Toward a Comprehensive Molecular Design Framework for Reduced Hazard

Toward Property-Based Regulation

An expanding web of adverse impacts on people and the environment has been steadily linked to anthropogenic chemicals and their proliferation. Central to this web are the regulatory structures intended to protect human and environmental health through the control of new molecules. Through chronically insufficient and inefficient action, the current chemical-by-chemical regulatory approach, which considers regulation at the level of chemical identity, has enabled many adverse impacts to develop and persist. Recognizing the link between fundamental physicochemical properties and hazards, we describe a new paradigm─property-based regulation. By regulating physicochemical properties, we show how governments can delineate and enforce safe chemical spaces, increasing the scalability of chemical assessments, reducing the time and resources to regulate a substance, and providing transparency for chemical designers. We highlight sparse existing property-based approaches and demonstrate their applicability using bioaccumulation as an example. Finally, we present a path to implementation in the United States, prescribing roles and steps for government, nongovernmental organizations, and industry to accelerate this transition, to the benefit of all.

Comparison of seven in silico tools for evaluating of daphnia and fish acute toxicity: case study on Chinese Priority Controlled Chemicals and new chemicals

BACKGROUND

A number of predictive models for aquatic toxicity are available, however, the accuracy and extent of easy to use of these in silico tools in risk assessment still need further studied. This study evaluated the performance of seven in silico tools to daphnia and fish: ECOSAR, T.E.S.T., Danish QSAR Database, VEGA, KATE, Read Across and Trent Analysis. 37 Priority Controlled Chemicals in China (PCCs) and 92 New Chemicals (NCs) were used as validation dataset.

RESULTS

In the quantitative evaluation to PCCs with the criteria of 10-fold difference between experimental value and estimated value, the accuracies of VEGA is the highest among all of the models, both in prediction of daphnia and fish acute toxicity, with accuracies of 100% and 90% after considering AD, respectively. The performance of KATE, ECOSAR and T.E.S.T. is similar, with accuracies are slightly lower than VEGA. The accuracy of Danish Q.D. is the lowest among the above tools with which QSAR is the main mechanism. The performance of Read Across and Trent Analysis is lowest among all of the tested in silico tools. The predictive ability of models to NCs was lower than that of PCCs possibly because never appeared in training set of the models, and ECOSAR perform best than other in silico tools.

CONCLUSION

QSAR based in silico tools had the greater prediction accuracy than category approach (Read Across and Trent Analysis) in predicting the acute toxicity of daphnia and fish. Category approach (Read Across and Trent Analysis) requires expert knowledge to be utilized effectively. ECOSAR performs well in both PCCs and NCs, and the application shoud be promoted in both risk assessment and priority activities. We suggest that distribution of multiple data and water solubility should be considered when developing in silico models. Both more intelligent in silico tools and testing are necessary to identify hazards of Chemicals.

Toward Sustainable Environmental Quality: Priority Research Questions for Asia

Environmental and human health challenges are pronounced in Asia, an exceptionally diverse and complex region where influences of global megatrends are extensive and numerous stresses to environmental quality exist. Identifying priorities necessary to engage grand challenges can be facilitated through horizon scanning exercises, and to this end we identified and examined 23 priority research questions needed to advance toward more sustainable environmental quality in Asia, as part of the Global Horizon Scanning Project. Advances in environmental toxicology, environmental chemistry, biological monitoring, and risk-assessment methodologies are necessary to address the adverse impacts of environmental stressors on ecosystem services and biodiversity, with Asia being home to numerous biodiversity hotspots. Intersections of the food-energy-water nexus are profound in Asia; innovative and aggressive technologies are necessary to provide clean water, ensure food safety, and stimulate energy efficiency, while improving ecological integrity and addressing legacy and emerging threats to public health and the environment, particularly with increased aquaculture production. Asia is the largest chemical-producing continent globally. Accordingly, sustainable and green chemistry and engineering present decided opportunities to stimulate innovation and realize a number of the United Nations Sustainable Development Goals. Engaging the priority research questions identified herein will require transdisciplinary coordination through existing and nontraditional partnerships within and among countries and sectors. Answering these questions will not be easy but is necessary to achieve more sustainable environmental quality in Asia. Environ Toxicol Chem 2020;39:1485-1505. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Going All In: A Strategic Investment in In Silico Toxicology

As vast numbers of new chemicals are introduced to market annually, we are faced with the grand challenge of protecting humans and the environment while minimizing economically and ethically costly animal testing. In silico models promise to be the solution we seek, but we find ourselves at crossroads of future development efforts that would ensure standalone applicability and reliability of these tools. A conscientious effort that prioritizes experimental testing to support the needs of in silico models (versus regulatory needs) is called for to achieve this goal. Using economic analogy in the title of this work, we argue that a prudent investment is to go all-in to support in silico model development, rather than gamble our future by keeping the status quo of a "balanced portfolio" of testing approaches. We discuss two paths to future in silico toxicology-one based on big-data statistics ("broadsword"), and the other based on direct modeling of molecular interactions ("scalpel")-and offer rationale that the latter approach is more transparent, is better aligned with our quest for fundamental knowledge, and has a greater potential to succeed if we are willing to transform our toxicity-testing paradigm.

Comparison of Small Molecule Biotransformation Half-Lives between Activated Sludge and Soil: Opportunities for Read-Across?

Compartment-specific degradation half-lives are essential pieces of information in the regulatory risk assessment of synthetic chemicals. However, their measurement according to regulatory testing guidelines is laborious and costly. Despite the obvious ecological and economic benefits of knowing environmental degradability as early as possible, its consideration in the early phases of rational chemical design is therefore challenging. Here, we explore the possibility to use half-lives determined in highly time- and work-efficient biotransformation experiments with activated sludge and mixtures of chemicals to predict soil half-lives from regulatory simulation studies. We experimentally determined half-lives for 52 structurally diverse agrochemical active ingredients in batch reactors with three concentrations of the same activated sludge. We then developed bi- and multivariate models for predicting half-lives in soil by regressing the experimentally determined half-lives in activated sludge against average soil half-lives of the same chemicals extracted from regulatory data. The models differed in how we accounted for sorption-related bioavailability differences in soil and activated sludge. The best-performing models exhibited good coefficients of determination (R² of around 0.8) and low average errors (<factor of 3 in half-life predictions) and were robust in cross-validation. From a practical perspective, these results suggest that it may indeed be possible to read across from half-lives determined in highly efficient biotransformation experiments in activated sludge to soil half-lives, which are obtained from much more work- and resource-intense regulatory studies, and that these predictions are clearly superior to predictions based on the output of BIOWIN, a publicly available quantitative structure-biodegradation relationship (QSBR) model. From a theoretical perspective, these results suggest that soil and activated sludge microbial communities, although certainly different in terms of taxonomic composition, may be functionally similar with respect to the enzymatic transformation of environmentally relevant concentrations of a diverse range of chemical compounds.

Toward Less Hazardous Industrial Compounds: Coupling Quantum Mechanical Computations, Biomarker Responses, and Behavioral Profiles To Identify Bioactivity of SN2 Electrophiles in Alternative Vertebrate Models

Sustainable molecular design of less hazardous chemicals promises to reduce risks to public health and the environment. Computational chemistry modeling coupled with alternative toxicology models (e.g., larval fish) present unique high-throughput opportunities to understand structural characteristics eliciting adverse outcomes. Numerous environmental contaminants with reactive properties can elicit oxidative stress, an important toxicological response associated with diverse adverse outcomes (i.e., cancer, diabetes, neurodegenerative disorders, etc.). We examined a common chemical mechanism (bimolecular nucleophilic substitution (S_N2)) associated with oxidative stress using property-based computational modeling coupled with acute (mortality) and sublethal (glutathione, photomotor behavior) responses in the zebrafish (Danio rerio) and the fathead minnow (Pimephales promelas) models to identify whether relationships exist among biological responses and molecular attributes of industrial chemicals. Following standardized methods, embryonic zebrafish and larval fathead minnows were exposed separately to eight different S_N2 compounds for 96 h. Acute and sublethal responses were compared to computationally derived in silico chemical descriptors. Specifically, frontier molecular orbital energies were significantly related to acute LC₅₀ values and photomotor response (PMR) no observed effect concentrations (NOECs) in both fathead minnow and zebrafish. This reactivity index, LC₅₀ values, and PMR NOECs were also significantly related to whole body glutathione (GSH) levels, suggesting that acute and chronic toxicity results from protein adduct formation for S_N2 electrophiles. Shared refractory locomotor response patterns among study compounds and two alternative vertebrate models appear informative of electrophilic properties associated with oxidative stress for S_N2 chemicals. Electrophilic parameters derived from frontier molecular orbitals were predictive of experimental in vivo acute and sublethal toxicity. These observations provide important implications for identifying and designing less hazardous industrial chemicals with reduced potential to elicit oxidative stress through bimolecular nucleophilic substitution.

Polysulfonate Cappings on Upconversion Nanoparticles Prevent Their Disintegration in Water and Provide Superior Stability in a Highly Acidic Medium

The stability of organic cappings on hexagonal NaYF4:Ln3+ upconversion nanoparticles (UCNPs) is crucial for their luminescence efficiency in aqueous solutions. The capping removal quickens as the acidity of the medium increases. We demonstrate here that polysulfonates, namely poly(2-acrylamido-2-methyl-1-propanesulfonate) (PAMPS) and poly(sodium 4-styrene sulfonate) (PSS), remain anchored to the surface of NaYF4:Yb3+,Er3+/Tm3 UCNPs even at a pH as low as 2 due to strong acidity of the sulfonate anchoring groups (pK a of ca. -3). Bare UCNPs progressively disintegrate into their compositional F-, Na+, Y3+, and Ln3+ ions. Their disintegration is particularly worrying in highly diluted dispersions of nanoparticles because both the lanthanide ions and/or the bare UCNPs can cause undesirable interference in a chemical or biological environment. Remarkably, the UC@PSS nanohybrid is particularly chemically stable, exhibiting an amazingly low release of Y3+ and Ln3+ ions for up to 96 h in highly diluted water dispersions (10 μg/mL). Additional advantages of the use of PSS as capping layer are its biocompatibility and its high dispersibility in water, together with easy further functionalization of the UCNP@PSS nanohybrids.

The Impact of Novel Assessment Methodologies in Toxicology on Green Chemistry and Chemical Alternatives

The field of experimental toxicology is rapidly advancing by incorporating novel techniques and methods that provide a much more granular view into the mechanisms of potential adverse effects of chemical exposures on human health. The data from various in vitro assays and computational models are useful not only for increasing confidence in hazard and risk decisions, but also are enabling better, faster and cheaper assessment of a greater number of compounds, mixtures, and complex products. This is of special value to the field of green chemistry where design of new materials or alternative uses of existing ones is driven, at least in part, by considerations of safety. This article reviews the state of the science and decision-making in scenarios when little to no data may be available to draw conclusions about which choice in green chemistry is "safer." It is clear that there is no "one size fits all" solution and multiple data streams need to be weighed in making a decision. Moreover, the overall level of familiarity of the decision-makers and scientists alike with new assessment methodologies, their validity, value and limitations is evolving. Thus, while the "impact" of the new developments in toxicology on the field of green chemistry is great already, it is premature to conclude that the data from new assessment methodologies have been widely accepted yet.

Kinetics of Glutathione Depletion and Antioxidant Gene Expression as Indicators of Chemical Modes of Action Assessed in Vitro in Mouse Hepatocytes with Enhanced Glutathione Synthesis

Here we report a vertically integrated in vitro - in silico study that aims to elucidate the molecular initiating events involved in the induction of oxidative stress (OS) by seven diverse chemicals (cumene hydroperoxide, t-butyl hydroperoxide, hydroquinone, t-butyl hydroquinone, bisphenol A, Dinoseb, and perfluorooctanoic acid). To that end, we probe the relationship between chemical properties, cell viability, glutathione (GSH) depletion, and antioxidant gene expression. Concentration-dependent effects on cell viability were assessed by MTT assay in two Hepa-1 derived mouse liver cell lines: a control plasmid vector transfected cell line (Hepa-V), and a cell line with increased glutamate-cysteine ligase (GCL) activity and GSH content (CR17). Changes to intracellular GSH content and mRNA expression levels for the Nrf2-driven antioxidant genes Gclc, Gclm, heme oxygenase-1 ( Hmox1), and NADPH quinone oxidoreductase-1 ( Nqo1) were monitored after sublethal exposure to the chemicals. In silico models of covalent and redox reactivity were used to rationalize differences in activity of quinones and peroxides. Our findings show CR17 cells were generally more resistant to chemical toxicity and showed markedly attenuated induction of OS biomarkers; however, differences in viability effects between the two cell lines were not the same for all chemicals. The results highlight the vital role of GSH in protecting against oxidative stress-inducing chemicals as well as the importance of probing molecular initiating events in order to identify chemicals with lower potential to cause oxidative stress.

Comparative behavioral toxicology with two common larval fish models: Exploring relationships among modes of action and locomotor responses

Behavioral responses inform toxicology studies by rapidly and sensitively detecting molecular initiation events that propagate to physiological changes in individuals. These behavioral responses can be unique to chemical specific mechanisms and modes of action (MOA) and thus present diagnostic utility. In an initial effort to explore the use of larval fish behavioral response patterns in screening environmental contaminants for toxicity and to identify behavioral responses associated with common chemical specific MOAs, we employed the two most common fish models, the zebrafish and the fathead minnow, to define toxicant induced swimming activity alterations during interchanging photoperiods. Though the fathead minnow (Pimephales promelas) is a common model for aquatic toxicology research and regulatory toxicology practice, this model has received little attention in behavioral studies compared to the zebrafish, a common biomedical model. We specifically compared behavioral responses among 7 different chemicals (1-heptanol, phenol, R-(-)-carvone, citalopram, diazinon, pentylenetetrazole (PTZ), and xylazine) that were selected and classified based on anticipated MOA (nonpolar narcosis, polar narcosis, electrophile, specific mechanism) according to traditional approaches to examine whether these comparative responses differ among chemicals with various structure-based predicted toxicity. Following standardized experimental guidelines, zebrafish embryos and fathead minnow larvae were exposed for 96 h to each compound then were observed using digital behavioral analysis. Behavioral observations included photomotor responses, distance traveled, and stimulatory, refractory and cruising locomotor activity. Though fathead minnow larvae displayed greater behavioral sensitivity to 1-heptanol, phenol and citalopram, zebrafish were more sensitive to diazinon and R-(-)-carvone. Both fish models were equally sensitive to xylazine and PTZ. Further, the pharmaceuticals citalopram and xylazine significantly affected behavior at therapeutic hazard values, and each of the seven chemicals elicited unique behavioral response profiles. Larval fish behaviors appear useful as early tier diagnostics to identify mechanisms and pathways associated with diverse biological activities for chemicals lacking mechanistic data.

How Green is Your Plasticizer?

Plasticizers are additives that are used to impart flexibility to polymer blends and improve their processability. Plasticizers are typically not covalently bound to the polymers, allowing them to leach out over time, which results in human exposure and environmental contamination. Phthalates, in particular, have been the subject of increasing concern due to their established ubiquity in the environment and their suspected negative health effects, including endocrine disrupting and anti-androgenic effects. As there is mounting pressure to find safe replacement compounds, this review addresses the design and experimental elements that should be considered in order for a new or existing plasticizer to be considered green. Specifically, a multi-disciplinary and holistic approach should be taken which includes toxicity testing (both in vitro and in vivo), biodegradation testing (with attention to metabolites), as well as leaching studies. Special consideration should also be given to the design stages of producing a new molecule and the synthetic and scale-up processes should also be optimized. Only by taking a multi-faceted approach can a plasticizer be considered truly green.

The Need for, and the Role of the Toxicological Chemist in the Design of Safer Chemicals

During the past several decades, there has been an ever increasing emphasis for designers of new commercial (nonpharmaceutical) chemicals to include considerations of the potential impacts a planned chemical may have on human health and the environment as part of the design of the chemical, and to design chemicals such that they possess the desired use efficacy while minimizing threats to human health and the environment. Achievement of this goal would be facilitated by the availability of individuals specifically and formally trained to design such chemicals. Medicinal chemists are specifically trained to design and develop safe and clinically efficacious pharmaceutical substances. No such formally trained science hybrid exists for the design of safer commercial (nonpharmaceutical) chemicals. This article describes the need for and role of the "toxicological chemist," an individual who is formally trained in synthetic organic chemistry, biochemistry, physiology, toxicology, environmental science, and in the relationships between structure and commercial use efficacy, structure and toxicity, structure and environmental fate and effects, and global hazard, and trained to integrate this knowledge to design safer commercially efficacious chemicals. Using examples, this article illustrates the role of the toxicological chemist in designing commercially efficacious, safer chemical candidates.

Toward the Design of Less Hazardous Chemicals: Exploring Comparative Oxidative Stress in Two Common Animal Models

Sustainable molecular design of less hazardous chemicals presents a potentially transformative approach to protect public health and the environment. Relationships between molecular descriptors and toxicity thresholds previously identified the octanol-water distribution coefficient, log D, and the HOMO-LUMO energy gap, ΔE, as two useful properties in the identification of reduced aquatic toxicity. To determine whether these two property-based guidelines are applicable to sublethal oxidative stress (OS) responses, two common aquatic in vivo models, the fathead minnow (Pimephales promelas) and zebrafish (Danio rerio), were employed to examine traditional biochemical biomarkers (lipid peroxidation, DNA damage, and total glutathione) and antioxidant gene activation following exposure to eight structurally diverse industrial chemicals (bisphenol A, cumene hydroperoxide, dinoseb, hydroquinone, indene, perfluorooctanoic acid, R-(-)-carvone, and tert-butyl hydroperoxide). Bisphenol A, cumene hydroperoxide, dinoseb, and hydroquinone were consistent inducers of OS. Glutathione was the most consistently affected biomarker, suggesting its utility as a sensitivity response to support the design of less hazardous chemicals. Antioxidant gene expression (changes in nrf2, gclc, gst, and sod) was most significantly (p < 0.05) altered by R-(-)-carvone, cumene hydroperoxide, and bisphenol A. Results from the present study indicate that metabolism of parent chemicals and the role of their metabolites in molecular initiating events should be considered during the design of less hazardous chemicals. Current empirical and computational findings identify the need for future derivation of sustainable molecular design guidelines for electrophilic reactive chemicals (e.g., SN2 nucleophilic substitution and Michael addition reactivity) to reduce OS related adverse outcomes in vivo.

Ultrasound and green chemistry--Further comments

In the light of recent discussions regarding the association of sonochemistry and sustainable methods, as well as the controversial misuse and abuse of the "green" concept through the scientific literature, this manuscript provides further thoughts hoping to be of benefit to the broad readership of this journal and practitioners of sustainable chemistry in general.

Identifying and designing chemicals with minimal acute aquatic toxicity

Industrial ecology has revolutionized our understanding of material stocks and flows in our economy and society. For this important discipline to have even deeper impact, we must understand the inherent nature of these materials in terms of human health and the environment. This paper focuses on methods to design synthetic chemicals to reduce their intrinsic ability to cause adverse consequence to the biosphere. Advances in the fields of computational chemistry and molecular toxicology in recent decades allow the development of predictive models that inform the design of molecules with reduced potential to be toxic to humans or the environment. The approach presented herein builds on the important work in quantitative structure-activity relationships by linking toxicological and chemical mechanistic insights to the identification of critical physical-chemical properties needed to be modified. This in silico approach yields design guidelines using boundary values for physiochemical properties. Acute aquatic toxicity serves as a model endpoint in this study. Defining value ranges for properties related to bioavailability and reactivity eliminates 99% of the chemicals in the highest concern for acute aquatic toxicity category. This approach and its future implementations are expected to yield very powerful tools for life cycle assessment practitioners and molecular designers that allow rapid assessment of multiple environmental and human health endpoints and inform modifications to minimize hazard.

Advancing safer alternatives through functional substitution

To achieve the ultimate goal of sustainable chemicals management policy–the transition to safer chemicals, materials, products, and processes–current chemicals management approaches could benefit from a broader perspective. Starting with considerations of function, rather than characterizing and managing risks associated with a particular chemical, may provide a different, solutions-oriented lens to reduce risk associated with the uses of chemicals. It may also offer an efficient means, complementing existing tools, to reorient chemicals management approaches from time-intensive risk assessment and risk management based on single chemicals to comparative evaluation of the best options to fulfill a specific function. This article describes a functional approach to chemicals management we call “functional substitution” that encourages decision-makers to look beyond chemical by chemical substitution to find a range of alternatives to meet product performance. We define functional substitution, outline a rationale for greater use of this concept when considering risks posed by uses of chemicals, and provide examples of how functional approaches have been applied toward the identification of alternatives. We also discuss next steps for implementing functional substitution in chemical assessment and policy development.

Sterically Demanding Unsymmetrical Diaryl-λ(3)-iodanes for Electrophilic Pentafluorophenylation and an Approach to α-Pentafluorophenyl Carbonyl Compounds with an All-Carbon Stereocenter

A sterically demanding unsymmetrical pentafluorophenyl-triisopropylphenyl-λ(3)-iodane was developed as an effective reagent for the electrophilic pentafluorophenylation of various β-keto esters and a β-keto amide. 17 examples of α-pentafluorophenylated 1,3-dicarbonyl compounds 3 having a quaternary carbon center are provided. The resulting compounds were nicely transformed into chiral α-pentafluorophenyl ketones with an all-carbon stereogenic center in high yields and high enantioselectivities using asymmetric organocatalysis (up to 98 % ee) or asymmetric metal catalysis (up to 82 % ee).

Designing nanomaterials to maximize performance and minimize undesirable implications guided by the Principles of Green Chemistry

A sustainable material design framework is proposed that emphasizes the importance of establishing structure–property–function (SPF) and structure–property–hazard (SPH) relationships to guide the rational design of ENMs.

Reducing aquatic hazards of industrial chemicals: probabilistic assessment of sustainable molecular design guidelines

Basic toxicological information is lacking for the majority of industrial chemicals. In addition to increasing empirical toxicity data through additional testing, prospective computational approaches to drug development aim to serve as a rational basis for the design of chemicals with reduced toxicity. Recent work has resulted in the derivation of a "rule of 2," wherein chemicals with an octanol-water partition coefficient (log P) less than 2 and a difference between the lowest unoccupied molecular orbital and the highest occupied molecular orbital (ΔE) greater than 9 (log P<2 and ΔE >9 eV) are predicted to be 4 to 5 times less likely to elicit acute or chronic toxicity to model aquatic organisms. The present study examines potential reduction of aquatic toxicity hazards from industrial chemicals if these 2 molecular design guidelines were employed. Probabilistic hazard assessment approaches were used to model the likelihood of encountering industrial chemicals exceeding toxicological categories of concern both with and without the rule of 2. Modeling predicted that utilization of these molecular design guidelines for log P and ΔE would appreciably decrease the number of chemicals that would be designated to be of "high" and "very high" concern for acute and chronic toxicity to standard model aquatic organisms and end points as defined by the US Environmental Protection Agency. For example, 14.5% of chemicals were categorized as having high and very high acute toxicity to the fathead minnow model, whereas only 3.3% of chemicals conforming to the design guidelines were predicted to be in these categories. Considerations of specific chemical classes (e.g., aldehydes), chemical attributes (e.g., ionization), and adverse outcome pathways in representative species (e.g., receptor-mediated responses) could be used to derive future property guidelines for broader classes of contaminants.

Progress in computational toxicology

INTRODUCTION

Computational methods have been widely applied to toxicology across pharmaceutical, consumer product and environmental fields over the past decade. Progress in computational toxicology is now reviewed.

METHODS

A literature review was performed on computational models for hepatotoxicity (e.g. for drug-induced liver injury (DILI)), cardiotoxicity, renal toxicity and genotoxicity. In addition various publications have been highlighted that use machine learning methods. Several computational toxicology model datasets from past publications were used to compare Bayesian and Support Vector Machine (SVM) learning methods.

RESULTS

The increasing amounts of data for defined toxicology endpoints have enabled machine learning models that have been increasingly used for predictions. It is shown that across many different models Bayesian and SVM perform similarly based on cross validation data.

DISCUSSION

Considerable progress has been made in computational toxicology in a decade in both model development and availability of larger scale or 'big data' models. The future efforts in toxicology data generation will likely provide us with hundreds of thousands of compounds that are readily accessible for machine learning models. These models will cover relevant chemistry space for pharmaceutical, consumer product and environmental applications.

Effects of HO-/MeO-PBDEs on androgen receptor: in vitro investigation and helix 12-involved MD simulation

Hydroxylated and methoxylated polybrominated diphenyl ethers (HO-/MeO-PBDEs) have received increasing attention for their potential endocrine disrupting activities and widely environmental distribution. However, little information is available for the anti-androgenic activities, and the molecular mechanism of interactions with androgen receptor (AR) is not fully understood. In the present study, cell line assay and computational simulation were integrated to systematically explore the molecular mechanism of interactions between chemicals and AR. The metabolites with similar molecular structures exhibited different anti-androgenic activity while none of them showed androgenic activity. According to the multisystem molecular dynamics simulation, minute differences in the structure of ligands induced dramatic different conformational transition of AR-ligand binding domain (LBD). The Helix12 (H12) component of active ligands occupied AR-LBD could become stable, but this component continued to fluctuate in inactive ligands occupied AR-LBD. Settling time and reposition of H12 obtained in dynamics process are important factors governing anti-androgenic activities. The related settling times were characteristic of anti-androgenic potencies of the tested chemicals. Overall, in our study, the stable reposition of H12 is characterized as a computational mark for identifying AR antagonists from PBDE metabolites, or even other various environmental pollutants.

Integrative chemical-biological read-across approach for chemical hazard classification

Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here, we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays ("biological" similarity). The Chemical-Biological Read-Across (CBRA) approach infers each compound's toxicity from both chemical and biological analogues whose similarities are determined by the Tanimoto coefficient. Classification accuracy of CBRA was compared to that of classical RA and other methods using chemical descriptors alone or in combination with biological data. Different types of adverse effects (hepatotoxicity, hepatocarcinogenicity, mutagenicity, and acute lethality) were classified using several biological data types (gene expression profiling and cytotoxicity screening). CBRA-based hazard classification exhibited consistently high external classification accuracy and applicability to diverse chemicals. Transparency of the CBRA approach is aided by the use of radial plots that show the relative contribution of analogous chemical and biological neighbors. Identification of both chemical and biological features that give rise to the high accuracy of CBRA-based toxicity prediction facilitates mechanistic interpretation of the models.

LASSO-ing Potential Nuclear Receptor Agonists and Antagonists: A New Computational Method for Database Screening

Nuclear receptors (NRs) are important biological macromolecular transcription factors that are implicated in multiple biological pathways and may interact with other xenobiotics that are endocrine disruptors present in the environment. Examples of important NRs include the androgen receptor (AR), estrogen receptors (ER), and the pregnane X receptor (PXR). In this study we have utilized the Ligand Activity by Surface Similarity Order (LASSO) method, a ligand-based virtual screening strategy to derive structural (surface/shape) molecular features used to generate predictive models of biomolecular activity for AR, ER, and PXR. For PXR, twenty-five models were built using between 8 to 128 agonists and tested using 3000, 8000, and 24,000 drug-like decoys including PXR inactive compounds (N=228). Preliminary studies with AR and ER using LASSO suggested the utility of this approach with 2-fold enrichment factors at 20%. We found that models with 64–128 PXR actives provided enrichment factors of 10-fold (10% actives in the top 1% of compounds screened). The LASSO models for AR and ER have been deployed and are freely available online, and they represent a ligand-based prediction method for putative NR activity of compounds in this database.

Informing mechanistic toxicology with computational molecular models

Computational molecular models of chemicals interacting with biomolecular targets provides toxicologists a valuable, affordable, and sustainable source of in silico molecular level information that augments, enriches, and complements in vitro and in vivo efforts. From a molecular biophysical ansatz, we describe how 3D molecular modeling methods used to numerically evaluate the classical pair-wise potential at the chemical/biological interface can inform mechanism of action and the dose-response paradigm of modern toxicology. With an emphasis on molecular docking, 3D-QSAR and pharmacophore/toxicophore approaches, we demonstrate how these methods can be integrated with chemoinformatic and toxicogenomic efforts into a tiered computational toxicology workflow. We describe generalized protocols in which 3D computational molecular modeling is used to enhance our ability to predict and model the most relevant toxicokinetic, metabolic, and molecular toxicological endpoints, thereby accelerating the computational toxicology-driven basis of modern risk assessment while providing a starting point for rational sustainable molecular design.

Plastics additives and green chemistry

The plastics enterprise depends on a small number of commodity polymers to perform in diverse applications, requiring additives to produce desired properties and performance. Toxic effects and environmental persistence of certain additive chemicals impact the sustainability of the industry. Green chemistry has been and will continue to be applied to find solutions to these issues. This review focuses on alternatives to phthalate plasticizers and halogenated flame retardants, two categories that together account for a significant portion of the global additives market and the global dispersion of endocrine-disrupting chemicals. Small-molecule alternatives that exist in various stages of research and commercialization will be discussed, with emphasis on the use of renewable resources. The rise of biorefineries and new bio-based monomers may help overcome existing economic barriers to adoption of alternatives. Increasing the molecular weight of additives or covalently linking them to polymer backbones are two promising strategies for reducing both mobility and toxicity that will also be discussed. Finally, the design of new polymers that show desirable properties without the use of additives will be considered. The substances put forward as “green” alternatives have yet to receive the same level of scrutiny as diethylhexyl phthalate (DEHP, also known as dioctyl phthalate) or polybrominated diphenyl ethers (PBDEs). Cooperation between chemists, engineers, and the environmental health community will be critical to ensure the safety and sustainability of new technologies.

Designing Endocrine Disruption Out of the Next Generation of Chemicals

A central goal of green chemistry is to avoid hazard in the design of new chemicals. This objective is best achieved when information about a chemical's potential hazardous effects is obtained as early in the design process as feasible. Endocrine disruption is a type of hazard that to date has been inadequately addressed by both industrial and regulatory science. To aid chemists in avoiding this hazard, we propose an endocrine disruption testing protocol for use by chemists in the design of new chemicals. The Tiered Protocol for Endocrine Disruption (TiPED) has been created under the oversight of a scientific advisory committee composed of leading representatives from both green chemistry and the environmental health sciences. TiPED is conceived as a tool for new chemical design, thus it starts with a chemist theoretically at "the drawing board." It consists of five testing tiers ranging from broad in silico evaluation up through specific cell- and whole organism-based assays. To be effective at detecting endocrine disruption, a testing protocol must be able to measure potential hormone-like or hormone-inhibiting effects of chemicals, as well as the many possible interactions and signaling sequellae such chemicals may have with cell-based receptors. Accordingly, we have designed this protocol to broadly interrogate the endocrine system. The proposed protocol will not detect all possible mechanisms of endocrine disruption, because scientific understanding of these phenomena is advancing rapidly. To ensure that the protocol remains current, we have established a plan for incorporating new assays into the protocol as the science advances. In this paper we present the principles that should guide the science of testing new chemicals for endocrine disruption, as well as principles by which to evaluate individual assays for applicability, and laboratories for reliability. In a 'proof-of-principle' test, we ran 6 endocrine disrupting chemicals (EDCs) that act via different endocrinological mechanisms through the protocol using published literature. Each was identified as endocrine active by one or more tiers. We believe that this voluntary testing protocol will be a dynamic tool to facilitate efficient and early identification of potentially problematic chemicals, while ultimately reducing the risks to public health.

Accessing, using, and creating chemical property databases for computational toxicology modeling

Toxicity data is expensive to generate, is increasingly seen as precompetitive, and is frequently used for the generation of computational models in a discipline known as computational toxicology. Repositories of chemical property data are valuable for supporting computational toxicologists by providing access to data regarding potential toxicity issues with compounds as well as for the purpose of building structure-toxicity relationships and associated prediction models. These relationships use mathematical, statistical, and modeling computational approaches and can be used to understand the mechanisms by which chemicals cause harm and, ultimately, enable prediction of adverse effects of these chemicals to human health and/or the environment. Such approaches are of value as they offer an opportunity to prioritize chemicals for testing. An increasing amount of data used by computational toxicologists is being published into the public domain and, in parallel, there is a greater availability of Open Source software for the generation of computational models. This chapter provides an overview of the types of data and software available and how these may be used to produce predictive toxicology models for the community.

Pharmaceuticals in the environment: an educational perspective

PURPOSE

Pharmaceuticals are an integral part of a dignified life. However, a lack of degradability and threats to the welfare of living beings cause concern due to their emission into the environment. There is also a lack of knowledge about cause and consequence. Therefore, we intend to contribute to the development of educational programmes which should increasingly include the topic 'pharmaceuticals in the environment'.

METHODS

Considering the current literature, we developed a corresponding series of worksheets (Online Resource) and sample solutions on an introductory level and integrated them into our curriculum.

RESULTS

The material compiled for the worksheets was arranged in a logical order and considers several subtopics. The worksheets aim to support the examination of related aspects such as environmental effects, emissions, wastewater treatment plants, degradation, degradation by-products, advanced oxidation processes, hydraulic retention times, half-life times, biosolids, exposition pathways, precautionary principle, classification schemes for pharmaceuticals and, related to the structure-activity relationship, the design for degradability. The students managed to work on the tasks in an appropriate manner and received a good overview of the occurrence and fate of pharmaceuticals in the environment.

CONCLUSIONS

Tasks that were presented to students regarding the topic 'pharmaceuticals in the environment' contributed to a better understanding of the possible risks of medical care on an introductory level. The tasks have been incorporated into a logic series of worksheets (Online Resource) with sample solutions available. Alternatively, the material would be appropriate for the preparation of a corresponding lecture on this topic.