1
|
Devillers J, Sartor V, Doucet JP, Doucet-Panaye A, Devillers H. In silico prediction of mosquito repellents for clothing application. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:239-257. [PMID: 35532305 DOI: 10.1080/1062936x.2022.2062871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Use of protective clothing is a simple and efficient way to reduce the contacts with mosquitoes and consequently the probability of transmission of diseases spread by them. This mechanical barrier can be enhanced by the application of repellents. Unfortunately the number of available repellents is limited. As a result, there is a crucial need to find new active and safer molecules repelling mosquitoes. In this context, a structure-activity relationship (SAR) model was proposed for the design of repellents active on clothing. It was computed from a dataset of 2027 chemicals for which repellent activity on clothing was measured against Aedes aegypti. Molecules were described by means of 20 molecular descriptors encoding physicochemical properties, topological information and structural features. A three-layer perceptron was used as statistical tool. An accuracy of 87% was obtained for both the training and test sets. Most of the wrong predictions can be explained. Avenues for increasing the performances of the model have been proposed.
Collapse
Affiliation(s)
| | - V Sartor
- Laboratoire des IMRCP, Université de Toulouse, Toulouse, France
| | - J P Doucet
- Université de Paris, ITODYS, CNRS, Paris, France
| | | | - H Devillers
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| |
Collapse
|
2
|
|
3
|
Schaduangrat N, Lampa S, Simeon S, Gleeson MP, Spjuth O, Nantasenamat C. Towards reproducible computational drug discovery. J Cheminform 2020; 12:9. [PMID: 33430992 PMCID: PMC6988305 DOI: 10.1186/s13321-020-0408-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022] Open
Abstract
The reproducibility of experiments has been a long standing impediment for further scientific progress. Computational methods have been instrumental in drug discovery efforts owing to its multifaceted utilization for data collection, pre-processing, analysis and inference. This article provides an in-depth coverage on the reproducibility of computational drug discovery. This review explores the following topics: (1) the current state-of-the-art on reproducible research, (2) research documentation (e.g. electronic laboratory notebook, Jupyter notebook, etc.), (3) science of reproducible research (i.e. comparison and contrast with related concepts as replicability, reusability and reliability), (4) model development in computational drug discovery, (5) computational issues on model development and deployment, (6) use case scenarios for streamlining the computational drug discovery protocol. In computational disciplines, it has become common practice to share data and programming codes used for numerical calculations as to not only facilitate reproducibility, but also to foster collaborations (i.e. to drive the project further by introducing new ideas, growing the data, augmenting the code, etc.). It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code.
Collapse
Affiliation(s)
- Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, 10700, Bangkok, Thailand
| | - Samuel Lampa
- Department of Pharmaceutical Biosciences, Uppsala University, 751 24, Uppsala, Sweden
| | - Saw Simeon
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 10900, Bangkok, Thailand
| | - Matthew Paul Gleeson
- Department of Biomedical Engineering, Faculty of Engineering, King Mongkut's Institute of Technology Ladkrabang, 10520, Bangkok, Thailand.
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, 751 24, Uppsala, Sweden.
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, 10700, Bangkok, Thailand.
| |
Collapse
|
4
|
Ecotoxicological QSARs of Personal Care Products and Biocides. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2020. [DOI: 10.1007/978-1-0716-0150-1_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
5
|
Devillers J, Devillers H. Toxicity profiling and prioritization of plant-derived antimalarial agents. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:801-824. [PMID: 31565973 DOI: 10.1080/1062936x.2019.1665844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Human malaria is the most widespread mosquito-borne life-threatening disease worldwide. In the absence of effective vaccines, prevention and treatment of malaria only depend on prophylaxis and drug-based therapy either in monotherapy or in combination. Unfortunately, the number of available antimalarial drugs presenting different mechanisms of action is rather limited. In addition, the appearance of drug-resistance in the parasite strains impacts the efficacy of the treatments. As a result, there is a crucial need to find new drugs to circumvent resistance problems. In the quest to identify new antimalarial agents a huge number of plant-derived compounds (PDCs) have been investigated. Surprisingly in the in silico PDC screening programs, toxicity filters are either never used or so simple that their interest is limited. In this context, the goal of this study was to show how to take advantage of validated toxicity QSAR models for refining the selection of PDCs. From an original data set of 507 PDCs collected from the literature, the use of toxicity filters for endocrine disruption, developmental toxicity, and hepatotoxicity in conjunction with classical pharmacokinetic filters allowed us to obtain a list of 31 compounds of potential interest. The pros and cons of such a strategy have been discussed.
Collapse
Affiliation(s)
| | - H Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
| |
Collapse
|
6
|
Khan K, Khan PM, Lavado G, Valsecchi C, Pasqualini J, Baderna D, Marzo M, Lombardo A, Roy K, Benfenati E. QSAR modeling of Daphnia magna and fish toxicities of biocides using 2D descriptors. CHEMOSPHERE 2019; 229:8-17. [PMID: 31063877 DOI: 10.1016/j.chemosphere.2019.04.204] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 05/25/2023]
Abstract
In the recent years, ecotoxicological hazard potential of biocidal products has been receiving increasing attention in the industries and regulatory agencies. Biocides/pesticides are currently one of the most studied groups of compounds, and their registration cannot be done without the empirical toxicity information. In view of limited experimental data available for these compounds, we have developed Quantitative Structure-Activity Relationship (QSAR) models for the toxicity of biocides to fish and Daphnia magna following principles of QSAR modeling recommended by the OECD (Organization for Economic Cooperation and Development). The models were developed using simple and interpretable 2D descriptors and validated using stringent tests. Both models showed encouraging statistical quality in terms of determination coefficient R2 (0.800 and 0.648), cross-validated leave-one-out Q2 (0.760 and 0.602) and predictive R2pred or Q2ext (0.875 and 0.817) for fish (nTraining = 66, nTest = 22) and Daphnia magna (nTraining = 100, nTest = 33) toxicity datasets, respectively. These models should be applicable for data gap filling in case of new or untested biocidal compounds falling within the applicability domain of the models. In general, the models indicate that the toxicity increases with lipophilicity and decreases with polarity, branching and unsaturation. We have also developed interspecies toxicity models for biocides using the daphnia and fish toxicity data and used the models for data gap filling.
Collapse
Affiliation(s)
- Kabiruddin Khan
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, 188 Raja S C Mullick Road, 700032, Kolkata, India
| | - Pathan Mohsin Khan
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Educational and Research (NIPER), Chunilal Bhawan, 168, Manikata Main Road, 700054, Kolkata, India
| | - Giovanna Lavado
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy
| | - Cecile Valsecchi
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy
| | - Julia Pasqualini
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy
| | - Diego Baderna
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy
| | - Marco Marzo
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy
| | - Anna Lombardo
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, 188 Raja S C Mullick Road, 700032, Kolkata, India; Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy.
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy.
| |
Collapse
|
7
|
Bhilwadikar T, Pounraj S, Manivannan S, Rastogi NK, Negi PS. Decontamination of Microorganisms and Pesticides from Fresh Fruits and Vegetables: A Comprehensive Review from Common Household Processes to Modern Techniques. Compr Rev Food Sci Food Saf 2019; 18:1003-1038. [DOI: 10.1111/1541-4337.12453] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/26/2019] [Accepted: 04/11/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Tanmayee Bhilwadikar
- Dept. of Fruit and Vegetable TechnologyCSIR ‐ Central Food Technological Research Inst. Mysuru 570020 India
| | - Saranya Pounraj
- Dept. of Fruit and Vegetable TechnologyCSIR ‐ Central Food Technological Research Inst. Mysuru 570020 India
| | - S. Manivannan
- Dept. of Food Protectant and Infestation ControlCSIR ‐ Central Food Technological Research Inst. Mysuru 570020 India
| | - N. K. Rastogi
- Dept. of Food EngineeringCSIR ‐ Central Food Technological Research Inst. Mysuru 570020 India
| | - P. S. Negi
- Dept. of Fruit and Vegetable TechnologyCSIR ‐ Central Food Technological Research Inst. Mysuru 570020 India
| |
Collapse
|
8
|
Khan PM, Roy K, Benfenati E. Chemometric modeling of Daphnia magna toxicity of agrochemicals. CHEMOSPHERE 2019; 224:470-479. [PMID: 30831498 DOI: 10.1016/j.chemosphere.2019.02.147] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
Over the past few years, the ecotoxicological hazard potential of agrochemicals has received much attention in the industries and regulatory agencies. In the current work, we have developed quantitative structure-activity relationship (QSAR) models for Daphnia magna toxicities of different classes of agrochemicals (fungicides, herbicides, insecticides and microbiocides) individually as well as for the combined set with the application of Organization for Economic Co-operation and Development (OECD) recommended guidelines. The models for the individual data sets as well as for the combined set were generated employing only simple and interpretable two-dimensional descriptors, and subsequently strictly validated using test set compounds. The validated individual models were used to generate consensus models, with the objective to improve the prediction quality and reduced prediction errors. All the individual models of different classes of agrochemicals as well as the global set of agrochemicals showed encouraging statistical quality and prediction ability. The general observations from the derived models suggest that the toxicity increases with lipophilicity and decreases with polarity. The generated models of different classes of agrochemicals and also for the combined set should be applicable for data gap filling for new or untested agrochemical compounds falling within the applicability domain of the developed models.
Collapse
Affiliation(s)
- Pathan Mohsin Khan
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Educational and Research (NIPER), Chunilal Bhawan, 168, Manikata Main Road, 700054, Kolkata, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, 188 Raja S C Mullick Road, 700032, Kolkata, India; Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy.
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa, 19, 20156, Milano, Italy
| |
Collapse
|
9
|
Cheluvappa R, Scowen P, Eri R. Ethics of animal research in human disease remediation, its institutional teaching; and alternatives to animal experimentation. Pharmacol Res Perspect 2017; 5. [PMID: 28805976 PMCID: PMC5684868 DOI: 10.1002/prp2.332] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 05/23/2017] [Indexed: 11/09/2022] Open
Abstract
Animals have been used in research and teaching for a long time. However, clear ethical guidelines and pertinent legislation were instated only in the past few decades, even in developed countries with Judeo-Christian ethical roots. We compactly cover the basics of animal research ethics, ethical reviewing and compliance guidelines for animal experimentation across the developed world, "our" fundamentals of institutional animal research ethics teaching, and emerging alternatives to animal research. This treatise was meticulously constructed for scientists interested/involved in animal research. Herein, we discuss key animal ethics principles - Replacement/Reduction/Refinement. Despite similar undergirding principles across developed countries, ethical reviewing and compliance guidelines for animal experimentation vary. The chronology and evolution of mandatory institutional ethical reviewing of animal experimentation (in its pioneering nations) are summarised. This is followed by a concise rendition of the fundamentals of teaching animal research ethics in institutions. With the advent of newer methodologies in human cell-culturing, novel/emerging methods aim to minimise, if not avoid the usage of animals in experimentation. Relevant to this, we discuss key extant/emerging alternatives to animal use in research; including organs on chips, human-derived three-dimensional tissue models, human blood derivates, microdosing, and computer modelling of various hues.
Collapse
Affiliation(s)
- Rajkumar Cheluvappa
- Department of Medicine, St. George Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul Scowen
- Department of Animal Services, University of Tasmania, Hobart, Tasmania, Australia
| | - Rajaraman Eri
- Mucosal Biology Laboratory, School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| |
Collapse
|
10
|
Bro E, Millot F, Decors A, Devillers J. Quantification of potential exposure of gray partridge (Perdix perdix) to pesticide active substances in farmlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 521-522:315-25. [PMID: 25847175 DOI: 10.1016/j.scitotenv.2015.03.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 05/15/2023]
Abstract
Estimating exposure of wild birds to plant protection products is of key importance in the risk assessment process evaluating their harmful potential. In this paper, we propose an ecologically-relevant methodology to estimate potential exposure to active substances (ASs) of a farmland focal bird, the gray partridge Perdix perdix. It is based on bird habitat use of fields at the time of pesticide applications. It accounts for spatio-temporal heterogeneity at population and landscape scales. We identify and quantify the potential exposure to 179 ASs of 140 clutches during pre-laying, laying, and incubation phases, and of 75 coveys. The data come from a large scale field study combining radiotelemetry and a farmer survey. They were collected in 12 different representative sites. The proportion of clutches potentially exposed to a given chemical was ≥5% for 32 ASs; prothioconazole and epoxiconazole ranking first. 71% of clutches were potentially exposed to ≥1 AS and 67% to ≥2 ASs. Mixtures involved 2 to 22 ASs. They emerged from commercial formulations, tank mixtures, bird habitat use, and combinations. ASs were fungicides (53%), herbicides (25%), and insecticides (16%) used on a variety of crops in April-June, when ground-nesting birds are breeding. The European Food Safety Authority conclusions report a long-term first-tier toxicity-to-exposure ratio (TERlt) <5 for 11 out of 19 documented ASs, and higher-tier TERlt <5 for 5 out of 10 ASs. This suggests a potential risk for bird reproduction in farmlands. Globally 13% of coveys were potentially exposed to 18 ASs during the first month (1-4 coveys per AS). The use of our field data in future research and risk assessment is discussed.
Collapse
Affiliation(s)
- Elisabeth Bro
- National Game and Wildlife Institute (ONCFS), Research Department, Saint Benoist, BP 20, F 78 612 Le Perray en Yvelines Cedex, France.
| | - Florian Millot
- National Game and Wildlife Institute (ONCFS), Research Department, Saint Benoist, BP 20, F 78 612 Le Perray en Yvelines Cedex, France.
| | - Anouk Decors
- National Game and Wildlife Institute (ONCFS), Research Department, Saint Benoist, BP 20, F 78 612 Le Perray en Yvelines Cedex, France.
| | - James Devillers
- Centre de Traitement de l'Information Scientifique (CTIS), 3 chemin de la Gravière, 69140 Rillieux La Pape, France.
| |
Collapse
|
11
|
Ovchinnikova SI, Bykov AA, Tsivadze AY, Dyachkov EP, Kireeva NV. Supervised extensions of chemography approaches: case studies of chemical liabilities assessment. J Cheminform 2014; 6:20. [PMID: 24868246 PMCID: PMC4018504 DOI: 10.1186/1758-2946-6-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 04/28/2014] [Indexed: 12/04/2022] Open
Abstract
Chemical liabilities, such as adverse effects and toxicity, play a significant role in modern drug discovery process. In silico assessment of chemical liabilities is an important step aimed to reduce costs and animal testing by complementing or replacing in vitro and in vivo experiments. Herein, we propose an approach combining several classification and chemography methods to be able to predict chemical liabilities and to interpret obtained results in the context of impact of structural changes of compounds on their pharmacological profile. To our knowledge for the first time, the supervised extension of Generative Topographic Mapping is proposed as an effective new chemography method. New approach for mapping new data using supervised Isomap without re-building models from the scratch has been proposed. Two approaches for estimation of model's applicability domain are used in our study to our knowledge for the first time in chemoinformatics. The structural alerts responsible for the negative characteristics of pharmacological profile of chemical compounds has been found as a result of model interpretation.
Collapse
Affiliation(s)
- Svetlana I Ovchinnikova
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky pr-t 31-4, 119071 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudny, Russia
| | - Arseniy A Bykov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky pr-t 31-4, 119071 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudny, Russia
| | - Aslan Yu Tsivadze
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky pr-t 31-4, 119071 Moscow, Russia
| | - Evgeny P Dyachkov
- Kurnakov Institute of General and Inorganic Chemistry RAS, Leninsky pr-t 31, 119071 Moscow, Russia
| | - Natalia V Kireeva
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninsky pr-t 31-4, 119071 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutsky per., 9, 141700 Dolgoprudny, Russia
| |
Collapse
|
12
|
Fjodorova N, Novič M. Comparison of criteria used to access carcinogenicity in CPANN QSAR models versus the knowledge-based expert system Toxtree. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:423-441. [PMID: 24716754 DOI: 10.1080/1062936x.2014.898687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The primary goal of this study was to describe and compare the criteria used to assess carcinogenic activity. The statistically-based predictive quantitative structure-activity relationship (QSAR) models based on the counter propagation artificial neural network (CPANN) algorithm, and knowledge-based expert systems based on a decision tree structural alert (SA) approach (Toxtree application), were considered. The integration of the QSAR (CPANN models) and SAR (Toxtree SA application) approach contributed to the mechanistic understanding of the QSAR model considered. The mapping technique inherent to CPANN Kohonen enables us to relate the similarities or dissimilarities within a congeneric set of chemicals with particular SAs for carcinogenicity. The focus of our investigations was the similarities and dissimilarities of the features used in the QSAR and SAR methods. Due to the complexity of the carcinogenic endpoint, the integration of different approaches allows the models to be improved and provides a valuable technique for evaluating the safety of chemicals.
Collapse
Affiliation(s)
- N Fjodorova
- a National Institute of Chemistry , Hajdrihova, Ljubljana , Slovenia
| | | |
Collapse
|
13
|
Tanabe K, Kurita T, Nishida K, Lučić B, Amić D, Suzuki T. Improvement of carcinogenicity prediction performances based on sensitivity analysis in variable selection of SVM models. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:565-580. [PMID: 23350528 DOI: 10.1080/1062936x.2012.762425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A new sensitivity analysis (SA) method for variable selection in support vector machine (SVM) was proposed to improve the performance level of the QSAR model to predict carcinogenicity based on the correlation coefficient (CC) method used in our preceding study. The performances of both methods were also compared with that of the F-score (FS) method proposed by Chang and Lin. The 911 non-congeneric chemicals were classified into 20 mutually overlapping groups according to contained substructures, and a specific SVM model created on chemicals belonging to each group was optimized by searching the best set of SVM parameters while successively omitting descriptors of lower absolute values of sensitivity, CC or FS until the maximum predictive performance was obtained. The SA method improves the overall accuracy from 80% of CC and FS to 84%, which is considerably higher than those of existing models for predicting the carcinogenicity of non-congeneric chemicals. It selects the optimum sets of effective descriptors fewer than the CC and FS methods, and is not time-consuming and can be applied to a large set of initial descriptors. It is concluded that SA is superior as a variable selection method in SVM models.
Collapse
Affiliation(s)
- K Tanabe
- Neuroscience Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | | | | | | | | | | |
Collapse
|
14
|
Devillers J, Pandard P, Richard B. External validation of structure-biodegradation relationship (SBR) models for predicting the biodegradability of xenobiotics. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:979-993. [PMID: 24313438 DOI: 10.1080/1062936x.2013.848632] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Biodegradation is an important mechanism for eliminating xenobiotics by biotransforming them into simple organic and inorganic products. Faced with the ever growing number of chemicals available on the market, structure-biodegradation relationship (SBR) and quantitative structure-biodegradation relationship (QSBR) models are increasingly used as surrogates of the biodegradation tests. Such models have great potential for a quick and cheap estimation of the biodegradation potential of chemicals. The Estimation Programs Interface (EPI) Suite™ includes different models for predicting the potential aerobic biodegradability of organic substances. They are based on different endpoints, methodologies and/or statistical approaches. Among them, Biowin 5 and 6 appeared the most robust, being derived from the largest biodegradation database with results obtained only from the Ministry of International Trade and Industry (MITI) test. The aim of this study was to assess the predictive performances of these two models from a set of 356 chemicals extracted from notification dossiers including compatible biodegradation data. Another set of molecules with no more than four carbon atoms and substituted by various heteroatoms and/or functional groups was also embodied in the validation exercise. Comparisons were made with the predictions obtained with START (Structural Alerts for Reactivity in Toxtree). Biowin 5 and Biowin 6 gave satisfactorily prediction results except for the prediction of readily degradable chemicals. A consensus model built with Biowin 1 allowed the diminution of this tendency.
Collapse
|
15
|
Abstract
Structure-activity relationship (SAR) and quantitative structure-activity relationship (QSAR) models are increasingly used in toxicology, ecotoxicology, and pharmacology for predicting the activity of the molecules from their physicochemical properties and/or their structural characteristics. However, the design of such models has many traps for unwary practitioners. Consequently, the purpose of this chapter is to give a practical guide for the computation of SAR and QSAR models, point out problems that may be encountered, and suggest ways of solving them. Attempts are also made to see how these models can be validated and interpreted.
Collapse
|
16
|
Mombelli E. Evaluation of the OECD (Q)SAR Application Toolbox for the profiling of estrogen receptor binding affinities. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:37-57. [PMID: 22014213 DOI: 10.1080/1062936x.2011.623325] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The determination of binding affinities for the estrogen receptor (ER) is used extensively to assess potential hazards to human health and the environment arising from chemicals that can interfere with natural hormone homeostasis. Given the great number of chemicals to which humans and wildlife are exposed, (quantitative) structure-activity relationship (Q)SAR models for the characterization of ER disruptors represent a fast and cost-efficient alternative to experimental testing. In this toxicological context, the freely available Organisation for Economic Co-operation and Development (OECD) (Q)SAR Application Toolbox provides a profiler for the categorical profiling of chemicals according to their ER binding propensities. The aim of this study was to evaluate the predictive performances of this profiler. To achieve such a purpose, prediction results with the ER-profiler were compared with experimental binding affinities relative to two large datasets of chemicals (rat and human). The resulting Cooper statistics indicated that the binding affinities of the majority of chemicals included in the retained datasets could be correctly predicted.
Collapse
Affiliation(s)
- E Mombelli
- a Unité Modèles pour l'Ecotoxicologie et la Toxicologie (METO), Institut National de l'Environnement Industriel et des Risques (INERIS) , Verneuil-en-Halatte , France
| |
Collapse
|
17
|
Schirhagl R, Latif U, Dickert FL. Atrazine detection based on antibody replicas. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm11576f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|