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Rajiv Gandhi G, Sharanya CS, Jayanandan A, Haridas M, Edwin Hillary V, Rajiv Gandhi S, Sridharan G, Sivasubramanian R, Silva Vasconcelos AB, Montalvão MM, Antony Ceasar S, Sousa NFD, Scotti L, Scotti MT, Gurgel RQ, Quintans-Júnior LJ. Multitargeted molecular docking and dynamics simulation studies of flavonoids and volatile components from the peel of Citrus sinensis L. (Osbeck) against specific tumor protein markers. J Biomol Struct Dyn 2024; 42:3051-3080. [PMID: 37203996 DOI: 10.1080/07391102.2023.2212062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/01/2023] [Indexed: 05/20/2023]
Abstract
Citrus sinensis (L.) Osbeck (Rutaceae), commonly known as the sweet orange, is a popular and widely consumed fruit with several medicinal properties. The present study aimed to perform the in silico screening of 18 flavonoids and eight volatile components from the peel of C. sinensis against apoptotic and inflammatory proteins, metalloprotease, and tumor suppressor markers. Flavonoids obtained higher probabilities than volatile components against selected anti-cancer drug targets. Hence, the data from the binding energies against the essential apoptotic and cell proliferation proteins substantiate that they may be promising compounds in developing effective candidates to block cell growth, proliferation, and induced cell death by activating the apoptotic pathway. Further, the binding stability of the selected targets and the corresponding molecules were analyzed by 100 ns molecular dynamics (MD) simulations. Chlorogenic acid has the most binding affinity against the important anti-cancer targets iNOS, MMP-9, and p53. The congruent binding mode to different drug targets focused on cancer shown by chlorogenic acid suggests that it may be a compound with significant therapeutic potential. Moreover, the binding energy predictions indicated that the compound had stable electrostatic and van der Waal energies. Thus, our data reinforce the medicinal importance of flavonoids from C. sinensis and expand the need for more studies, seeking to optimize results and amplify the impacts of further in vitro and in vivo studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gopalsamy Rajiv Gandhi
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Chelankara Suresh Sharanya
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Abhithaj Jayanandan
- Department of Biotechnology and Microbiology, Dr. Janaki Ammal Campus, Kannur University, Thalassery, Kannur, India
| | - Madathilkovilakath Haridas
- Department of Biotechnology and Microbiology, Dr. Janaki Ammal Campus, Kannur University, Thalassery, Kannur, India
| | - Varghese Edwin Hillary
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Sathiyabama Rajiv Gandhi
- Laboratory of Neuroscience and Pharmacological Assays (LANEF), Department of Physiology (DFS), Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Gurunagarajan Sridharan
- Department of Biochemistry, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirapalli, India
| | - Rengaraju Sivasubramanian
- Department of Biochemistry, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirapalli, India
| | - Alan Bruno Silva Vasconcelos
- Postgraduate Program of Physiological Sciences (PROCFIS), Federal University of Sergipe (UFS), São Cristóvão, Sergipe, Brazil
| | - Monalisa Martins Montalvão
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Natália Ferreira de Sousa
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Paraíba, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Paraíba, Brazil
| | - Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Paraíba, Brazil
| | - Ricardo Queiroz Gurgel
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Lucindo José Quintans-Júnior
- Laboratory of Neuroscience and Pharmacological Assays (LANEF), Department of Physiology (DFS), Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
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de Sousa NF, da Silva Souza HD, de Menezes RPB, da Silva Alves F, Acevedo CAH, de Lima Nunes TA, Sessions ZL, Scotti L, Muratov EN, Mendonça-Junior FJB, da Franca Rodrigues KA, de Athayde Filho PF, Scotti MT. Selene-Ethylenelacticamides and N-Aryl-Propanamides as Broad-Spectrum Leishmanicidal Agents. Pathogens 2023; 12:pathogens12010136. [PMID: 36678484 PMCID: PMC9860784 DOI: 10.3390/pathogens12010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/18/2023] Open
Abstract
The World Health Organization classifies Leishmania as one of the 17 “neglected diseases” that burden tropical and sub-tropical climate regions with over half a million diagnosed cases each year. Despite this, currently available anti-leishmania drugs have high toxicity and the potential to be made obsolete by parasite drug resistance. We chose to analyze organoselenides for leishmanicidal potential given the reduced toxicity inherent to selenium and the displayed biological activity of organoselenides against Leishmania. Thus, the biological activities of 77 selenoesters and their N-aryl-propanamide derivatives were predicted using robust in silico models of Leishmania infantum, Leishmania amazonensis, Leishmania major, and Leishmania (Viannia) braziliensis. The models identified 28 compounds with >60% probability of demonstrating leishmanicidal activity against L. infantum, and likewise, 26 for L. amazonesis, 25 for L. braziliensis, and 23 for L. major. The in silico prediction of ADMET properties suggests high rates of oral absorption and good bioavailability for these compounds. In the in silico toxicity evaluation, only seven compounds showed signs of toxicity in up to one or two parameters. The methodology was corroborated with the ensuing experimental validation, which evaluated the inhibition of the Promastigote form of the Leishmania species under study. The activity of the molecules was determined by the IC50 value (µM); IC50 values < 20 µM indicated better inhibition profiles. Sixteen compounds were synthesized and tested for their activity. Eight molecules presented IC50 values < 20 µM for at least one of the Leishmania species under study, with compound NC34 presenting the strongest parasite inhibition profile. Furthermore, the methodology used was effective, as many of the compounds with the highest probability of activity were confirmed by the in vitro tests performed.
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Affiliation(s)
- Natália Ferreira de Sousa
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | | | | | - Francinara da Silva Alves
- Post-Graduate Program in Chemistry, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Chonny Alexander Herrera Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Thaís Amanda de Lima Nunes
- Infectious Diseases Laboratory, Federal University of Delta of Parnaíba, Av. São Sebastião, nº 2819-Nossa Sra. de Fátima, Parnaíba 64202-020, PI, Brazil
| | - Zoe L. Sessions
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Eugene N. Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Klinger Antônio da Franca Rodrigues
- Infectious Diseases Laboratory, Federal University of Delta of Parnaíba, Av. São Sebastião, nº 2819-Nossa Sra. de Fátima, Parnaíba 64202-020, PI, Brazil
| | | | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
- Correspondence: ; Tel.: +55-83-99869-0415
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Rayff da Silva P, de Andrade JC, de Sousa NF, Portela ACR, Oliveira Pires HF, Remígio MCRB, da Nóbrega Alves D, de Andrade HHN, Dias AL, Salvadori MGDSS, de Oliveira Golzio AMF, de Castro RD, Scotti MT, Felipe CFB, de Almeida RN, Scotti L. Computational Studies Applied to Linalool and Citronellal Derivatives Against Alzheimer's and Parkinson's Disorders: A Review with Experimental Approach. Curr Neuropharmacol 2023; 21:842-866. [PMID: 36809939 PMCID: PMC10227923 DOI: 10.2174/1570159x21666230221123059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 02/24/2023] Open
Abstract
Alzheimer's and Parkinson's are neurodegenerative disorders that affect a great number of people around the world, seriously compromising the quality of life of individuals, due to motor and cognitive damage. In these diseases, pharmacological treatment is used only to alleviate symptoms. This emphasizes the need to discover alternative molecules for use in prevention. Using Molecular Docking, this review aimed to evaluate the anti-Alzheimer's and anti-Parkinson's activity of linalool and citronellal, as well as their derivatives. Before performing Molecular Docking simulations, the compounds' pharmacokinetic characteristics were evaluated. For Molecular Docking, 7 chemical compounds derived from citronellal, and 10 compounds derived from linalool, and molecular targets involved in Alzheimer's and Parkinson's pathophysiology were selected. According to the Lipinski rules, the compounds under study presented good oral absorption and bioavailability. For toxicity, some tissue irritability was observed. For Parkinson-related targets, the citronellal and linalool derived compounds revealed excellent energetic affinity for α-Synuclein, Adenosine Receptors, Monoamine Oxidase (MAO), and Dopamine D1 receptor proteins. For Alzheimer disease targets, only linalool and its derivatives presented promise against BACE enzyme activity. The compounds studied presented high probability of modulatory activity against the disease targets under study, and are potential candidates for future drugs.
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Affiliation(s)
- Pablo Rayff da Silva
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Jéssica Cabral de Andrade
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Natália Ferreira de Sousa
- Cheminformatics Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-900, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Anne Caroline Ribeiro Portela
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Hugo Fernandes Oliveira Pires
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Maria Caroline Rodrigues Bezerra Remígio
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Danielle da Nóbrega Alves
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Humberto Hugo Nunes de Andrade
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Arthur Lins Dias
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | | | | | - Ricardo Dias de Castro
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Marcus T. Scotti
- Cheminformatics Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-900, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Cícero Francisco Bezerra Felipe
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Reinaldo Nóbrega de Almeida
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Luciana Scotti
- Cheminformatics Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-900, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
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In Silico Studies of Lamiaceae Diterpenes with Bioinsecticide Potential against Aphis gossypii and Drosophila melanogaster. Molecules 2021; 26:molecules26030766. [PMID: 33540716 PMCID: PMC7867283 DOI: 10.3390/molecules26030766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 12/19/2022] Open
Abstract
Background: The growing demand for agricultural products has led to the misuse/overuse of insecticides; resulting in the use of higher concentrations and the need for ever more toxic products. Ecologically, bioinsecticides are considered better and safer than synthetic insecticides; they must be toxic to the target organism, yet with low or no toxicity to non-target organisms. Many plant extracts have seen their high insecticide potential confirmed under laboratory conditions, and in the search for plant compounds with bioinsecticidal activity, the Lamiaceae family has yielded satisfactory results. Objective: The aim of our study was to develop computer-assisted predictions for compounds with known insecticidal activity against Aphis gossypii and Drosophila melanogaster. Results and conclusion: Structure analysis revealed ent-kaurane, kaurene, and clerodane diterpenes as the most active, showing excellent results. We also found that the interactions formed by these compounds were more stable, or presented similar stability to the commercialized insecticides tested. Overall, we concluded that the compounds bistenuifolin L (1836) and bistenuifolin K (1931), were potentially active against A. gossypii enzymes; and salvisplendin C (1086) and salvixalapadiene (1195), are potentially active against D. melanogaster. We observed and highlight that the diterpenes bistenuifolin L (1836), bistenuifolin K (1931), salvisplendin C (1086), and salvixalapadiene (1195), present a high probability of activity and low toxicity against the species studied.
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Basketter DA, Kimber I, Ezendam J. Predictive Tests for Irritants and Allergens: Human, Animal, and In Vitro Tests. Contact Dermatitis 2021. [DOI: 10.1007/978-3-030-36335-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Tintó-Moliner A, Martin M. Quantitative weight of evidence method for combining predictions of quantitative structure-activity relationship models. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:261-279. [PMID: 32065534 DOI: 10.1080/1062936x.2020.1725116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
A method for combining statistical-based QSAR predictions of two or more binary classification models is presented. It was assumed that all models were independent. This facilitated the combination of positive and negative predictions using a quantitative weight of evidence (qWoE) procedure based on Bayesian statistics and the additivity of the logarithms of the likelihood ratios. Previous studies combined more than one prediction but used arbitrary strengths for positive and negative predictions. In our approach, the combined models were validated by determining the sensitivity and specificity values, which are performance metrics that are a point of departure for obtaining values that measure the weight of evidence of positive and negative predictions. The developed method was experimentally applied in the prediction of Ames mutagenicity. The method achieved a similar accuracy to that of the experimental Ames test for this endpoint when the overall prediction was determined using a combination of the individual predictions of more than one model. Calculating the qWoE value would reduce the requirement for expert knowledge and decrease the subjectivity of the prediction. This method could be applied to other endpoints such as developmental toxicity and skin sensitisation with binary classification models.
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Affiliation(s)
- A Tintó-Moliner
- Department of Analytical Resources, Moehs Ibérica S.L., Barcelona, Spain
| | - M Martin
- Department of Analytical Resources, Moehs Ibérica S.L., Barcelona, Spain
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Kennedy MC, Hart ADM, Kruisselbrink JW, van Lenthe M, de Boer WJ, van der Voet H, Rorije E, Sprong C, van Klaveren J. A retain and refine approach to cumulative risk assessment. Food Chem Toxicol 2020; 138:111223. [PMID: 32088251 DOI: 10.1016/j.fct.2020.111223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/07/2020] [Accepted: 02/17/2020] [Indexed: 12/27/2022]
Abstract
Mixtures of substances to which humans are exposed may lead to cumulative exposure and health effects. To study their effects, it is first necessary to identify a cumulative assessment group (CAG) of substances for risk assessment or hazard testing. Excluding substances from consideration before there is sufficient evidence may underestimate the risk. Conversely, including everything and treating the inevitable uncertainties using conservative assumptions is inefficient and may overestimate the risk, with an unknown level of protection. An efficient, transparent strategy is described to retain a large group, quantifying the uncertainty of group membership and other uncertainties. Iterative refinement of the CAG then focuses on adding information for the substances with high probability of contributing significantly to the risk. Probabilities can be estimated using expert opinion or derived from data on substance properties. An example is presented with 100 pesticides, in which the retain step identified a single substance to target refinement. Using an updated hazard characterisation for this substance reduced the mean exposure estimate from 0.43 to 0.28 μg kg-bw-1 day-1 and reduced the 99.99th percentile exposure from 24.9 to 5.1 μg kg-bw-1 day-1. Other retained substances contributed little to the risk estimates, even after accounting for uncertainty.
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Affiliation(s)
- Marc C Kennedy
- Fera Science Ltd, Sand Hutton, York, YO41 1LZ, United Kingdom.
| | - Andy D M Hart
- Fera Science Ltd, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Johannes W Kruisselbrink
- Wageningen University & Research, Biometrics, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Marco van Lenthe
- Wageningen University & Research, Biometrics, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Waldo J de Boer
- Wageningen University & Research, Biometrics, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Hilko van der Voet
- Wageningen University & Research, Biometrics, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Emiel Rorije
- RIVM, National Institute for Public Health and the Environment, The Netherlands, PO Box 1, 3720 BA, Bilthoven, the Netherlands
| | - Corinne Sprong
- RIVM, National Institute for Public Health and the Environment, The Netherlands, PO Box 1, 3720 BA, Bilthoven, the Netherlands
| | - Jacob van Klaveren
- RIVM, National Institute for Public Health and the Environment, The Netherlands, PO Box 1, 3720 BA, Bilthoven, the Netherlands
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Benfenati E, Chaudhry Q, Gini G, Dorne JL. Integrating in silico models and read-across methods for predicting toxicity of chemicals: A step-wise strategy. ENVIRONMENT INTERNATIONAL 2019; 131:105060. [PMID: 31377600 DOI: 10.1016/j.envint.2019.105060] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/26/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
In silico methods and models are increasingly used for predicting properties of chemicals for hazard identification and hazard characterisation in the absence of experimental toxicity data. Many in silico models are available and can be used individually or in an integrated fashion. Whilst such models offer major benefits to toxicologists, risk assessors and the global scientific community, the lack of a consistent framework for the integration of in silico results can lead to uncertainty and even contradictions across models and users, even for the same chemicals. In this context, a range of methods for integrating in silico results have been proposed on a statistical or case-specific basis. Read-across constitutes another strategy for deriving reference points or points of departure for hazard characterisation of untested chemicals, from the available experimental data for structurally-similar compounds, mostly using expert judgment. Recently a number of software systems have been developed to support experts in this task providing a formalised and structured procedure. Such a procedure could also facilitate further integration of the results generated from in silico models and read-across. This article discusses a framework on weight of evidence published by EFSA to identify the stepwise approach for systematic integration of results or values obtained from these "non-testing methods". Key criteria and best practices for selecting and evaluating individual in silico models are also described, together with the means to combining the results, taking into account any limitations, and identifying strategies that are likely to provide consistent results.
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Affiliation(s)
- Emilio Benfenati
- Department of Environmental and Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, Milano, Italy.
| | - Qasim Chaudhry
- University of Chester, Parkgate Road, Chester CH1 4BJ, United Kingdom
| | | | - Jean Lou Dorne
- Scientific Committee and Emerging Risks Unit, European Food Safety Authority, Via Carlo Magno 1A, Parma, Italy
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Liu L, Yang H, Cai Y, Cao Q, Sun L, Wang Z, Li W, Liu G, Lee PW, Tang Y. In silico prediction of chemical aquatic toxicity for marine crustaceans via machine learning. Toxicol Res (Camb) 2019; 8:341-352. [PMID: 31160968 PMCID: PMC6505403 DOI: 10.1039/c8tx00331a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/24/2019] [Indexed: 12/30/2022] Open
Abstract
Aquatic toxicity is a crucial endpoint for evaluating chemically adverse effects on ecosystems. Therefore, we developed in silico methods for the prediction of chemical aquatic toxicity in marine environment. At first, a diverse data set including different crustacean species was constructed. We then built local binary models using Mysidae data and global binary models using Mysidae, Palaemonidae, and Penaeidae data. Molecular fingerprints and descriptors were employed to represent chemical structures separately. All the models were built by six machine learning methods. The AUC (area under the receiver operating characteristic curve) values of the better local and global models were around 0.8 and 0.9 for the test sets, respectively. We also identified several chemicals with selective toxicity on different species. The analysis of selective toxicity would promote to design greener chemicals in a specific environment. Finally, to understand and interpret the models, we explored the relationships between chemical aquatic toxicity and the molecular descriptors. Our study would be helpful in gaining further insights into marine organisms, prediction of chemical aquatic toxicity and prioritization of environmental hazard assessment.
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Affiliation(s)
- Lin Liu
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
| | - Hongbin Yang
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
| | - Yingchun Cai
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
| | - Qianqian Cao
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
| | - Lixia Sun
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
| | - Zhuang Wang
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
| | - Philip W Lee
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China .
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Predictive Tests for Irritants and Allergens: Human, Animal, and In Vitro Tests. Contact Dermatitis 2019. [DOI: 10.1007/978-3-319-72451-5_13-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Wilm A, Kühnl J, Kirchmair J. Computational approaches for skin sensitization prediction. Crit Rev Toxicol 2018; 48:738-760. [DOI: 10.1080/10408444.2018.1528207] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Anke Wilm
- Center for Bioinformatics, Universität Hamburg, Hamburg, Germany
- HITeC e.V, Hamburg, Germany
| | - Jochen Kühnl
- Front End Innovation, Beiersdorf AG, Hamburg, Germany
| | - Johannes Kirchmair
- Center for Bioinformatics, Universität Hamburg, Hamburg, Germany
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), University of Bergen, Bergen, Norway
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Gabbert S, Leontaridou M, Landsiedel R. A Critical Review of Adverse Outcome Pathway-Based Concepts and Tools for Integrating Information from Nonanimal Testing Methods: The Case of Skin Sensitization. ACTA ACUST UNITED AC 2017. [DOI: 10.1089/aivt.2017.0015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Silke Gabbert
- Environmental Economics and Natural Resources Group, Wageningen University, Wageningen, The Netherlands
| | - Maria Leontaridou
- Environmental Economics and Natural Resources Group, Wageningen University, Wageningen, The Netherlands
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Schultz TW, Dimitrova G, Dimitrov S, Mekenyan OG. The adverse outcome pathway for skin sensitisation: Moving closer to replacing animal testing. Altern Lab Anim 2017; 44:453-460. [PMID: 27805828 DOI: 10.1177/026119291604400515] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This article outlines the work of the Organisation for Economic Co-operation and Development (OECD) that led to being jointly awarded the 2015 Lush Black Box Prize. The award-winning work centred on the development of 'The Adverse Outcome Pathway for Skin Sensitisation Initiated by Covalent Binding to Proteins'. This Adverse Outcome Pathway (AOP) has provided the mechanistic basis for the integration of skin sensitisation-related information. Recent developments in integrated approaches to testing and assessment, based on the AOP, are summarised. The impact of the AOP on regulatory policy and on the Three Rs are discussed. An overview of the next generation of the skin sensitisation AOP module in the OECD QSAR Toolbox, based on more-recent work at the Laboratory of Mathematical Chemistry, is also presented.
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Affiliation(s)
- Terry W Schultz
- The University of Tennessee, College of Veterinary Medicine, Knoxville, TN, USA
| | - Gergana Dimitrova
- Laboratory of Mathematical Chemistry (LMC), As. Zlatarov University, Bourgas, Bulgaria
| | - Sabcho Dimitrov
- Laboratory of Mathematical Chemistry (LMC), As. Zlatarov University, Bourgas, Bulgaria
| | - Ovanes G Mekenyan
- Laboratory of Mathematical Chemistry (LMC), As. Zlatarov University, Bourgas, Bulgaria
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14
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Ezendam J, Braakhuis HM, Vandebriel RJ. State of the art in non-animal approaches for skin sensitization testing: from individual test methods towards testing strategies. Arch Toxicol 2016; 90:2861-2883. [PMID: 27629427 DOI: 10.1007/s00204-016-1842-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/29/2016] [Indexed: 11/28/2022]
Abstract
The hazard assessment of skin sensitizers relies mainly on animal testing, but much progress is made in the development, validation and regulatory acceptance and implementation of non-animal predictive approaches. In this review, we provide an update on the available computational tools and animal-free test methods for the prediction of skin sensitization hazard. These individual test methods address mostly one mechanistic step of the process of skin sensitization induction. The adverse outcome pathway (AOP) for skin sensitization describes the key events (KEs) that lead to skin sensitization. In our review, we have clustered the available test methods according to the KE they inform: the molecular initiating event (MIE/KE1)-protein binding, KE2-keratinocyte activation, KE3-dendritic cell activation and KE4-T cell activation and proliferation. In recent years, most progress has been made in the development and validation of in vitro assays that address KE2 and KE3. No standardized in vitro assays for T cell activation are available; thus, KE4 cannot be measured in vitro. Three non-animal test methods, addressing either the MIE, KE2 or KE3, are accepted as OECD test guidelines, and this has accelerated the development of integrated or defined approaches for testing and assessment (e.g. testing strategies). The majority of these approaches are mechanism-based, since they combine results from multiple test methods and/or computational tools that address different KEs of the AOP to estimate skin sensitization potential and sometimes potency. Other approaches are based on statistical tools. Until now, eleven different testing strategies have been published, the majority using the same individual information sources. Our review shows that some of the defined approaches to testing and assessment are able to accurately predict skin sensitization hazard, sometimes even more accurate than the currently used animal test. A few defined approaches are developed to provide an estimate of the potency sub-category of a skin sensitizer as well, but these approaches need further independent evaluation with a new dataset of chemicals. To conclude, this update shows that the field of non-animal approaches for skin sensitization has evolved greatly in recent years and that it is possible to predict skin sensitization hazard without animal testing.
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Affiliation(s)
- Janine Ezendam
- Department of Innovative Testing Strategies, Center for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA, Bilthoven, The Netherlands.
| | - Hedwig M Braakhuis
- Department of Innovative Testing Strategies, Center for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Rob J Vandebriel
- Department of Innovative Testing Strategies, Center for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA, Bilthoven, The Netherlands
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15
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Leontaridou M, Gabbert S, Van Ierland EC, Worth AP, Landsiedel R. Evaluation of Non-animal Methods for Assessing Skin Sensitisation Hazard: A Bayesian Value-of-Information Analysis. Altern Lab Anim 2016; 44:255-69. [DOI: 10.1177/026119291604400309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper offers a Bayesian Value-of-Information (VOI) analysis for guiding the development of non-animal testing strategies, balancing information gains from testing with the expected social gains and costs from the adoption of regulatory decisions. Testing is assumed to have value, if, and only if, the information revealed from testing triggers a welfare-improving decision on the use (or non-use) of a substance. As an illustration, our VOI model is applied to a set of five individual non-animal prediction methods used for skin sensitisation hazard assessment, seven battery combinations of these methods, and 236 sequential 2-test and 3-test strategies. Their expected values are quantified and compared to the expected value of the local lymph node assay (LLNA) as the animal method. We find that battery and sequential combinations of non-animal prediction methods reveal a significantly higher expected value than the LLNA. This holds for the entire range of prior beliefs. Furthermore, our results illustrate that the testing strategy with the highest expected value does not necessarily have to follow the order of key events in the sensitisation adverse outcome pathway (AOP).
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Affiliation(s)
- Maria Leontaridou
- Wageningen University, Environmental Economics and Natural Resources Group, Wageningen, The Netherlands
- BASF SE, Experimental Toxicology and Ecology, Ludwigshafen, Germany
| | - Silke Gabbert
- Wageningen University, Environmental Economics and Natural Resources Group, Wageningen, The Netherlands
| | - Ekko C. Van Ierland
- Wageningen University, Environmental Economics and Natural Resources Group, Wageningen, The Netherlands
| | - Andrew P. Worth
- European Commission, Joint Research Centre, Directorate F — Health, Consumer and Reference Materials, EURL ECVAM, Ispra, Italy
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16
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Macmillan DS, Canipa SJ, Chilton ML, Williams RV, Barber CG. Predicting skin sensitisation using a decision tree integrated testing strategy with an in silico model and in chemico/in vitro assays. Regul Toxicol Pharmacol 2016; 76:30-8. [PMID: 26796566 DOI: 10.1016/j.yrtph.2016.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 11/19/2022]
Abstract
There is a pressing need for non-animal methods to predict skin sensitisation potential and a number of in chemico and in vitro assays have been designed with this in mind. However, some compounds can fall outside the applicability domain of these in chemico/in vitro assays and may not be predicted accurately. Rule-based in silico models such as Derek Nexus are expert-derived from animal and/or human data and the mechanism-based alert domain can take a number of factors into account (e.g. abiotic/biotic activation). Therefore, Derek Nexus may be able to predict for compounds outside the applicability domain of in chemico/in vitro assays. To this end, an integrated testing strategy (ITS) decision tree using Derek Nexus and a maximum of two assays (from DPRA, KeratinoSens, LuSens, h-CLAT and U-SENS) was developed. Generally, the decision tree improved upon other ITS evaluated in this study with positive and negative predictivity calculated as 86% and 81%, respectively. Our results demonstrate that an ITS using an in silico model such as Derek Nexus with a maximum of two in chemico/in vitro assays can predict the sensitising potential of a number of chemicals, including those outside the applicability domain of existing non-animal assays.
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Affiliation(s)
- Donna S Macmillan
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds, LS11 5PS, UK.
| | - Steven J Canipa
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds, LS11 5PS, UK
| | - Martyn L Chilton
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds, LS11 5PS, UK
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Integrated Approaches to Testing and Assessment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 856:317-342. [PMID: 27671729 DOI: 10.1007/978-3-319-33826-2_13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this chapter, we explain how Integrated Approaches to Testing and Assessment (IATA) offer a means of integrating and translating the data generated by toxicity testing methods, thereby serving as flexible and suitable tools for toxicological decision making in the twenty-first century. In addition to traditional in vitro and in vivo testing methods, IATA are increasingly incorporating newly developed in vitro systems and measurement technologies such as high throughput screening and high content imaging. Computational approaches are also being used in IATA development, both as a means of generating data (e.g. QSARs), interpreting data (bioinformatics and chemoinformatics), and as a means of integrating multiple sources of data (e.g. expert systems, bayesian models). Decision analytic methods derived from socioeconomic theory can also play a role in developing flexible and optimal IATA solutions. Some of the challenges involved in the development, validation and implementation of IATA are also discussed.
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Linkov I, Massey O, Keisler J, Rusyn I, Hartung T. From "weight of evidence" to quantitative data integration using multicriteria decision analysis and Bayesian methods. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION 2015; 32:3-8. [PMID: 25592482 PMCID: PMC5317204 DOI: 10.14573/altex.1412231] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
“Weighing” available evidence in the process of decision-making is unavoidable, yet it is one step that routinely raises suspicions: what evidence should be used, how much does it weigh, and whose thumb may be tipping the scales? This commentary aims to evaluate the current state and future roles of various types of evidence for hazard assessment as it applies to environmental health. In its recent evaluation of the US Environmental Protection Agency’s Integrated Risk Information System assessment process, the National Research Council committee singled out the term “weight of evidence” (WoE) for critique, deeming the process too vague and detractive to the practice of evaluating human health risks of chemicals. Moving the methodology away from qualitative, vague and controversial methods towards generalizable, quantitative and transparent methods for appropriately managing diverse lines of evidence is paramount for both regulatory and public acceptance of the hazard assessments. The choice of terminology notwithstanding, a number of recent Bayesian WoE-based methods, the emergence of multi criteria decision analysis for WoE applications, as well as the general principles behind the foundational concepts of WoE, show promise in how to move forward and regain trust in the data integration step of the assessments. We offer our thoughts on the current state of WoE as a whole and while we acknowledge that many WoE applications have been largely qualitative and subjective in nature, we see this as an opportunity to turn WoE towards a quantitative direction that includes Bayesian and multi criteria decision analysis.
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Affiliation(s)
- Igor Linkov
- US Army Engineer Research and Development Center, Concord, MA, USA
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19
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Patlewicz G, Simon TW, Rowlands JC, Budinsky RA, Becker RA. Proposing a scientific confidence framework to help support the application of adverse outcome pathways for regulatory purposes. Regul Toxicol Pharmacol 2015; 71:463-77. [PMID: 25707856 DOI: 10.1016/j.yrtph.2015.02.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/13/2015] [Accepted: 02/16/2015] [Indexed: 10/24/2022]
Abstract
An adverse outcome pathway (AOP) describes the causal linkage between initial molecular events and an adverse outcome at individual or population levels. Whilst there has been considerable momentum in AOP development, far less attention has been paid to how AOPs might be practically applied for different regulatory purposes. This paper proposes a scientific confidence framework (SCF) for evaluating and applying a given AOP for different regulatory purposes ranging from prioritizing chemicals for further evaluation, to hazard prediction, and ultimately, risk assessment. The framework is illustrated using three different AOPs for several typical regulatory applications. The AOPs chosen are ones that have been recently developed and/or published, namely those for estrogenic effects, skin sensitisation, and rodent liver tumor promotion. The examples confirm how critical the data-richness of an AOP is for driving its practical application. In terms of performing risk assessment, human dosimetry methods are necessary to inform meaningful comparisons with human exposures; dosimetry is applied to effect levels based on non-testing approaches and in vitro data. Such a comparison is presented in the form of an exposure:activity ratio (EAR) to interpret biological activity in the context of exposure and to provide a basis for product stewardship and regulatory decision making.
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Affiliation(s)
- Grace Patlewicz
- DuPont Haskell Global Centers for Health and Environmental Sciences, 1090 Elkton Road, Newark, DE 19711, USA.
| | - Ted W Simon
- Ted Simon LLC, 4184 Johnston Road, Winston, GA 30187, USA
| | - J Craig Rowlands
- The Dow Chemical Company, Toxicology & Environmental Research & Consulting, 1803 Building Washington Street, Midland, MI 48674, USA
| | - Robert A Budinsky
- The Dow Chemical Company, Toxicology & Environmental Research & Consulting, 1803 Building Washington Street, Midland, MI 48674, USA
| | - Richard A Becker
- Regulatory and Technical Affairs Department, American Chemistry Council (ACC), Washington, DC 20002, USA
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20
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Dik S, Ezendam J, Cunningham AR, Carrasquer CA, van Loveren H, Rorije E. Evaluation of in silico models for the identification of respiratory sensitizers. Toxicol Sci 2014; 142:385-94. [PMID: 25239631 DOI: 10.1093/toxsci/kfu188] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Low molecular weight (LMW) respiratory sensitizers can cause occupational asthma but due to a lack of adequate test methods, prospective identification of respiratory sensitizers is currently not possible. This article presents the evaluation of structure-activity relationship (SAR) models as potential methods to prospectively conclude on the sensitization potential of LMW chemicals. The predictive performance of the SARs calculated from their training sets was compared to their performance on a dataset of newly identified respiratory sensitizers and nonsensitizers, derived from literature. The predictivity of the available SARs for new substances was markedly lower than their published predictive performance. For that reason, no single SAR model can be considered sufficiently reliable to conclude on potential LMW respiratory sensitization properties of a substance. The individual applicability domains (ADs) of the models were analyzed for adequacies and deficiencies. Based on these findings, a tiered prediction approach is subsequently proposed. This approach combines the two SARs with the highest positive and negative predictivity taking into account model specific chemical AD issues. The tiered approach provided reliable predictions for one-third of the respiratory sensitizers and nonsensitizers of the external validation set compiled by us. For these chemicals, a positive predictive value of 96% and a negative predictive value of 89% were obtained. The tiered approach was not able to predict the other two-thirds of the chemicals, meaning that additional information is required and that there is an urgent need for other test methods, e.g., in chemico or in vitro, to reach a reliable conclusion.
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Affiliation(s)
- Sander Dik
- *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Janine Ezendam
- *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Albert R Cunningham
- *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Carl Alex Carrasquer
- *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Henk van Loveren
- *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Emiel Rorije
- *Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands, Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands, James Graham Brown Cancer Center, Department of Medicine, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, and Centre for Safety of Substances and Products, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
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21
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Lombardo A, Roncaglioni A, Benfentati E, Nendza M, Segner H, Fernández A, Kühne R, Franco A, Pauné E, Schüürmann G. Integrated testing strategy (ITS) for bioaccumulation assessment under REACH. ENVIRONMENT INTERNATIONAL 2014; 69:40-50. [PMID: 24806447 DOI: 10.1016/j.envint.2014.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 04/02/2014] [Accepted: 04/10/2014] [Indexed: 06/03/2023]
Abstract
REACH (registration, evaluation, authorisation and restriction of chemicals) regulation requires that all the chemicals produced or imported in Europe above 1 tonne/year are registered. To register a chemical, physicochemical, toxicological and ecotoxicological information needs to be reported in a dossier. REACH promotes the use of alternative methods to replace, refine and reduce the use of animal (eco)toxicity testing. Within the EU OSIRIS project, integrated testing strategies (ITSs) have been developed for the rational use of non-animal testing approaches in chemical hazard assessment. Here we present an ITS for evaluating the bioaccumulation potential of organic chemicals. The scheme includes the use of all available data (also the non-optimal ones), waiving schemes, analysis of physicochemical properties related to the end point and alternative methods (both in silico and in vitro). In vivo methods are used only as last resort. Using the ITS, in vivo testing could be waived for about 67% of the examined compounds, but bioaccumulation potential could be estimated on the basis of non-animal methods. The presented ITS is freely available through a web tool.
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Affiliation(s)
- Anna Lombardo
- Laboratory of Evironmental Chemistry and Toxicology, Department of Environmental Health Science, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri," Via G. La Masa 19, Milan 20156, Italy
| | - Alessandra Roncaglioni
- Laboratory of Evironmental Chemistry and Toxicology, Department of Environmental Health Science, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri," Via G. La Masa 19, Milan 20156, Italy
| | - Emilio Benfentati
- Laboratory of Evironmental Chemistry and Toxicology, Department of Environmental Health Science, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri," Via G. La Masa 19, Milan 20156, Italy.
| | - Monika Nendza
- Analytisches Laboratorium, Bahnhofstr. 1, Luhnstedt 24816, Germany
| | - Helmut Segner
- Centre for Fish and Wildlife Health, University of Bern, PO Box 8466, Bern CH-3001, Switzerland
| | - Alberto Fernández
- Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, Av. Països Catalans 26, Catalunya, Tarragona 43007, Spain
| | - Ralph Kühne
- Department of Ecological Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, Leipzig 04318, Germany
| | - Antonio Franco
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej, Kgs. Lyngby DK-2800, Denmark; Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Eduard Pauné
- SIMPPLE S.L., Cr Joan Maragall 1 1r, Catalunya, Tarragona 43003, Spain
| | - Gerrit Schüürmann
- Department of Ecological Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, Leipzig 04318, Germany; Institute for Organic Chemistry, Technical University Bergakademie Freiberg, Leipziger Strasse 29, Freiberg 09596, Germany
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22
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Towards AOP application--implementation of an integrated approach to testing and assessment (IATA) into a pipeline tool for skin sensitization. Regul Toxicol Pharmacol 2014; 69:529-45. [PMID: 24928565 DOI: 10.1016/j.yrtph.2014.06.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/27/2014] [Accepted: 06/01/2014] [Indexed: 12/13/2022]
Abstract
Since the OECD published the Adverse Outcome Pathway (AOP) for skin sensitization, many efforts have focused on how to integrate and interpret nonstandard information generated for key events in a manner that can be practically useful for decision making. These types of frameworks are known as Integrated Approaches to Testing and Assessment (IATA). Here we have outlined an IATA for skin sensitization which focuses on existing information including non testing approaches such as QSAR and read-across. The IATA was implemented into a pipeline tool using OASIS technology to provide a means of systematically collating and compiling relevant information which could be used in an assessment of skin sensitization potential. A test set of 100 substances with available skin sensitization information was profiled using the pipeline IATA. In silico and in chemico profiling information alone was able to correctly predict skin sensitization potential, with a preliminary accuracy of 73.85%. Information from other relevant endpoints (e.g., Ames mutagenicity) was found to improve the accuracy (to 87.6%) when coupled with a reaction chemistry mechanistic understanding. This pipeline platform could be useful in the assessment of skin sensitization potential and marks a step change in how non testing approaches can be practically applied.
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23
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van der Veen JW, Rorije E, Emter R, Natsch A, van Loveren H, Ezendam J. Evaluating the performance of integrated approaches for hazard identification of skin sensitizing chemicals. Regul Toxicol Pharmacol 2014; 69:371-9. [PMID: 24813372 DOI: 10.1016/j.yrtph.2014.04.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/14/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
Abstract
The currently available animal-free methods for the detection of skin sensitizing potential of chemicals seem promising. However, no single method is able to comprehensively represent the complexity of the processes involved in skin sensitization. To ensure a mechanistic basis and cover the complexity, multiple methods should be integrated into a testing strategy, in accordance with the adverse outcome pathway that describes all key events in skin sensitization. Although current majority voting testing strategies have proven effective, the performance of individual methods is not taken into account. To that end, we designed a tiered strategy based on complementary characteristics of the included methods, and compared it to a majority voting approach. This tiered testing strategy was able to correctly identify all 41 chemicals tested. In terms of total number of experiments required, the tiered testing strategy requires less experiments compared to the majority voting approach. On the other hand, this tiered strategy is more complex due the number of different alternative methods required, and predicted costs are similar for both strategies. Both the tiered and majority voting strategies provide a mechanistic basis for skin sensitization testing, but the strategy most suitable for regulatory decision-making remains to be determined.
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Affiliation(s)
- Jochem W van der Veen
- National Institute for Public Health and the Environment (RIVM), PO Box 1, NL-3720BA Bilthoven, The Netherlands; Department of Toxicogenomics, Maastricht University, PO Box 616, NL-6200 MD Maastricht, The Netherlands
| | - Emiel Rorije
- National Institute for Public Health and the Environment (RIVM), PO Box 1, NL-3720BA Bilthoven, The Netherlands
| | - Roger Emter
- Givaudan Schweiz AG, Ueberlandstrasse 138, CH-8600 Dübendorf, Switzerland
| | - Andreas Natsch
- Givaudan Schweiz AG, Ueberlandstrasse 138, CH-8600 Dübendorf, Switzerland
| | - Henk van Loveren
- National Institute for Public Health and the Environment (RIVM), PO Box 1, NL-3720BA Bilthoven, The Netherlands; Department of Toxicogenomics, Maastricht University, PO Box 616, NL-6200 MD Maastricht, The Netherlands
| | - Janine Ezendam
- National Institute for Public Health and the Environment (RIVM), PO Box 1, NL-3720BA Bilthoven, The Netherlands.
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24
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Scholz S, Sela E, Blaha L, Braunbeck T, Galay-Burgos M, García-Franco M, Guinea J, Klüver N, Schirmer K, Tanneberger K, Tobor-Kapłon M, Witters H, Belanger S, Benfenati E, Creton S, Cronin MT, Eggen RI, Embry M, Ekman D, Gourmelon A, Halder M, Hardy B, Hartung T, Hubesch B, Jungmann D, Lampi MA, Lee L, Léonard M, Küster E, Lillicrap A, Luckenbach T, Murk AJ, Navas JM, Peijnenburg W, Repetto G, Salinas E, Schüürmann G, Spielmann H, Tollefsen KE, Walter-Rohde S, Whale G, Wheeler JR, Winter MJ. A European perspective on alternatives to animal testing for environmental hazard identification and risk assessment. Regul Toxicol Pharmacol 2013; 67:506-30. [DOI: 10.1016/j.yrtph.2013.10.003] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 10/02/2013] [Accepted: 10/16/2013] [Indexed: 12/20/2022]
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Buist H, Aldenberg T, Batke M, Escher S, Klein Entink R, Kühne R, Marquart H, Pauné E, Rorije E, Schüürmann G, Kroese D. The OSIRIS Weight of Evidence approach: ITS mutagenicity and ITS carcinogenicity. Regul Toxicol Pharmacol 2013; 67:170-81. [DOI: 10.1016/j.yrtph.2013.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 01/02/2013] [Accepted: 01/04/2013] [Indexed: 10/27/2022]
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Nendza M, Gabbert S, Kühne R, Lombardo A, Roncaglioni A, Benfenati E, Benigni R, Bossa C, Strempel S, Scheringer M, Fernández A, Rallo R, Giralt F, Dimitrov S, Mekenyan O, Bringezu F, Schüürmann G. A comparative survey of chemistry-driven in silico methods to identify hazardous substances under REACH. Regul Toxicol Pharmacol 2013; 66:301-14. [DOI: 10.1016/j.yrtph.2013.05.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 05/09/2013] [Accepted: 05/11/2013] [Indexed: 11/29/2022]
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Vermeire T, Aldenberg T, Buist H, Escher S, Mangelsdorf I, Pauné E, Rorije E, Kroese D. OSIRIS, a quest for proof of principle for integrated testing strategies of chemicals for four human health endpoints. Regul Toxicol Pharmacol 2013; 67:136-45. [PMID: 23385135 DOI: 10.1016/j.yrtph.2013.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 01/20/2013] [Accepted: 01/23/2013] [Indexed: 01/07/2023]
Abstract
Chemical substances policies in Europe are aiming towards chemical safety and at the same time a reduction in animal testing. These goals are alleged to be reachable by mining as many relevant data as possible, evaluate these data with regard to validity, reliability and relevance, and use of these data in so-called Integrated Testing Strategies (ITS). This paper offers an overview of four human health endpoints that were part of the EU-funded OSIRIS project, aiming to develop ITS fit for the EU chemicals legislation REACH. The endpoints considered cover their categorical as well as continuous characteristics: skin sensitisation, repeated dose toxicity, mutagenicity and carcinogenicity. Detailed papers are published elsewhere in this volume. The stepwise ITS approach developed takes advantage of existing information, groups information about similar substances and integrates exposure considerations. The different and possibly contradictory information is weighted and the respective uncertainties taken into account in a weight of evidence (WoE) approach. In case of data gaps, the ITS proposes the most appropriate method to acquire the missing information. Each building block for the ITS, i.e. each in vivo test, in vitro test, (Q)SAR model or human evidence, is evaluated with regard to quality.
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Affiliation(s)
- Theo Vermeire
- National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.
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