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Mode of Action (MOA) Assignment Classifications for Ecotoxicology: An Evaluation of Approaches Aude Kienzler, Mace G. Barron, Scott E Belanger, Amy Beasley, and Michelle R Embry Environ. Sci. Technol., Just Accepted Manuscript • DOI: 10.1021/acs.est.7b02337 • Publication Date (Web): 31 Jul 2017 Downloaded from http://pubs.acs.org on August 6, 2017

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Environmental Science & Technology

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TITLE: Mode of Action (MOA) Assignment Classifications for Ecotoxicology: An Evaluation of

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Approaches

AUTHORS: A. Kienzlera, M. G. Barronb, S. E. Belangerc, A. Beasleyd, M.R. Embrye*

a

Scientific officer, Joint Research Centre, Directorate F – Health, Consumers and Reference

Materials, F.3 Chemicals Safety & Alternative Methods, TP 126, Via E. Fermi, 2749, I-21027 Ispra, Italy b

Research Toxicologist, United States Environmental Protection Agency, 1 Sabine Island Dr,

Gulf Breeze, FL 32561, USA c

Research Fellow, The Procter & Gamble Company, Mason Business Center, 8700 S Mason-

Montgomery Road, Mason, OH 45040, USA d

Product Sustainability Consultant, TERC Toxicology and Environmental Research and

Consulting, The Dow Chemical Company. 1803 Building, Midland, MI 48674, USA e*

Associate Director, Environmental Science, International Life Sciences Institute Health and Environmental Sciences Institute (HESI). 1156 15th Street, NW, Suite 200, Washington, DC, 20005, USA

*Corresponding author: HESI, 1156 15th Street, NW, Washington, DC 20005, USA; +1 202 659 3306 x183 (P); +1 202 659 3617 (F); [email protected]

1 ACS Paragon Plus Environment


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ABSTRACT

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The mode of toxic action (MOA) is recognized as a key determinant of chemical toxicity and as

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an alternative to chemical class-based predictive toxicity modeling. However, MOA classification

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has never been standardized in ecotoxicology, and a comprehensive comparison of

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classification tools and approaches has never been reported. Here we critically evaluate three

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MOA classification methodologies using an aquatic toxicity dataset of 3488 chemicals, compare

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the approaches, and assess utility and limitations in screening and early tier assessments. The

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comparisons focused on three commonly used tools: Verhaar prediction of toxicity MOA, the

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U.S. Environmental Protection Agency (EPA) ASsessment Tool for Evaluating Risk (ASTER)

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QSAR (quantitative structure activity relationship) application, and the EPA Mode of Action and

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Toxicity (MOATox) database. Of the 3448 MOAs predicted using the Verhaar scheme, 1165

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were classified by ASTER and 802 were available in MOAtox. Of the subset of 432 chemicals

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with MOA assignments for each of the three schemes, 42% had complete concordance in MOA

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classification, and there was no agreement for 7% of the chemicals. The research shows

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the potential for large differences in MOA classification between the five broad groups of the

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Verhaar scheme and the more mechanism-based assignments of ASTER and MOAtox.

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Harmonization of classification schemes is needed to use MOA classification in chemical hazard

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and risk assessment more broadly.


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TOC ART

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INTRODUCTION

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There has been a shift in the risk assessment paradigm towards a more mechanistically based

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understanding of the mechanism and mode of action of chemicals.1 Improved understanding of

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toxicological mechanisms would reduce reliance on traditional animal testing, allow chemical

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grouping to increase assessment efficiency, and improve toxicity extrapolations.2,3 These

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outcomes would increase the potential use of animal alternative methods, which is a long-term

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policy goal of most chemical management programs.4,5.

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Various structure-based classification schemes have been developed to categorize chemicals

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based on the mode of toxic action (MOA). Thousands of chemicals are in commerce and most

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have little available information other than structure. Understanding how the available MOA

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schemes were devised, what information they are based on, and the limitations of each

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approach are critical. The various MOA classification schemes provide information on a key

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determinant of chemical toxicity and as an alternative to chemical class-based predictive toxicity

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modeling. Direct regulatory application of these MOA classifications has been seen most

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directly in chemical classification and in the use of Quantitative Structure-Activity Relationship

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(QSAR) models in risk assessment. 6 MOA also plays a role in mixture risk assessment, where

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both the grouping of chemicals and the choice of the concentration addition or independent

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action hypothesis can be based on knowledge of the MOA. 7

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MOA is an operational term that has been loosely defined in both human health and

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ecotoxicology as a functional change at the cellular level, in contrast to the mechanism of action

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or molecular initiating event. The definition of MOA is critical in the context of Adverse Outcome

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Pathways (AOPs). Generally, MOA describes key events at various levels of biological

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organization, starting with cellular interaction and leading to functional and/or anatomical

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changes.8 MOA is important in classifying chemicals because it represents an intermediate level


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of complexity between molecular mechanisms and physiological or organismal outcomes and

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provides an organizing scheme for chemical classification.9 MOA has also been used to classify

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pesticides by the interaction with the receptor of the target species10 and to describe the

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toxicology of human cancer and non-cancer agents by key cytological and biochemical

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events.11,12 The definitions of MOA used are unique to each of the classification schemes

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investigated: Verhaar used five broad categories based on general toxicological responses,13

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whereas the U.S. Environmental Protection Agency (EPA) ASsessment Tool for Evaluating Risk

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(ASTER) QSAR (quantitative structure activity relationship) application14 and the EPA Mode of

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Action and Toxicity (MOAtox) database15 have a high degree of specificity based on fish

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behavioral responses or weight of evidence classification, respectively. It is also important to

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note that both within and between classification schemes, different levels of biological

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organization may be represented (e.g., at the molecular, cellular, and organism-level).

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Research to develop screening and early tier methods to more easily classify or assess

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chemicals using approaches such as the ecological threshold of toxicological concern (eco-

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TTC)16 and chemical activity17 is ongoing. Evaluation of these approaches and determination of

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their domain of applicability is partly dependent on the MOA classification used to group

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chemicals.

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The objectives of this study were to critically evaluate available MOA classification

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methodologies using a set of unique chemicals from a large aquatic toxicity dataset, compare

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the various approaches, and evaluate their utility and limitations in screening early tier

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assessments.

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OVERVIEW OF MOA SCHEMES

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The comparison of classification approaches focused on three currently available schemes: the

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Verhaar scheme for prediction of toxicity MOA,13 the EPA ASTER QSAR application,18 and the 5 ACS Paragon Plus Environment


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EPA MOAtox database15 (Table S1). The Verhaar scheme classifies organic compounds into

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one of four categories: inert chemicals (Class 1), less inert chemicals (Class 2), reactive

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chemicals (Class 3), and chemicals acting by a specific mechanism (Class 4). Chemicals in

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Class 1 exhibit non-polar narcosis or baseline toxicity and can only be predicted if they have log

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octanol:water partition coefficient (Kow) values between 0 and 6 (e.g., benzenes).

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Chemicals in Class 2 are more toxic and cause polar narcosis, and typically possess hydrogen

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bond donor acidity (e.g. phenols & anilines).13 Chemicals in Class 3 demonstrate enhanced

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toxicity as compared to baseline toxicity that react non-specifically with biomolecules (e.g.

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epoxides) or are metabolized into more toxic species (e.g., nitriles).13 Chemicals in Class 4

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cause toxicity through a specific mechanism such as acetylcholinesterase (AChE) inhibition by

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carbamate insecticides. The assignment of a chemical to a class is based on a decision tree

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that utilizes the presence or absence of certain chemical structures and moieties. The Verhaar

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classification scheme has been further modified by changing the order of some classification

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rules in the decision tree and by adding a fifth class to which chemicals are assigned if the

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chemical could not be placed in Class 1–4.19

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Verhaar and modified Verhaar schemes have been implemented into online tools in the public

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domain such as the Organization for Economic Cooperation and Development (OECD) QSAR

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Toolbox (https://www.qsartoolbox.org/home) and Toxtree (https://eurl-

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ecvam.jrc.ec.europa.eu/laboratories-research/predictive_toxicology/qsar_tools/toxtree).20 The

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OECD QSAR Toolbox is a software application used in the grouping of chemicals and in filling

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(eco)toxicity data gaps for assessing the hazards of chemicals. Chemical profiling is based on

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the Chemical Abstracts Service numbers (CAS) and/or SMILES (Simplified Molecular Line Entry

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System). Toxtree, an open-source application, groups chemicals into categories using several

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schemes based on SMILES notation and decision trees. A post-processing filter encoded as a

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KNIME (Konstanz Information Miner) workflow adds amendments to the classification rules21 to 6 ACS Paragon Plus Environment

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improve the Toxtree classification. The post-filter addresses three types of misclassification:

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Class 5 of some aliphatic alcohols, some halogenated compounds that should both be assigned

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to Class 1 (rule 1.5.2 and rule 1.7.1, respectively, of the Verhaar classification scheme), and

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non- or weakly acidic phenols (rule 2.1). Fewer compounds are misclassified as outside of the

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model domain, further improving the prediction accuracy of the scheme.

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ASTER is a rule-based expert system that screens a chemical structure for structural fragments

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to determine MOA.18 The tool uses acute toxicity of over 600 chemicals in fathead minnows.

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Non-polar narcosis is the default MOA if no MOA specific structural fragments are identified. If

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fragments satisfy requirements for more than one MOA, then the QSAR for the most potent

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toxicity prediction is selected.18 ASTER is based on the MOA categories in Russom et al.22 and

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contains information on over 50,000 molecular structures. ASTER was primarily developed with

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neutral industrial organic chemicals acting through narcosis and has a more limited

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representation of pesticides and other chemicals with more specific modes of action. The tool is

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not publicly available.

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MOAtox is comprised of a database of MOA assignments for 1208 chemicals including metals,

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organometallics, pesticides, and other organic compounds.15 The categorization scheme was

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based on earlier work determining chemical modes of acute toxic action in fish and

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encompasses six broad and 31 specific MOAs.23 The resulting dataset used a combination of

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high-confidence MOA assignments, including biological responses in fish acute toxicity

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assays,22 pesticide classifications schemes (e.g., Insecticide Resistance Action Committee

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[IRAC]), QSAR predictions (e.g., ASTER), and weight of evidence professional judgement

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incorporating an assessment of chemical structure (e.g., analogous structure; moiety/functional

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group presence) and available information on MOA, mechanism of action, and toxicity

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pathways. Chemicals with an uncertain MOA assignment and MOAs specific to invertebrates



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were excluded. Specific MOAs were developed as subcategories of the broad MOAs based on

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either chemical structure or known mechanism of action.

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MATERIALS AND METHODS

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Figure S1 provides an overview of the materials and methods used in this analysis.

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Database Construction and Curation

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A master dataset was constructed using pre-determined inclusion criteria (Figure S2) following

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the Stepwise Information-Filtering Tool (SIFT) of Beasley et al.24 An initial dataset of

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approximately 200,000 studies and chemical property information was compiled, including

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MOA classification. Approximately 110,000 toxicity data records meeting inclusion criteria was

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prepared to inform the MOA assignment objectives.

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Records in the final dataset were subjected to additional curation steps:

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Harmonization of data (e.g., taxonomic name, duration, test statistic units)

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Spot verification of source information, durations, test organism

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Determination of acute/chronic test type and toxicity endpoint

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CAS numbers were extracted from the working dataset to inform the MOA assignment

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investigation. A total of 5638 unique CAS were subjected to further reconciliation, including

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identification of duplicates and mismatches.

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The CAS list was processed with OECD QSAR Toolbox 3.4 to obtain the related SMILES code,

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the EPA Ecological Structure Activity Relationships (ECOSAR)25 chemical classification, and the

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aquatic MOA according to the modified Verhaar classification. The SMILES are essential as the


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two-dimensional representation of the molecule processed by the MOA assignment tools. The

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CAS list was also employed to obtain the ASTER and the MOATox classifications.

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257 CAS were not recognized (no match, no name, and no SMILES were retrieved in the

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various databases) and therefore could not be processed. 151 CAS were linked to a chemical

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name without a corresponding SMILES and therefore resulted as “blank” or “non-applicable”

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regarding the MOA assignment. For some CAS, several SMILES matched, which was either

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linked to the presence of a salt form of the chemical or to an error in the SMILES. In some rare

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cases, the same SMILES linked to two different CAS, which was mainly related to different

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enantiomeric forms of the chemical.

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Once the CAS list was scrubbed to remove incorrect or unrecognized CAS, 3448 of the original

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5638 chemicals remained (61%) for which there were CAS matched to a name and a correct

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SMILES notation.

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MOA Assignment

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Two different tools (OECD QSAR Toolbox 3.4 and Toxtree 2.6.620) were used to compare the

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MOA assignment results for the modified Verhaar scheme, as Bhatia et al.26 showed that

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discrepancies might exist between the tools. The CAS was used as an input in the OECD

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QSAR Toolbox, which also retrieves the name and SMILES for each chemical. The SMILES

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were then processed with Toxtree 2.6.6, to obtain the Verhaar classification. The results

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obtained with the Toxtree software were then processed through a KNIME post-filter workflow,21

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which aims at lowering the number of compounds being classified as outside of the model

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domain and further improving the prediction accuracy of the scheme.

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To obtain ASTER classifications, the SMILES corresponding to the listed CAS were first

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processed through the proprietary ASTER tool. If SMILES was not present or returned an error,



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the corresponding CAS was submitted to maximize the number of CAS given an ASTER

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assignment. When the SMILES represented a structure described as “impossible,” ASTER

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returned an error message describing the structure discrepancies and no MOA was assigned.

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When the SMILES represented a mixture, no MOA was assigned, as mixtures are outside the

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ASTER applicability domain. When no match was found from the SMILES or CAS, no MOA

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assignment was returned.

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MOATox assignments were obtained from previously published tables,15 rather than from model

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predictions. The individual CAS numbers of all chemicals in the database were cross-referenced

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to the curated CAS-linked MOA classifications in Table S2.15

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Along with the MOA, the ECOSAR classes of the chemicals also were extracted to characterize

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the dataset and to identify the chemicals and classes present in the dataset. The ECOSAR

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classification distinguishes up to 111 classes of organic chemicals, including neutral organics,

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organic chemicals with excess toxicity, and chemicals that are determined to be surfactants.

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Analysis

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The Verhaar MOAs obtained with the OECD QSAR Toolbox and the Toxtree software for each

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chemical were compared to identify potential discrepancies (n = 3448). The result of the use of

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the KNIME post-filter on the classification given by Toxtree was also evaluated for

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discrepancies.

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Mapping the three classification schemes shows how they correspond and where they overlap

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(Table 1). The subset of chemicals for which at least three classifications were obtained using

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Verhaar, OECD QSAR Toolbox, ASTER, and the MOATox classifications (n = 432) was further

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analyzed to compare the MOA assigned according to the various schemes, specifically where

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those classification assignments overlap. The complete dataset is given in Table S2.

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Table 1. Comparison of the Three MOA Classification Schemes Verhaar (Modified) Class 1 (narcosis or baseline toxicity) Class 2 (less inert compounds)

Class 3 (unspecific reactivity)

ASTER MOA

MOATox Broad

Non-polar narcosis

Non-polar Narcosis

Polar narcosis Ester narcosis Diester toxicity Reactive Chloro-diester-based reactivity Carbonyl (C=O)-based reactivity Carbonyl reactivity Alkylation/arylation-based reactivity Acylation-based reactivity Sulfhydryl (-S-H)-based reactivity Reactive dinitroaromatic group Nitroso-based reactivity Quinoline reactivity Acetamidophenol reactivity Reactive diketones Acrylate toxicity N-halogenated acetophenone inhibition Hydrazine-based reactivity

Isocyanate (-N=C=O)-based reactivity Pyridinium compounds

Polar Ester

Reactivity Reactivity

Carbonyl Carbonyl

Reactivity

Alkylation

Reactivity

Di/trinitroaromatic

Reactivity

Acrylate

Reactivity Reactivity Reactivity Reactivity

Hydrazine Chromate Phosphide Other

Reactivity

Neurotoxicant: DDT-type Neurotoxicant: pyrethroid Neurotoxicant: cyclodiene-type Neurotoxicity Neurotoxicant: strychnine Neurotoxicant: nicotine Class 4 (compounds and groups Organophosphate-mediated AChE of compounds acting by a inhibition AChE inhibition Carbamate-mediated AChE specific mechanism) inhibition Uncoupler of oxidative phosphorylation Electron transport inhibition Respiratory blocker: azides and cyanides Iono/osmoregulatory/ circulatory impairment Class 5

MOATox Specific

Unknown mode of action

Unknown

Cyanate/nitrile (OCN-; CΞN) Sodium channel blocking Diphenyl sodium channel modulation Pyrethroid sodium channel modulation Alicyclic GABA antagonism Pyrazole GABA antagonism GABA agonism Strychnine Nicotinic acetylcholine receptor agonism Other Organophosphate Carbamate Uncoupling oxidative phosphorylation Arsenical respiratory inhibition Oxidative phosphorylation inhibition Metallic iono/osmoregulatory impairment Methemoglobinemia Anticoagulation Other osmoregulatory Unknown



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AChE, acetylcholinesterase; ASTER, Assessment Tool for Evaluating Risk; MOA, mode of toxic action; MOATox,

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Mode of Action and Toxicity database.

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RESULTS

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Chemical Classes in Dataset

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The dataset of 3448 chemicals was evaluated using ECOSAR to provide an overview of the

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chemical class coverage. For chemicals where multiple classifications were generated by

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ECOSAR, the first reported was used. These 89 categories were further collapsed into 46 more

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general categories. Collapsed ECOSAR classifications that each represent >4% of the total

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dataset are shown in Figure 1. Figure 1 includes the seven major categories in which the most

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chemicals were classified (e.g., those individual categories in which ≥4% of the total number of

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chemicals were classified). 24% of chemicals in the dataset were classified as neutral organics,

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with the second most common category being esters (13%). Importantly, approximately 6% of

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chemicals were classified as “should not be profiled” and therefore were not assigned a

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chemical category. The “Other” category (24%) represents other non-major chemical categories

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that are each represented by

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