viewed by 266
Abstract
Diesel fuel is among the most persistent petroleum-derived pollutants in soils, posing long-term ecological and toxicological risks, especially in cold-climate regions where natural degradation is limited. Reliable assessment of diesel-contaminated soils remains difficult because conventional solvent-based analyses are incompatible with bioassays, while aqueous [...] Read more.
Diesel fuel is among the most persistent petroleum-derived pollutants in soils, posing long-term ecological and toxicological risks, especially in cold-climate regions where natural degradation is limited. Reliable assessment of diesel-contaminated soils remains difficult because conventional solvent-based analyses are incompatible with bioassays, while aqueous extracts underestimate hydrocarbon toxicity. This study evaluated dimethyl sulfoxide (DMSO) as a biocompatible extractant for enzymatic bioluminescent toxicity assays employing the coupled NAD(P)H:FMN-oxidoreductase and bacterial luciferase (BLuc–Red) system. Soil samples artificially contaminated with diesel fuel were analyzed using DMSO extracts in combination with molecular dynamics (MD) simulations to examine enzyme stability in solvent environments. Moderate DMSO concentrations (4–6% v/v) maintained enzymatic activity, whereas higher levels caused partial inhibition. Diesel hydrocarbons dissolved in DMSO strongly suppressed luminescence, and soil extracts exhibited a clear dose–response relationship between contamination level and enzymatic inhibition. MD simulations confirmed that neither DMSO nor diesel induced large-scale unfolding of luciferase or reductase, though localized flexibility changes and partial dehydration of active site residues was observed, which may account for the detected inhibition of luminescence at higher DMSO concentrations. These results demonstrate that DMSO provides an effective and biocompatible extraction medium for enzymatic bioluminescent assays, enabling accurate toxicity evaluation of petroleum-contaminated soils and offering a promising tool for ecotoxicological risk assessment in oil-impacted environments. Full article
(This article belongs to the Special Issue Advances in Computational Methods of Studying Exposure to Chemicals)
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18 pages, 2423 KB  
Article
Toxicokinetic Characterization of MDM Hydantoin via Stable Metabolite DMH: Population Modeling for Predicting Dermal Formaldehyde Formation
by Woohyung Jung, Jaewoong Lee, Woojin Kim, Seongwon Kim, Woojin Nam, In-Soo Myeong, Kwang Ho Kim, Soyoung Shin and Tae Hwan Kim
Toxics 2025, 13(11), 917; https://doi.org/10.3390/toxics13110917 - 25 Oct 2025
Viewed by 589
Abstract
MDM hydantoin (MDMH), a formaldehyde-releasing preservative widely used in cosmetics, poses potential health risks due to its conversion to formaldehyde and systemically absorbed metabolites. Current safety assessments lack quantitative exposure data due to rapid degradation of MDMH in biological matrices. In the present [...] Read more.
MDM hydantoin (MDMH), a formaldehyde-releasing preservative widely used in cosmetics, poses potential health risks due to its conversion to formaldehyde and systemically absorbed metabolites. Current safety assessments lack quantitative exposure data due to rapid degradation of MDMH in biological matrices. In the present study, we developed a validated LC-MS/MS assay for simultaneous determination of MDMH and its stable metabolite DMH in rat plasma, and characterized their toxicokinetics using population modeling following intravenous and transdermal administration. MDMH exhibited extremely rapid elimination (t1/2 = 0.4 ± 0.1 min) with near-complete conversion to DMH (97.6 ± 9.6%), while DMH demonstrated prolonged retention (t1/2 = 174.2 ± 12.2 min) and complete bioavailability (100.9 ± 18.0%) after transdermal application. Population modeling estimated that 84% (relative standard error: 42.8%) of applied MDMH undergoes cutaneous absorption and metabolism to DMH and formaldehyde within skin tissues. This study demonstrates that stable metabolite monitoring combined with population modeling enables toxicokinetic characterization of rapidly degrading compounds following dermal exposure. Full article
(This article belongs to the Special Issue Advances in Computational Methods of Studying Exposure to Chemicals)
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24 pages, 4143 KB  
Article
The Role of Simulation Science in Public Health at the Agency for Toxic Substances and Disease Registry: An Overview and Analysis of the Last Decade
by Siddhi Desai, Jewell Wilson, Chao Ji, Jason Sautner, Andrew J. Prussia, Eugene Demchuk, M. Moiz Mumtaz and Patricia Ruiz
Toxics 2024, 12(11), 811; https://doi.org/10.3390/toxics12110811 - 12 Nov 2024
Cited by 2 | Viewed by 2779
Abstract
Environmental exposures are ubiquitous and play a significant, and sometimes understated, role in public health as they can lead to the development of various chronic and infectious diseases. In an ideal world, there would be sufficient experimental data to determine the health effects [...] Read more.
Environmental exposures are ubiquitous and play a significant, and sometimes understated, role in public health as they can lead to the development of various chronic and infectious diseases. In an ideal world, there would be sufficient experimental data to determine the health effects of exposure to priority environmental contaminants. However, this is not the case, as emerging chemicals are continuously added to this list, furthering the data gaps. Recently, simulation science has evolved and can provide appropriate solutions using a multitude of computational methods and tools. In its quest to protect communities across the country from environmental health threats, ATSDR employs a variety of simulation science tools such as Physiologically Based Pharmacokinetic (PBPK) modeling, Quantitative Structure–Activity Relationship (QSAR) modeling, and benchmark dose (BMD) modeling, among others. ATSDR’s use of such tools has enabled the agency to evaluate exposures in a timely, efficient, and effective manner. ATSDR’s work in simulation science has also had a notable impact beyond the agency, as evidenced by external researchers’ widespread appraisal and adaptation of the agency’s methodology. ATSDR continues to advance simulation science tools and their applications by collaborating with researchers within and outside the agency, including other federal/state agencies, NGOs, the private sector, and academia. Full article
(This article belongs to the Special Issue Advances in Computational Methods of Studying Exposure to Chemicals)
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