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Application of Computational Tools to Health and Environmental Sciences, Volume II

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Editorial01 December 2022
Editorial: Application of computational tools to health and environmental sciences, Volume II

The scarcity of human data, the limitation of time and resources for experimental testing, and societal pressure to develop animal-free testing strategies are driving the field of toxicology toward new methods to generate and interpret data for chemical risk assessment (1). Computational toxicology is an emerging multi-disciplinary research field that incorporates diverse disciplines such as computational sciences, bioinformatics, machine learning, chemo-informatics, systems biology, toxicogenomics, and toxicokinetics (2,3).The ability to rapidly screen chemicals for biological activity and reduce the use of animals in toxicity testing has been the goal of regulatory toxicology for several decades. With current technological and scientific advances, scientists seek to apply high throughput screening assays and computational toxicology techniques to evaluate and screen large numbers of chemicals and drug data sets for biological activity (3)(4)(5).The availability of in vitro toxicokinetic data is essential to meet the growing regulatory need to improve chemical safety assessments (6,7). With the availability of a growing number of commercial and opensource computational tools and databases for quantitative structure-activity relationship (QSAR) and physiologically-based pharmacokinetic (PBPK) modeling, scientists are developing workflows that integrate new approach methodologies (NAMs), in silico techniques and in vitro data to predict biological activity in humans (8,9). This research topic on applying computational tools to health and environmental sciences brings together exemplars of current modeling efforts that seek to play an important role in next-generation risk assessment, such as:• Understanding toxicokinetics of xenobiotics based on omics approaches • Development and acceptance of high-throughput computational tools • Building data-driven models to identify chemicals associated with adverse outcome pathways (AOPs) and toxicity• Development and application of a computational workflow for probabilistic quantitative in vitro to in vivo extrapolation (QIVIVE) in environmental risk assessment

The overall aim is to develop and engage model developers and users to promote and maximize benefits from basic and applied research that is being undertaken to protect public and environmental health.Nicolas et al. presented a case study demonstrating the utility of exploiting existing computational methods (ratio of surrogate hazard and exposure data, called margins of exposure) at the preassessment phase of a tiered risk-based approach to prioritize thousands of untested chemicals quickly and conservatively for further research. In summary, this research topic presents some recent developments and perspectives on the challenges in computational toxicological modeling, their applications, integration of data and tools, and their potential to meet different case scenarios within environmental and human health risk assessment. The development of computational toxicology tools and approaches should accelerate with the availability of open-source toxicological databases to provide a more quantitative, biologically based assessment of the risk of chemicals in the environment.

1,667 views

4 citations

Estimating provisional margins of exposure for data-poor chemicals using high-throughput computational methods
Current computational technologies hold promise for prioritizing the testing of the thousands of chemicals in commerce. Here, a case study is presented demonstrating comparative risk-prioritization approaches based on the ratio of surrogate hazard and exposure data, called margins of exposure (MoEs). Exposures were estimated using a U.S. EPA’s ExpoCast predictive model (SEEM3) results and estimates of bioactivity were predicted using: (1) oral equivalent doses (OEDs) derived from U.S. EPA’s ToxCast high-throughput screening program, together with in vitro to in vivo extrapolation and (2) thresholds of toxicological concern (TTCs) determined using a structure-based decision-tree using the Toxtree open source software. To ground-truth these computational approaches, we compared the MoEs based on predicted noncancer TTC and OED values to those derived using the traditional method of deriving points of departure from no-observed adverse effect levels (NOAELs) from in vivo oral exposures in rodents. TTC-based MoEs were lower than NOAEL-based MoEs for 520 out of 522 (99.6%) compounds in this smaller overlapping dataset, but were relatively well correlated with the same (r2 = 0.59). TTC-based MoEs were also lower than OED-based MoEs for 590 (83.2%) of the 709 evaluated chemicals, indicating that TTCs may serve as a conservative surrogate in the absence of chemical-specific experimental data. The TTC-based MoE prioritization process was then applied to over 45,000 curated environmental chemical structures as a proof-of-concept for high-throughput prioritization using TTC-based MoEs. This study demonstrates the utility of exploiting existing computational methods at the pre-assessment phase of a tiered risk-based approach to quickly, and conservatively, prioritize thousands of untested chemicals for further study.

4,380 views

12 citations

SimRFlow: An R-based workflow for automated high-throughput PBPK simulation with the Simcyp® simulator
TECHNOLOGY AND CODE
25 August 2022
SimRFlow: An R-based workflow for automated high-throughput PBPK simulation with the Simcyp® simulator
Hiba Khalidi, 6 more and Frederic Y. Bois
SimRFlow is a high-throughput physiologically based pharmacokinetic (PBPK) modelling tool which uses Certara’s Simcyp® simulator. The workflow is comprised of three main modules: 1) a Data Collection module for automated curation of physicochemical (from ChEMBL and the Norman Suspect List databases) and experimental data (i.e.: clearance, plasma-protein binding, and blood-to-plasma ratio, from httk-R package databases), 2) a Simulation module which activates the Simcyp® simulator and runs Monte Carlo simulations on virtual subjects using the curated data, and 3) a Data Visualisation module for understanding the simulated compound-specific profiles and predictions. SimRFlow has three administration routes (oral, intravenous, dermal) and allows users to change some simulation parameters including the number of subjects, simulation duration, and dosing. Users are only expected to provide a file of the compounds they wish to simulate, and in return the workflow provides summary statistics, concentration-time profiles of various tissue types, and a database file (containing in-depth results) for each simulated compound. This is presented within a guided and easy-to-use R Shiny interface which provides many plotting options for the visualisation of concentration-time profiles, parameter distributions, trends between the different parameters, as well as comparison of predicted parameters across all batch-simulated compounds. The in-built R functions can be assembled in user-customised scripts which allows for the modification of the workflow for different purposes. SimRFlow proves to be a time-efficient tool for simulating a large number of compounds without any manual curation of physicochemical or experimental data necessary to run Simcyp® simulations.

7,271 views

19 citations

Derivation of a Human In Vivo Benchmark Dose for Bisphenol A from ToxCast In Vitro Concentration Response Data Using a Computational Workflow for Probabilistic Quantitative In Vitro to In Vivo Extrapolation
A computational workflow which integrates physiologically based kinetic (PBK) modelling; global sensitivity analysis (GSA), Approximate Bayesian Computation (ABC), Markov Chain Monte Carlo (MCMC) simulation and the Virtual Cell Based Assay (VCBA) for the estimation of the active, free in vitro concentration of chemical in the reaction medium was developed to facilitate quantitative in vitro to in vivo extrapolation (QIVIVE). The workflow was designed to estimate parameter and model uncertainty within a computationally efficient framework. The workflow was tested using a human PBK model for bisphenol A (BPA) and high throughput screening (HTS) in vitro concentration-response data, for estrogen and pregnane X receptor activation determined in human liver and kidney cell lines, from the ToxCast/Tox21 database. In vivo benchmark dose 10% lower confidence limits (BMDL10) for oral uptake of BPA (ng/kg BW/day) were calculated from the in vivo dose-responses and compared to the human equivalent dose (HED) BMDL10 for relative kidney weight change in the mouse derived by European Food Safety Authority (EFSA). Three from four in vivo BMDL10 values calculated in this study were similar to the EFSA values whereas the fourth was much smaller. The derivation of an uncertainty factor (UF) to accommodate the uncertainties associated with measurements using human cell lines in vitro, extrapolated to in vivo, could be useful for the derivation of Health Based Guidance Values (HBGV).

4,716 views

11 citations

ORIGINAL RESEARCH
11 July 2022
Correlation Analysis of Variables From the Atherosclerosis Risk in Communities Study
Meisha Mandal, 9 more and Stephen Edwards

2,429 views

1 citations

Physiologically Based Pharmacokinetic Modeling of Cefadroxil in Mouse, Rat, and Human to Predict Concentration–Time Profile at Infected Tissue
ORIGINAL RESEARCH
23 December 2021
Physiologically Based Pharmacokinetic Modeling of Cefadroxil in Mouse, Rat, and Human to Predict Concentration–Time Profile at Infected Tissue
Zhongxia Tan, 2 more and Le Sun
The aim of this study was to develop physiologically based pharmacokinetic (PBPK) models capable of simulating cefadroxil concentrations in plasma and tissues in mouse, rat and human. PBPK models in this study were consist of 14 tissues and 2 blood compartments. They were established using measured Kp in mouse and rat, absolute expression levels of hPEPT1 along the entire length of the human intestine, as well as the transporter kinetic parameters. The PBPK models also assumed that all the tissues were well-stirred compartments with perfusion rate limitations, and the ratio of the concentration in tissue to the unbound concentration in plasma is identical across species. These PBPK models were validated strictly by a series of observed plasma concentration - time profile data. The average fold error (AFE) and absolute average fold error (AAFE) values were all smaller than 2. The models’ rationality and accuracy were further demonstrated by the almost consistent Vss calculated by PBPK model and noncompartmental method, as well as good allometric scaling relationship of Vss and CL. The model suggests that hPEPT1 is the major transporter responsible for the oral absorption of cefadroxil in human, and the plasma concentration-time profiles of cefadroxil was not sensitive to dissolution rate faster than T85% = 2 h. The cefadroxil PBPK model in human is reliable, and can be used to predict concentration-time profile at infected tissue. It may be useful for dose selection and informative decision making during clinical trials, dosage forms design of cefadroxil, and provide a reference for the PBPK model establishment of hPEPT1 substrate.

7,437 views

18 citations

ORIGINAL RESEARCH
22 December 2021
Toxicokinetics of Arenobufagin and its Cardiotoxicity Mechanism Exploration Based on Lipidomics and Proteomics Approaches in Rats
Lijuan Zhao, 8 more and Haiyu Zhao
Arenobufagin (ArBu), one of the main active bufadienolides of toad venom with cardiotonic effect, analgesic effect, and outstanding anti-tumor potentiality, is also a potential cardiotoxic component. In the present study, the cardiac effect of ArBu and its underlying mechanism were explored by integrating data such as heart rates, toxicokinetics, myocardial enzyme and brain natriuretic peptide (BNP) activity, pathological sections, lipidomics and proteomics. Under different doses, the cardiac effects turned out to be different. The oral dose of 60 mg/kg of ArBu sped up the heart rate. However, 120 mg/kg ArBu mainly reduced the heart rate. Over time, they all returned to normal, consisting of the trend of ArBu concentration-time curve. High concentrations of myocardial enzymes and BNP indicated that ArBu inhibited or impaired the cardiac function of rats. Pathological sections of hearts also showed that ArBu caused myocardial fiber disorder and rupture, in which the high-dose group was more serious. At the same time, serum and heart tissue lipidomics were used to explore the changes in body lipid metabolism under different doses. The data indicated a larger difference in the high-dose ArBu group. There were likewise many significant differences in the proteomics of the heart. Furthermore, a multi-layered network was used to integrate the above information to explore the potential mechanism. Finally, 4 proteins that were shown to be significantly and differentially expressed were validated by targeted proteomics using parallel reaction monitoring (PRM) analysis. Our findings indicated that ArBu behaved as a bidirectional regulation of the heart. The potential mechanism of cardiac action was revealed with the increased dose, which provided a useful reference for the safety of clinical application of ArBu.
Toxicokinetics of Arenobufagin and its Cardiotoxicity Mechanism Exploration Based on Lipidomics and Proteomics Approaches in Rats

5,606 views

5 citations