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Yang H, Li J, Wu Z, Li W, Liu G, Tang Y. Evaluation of Different Methods for Identification of Structural Alerts Using Chemical Ames Mutagenicity Data Set as a Benchmark. Chem Res Toxicol 2017; 30:1355-1364. [DOI: 10.1021/acs.chemrestox.7b00083] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hongbin Yang
- Shanghai Key Laboratory of
New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jie Li
- Shanghai Key Laboratory of
New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- 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
| | - 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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Raies AB, Bajic VB. In silico toxicology: computational methods for the prediction of chemical toxicity. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2016; 6:147-172. [PMID: 27066112 PMCID: PMC4785608 DOI: 10.1002/wcms.1240] [Citation(s) in RCA: 344] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/27/2015] [Accepted: 11/10/2015] [Indexed: 01/08/2023]
Abstract
Determining the toxicity of chemicals is necessary to identify their harmful effects on humans, animals, plants, or the environment. It is also one of the main steps in drug design. Animal models have been used for a long time for toxicity testing. However, in vivo animal tests are constrained by time, ethical considerations, and financial burden. Therefore, computational methods for estimating the toxicity of chemicals are considered useful. In silico toxicology is one type of toxicity assessment that uses computational methods to analyze, simulate, visualize, or predict the toxicity of chemicals. In silico toxicology aims to complement existing toxicity tests to predict toxicity, prioritize chemicals, guide toxicity tests, and minimize late-stage failures in drugs design. There are various methods for generating models to predict toxicity endpoints. We provide a comprehensive overview, explain, and compare the strengths and weaknesses of the existing modeling methods and algorithms for toxicity prediction with a particular (but not exclusive) emphasis on computational tools that can implement these methods and refer to expert systems that deploy the prediction models. Finally, we briefly review a number of new research directions in in silico toxicology and provide recommendations for designing in silico models. WIREs Comput Mol Sci 2016, 6:147-172. doi: 10.1002/wcms.1240 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Arwa B Raies
- King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Centre (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) Thuwal Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Centre (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) Thuwal Saudi Arabia
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Carrasquer CA, Batey K, Qamar S, Cunningham AR, Cunningham SL. Structure-activity relationship models for rat carcinogenesis and assessing the role mutagens play in model predictivity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:489-506. [PMID: 24697549 PMCID: PMC4830131 DOI: 10.1080/1062936x.2014.898694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We previously demonstrated that fragment based cat-SAR carcinogenesis models consisting solely of mutagenic or non-mutagenic carcinogens varied greatly in terms of their predictive accuracy. This led us to investigate how well the rat cancer cat-SAR model predicted mutagens and non-mutagens in their learning set. Four rat cancer cat-SAR models were developed: Complete Rat, Transgender Rat, Male Rat and Female Rat, with leave-one-out (LOO) validation concordance values of 69%, 74%, 67% and 73%, respectively. The mutagenic carcinogens produced concordance values in the range 69-76% compared with only 47-53% for non-mutagenic carcinogens. As a surrogate for mutagenicity, comparisons between single site and multiple site carcinogen SAR models were analysed. The LOO concordance values for models consisting of 1-site, 2-site and 4+-site carcinogens were 66%, 71% and 79%, respectively. As expected, the proportion of mutagens to non-mutagens also increased, rising from 54% for 1-site to 80% for 4+-site carcinogens. This study demonstrates that mutagenic chemicals, in both SAR learning sets and test sets, are influential in assessing model accuracy. This suggests that SAR models for carcinogens may require a two-step process in which mutagenicity is first determined before carcinogenicity can be accurately predicted.
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Affiliation(s)
| | - Kaylind Batey
- James Graham Brown Cancer Center, University of Louisville
| | - Shahid Qamar
- James Graham Brown Cancer Center, University of Louisville
| | - Albert R. Cunningham
- James Graham Brown Cancer Center, University of Louisville
- Department of Medicine, University of Louisville
- Department of Pharmacology and Toxicology, University of Louisville
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Kumar P, Carrasquer CA, Carter A, Song ZH, Cunningham AR. A categorical structure-activity relationship analysis of GPR119 ligands. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:891-903. [PMID: 25401513 PMCID: PMC4795450 DOI: 10.1080/1062936x.2014.967292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The categorical structure-activity relationship (cat-SAR) expert system has been successfully used in the analysis of chemical compounds that cause toxicity. Herein we describe the use of this fragment-based approach to model ligands for the G protein-coupled receptor 119 (GPR119). Using compounds that are known GPR119 agonists and compounds that we have confirmed experimentally that are not GPR119 agonists, four distinct cat-SAR models were developed. Using a leave-one-out validation routine, the best GPR119 model had an overall concordance of 99%, a sensitivity of 99%, and a specificity of 100%. Our findings from the in-depth fragment analysis of several known GPR119 agonists were consistent with previously reported GPR119 structure-activity relationship (SAR) analyses. Overall, while our results indicate that we have developed a highly predictive cat-SAR model that can be potentially used to rapidly screen for prospective GPR119 ligands, the applicability domain must be taken into consideration. Moreover, our study demonstrates for the first time that the cat-SAR expert system can be used to model G protein-coupled receptor ligands, many of which are important therapeutic agents.
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Affiliation(s)
- Pritesh Kumar
- Department of Pharmacology and Toxicology, University of Louisville Louisville, KY 40202
| | - Carl A. Carrasquer
- Department of Medicine, University of Louisville Louisville, KY 40202
- James Graham Brown Cancer Center, University of Louisville Louisville, KY 40202
| | - Arren Carter
- James Graham Brown Cancer Center, University of Louisville Louisville, KY 40202
- Department of Chemistry, University of Louisville Louisville, KY 40202
| | - Zhao-Hui Song
- Department of Pharmacology and Toxicology, University of Louisville Louisville, KY 40202
| | - Albert R. Cunningham
- Department of Pharmacology and Toxicology, University of Louisville Louisville, KY 40202
- Department of Medicine, University of Louisville Louisville, KY 40202
- James Graham Brown Cancer Center, University of Louisville Louisville, KY 40202
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Lepailleur A, Poezevara G, Bureau R. Automated detection of structural alerts (chemical fragments) in (eco)toxicology. Comput Struct Biotechnol J 2013; 5:e201302013. [PMID: 24688706 PMCID: PMC3962211 DOI: 10.5936/csbj.201302013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 02/09/2013] [Accepted: 02/20/2013] [Indexed: 11/22/2022] Open
Abstract
This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (eco)toxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data.
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Affiliation(s)
- Alban Lepailleur
- Normandie Univ, France ; UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie, FR CNRS INC3M - SF ICORE, Université de Caen Basse- Normandie, U.F.R. des Sciences Pharmaceutiques), F-14032 Caen, France
| | - Guillaume Poezevara
- Normandie Univ, France ; UNICAEN, GREYC (Groupe de Recherche en Informatique, Image, Automatique et Instrumentation de Caen, CNRS UMR 6072, Université de Caen Basse-Normandie), F-14032 Caen, France
| | - Ronan Bureau
- Normandie Univ, France ; UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie, FR CNRS INC3M - SF ICORE, Université de Caen Basse- Normandie, U.F.R. des Sciences Pharmaceutiques), F-14032 Caen, France
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Carrasquer CA, Malik N, States G, Qamar S, Cunningham S, Cunningham A. Chemical structure determines target organ carcinogenesis in rats. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:775-795. [PMID: 23066888 PMCID: PMC3547634 DOI: 10.1080/1062936x.2012.728996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
SAR models were developed for 12 rat tumour sites using data derived from the Carcinogenic Potency Database. Essentially, the models fall into two categories: Target Site Carcinogen-Non-Carcinogen (TSC-NC) and Target Site Carcinogen-Non-Target Site Carcinogen (TSC-NTSC). The TSC-NC models were composed of active chemicals that were carcinogenic to a specific target site and inactive ones that were whole animal non-carcinogens. On the other hand, the TSC-NTSC models used an inactive category also composed of carcinogens but to any/all other sites but the target site. Leave one out (LOO) validations produced an overall average concordance value for all 12 models of 0.77 for the TSC-NC models and 0.73 for the TSC-NTSC models. Overall, these findings suggest that while the TSC-NC models are able to distinguish between carcinogens and non-carcinogens, the TSC-NTSC models are identifying structural attributes that associate carcinogens to specific tumour sites. Since the TSC-NTSC models are composed of active and inactive compounds that are genotoxic and non-genotoxic carcinogens, the TSC-NTSC models may be capable of deciphering non-genotoxic mechanisms of carcinogenesis. Together, models of this type may also prove useful in anticancer drug development since they essentially contain chemical moieties that target a specific tumour site.
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Affiliation(s)
- C. A. Carrasquer
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - N. Malik
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - G. States
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - S. Qamar
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - S.L. Cunningham
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| | - A.R. Cunningham
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
- Department of Medicine, University of Louisville, Louisville, KY 40202
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202
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Stewart BW. Priorities for cancer prevention: lifestyle choices versus unavoidable exposures. Lancet Oncol 2012; 13:e126-33. [DOI: 10.1016/s1470-2045(11)70221-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Cunningham A, Qamar S, Carrasquer C, Holt P, Maguire J, Cunningham S, Trent J. Mammary carcinogen-protein binding potentials: novel and biologically relevant structure-activity relationship model descriptors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2010; 21:463-479. [PMID: 20818582 PMCID: PMC3383027 DOI: 10.1080/1062936x.2010.501818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Previously, SAR models for carcinogenesis used descriptors that are essentially chemical descriptors. Herein we report the development of models with the cat-SAR expert system using biological descriptors (i.e., ligand-receptor interactions) rat mammary carcinogens. These new descriptors are derived from the virtual screening for ligand-receptor interactions of carcinogens, non-carcinogens, and mammary carcinogens to a set of 5494 target proteins. Leave-one-out validations of the ligand mammary carcinogen-non-carcinogen model had a concordance between experimental and predicted results of 71%, and the mammary carcinogen-non-mammary carcinogen model was 72% concordant. The development of a hybrid fragment-ligand model improved the concordances to 85 and 83%, respectively. In a separate external validation exercise, hybrid fragment-ligand models had concordances of 81 and 76%. Analyses of example rat mammary carcinogens including the food mutagen and oestrogenic compound PhIP, the herbicide atrazine, and the drug indomethacin; the ligand model identified a number of proteins associated with each compound that had previously been referenced in Medline in conjunction with the test chemical and separately with association to breast cancer. This new modelling approach can enhance model predictivity and help bridge the gap between chemical structure and carcinogenic activity by descriptors that are related to biological targets.
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Affiliation(s)
- A.R. Cunningham
- James Graham Brown Cancer Center, University of Louisville, USA
- Department of Medicine, University of Louisville, USA
- Department of Pharmacology and Toxicology, University of Louisville, USA
| | - S. Qamar
- James Graham Brown Cancer Center, University of Louisville, USA
| | - C.A. Carrasquer
- James Graham Brown Cancer Center, University of Louisville, USA
| | - P.A. Holt
- James Graham Brown Cancer Center, University of Louisville, USA
| | - J.M. Maguire
- James Graham Brown Cancer Center, University of Louisville, USA
| | - S.L. Cunningham
- James Graham Brown Cancer Center, University of Louisville, USA
| | - J.O. Trent
- James Graham Brown Cancer Center, University of Louisville, USA
- Department of Medicine, University of Louisville, USA
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A categorical structure-activity relationship analysis of the developmental toxicity of antithyroid drugs. INTERNATIONAL JOURNAL OF PEDIATRIC ENDOCRINOLOGY 2010; 2009:936154. [PMID: 20111734 PMCID: PMC2810459 DOI: 10.1155/2009/936154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 09/18/2009] [Indexed: 11/18/2022]
Abstract
The choice of therapeutic strategies for hyperthyroidism during pregnancy is limited. Surgery and radioiodine are typically avoided, leaving propylthiouracil and methimazole in the US. Carbimazole, a metabolic precursor of methimazole, is available in some countries outside of the US. In the US propylthiouracil is recommended because of concern about developmental toxicity from methimazole and carbimazole. Despite this recommendation, the data on developmental toxicity of all three agents are extremely limited and insufficient to support a policy given the broad use of methimazole and carbimazole around the world. In the absence of new human or animal data we describe the development of a new structure-activity relationship (SAR) model for developmental toxicity using the cat-SAR expert system. The SAR model was developed from data for 323 compounds evaluated for human developmental toxicity with 130 categorized as developmental toxicants and 193 as nontoxicants. Model cross-validation yielded a concordance between observed and predicted results between 79% to 81%. Based on this model, propylthiouracil, methimazole, and carbimazole were observed to share some structural features relating to human developmental toxicity. Thus given the need to treat women with Graves's disease during pregnancy, new molecules with minimized risk for developmental toxicity are needed. To help meet this challenge, the cat-SAR method would be a useful in screening new drug candidates for developmental toxicity as well as for investigating their mechanism of action.
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