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Hamid N, Junaid M, Manzoor R, Sultan M, Chuan OM, Wang J. An integrated assessment of ecological and human health risks of per- and polyfluoroalkyl substances through toxicity prediction approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167213. [PMID: 37730032 DOI: 10.1016/j.scitotenv.2023.167213] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/06/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are also known as "forever chemicals" due to their persistence and ubiquitous environmental distribution. This review aims to summarize the global PFAS distribution in surface water and identify its ecological and human risks through integrated assessment. Moreover, it provides a holistic insight into the studies highlighting the human biomonitoring and toxicological screening of PFAS in freshwater and marine species using quantitative structure-activity relationship (QSAR) based models. Literature showed that PFOA and PFOS were the most prevalent chemicals found in surface water. The highest PFAS levels were reported in the US, China, and Australia. The TEST model showed relatively low LC50 of PFDA and PFOS for Pimephales promelas (0.36 and 0.91 mg/L) and high bioaccumulation factors (518 and 921), revealing an elevated associated toxicity. The risk quotients (RQs) values for P. promelas and Daphnia magna were found to be 269 and 23.7 for PFOS. Studies confirmed that long-chain PFAS such as PFOS and PFOA undergo bioaccumulation in aquatic organisms and induce toxicological effects such as oxidative stress, transgenerational epigenetic effects, disturbed genetic and enzymatic responses, perturbed immune system, hepatotoxicity, neurobehavioral toxicity, altered genetic and enzymatic responses, and metabolism abnormalities. Human biomonitoring studies found the highest PFOS, PFOA, and PFHxS levels in urine, cerebrospinal fluid, and serum samples. Further, long-chain PFOA and PFOS exposure create severe health implications such as hyperuricemia, reduced birth weight, and immunotoxicity in humans. Molecular docking analysis revealed that short-chain PFBS (-11.84 Kcal/mol) and long-chain PFUnDA (-10.53 Kcal/mol) displayed the strongest binding interactions with human serum albumin protein. Lastly, research challenges and future perspectives for PFAS toxicological implications were also discussed, which helps to mitigate associated pollution and ecological risks.
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Affiliation(s)
- Naima Hamid
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Ocean Pollution and Ecotoxicology (OPEC) Research Group, Universiti Malaysia Terengganu, Malaysia
| | - Muhammad Junaid
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Rakia Manzoor
- State key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Marriya Sultan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Ong Meng Chuan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Ocean Pollution and Ecotoxicology (OPEC) Research Group, Universiti Malaysia Terengganu, Malaysia
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China.
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2
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Balogun TA, Chukwudozie OS, Ogbodo UC, Junaid IO, Sunday OA, Ige OM, Aborode AT, Akintayo AD, Oluwarotimi EA, Oluwafemi IO, Saibu OA, Chuckwuemaka P, Omoboyowa DA, Alausa AO, Atasie NH, Ilesanmi A, Dairo G, Tiamiyu ZA, Batiha GE, Alkhuriji AF, Al-Megrin WAI, De Waard M, Sabatier JM. Discovery of putative inhibitors against main drivers of SARS-CoV-2 infection: Insight from quantum mechanical evaluation and molecular modeling. Front Chem 2022; 10:964446. [PMID: 36304744 PMCID: PMC9593047 DOI: 10.3389/fchem.2022.964446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 triggered a worldwide medical crisis, affecting the world’s social, emotional, physical, and economic equilibrium. However, treatment choices and targets for finding a solution to COVID-19’s threat are becoming limited. A viable approach to combating the threat of COVID-19 is by unraveling newer pharmacological and therapeutic targets pertinent in the viral survival and adaptive mechanisms within the host biological milieu which in turn provides the opportunity to discover promising inhibitors against COVID-19. Therefore, using high-throughput virtual screening, manually curated compounds library from some medicinal plants were screened against four main drivers of SARS-CoV-2 (spike glycoprotein, PLpro, 3CLpro, and RdRp). In addition, molecular docking, Prime MM/GBSA (molecular mechanics/generalized Born surface area) analysis, molecular dynamics (MD) simulation, and drug-likeness screening were performed to identify potential phytodrugs candidates for COVID-19 treatment. In support of these approaches, we used a series of computational modeling approaches to develop therapeutic agents against COVID-19. Out of the screened compounds against the selected SARS-CoV-2 therapeutic targets, only compounds with no violations of Lipinski’s rule of five and high binding affinity were considered as potential anti-COVID-19 drugs. However, lonchocarpol A, diplacol, and broussonol E (lead compounds) were recorded as the best compounds that satisfied this requirement, and they demonstrated their highest binding affinity against 3CLpro. Therefore, the 3CLpro target and the three lead compounds were selected for further analysis. Through protein–ligand mapping and interaction profiling, the three lead compounds formed essential interactions such as hydrogen bonds and hydrophobic interactions with amino acid residues at the binding pocket of 3CLpro. The key amino acid residues at the 3CLpro active site participating in the hydrophobic and polar inter/intra molecular interaction were TYR54, PRO52, CYS44, MET49, MET165, CYS145, HIS41, THR26, THR25, GLN189, and THR190. The compounds demonstrated stable protein–ligand complexes in the active site of the target (3CLpro) over a 100 ns simulation period with stable protein–ligand trajectories. Drug-likeness screening shows that the compounds are druggable molecules, and the toxicity descriptors established that the compounds demonstrated a good biosafety profile. Furthermore, the compounds were chemically reactive with promising molecular electron potential properties. Collectively, we propose that the discovered lead compounds may open the way for establishing phytodrugs to manage COVID-19 pandemics and new chemical libraries to prevent COVID-19 entry into the host based on the findings of this computational investigation.
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Affiliation(s)
- Toheeb A. Balogun
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- *Correspondence: Toheeb A. Balogun, ; Gaber E. Batiha,
| | - Onyeka S. Chukwudozie
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, United States
| | | | - Idris O. Junaid
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, United States
| | - Olugbodi A. Sunday
- Department of Environmental Toxicology, Universitat Duisburg-Essen, Essen, Germany
| | - Oluwasegun M. Ige
- Department of Marine Biological Resources, Ghent University, Ghent, Belgium
| | - Abdullahi T. Aborode
- Department of Chemistry, Mississippi State University, Starkville, MS, United States
| | - Abiola D. Akintayo
- Department of Chemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Emmanuel A. Oluwarotimi
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, United States
| | - Isaac O. Oluwafemi
- Department of Chemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Oluwatosin A. Saibu
- Department of Environmental Toxicology, Universitat Duisburg-Essen, Essen, Germany
| | - Prosper Chuckwuemaka
- Department of Biotechnology, Federal University of Technology Akure, Akure, Nigeria
| | | | | | - Nkechi H. Atasie
- Clinical Pharmacy Department, Nigeria Correctional Service, Enugu Custodial Centre, Enugu, Nigeria
| | - Ayooluwa Ilesanmi
- Department of Chemistry, Mississipi University for Women Columbus, Columbus, United States
| | - Gbenga Dairo
- Department of Biological Sciences, Western Illinois University, Macomb, IL, United States
| | - Zainab A. Tiamiyu
- Department of Biochemistry and Molecular Biology, Federal University Dutsin-ma, Dutsin-Ma, Nigeria
| | - Gaber E. Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
- *Correspondence: Toheeb A. Balogun, ; Gaber E. Batiha,
| | - Afrah Fahad Alkhuriji
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wafa Abdullah I. Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Michel De Waard
- Smartox Biotechnology, Saint-Egréve, France
- L‘institut du Thorax, INSERM, CNRS, Université de Nantes, Nantes, France
- LabEx Ion Channels, Science and Therapeutics, Université de Nice Sophia-Antipolis, Valbonne, France
| | - Jean-Marc Sabatier
- Institut de Neurophysiopathologie (INP), Faculté des Sciences Médicales et Paramédicales, Aix-Marseille Université, CNRS UMR 7051, Marseille, France
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3
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Koelmel JP, Lin EZ, DeLay K, Williams AJ, Zhou Y, Bornman R, Obida M, Chevrier J, Godri Pollitt KJ. Assessing the External Exposome Using Wearable Passive Samplers and High-Resolution Mass Spectrometry among South African Children Participating in the VHEMBE Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2191-2203. [PMID: 35089017 DOI: 10.1021/acs.est.1c06481] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Children in low- and middle-income countries are often exposed to higher levels of chemicals and are more vulnerable to the health effects of air pollution. Little is known about the diversity, toxicity, and dynamics of airborne chemical exposures at the molecular level. We developed a workflow employing state-of-the-art wearable passive sampling technology coupled with high-resolution mass spectrometry to comprehensively measure 147 children's personal exposures to airborne chemicals in Limpopo, South Africa, as part of the Venda Health Examination of Mothers, Babies, and Their Environment (VHEMBE). 637 environmental exposures were detected, many of which have never been measured in this population; of these 50 airborne chemical exposures of concern were detected, including pesticides, plasticizers, organophosphates, dyes, combustion products, and perfumes. Biocides detected in wristbands included p,p'-dichlorodiphenyltrichloroethane (p,p'-DDT), p,p'-dichlorodiphenyldichloroethane (p,p'-DDD), p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE), propoxur, piperonyl butoxide, and triclosan. Exposures differed across the assessment period with 27% of detected chemicals observed to be either higher or lower in the wet or dry seasons.
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Affiliation(s)
- Jeremy P Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, United States
| | - Elizabeth Z Lin
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, United States
| | - Kayley DeLay
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, United States
| | - Antony J Williams
- Center for Computational Toxicology and Exposure, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Yakun Zhou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, United States
| | - Riana Bornman
- University of Pretoria Institute for Sustainable Malaria Control and School of Health Systems and Public Health, University of Pretoria, Pretoria 0028, South Africa
| | - Muvhulawa Obida
- University of Pretoria Institute for Sustainable Malaria Control and School of Health Systems and Public Health, University of Pretoria, Pretoria 0028, South Africa
| | - Jonathan Chevrier
- Department of Epidemiology, Biostatistics and Occupational Health, Faculty of Medicine, McGill University, Montréal, Québec H3A 1A2, Canada
| | - Krystal J Godri Pollitt
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, United States
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4
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C S, S. DK, Ragunathan V, Tiwari P, A. S, P BD. Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease. J Biomol Struct Dyn 2022; 40:585-611. [PMID: 32897178 PMCID: PMC7573242 DOI: 10.1080/07391102.2020.1815584] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/21/2020] [Indexed: 12/31/2022]
Abstract
The study aims to evaluate the potency of two hundred natural antiviral phytocompounds against the active site of the Severe Acquired Respiratory Syndrome - Coronavirus - 2 (SARS-CoV-2) Main-Protease (Mpro) using AutoDock 4.2.6. The three- dimensional crystal structure of the Mpro (PDB Id: 6LU7) was retrieved from the Protein Data Bank (PDB), the active site was predicted using MetaPocket 2.0. Food and Drug Administration (FDA) approved viral protease inhibitors were used as standards for comparison of results. The compounds theaflavin-3-3'-digallate, rutin, hypericin, robustaflavone, and (-)-solenolide A with respective binding energy of -12.41 (Ki = 794.96 pM); -11.33 (Ki = 4.98 nM); -11.17 (Ki = 6.54 nM); -10.92 (Ki = 9.85 nM); and -10.82 kcal/mol (Ki = 11.88 nM) were ranked top as Coronavirus Disease - 2019 (COVID-19) Mpro inhibitors. The interacting amino acid residues were visualized using Discovery Studio 3.5 to elucidate the 2-dimensional and 3-dimensional interactions. The study was validated by i) re-docking the N3-peptide inhibitor-Mpro and superimposing them onto co-crystallized complex and ii) docking decoy ligands to Mpro. The ligands that showed low binding energy were further predicted for and pharmacokinetic properties and Lipinski's rule of 5 and the results are tabulated and discussed. Molecular dynamics simulations were performed for 50 ns for those compounds using the Desmond package, Schrödinger to assess the conformational stability and fluctuations of protein-ligand complexes during the simulation. Thus, the natural compounds could act as a lead for the COVID-19 regimen after in-vitro and in- vivo clinical trials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivanika C
- Department of Bio-Engineering, School of
Engineering, Vels Institute of Science Technology and Advanced Studies,
Chennai, Tamil Nadu, India
| | - Deepak Kumar S.
- Department of Biotechnology, Rajalakshmi
Engineering College, Thandalam, Tamil Nadu,
India
| | - Venkataraghavan Ragunathan
- Department of Chemical Engineering, Alagappa
College of Technology, Anna University, Chennai, Tamil
Nadu, India
| | - Pawan Tiwari
- Department of Pharmaceutical Science, Kumaun
University, Nainital, Uttarakhand,
India
| | - Sumitha A.
- Department of Pharmacology, ACS Medical
College and Hospital, Chennai, Tamil Nadu,
India
| | - Brindha Devi P
- Department of Bio-Engineering, School of
Engineering, Vels Institute of Science Technology and Advanced Studies,
Chennai, Tamil Nadu, India
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5
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Abstract
Screening compounds for potential carcinogenicity is of major importance for prevention of environmentally induced cancers. A large sequence of predictive models, ranging from short-term biological assays (e.g., mutagenicity tests) to theoretical models, has been attempted in this field. Theoretical approaches such as (Q)SAR are highly desirable for identifying carcinogens, since they actively promote the replacement, reduction, and refinement of animal tests. This chapter reports and describes some of the most noted (Q)SAR models based on human expert knowledge and statistical approaches, aiming at predicting the carcinogenicity of chemicals. Additionally, the performance of the selected models has been evaluated, and the results are interpreted in details by applying these predictive models to some pharmaceutical molecules.
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Affiliation(s)
- Azadi Golbamaki
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Emilio Benfenati
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
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6
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Artificial intelligence in drug design: algorithms, applications, challenges and ethics. FUTURE DRUG DISCOVERY 2021. [DOI: 10.4155/fdd-2020-0028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The discovery paradigm of drugs is rapidly growing due to advances in machine learning (ML) and artificial intelligence (AI). This review covers myriad faces of AI and ML in drug design. There is a plethora of AI algorithms, the most common of which are summarized in this review. In addition, AI is fraught with challenges that are highlighted along with plausible solutions to them. Examples are provided to illustrate the use of AI and ML in drug discovery and in predicting drug properties such as binding affinities and interactions, solubility, toxicology, blood–brain barrier permeability and chemical properties. The review also includes examples depicting the implementation of AI and ML in tackling intractable diseases such as COVID-19, cancer and Alzheimer’s disease. Ethical considerations and future perspectives of AI are also covered in this review.
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7
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Nathan VK, Rani ME. Natural dye from Caesalpinia sappan L. heartwood for eco-friendly coloring of recycled paper based packing material and its in silico toxicity analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:28713-28719. [PMID: 33543441 DOI: 10.1007/s11356-020-11827-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
The uses of natural dyes are getting popularized due to the increased awareness regarding the toxicity of many chemical colorants. The chemical colorants are being replaced by the natural colorants for the various industrial applications. The plant-based natural colorants are considered eco-friendly and toxic free. In the present study, we report a natural dye from the heartwood of Caesalpinia sappan suitable for paper based packing materials. This forms the first report on the study of natural dye obtained from the heartwood of C. sappan on paper material. The extracted dye had a good photostability and able to make imprints on recycled paper bags. Moreover, a significant inhibition of bacterial growth was observed at a higher dye concentration of 100 μg mL-1 against P. aeruginosa which was higher than the standard antibiotics. Growth inhibition was also observed in case of B. subtilis (22 ± 0.17 mm) and K. pneumonia (21 ± 0.53 mm) at 100 μg mL-1. The dye could be used in making medicated packing materials and have many other bio-potential which was validated through in silico toxicity analysis. The application of such natural dyes in paper material value addition will help in a cleaner and sustainable process during paper recycling.
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Affiliation(s)
- Vinod Kumar Nathan
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, 613401, India.
- Department of Botany and Microbiology, Lady Doak College, Madurai, Tamil Nadu, 625 002, India.
| | - Mary Esther Rani
- Department of Botany and Microbiology, Lady Doak College, Madurai, Tamil Nadu, 625 002, India
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8
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Koelmel JP, Lin EZ, Nichols A, Guo P, Zhou Y, Godri Pollitt KJ. Head, Shoulders, Knees, and Toes: Placement of Wearable Passive Samplers Alters Exposure Profiles Observed. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3796-3806. [PMID: 33625210 DOI: 10.1021/acs.est.0c05522] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical exposures are a major risk factor for many diseases. Comprehensive characterization of personal exposures is necessary to highlight chemicals of concern and factors that influence these chemical exposure dynamics. For this purpose, wearable passive samplers can be applied to assess longitudinal personal exposures to airborne contaminants. Questions remain regarding the impact of sampler placement at different locations of the body on the exposure profiles observed and how these placements affect the monitoring of seasonal dynamics in exposures. This study assessed personal air contaminant exposure using passive samplers worn in parallel across 32 participant's wrists, chest, and shoes over 24 h. Samplers were analyzed by thermal desorption gas chromatography high-resolution mass spectrometry. Personal exposure profiles were similar for about one-third of the 275 identified chemicals, irrespective of sampler placement. Signals of certain semivolatile organic compounds (SVOCs) were enhanced in shoes and, to a lesser extent, wrist samplers, as compared to those in chest samplers. Signals of volatile organic compounds were less impacted by sampler placement. Results showed that chest samplers predominantly captured more volatile exposures, as compared to those of particle-bound exposures, which may indicate predominant monitoring of chemicals via the inhalation route of exposure for chest samplers. In contrast, shoe samplers were more sensitive to particle-bound SVOCs. Seventy-one chemicals changed across participants between winter and summer in the same manner for two or more different sampler placements on the body, whereas 122 chemicals were observed to have seasonal differences in only one placement. Hence, the placement in certain cases significantly impacts exposure dynamics observed. This work shows that it is essential in epidemiological studies undertaking exposure assessment to consider the consequence of the placement of exposure monitors.
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Affiliation(s)
- Jeremy P Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College Street, New Haven, Connecticut 06510, United States
| | - Elizabeth Z Lin
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College Street, New Haven, Connecticut 06510, United States
| | - Amy Nichols
- Department of Chemical and Environmental Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06520, United States
| | - Pengfei Guo
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College Street, New Haven, Connecticut 06510, United States
| | - Yakun Zhou
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College Street, New Haven, Connecticut 06510, United States
| | - Krystal J Godri Pollitt
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College Street, New Haven, Connecticut 06510, United States
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9
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Koelmel JP, Lin EZ, Guo P, Zhou J, He J, Chen A, Gao Y, Deng F, Dong H, Liu Y, Cha Y, Fang J, Beecher C, Shi X, Tang S, Godri Pollitt KJ. Exploring the external exposome using wearable passive samplers - The China BAPE study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 270:116228. [PMID: 33360595 DOI: 10.1016/j.envpol.2020.116228] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Environmental exposures are one of the greatest threats to human health, yet we lack tools to answer simple questions about our exposures: what are our personal exposure profiles and how do they change overtime (external exposome), how toxic are these chemicals, and what are the sources of these exposures? To capture variation in personal exposures to airborne chemicals in the gas and particulate phases and identify exposures which pose the greatest health risk, wearable exposure monitors can be deployed. In this study, we deployed passive air sampler wristbands with 84 healthy participants (aged 60-69 years) as part of the Biomarkers for Air Pollutants Exposure (China BAPE) study. Participants wore the wristband samplers for 3 days each month for five consecutive months. Passive samplers were analyzed using a novel gas chromatography high resolution mass spectrometry data-processing workflow to overcome the bottleneck of processing large datasets and improve confidence in the resulting identified features. The toxicity of chemicals observed frequently in personal exposures were predicted to identify exposures of potential concern via inhalation route or other routes of airborne contaminant exposure. Three exposures were highlighted based on elevated toxicity: dichlorvos from insecticides (mosquito/malaria control), naphthalene partly from mothballs, and 183 polyaromatic hydrocarbons from multiple sources. Other exposures explored in this study are linked to diet and personal care products, cigarette smoke, sunscreen, and antimicrobial soaps. We highlight the potential for this workflow employing wearable passive samplers for prioritizing chemicals of concern at both the community and individual level, and characterizing sources of exposures for follow up interventions.
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Affiliation(s)
- Jeremy P Koelmel
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, 06520, USA
| | - Elizabeth Z Lin
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, 06520, USA
| | - Pengfei Guo
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, 06520, USA
| | - Jieqiong Zhou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, 06520, USA
| | - Jucong He
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, 06520, USA
| | - Alex Chen
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Ying Gao
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | - Fuchang Deng
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | - Haoran Dong
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | - Yuanyuan Liu
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | - Yu'e Cha
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | - Jianlong Fang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China
| | | | - Xiaoming Shi
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China; Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Song Tang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, 100021, China; Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Krystal J Godri Pollitt
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, 06520, USA.
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10
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Pandit S, Singh P, Sinha M, Parthasarathi R. Integrated QSAR and Adverse Outcome Pathway Analysis of Chemicals Released on 3D Printing Using Acrylonitrile Butadiene Styrene. Chem Res Toxicol 2021; 34:355-364. [PMID: 33416328 DOI: 10.1021/acs.chemrestox.0c00274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Additive manufacturing commonly known as 3D printing has numerous applications in several domains including material and biomedical technologies and has emerged as a tool of capabilities by providing fast, highly customized, and cost-effective solutions. However, the impact of the printing materials and chemicals present in the printing fumes has raised concerns about their adverse potential affecting humans and the environment. Thus, it is necessary to understand the properties of the chemicals emitted during additive manufacturing for developing safe and biocompatible fibers having controlled emission of fumes including its sustainable usage. Therefore, in this study, we have developed a computational predictive risk-assessment framework on the comprehensive list of chemicals released during 3D printing using the acrylonitrile butadiene styrene (ABS) filament. Our results showed that the chemicals present in the fumes of the ABS-based fiber used in additive manufacturing have the potential to lead to various toxicity end points such as inhalation toxicity, oral toxicity, carcinogenicity, hepatotoxicity, and teratogenicity. Moreover, because of their absorption, distribution in the body, metabolism, and excretion properties, most of the chemicals exhibited a high absorption level in the intestine and the potential to cross the blood-brain barrier. Furthermore, pathway analysis revealed that signaling like alpha-adrenergic receptor signaling, heterotrimeric G-protein signaling, and Alzheimer's disease-amyloid secretase pathway are significantly overrepresented given the identified target proteins of these chemicals. These findings signify the adversities associated with 3D printing fumes and the necessity for the development of biodegradable and considerably safer fibers for 3D printing technology.
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Affiliation(s)
- Shraddha Pandit
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prakrity Singh
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Meetali Sinha
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Toma C, Manganaro A, Raitano G, Marzo M, Gadaleta D, Baderna D, Roncaglioni A, Kramer N, Benfenati E. QSAR Models for Human Carcinogenicity: An Assessment Based on Oral and Inhalation Slope Factors. Molecules 2020; 26:E127. [PMID: 33383938 PMCID: PMC7796303 DOI: 10.3390/molecules26010127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 11/21/2022] Open
Abstract
Carcinogenicity is a crucial endpoint for the safety assessment of chemicals and products. During the last few decades, the development of quantitative structure-activity relationship ((Q)SAR) models has gained importance for regulatory use, in combination with in vitro testing or expert-based reasoning. Several classification models can now predict both human and rat carcinogenicity, but there are few models to quantitatively assess carcinogenicity in humans. To our knowledge, slope factor (SF), a parameter describing carcinogenicity potential used especially for human risk assessment of contaminated sites, has never been modeled for both inhalation and oral exposures. In this study, we developed classification and regression models for inhalation and oral SFs using data from the Risk Assessment Information System (RAIS) and different machine learning approaches. The models performed well in classification, with accuracies for the external set of 0.76 and 0.74 for oral and inhalation exposure, respectively, and r2 values of 0.57 and 0.65 in the regression models for oral and inhalation SFs in external validation. These models might therefore support regulators in (de)prioritizing substances for regulatory action and in weighing evidence in the context of chemical safety assessments. Moreover, these models are implemented on the VEGA platform and are now freely downloadable online.
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Affiliation(s)
- Cosimo Toma
- Laboratory of Chemistry and Environmental Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy; (C.T.); (G.R.); (M.M.); (D.G.); (A.R.)
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80177, 3508 TD Utrecht, The Netherlands;
| | | | - Giuseppa Raitano
- Laboratory of Chemistry and Environmental Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy; (C.T.); (G.R.); (M.M.); (D.G.); (A.R.)
| | - Marco Marzo
- Laboratory of Chemistry and Environmental Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy; (C.T.); (G.R.); (M.M.); (D.G.); (A.R.)
| | - Domenico Gadaleta
- Laboratory of Chemistry and Environmental Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy; (C.T.); (G.R.); (M.M.); (D.G.); (A.R.)
| | - Diego Baderna
- Laboratory of Chemistry and Environmental Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy; (C.T.); (G.R.); (M.M.); (D.G.); (A.R.)
| | - Alessandra Roncaglioni
- Laboratory of Chemistry and Environmental Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy; (C.T.); (G.R.); (M.M.); (D.G.); (A.R.)
| | - Nynke Kramer
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, P.O. Box 80177, 3508 TD Utrecht, The Netherlands;
| | - Emilio Benfenati
- Laboratory of Chemistry and Environmental Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milan, Italy; (C.T.); (G.R.); (M.M.); (D.G.); (A.R.)
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12
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Screening for Ames mutagenicity of food flavor chemicals by (quantitative) structure-activity relationship. Genes Environ 2020; 42:32. [PMID: 33292765 PMCID: PMC7706032 DOI: 10.1186/s41021-020-00171-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Background (Quantitative) Structure-Activity Relationship ((Q)SAR) is a promising approach to predict the potential adverse effects of chemicals based on their structure without performing toxicological studies. We evaluate the mutagenicity of food flavor chemicals by (Q) SAR tools, identify potentially mutagenic chemicals, and verify their mutagenicity by actual Ames test. Results The Ames mutagenicity of 3942 food flavor chemicals was predicted using two (Q)SAR) tools, DEREK Nexus and CASE Ultra. Three thousand five hundred seventy-five chemicals (91%) were judged to be negative in both (Q) SAR tools, and 75 chemicals (2%) were predicted to be positive in both (Q) SAR tools. When the Ames test was conducted on ten of these positive chemicals, nine showed positive results. Conclusion The (Q) SAR method can be used for screening the mutagenicity of food flavors. Supplementary Information The online version contains supplementary material available at 10.1186/s41021-020-00171-1.
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Young onset breast cancer in Southern China - a 5-year clinico-pathological study from a multi-centre database. Cancer Treat Res Commun 2020; 24:100182. [PMID: 32534410 DOI: 10.1016/j.ctarc.2020.100182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 11/23/2022]
Abstract
AIMS Breast cancer onset is known to be younger in China when compared to many westernized countries, the reason remains unknown. This study aims to evaluate the clinical and pathological characteristics of young breast cancer in Hong Kong and Shenzhen, China. METHODS This is a 5-year retrospective review of a prospectively-maintained region-wide database. Patients treated in Hong Kong and Shenzhen between 2013 and 2017 were analysed. RESULTS 1610 breast cancer patients were identified for analysis, 1108 patients were from Hong Kong and 502 patients were from Shenzhen. Median age of breast cancer onset was 60 years old in Hong Kong (Range 21 - 103), while that in Shenzhen was 46 years old (Range 23 - 85). 59 (5.3%) patients from the Hong Kong cohort were younger than 40 years old at the age of diagnosis (i.e. young breast cancer), comparing to 152 (30.3%) patients from the Shenzhen cohort (p < 0.0001). There were more nulliparity, positive family history and use of exogenous hormones in young breast cancer patients in Hong Kong (p = 0.0043, < 0.0001 and 0.0022). Pathological characteristics were however comparable between the two cohorts, apart from being more triple negative breast cancers in young breast cancer patients in Hong Kong (p = 0.05). CONCLUSION Age of onset of breast cancer tends to be younger in mainland China than in Hong Kong. Personal and familial risk factors were not significantly different. Environmental factor may play an important role.
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Baderna D, Gadaleta D, Lostaglio E, Selvestrel G, Raitano G, Golbamaki A, Lombardo A, Benfenati E. New in silico models to predict in vitro micronucleus induction as marker of genotoxicity. JOURNAL OF HAZARDOUS MATERIALS 2020; 385:121638. [PMID: 31757721 DOI: 10.1016/j.jhazmat.2019.121638] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/03/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
The evaluation of genotoxicity is a fundamental part of the safety assessment of chemicals due to the relevance of the potential health effects of genotoxicants. Among the testing methods available, the in vitro micronucleus assay with mammalian cells is one of the most used and required by regulations targeting several industrial sectors such as the cosmetic industry and food-related sectors. As an alternative to the testing methods, in recent years, lots in silico methods were developed to predict the genotoxicity of chemicals, including models for the Ames mutagenicity test, the in vitro chromosomal aberrations and the in vivo micronucleus assay. We developed several in silico models for the prediction of genotoxicity as reflected by the in vitro micronucleus assay. The resulting models include both statistical and knowledge-based models. The most promising model is the one based on fragments extracted with the SARpy platform. More than 100 structural alerts were extracted, including also fragments associated with the non-genotoxic activity. The model is characterized by high accuracy and the lowest false negative rate, making this tool suitable for chemical screening according to the regulators' needs. The SARpy model will be implemented on the VEGA platform (https://www.vegahub.eu) and will be freely available.
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Affiliation(s)
- Diego Baderna
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy.
| | - Domenico Gadaleta
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Eleonora Lostaglio
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Gianluca Selvestrel
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Giuseppa Raitano
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Azadi Golbamaki
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Anna Lombardo
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Environmental Health Department, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
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He W, Kong X, Qin N, He Q, Liu W, Bai Z, Wang Y, Xu F. Combining species sensitivity distribution (SSD) model and thermodynamic index (exergy) for system-level ecological risk assessment of contaminates in aquatic ecosystems. ENVIRONMENT INTERNATIONAL 2019; 133:105275. [PMID: 31675563 DOI: 10.1016/j.envint.2019.105275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/29/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
After reviewing the species- and community-level ecological risk assessments (ERAs) of chemicals in the aquatic environment, the present study attempted to propose a third stage of ERA, i.e., the ecosystem-level ERA. Based on the species sensitivity distribution model (SSD) and thermodynamic theory, the exergy and biomass indicators of communities from various trophic levels (TLs) were introduced to improve ecological connotation of SSDs. The species were classified into three TLs based on algae (TL1), invertebrates (TL2), and vertebrates (TL3), and the weight of each TL was determined based on relative biomass and β value, which indicated a holistic contribution of each species or community to the ecosystem. Then, a system-level ERA protocol was successfully established, and the community- and system-level ecological risks of 10 typical toxic micro-organic pollutants in the western area of Lake Chaohu and its inflowing rivers were evaluated. System-level ERA curves (ExSSD) were mainly affected by the community-level SSD at TL2 for most chemicals in the present study. The uncertain boundary of ExSSD was mostly related to TLs with a wider uncertain boundary, but had little relation to the weight of each TL. The results of system-level ERAs revealed that dibutyl phthalate had the highest eco-risk, whereas γ-hexachlorocyclohexane presented the lowest eco-risk. Results of the system-level ERA were not fully consistent with the those of community-level ERA owing to the lack of a sufficient dataset, SSD model type, and ecosystem structure, as indicated by the weight of each TL. The successful application of ExSSD in Lake Chaohu signifies the start of the third stage of ERA at the system-level, and it also provides a scientific basis for ecosystem-level ERA, aquatic ecosystem protection, and future water safety management. However, there were some limitations, including sufficient data dependence, neglect of ecological interactions, and neglect of environmental parameters such as natural organic matter. We propose to employ toxicogenomics to enrich the toxicity database, to simulate the interaction using the ecological dynamic model, and to introduce the chemical fate model into the system-level ERA.
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Affiliation(s)
- Wei He
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing 100083, China; MOE Key Laboratory for Earth Surface Process, College of Urban & Environmental Sciences, Peking University, Beijing 100871, China
| | - Xiangzhen Kong
- Department of Lake Research, Helmholtz Centre for Environmental Research (UFZ), Brückstr. 3a, 39114 Magdeburg, Germany
| | - Ning Qin
- School of Energy and Environmental Engineering, Beijing University of Science and Technology, Beijing 100083, China
| | - Qishuang He
- Beijing Municipal Key Laboratory of Agriculture Environment Monitoring, Beijing 100097, China
| | - WenXiu Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zelin Bai
- MOE Key Laboratory for Earth Surface Process, College of Urban & Environmental Sciences, Peking University, Beijing 100871, China
| | - Yin Wang
- MOE Key Laboratory for Earth Surface Process, College of Urban & Environmental Sciences, Peking University, Beijing 100871, China
| | - Fuliu Xu
- MOE Key Laboratory for Earth Surface Process, College of Urban & Environmental Sciences, Peking University, Beijing 100871, China.
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Sinha M, Dhawan A, Parthasarathi R. In Silico Approaches in Predictive Genetic Toxicology. Methods Mol Biol 2019; 2031:351-373. [PMID: 31473971 DOI: 10.1007/978-1-4939-9646-9_20] [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] [Indexed: 04/05/2023]
Abstract
Genetic toxicology testing is a weight-of-evidence approach to identify and characterize chemical substances that can cause genetic modifications in somatic and/or germ cells. Prediction of genetic toxicology using computational tools is gaining more attention and preferred by regulatory authorities as an alternate safety assessment for in vivo or in vitro approaches. Due to the cost and time associated with experimental genetic toxicity tests, it is essential to develop more robust in silico methods to predict chemical genetic toxicity. A number of in silico genotoxicity predictive tools/models are developed based on the experimental data gathered over the years. These in silico tools are divided into statistical quantitative structure-activity relationships (QSAR)-based approaches and expert-based systems. This chapter covers the state of the art in silico toxicology approaches and standardized protocols, essential for conducting genetic toxicity predictions of chemicals. This chapter also highlights various parameters for the validation of the prediction results obtained from QSAR models.
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Affiliation(s)
- Meetali Sinha
- Computational Toxicology Facility, Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
| | - Alok Dhawan
- Nanomaterials Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India.
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Abstract
Modern chemistry foundations were made in between the 18th and 19th centuries and have been extended in 20th century. R&D towards synthetic chemistry was introduced during the 1960s. Development of new molecular drugs from the herbal plants to synthetic chemistry is the fundamental scientific improvement. About 10-14 years are needed to develop a new molecule with an average cost of more than $800 million. Pharmaceutical industries spend the highest percentage of revenues, but the achievement of desired molecular entities into the market is not increasing proportionately. As a result, an approximate of 0.01% of new molecular entities are approved by the FDA. The highest failure rate is due to inadequate efficacy exhibited in Phase II of the drug discovery and development stage. Innovative technologies such as combinatorial chemistry, DNA sequencing, high-throughput screening, bioinformatics, computational drug design, and computer modeling are now utilized in the drug discovery. These technologies can accelerate the success rates in introducing new molecular entities into the market.
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Jean-Quartier C, Jeanquartier F, Jurisica I, Holzinger A. In silico cancer research towards 3R. BMC Cancer 2018; 18:408. [PMID: 29649981 PMCID: PMC5897933 DOI: 10.1186/s12885-018-4302-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 03/26/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Improving our understanding of cancer and other complex diseases requires integrating diverse data sets and algorithms. Intertwining in vivo and in vitro data and in silico models are paramount to overcome intrinsic difficulties given by data complexity. Importantly, this approach also helps to uncover underlying molecular mechanisms. Over the years, research has introduced multiple biochemical and computational methods to study the disease, many of which require animal experiments. However, modeling systems and the comparison of cellular processes in both eukaryotes and prokaryotes help to understand specific aspects of uncontrolled cell growth, eventually leading to improved planning of future experiments. According to the principles for humane techniques milestones in alternative animal testing involve in vitro methods such as cell-based models and microfluidic chips, as well as clinical tests of microdosing and imaging. Up-to-date, the range of alternative methods has expanded towards computational approaches, based on the use of information from past in vitro and in vivo experiments. In fact, in silico techniques are often underrated but can be vital to understanding fundamental processes in cancer. They can rival accuracy of biological assays, and they can provide essential focus and direction to reduce experimental cost. MAIN BODY We give an overview on in vivo, in vitro and in silico methods used in cancer research. Common models as cell-lines, xenografts, or genetically modified rodents reflect relevant pathological processes to a different degree, but can not replicate the full spectrum of human disease. There is an increasing importance of computational biology, advancing from the task of assisting biological analysis with network biology approaches as the basis for understanding a cell's functional organization up to model building for predictive systems. CONCLUSION Underlining and extending the in silico approach with respect to the 3Rs for replacement, reduction and refinement will lead cancer research towards efficient and effective precision medicine. Therefore, we suggest refined translational models and testing methods based on integrative analyses and the incorporation of computational biology within cancer research.
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Affiliation(s)
- Claire Jean-Quartier
- Holzinger Group, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Graz, Austria
| | - Fleur Jeanquartier
- Holzinger Group, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Graz, Austria
- Institute of Interactive Systems and Data Science, Graz University of Technology, Graz, Austria
| | - Igor Jurisica
- Krembil Research Institute, University Health Network; Depts. of Medical Bioph. and Comp. Sci., University of Toronto; Institute of Neuroimmunology, Slovak Academy of Sciences, Toronto, Canada
| | - Andreas Holzinger
- Holzinger Group, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Graz, Austria
- Institute of Interactive Systems and Data Science, Graz University of Technology, Graz, Austria
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Abstract
Screening compounds for potential carcinogenicity is of major importance for prevention of environmentally induced cancers. A large sequence of alternative predictive models, ranging from short-term biological assays (e.g. mutagenicity tests) to theoretical models, have been attempted in this field. Theoretical approaches such as (Q)SAR are highly desirable for identifying carcinogens, since they actively promote the replacement, reduction, and refinement of animal tests. This chapter reports and describes some of the most noted (Q)SAR models based on the human expert knowledge and statistically approach, aiming at predicting the carcinogenicity of chemicals. Additionally, the performance of the selected models has been evaluated and the results are interpreted in details by applying these prediction models to some pharmaceutical molecules.
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Vračko M, Drgan V. Grouping of CoMPARA data with respect to compounds from the carcinogenic potency database. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:801-813. [PMID: 29156996 DOI: 10.1080/1062936x.2017.1398184] [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: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 06/07/2023]
Abstract
Methods for clustering and measures of similarity of chemical structures have become an important supporting tool in chemoinformatics. They represent the basis for categorization of chemicals and read-across, where a molecular property is estimated from 'similar molecules'. This study proposes a clustering scheme within the given dataset with respect to a reference dataset. The scheme was applied on two datasets ToxCast_AR_Agonist and ToxCast_AR_Antagonists with 1654 and 1522 compounds, respectively. The compounds are tested to androgen receptor activity (AR) in 11 high throughput screening assays. The carcinogenic dataset was used as the reference set.
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Affiliation(s)
- M Vračko
- a National Institute of Chemistry , Kemijski Inštitut , Ljubljana , Slovenia
| | - V Drgan
- a National Institute of Chemistry , Kemijski Inštitut , Ljubljana , Slovenia
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Alves VM, Muratov EN, Zakharov A, Muratov NN, Andrade CH, Tropsha A. Chemical toxicity prediction for major classes of industrial chemicals: Is it possible to develop universal models covering cosmetics, drugs, and pesticides? Food Chem Toxicol 2017; 112:526-534. [PMID: 28412406 DOI: 10.1016/j.fct.2017.04.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/16/2017] [Accepted: 04/10/2017] [Indexed: 01/15/2023]
Abstract
Computational models have earned broad acceptance for assessing chemical toxicity during early stages of drug discovery or environmental safety assessment. The majority of publicly available QSAR toxicity models have been developed for datasets including mostly drugs or drug-like compounds. We have evaluated and compared chemical spaces occupied by cosmetics, drugs, and pesticides, and explored whether current computational models of toxicity endpoints can be universally applied to all these chemicals. Our analysis of the chemical space overlap and applicability domain (AD) of models built previously for twenty different toxicity endpoints showed that most of these models afforded high coverage (>90%) for all three classes of compounds analyzed herein. Only T. pyriformis models demonstrated lower coverage for drugs and pesticides (38% and 54%, respectively). These results show that, for the most part, historical QSAR models built with data available for different toxicity endpoints can be used for toxicity assessment of novel chemicals irrespective of the intended commercial use; however, the AD restriction is necessary to assure the expected prediction accuracy. Local models may need to be developed to capture chemicals that appear as outliers with respect to global models.
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Affiliation(s)
- Vinicius M Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA; Laboratory of Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, 74605-170, Brazil
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA; Department of Chemical Technology, Odessa National Polytechnic University, Odessa, 65000, Ukraine
| | - Alexey Zakharov
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, 20850, USA
| | - Nail N Muratov
- Department of Chemical Technology, Odessa National Polytechnic University, Odessa, 65000, Ukraine
| | - Carolina H Andrade
- Laboratory of Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, 74605-170, Brazil
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.
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Use of in silico models for prioritization of heat-induced food contaminants in mutagenicity and carcinogenicity testing. Arch Toxicol 2017; 91:3157-3174. [PMID: 28091709 DOI: 10.1007/s00204-016-1924-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/20/2016] [Indexed: 01/01/2023]
Abstract
Numerous Maillard reaction and lipid oxidation products are present in processed foods such as heated cereals, roasted meat, refined oils, coffee, and juices. Due to the lack of experimental toxicological data, risk assessment is hardly possible for most of these compounds. In the present study, an in silico approach was employed for the prediction of the toxicological endpoints mutagenicity and carcinogenicity on the basis of the structure of the respective compound, to examine (quantitative) structure-activity relationships for more than 800 compounds. Five software tools for mutagenicity prediction (T.E.S.T., SARpy, CAESAR, Benigni-Bossa, and LAZAR) and three carcinogenicity prediction tools (CAESAR, Benigni-Bossa, and LAZAR) were combined to yield so-called mutagenic or carcinogenic scores for every single substance. Alcohols, ketones, acids, lactones, and esters were predicted to be mutagenic and carcinogenic with low probability, whereas the software tools tended to predict a considerable mutagenic and carcinogenic potential for thiazoles. To verify the in silico predictions for the endpoint mutagenicity experimentally, twelve selected compounds were examined for their mutagenic potential using two different validated in vitro test systems, the bacterial reverse mutation assay (Ames test) and the in vitro micronucleus assay. There was a good correlation between the results of the Ames test and the in silico predictions. However, in the case of the micronucleus assay, at least three substances, 2-amino-6-methylpyridine, 6-heptenoic acid, and 2-methylphenol, were clearly positive although they were predicted to be non-mutagenic. Thus, software tools for mutagenicity prediction are suitable for prioritization among large numbers of substances, but these predictions still need experimental verification.
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Ford KA. Refinement, Reduction, and Replacement of Animal Toxicity Tests by Computational Methods. ILAR J 2017; 57:226-233. [DOI: 10.1093/ilar/ilw031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/12/2016] [Indexed: 12/16/2022] Open
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Powroźnik B, Słoczyńska K, Marciniec K, Zajdel P, Pękala E. Preliminary Safety Assessment of New Azinesulfonamide Analogs of Aripiprazole using Prokaryotic Models. Adv Pharm Bull 2016; 6:377-384. [DOI: 10.15171/apb.2016.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/13/2016] [Accepted: 08/04/2016] [Indexed: 01/29/2023] Open
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AutoQSAR: an automated machine learning tool for best-practice quantitative structure-activity relationship modeling. Future Med Chem 2016; 8:1825-1839. [PMID: 27643715 DOI: 10.4155/fmc-2016-0093] [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] [Indexed: 11/17/2022] Open
Abstract
AIM We introduce AutoQSAR, an automated machine-learning application to build, validate and deploy quantitative structure-activity relationship (QSAR) models. METHODOLOGY/RESULTS The process of descriptor generation, feature selection and the creation of a large number of QSAR models has been automated into a single workflow within AutoQSAR. The models are built using a variety of machine-learning methods, and each model is scored using a novel approach. Effectiveness of the method is demonstrated through comparison with literature QSAR models using identical datasets for six end points: protein-ligand binding affinity, solubility, blood-brain barrier permeability, carcinogenicity, mutagenicity and bioaccumulation in fish. CONCLUSION AutoQSAR demonstrates similar or better predictive performance as compared with published results for four of the six endpoints while requiring minimal human time and expertise.
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Molecular mechanisms of endocrine and metabolic disruption: An in silico study on antitrypanosomal natural products and some derivatives. Toxicol Lett 2016; 252:29-41. [PMID: 27091077 DOI: 10.1016/j.toxlet.2016.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 11/24/2022]
Abstract
The VirtualToxLab is an in silico technology for estimating the toxic potential - endocrine and metabolic disruption, as well as aspects of carcinogenicity and cardiotoxicity - of drugs, chemicals and natural products. The technology is based on an automated protocol that simulates and quantifies the binding of small molecules towards a series of currently 16 proteins, known or suspected to trigger adverse effects. The simulations are conducted at the atomic level and explicitly allow for a mechanistic interpretation of the results (in real-time 3D/4D), thereby complying with the Setubal principles put forward in 2002 for computational approaches to toxicology. Moreover, the underlying "ab-initio" protocol is independent from any training data and makes the approach universal with respect to the applicability domain. The VirtualToxLab runs in client-server mode and is freely available to academic and non-profit organizations. As the underlying technology yields a thermodynamic estimate of the binding affinity, the associated ligand-protein complexes have been challenged by molecular-dynamics simulations to probe their kinetic stability. Human African trypanosomiasis is a neglected tropical disease caused by two subspecies of Trypanosoma brucei. The control of this parasitic infection relies on a few chemotherapeutic agents, most of which were discovered decades ago and pose many challenges including adverse side effects, poor efficacy, and the occurrence of drug resistances. Natural products, on the other hand, offer a high potential for the discovery of new drug leads due to their chemical diversity. In this in silico study, we analyze a series of 89 natural products and derivatives displaying anti-trypanosomal activity for their potential to trigger adverse effects. Our results indicate a moderate potential for a number of those compounds to bind to nuclear receptors and thereby ease the development of endocrine disregulation. A few others would seem to inhibit enzymes of the cytochrome P450 family and, hence, sustain drug-drug interactions.
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Ates G, Raitano G, Heymans A, Van Bossuyt M, Vanparys P, Mertens B, Chesne C, Roncaglioni A, Milushev D, Benfenati E, Rogiers V, Doktorova TY. In silico tools and transcriptomics analyses in the mutagenicity assessment of cosmetic ingredients: a proof-of-principle on how to add weight to the evidence. Mutagenesis 2016; 31:453-61. [PMID: 26980085 DOI: 10.1093/mutage/gew008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Prior to the downstream development of chemical substances, including pharmaceuticals and cosmetics, their influence on the genetic apparatus has to be tested. Several in vitro and in vivo assays have been developed to test for genotoxicity. In a first tier, a battery of two to three in vitro tests is recommended to cover mutagenicity, clastogenicity and aneugenicity as main endpoints. This regulatory in vitro test battery is known to have a high sensitivity, which is at the expense of the specificity. The high number of false positive in vitro results leads to excessive in vivo follow-up studies. In the case of cosmetics it may even induce the ban of the particular compound since in Europe the use of experimental animals is no longer allowed for cosmetics. In this article, an alternative approach to derisk a misleading positive Ames test is explored. Hereto we first tested the performance of five existing computational tools to predict the potential mutagenicity of a data set of 132 cosmetic compounds with a known genotoxicity profile. Furthermore, we present, as a proof-of-principle, a strategy in which a combination of computational tools and mechanistic information derived from in vitro transcriptomics analyses is used to derisk a misleading positive Ames test result. Our data shows that this strategy may represent a valuable tool in a weight-of-evidence approach to further evaluate a positive outcome in an Ames test.
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Affiliation(s)
| | - Giuseppa Raitano
- IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milan, Italy
| | | | - Melissa Van Bossuyt
- Unit of Toxicology, Scientific Institute of Public Health (WIV-ISP), Juliette Wytsmanstraat 14, B-1050, Brussels, Belgium
| | | | - Birgit Mertens
- Unit of Toxicology, Scientific Institute of Public Health (WIV-ISP), Juliette Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Christophe Chesne
- Biopredic International, Parc d'activité de la Bretèche Bâtiment A4, 35760 Saint Grégoire, France and
| | - Alessandra Roncaglioni
- IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milan, Italy
| | | | - Emilio Benfenati
- IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milan, Italy
| | | | - Tatyana Y Doktorova
- Unit of Toxicology, Scientific Institute of Public Health (WIV-ISP), Juliette Wytsmanstraat 14, B-1050, Brussels, Belgium
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Chemoinformatics: Achievements and Challenges, a Personal View. Molecules 2016; 21:151. [PMID: 26828468 PMCID: PMC6273366 DOI: 10.3390/molecules21020151] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/14/2016] [Accepted: 01/20/2016] [Indexed: 11/16/2022] Open
Abstract
Chemoinformatics provides computer methods for learning from chemical data and for modeling tasks a chemist is facing. The field has evolved in the past 50 years and has substantially shaped how chemical research is performed by providing access to chemical information on a scale unattainable by traditional methods. Many physical, chemical and biological data have been predicted from structural data. For the early phases of drug design, methods have been developed that are used in all major pharmaceutical companies. However, all domains of chemistry can benefit from chemoinformatics methods; many areas that are not yet well developed, but could substantially gain from the use of chemoinformatics methods. The quality of data is of crucial importance for successful results. Computer-assisted structure elucidation and computer-assisted synthesis design have been attempted in the early years of chemoinformatics. Because of the importance of these fields to the chemist, new approaches should be made with better hardware and software techniques. Society's concern about the impact of chemicals on human health and the environment could be met by the development of methods for toxicity prediction and risk assessment. In conjunction with bioinformatics, our understanding of the events in living organisms could be deepened and, thus, novel strategies for curing diseases developed. With so many challenging tasks awaiting solutions, the future is bright for chemoinformatics.
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Chen B, Zhang T, Bond T, Gan Y. Development of quantitative structure activity relationship (QSAR) model for disinfection byproduct (DBP) research: A review of methods and resources. JOURNAL OF HAZARDOUS MATERIALS 2015; 299:260-79. [PMID: 26142156 DOI: 10.1016/j.jhazmat.2015.06.054] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/17/2015] [Accepted: 06/21/2015] [Indexed: 05/19/2023]
Abstract
Quantitative structure-activity relationship (QSAR) models are tools for linking chemical activities with molecular structures and compositions. Due to the concern about the proliferating number of disinfection byproducts (DBPs) in water and the associated financial and technical burden, researchers have recently begun to develop QSAR models to investigate the toxicity, formation, property, and removal of DBPs. However, there are no standard procedures or best practices regarding how to develop QSAR models, which potentially limit their wide acceptance. In order to facilitate more frequent use of QSAR models in future DBP research, this article reviews the processes required for QSAR model development, summarizes recent trends in QSAR-DBP studies, and shares some important resources for QSAR development (e.g., free databases and QSAR programs). The paper follows the four steps of QSAR model development, i.e., data collection, descriptor filtration, algorithm selection, and model validation; and finishes by highlighting several research needs. Because QSAR models may have an important role in progressing our understanding of DBP issues, it is hoped that this paper will encourage their future use for this application.
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Affiliation(s)
- Baiyang Chen
- Harbin Institute of Technology Shenzhen Graduate School, Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Shenzhen 518055, China.
| | - Tian Zhang
- Harbin Institute of Technology Shenzhen Graduate School, Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Shenzhen 518055, China
| | - Tom Bond
- Department of Civil and Environmental Engineering, Imperial College, London SW7 2AZ, United Kingdom
| | - Yiqun Gan
- Harbin Institute of Technology Shenzhen Graduate School, Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Shenzhen 518055, China
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31
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Schwarzman MR, Ackerman JM, Dairkee SH, Fenton SE, Johnson D, Navarro KM, Osborne G, Rudel RA, Solomon GM, Zeise L, Janssen S. Screening for Chemical Contributions to Breast Cancer Risk: A Case Study for Chemical Safety Evaluation. ENVIRONMENTAL HEALTH PERSPECTIVES 2015; 123:1255-64. [PMID: 26032647 PMCID: PMC4671249 DOI: 10.1289/ehp.1408337] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/20/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND Current approaches to chemical screening, prioritization, and assessment are being reenvisioned, driven by innovations in chemical safety testing, new chemical regulations, and demand for information on human and environmental impacts of chemicals. To conceptualize these changes through the lens of a prevalent disease, the Breast Cancer and Chemicals Policy project convened an interdisciplinary expert panel to investigate methods for identifying chemicals that may increase breast cancer risk. METHODS Based on a review of current evidence, the panel identified key biological processes whose perturbation may alter breast cancer risk. We identified corresponding assays to develop the Hazard Identification Approach for Breast Carcinogens (HIA-BC), a method for detecting chemicals that may raise breast cancer risk. Finally, we conducted a literature-based pilot test of the HIA-BC. RESULTS The HIA-BC identifies assays capable of detecting alterations to biological processes relevant to breast cancer, including cellular and molecular events, tissue changes, and factors that alter susceptibility. In the pilot test of the HIA-BC, chemicals associated with breast cancer all demonstrated genotoxic or endocrine activity, but not necessarily both. Significant data gaps persist. CONCLUSIONS This approach could inform the development of toxicity testing that targets mechanisms relevant to breast cancer, providing a basis for identifying safer chemicals. The study identified important end points not currently evaluated by federal testing programs, including altered mammary gland development, Her2 activation, progesterone receptor activity, prolactin effects, and aspects of estrogen receptor β activity. This approach could be extended to identify the biological processes and screening methods relevant for other common diseases.
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Affiliation(s)
- Megan R Schwarzman
- Center for Occupational and Environmental Health, School of Public Health, University of California, Berkeley, Berkeley, California, USA
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Powroźnik B, Słoczyńska K, Canale V, Grychowska K, Zajdel P, Pękala E. Preliminary mutagenicity and genotoxicity evaluation of selected arylsulfonamide derivatives of (aryloxy)alkylamines with potential psychotropic properties. J Appl Genet 2015; 57:263-70. [PMID: 26440375 DOI: 10.1007/s13353-015-0322-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 09/07/2015] [Accepted: 09/25/2015] [Indexed: 11/24/2022]
Abstract
Determination of the mutagenic and genotoxic liability of biologically active compounds is of great concern for preliminary toxicity testing and drug development. In this study, we focused on the evaluation of the mutagenic and genotoxic effects of selected arylsulfonamide derivatives of aryloxyethyl piperidines and pyrrolidines (1-8), classified as 5-HT7 receptor antagonist with antidepressant and procognitive properties, using in silico and in vitro methods: the Vibrio harveyi assay and the SOS/umu-test (umuC Easy CS test). Finally, the antimutagenic potential of tested compounds was evaluated with the V. harveyi assay. It was demonstrated that none of the examined compounds produced a positive response in in vitro assays and these results were in line with in silico prediction. Additionally, all the tested compounds demonstrated various antimutagenic potential, with compound 1 (5-chloro-N-((1-(2-phenoxyethyl)piperidin-4-yl)methyl)thiophene-2-sulfonamide) being the most active against NQNO-induced mutagenicity.
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Affiliation(s)
- Beata Powroźnik
- Department of Pharmaceutical Biochemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688, Krakow, Poland
| | - Karolina Słoczyńska
- Department of Pharmaceutical Biochemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688, Krakow, Poland
| | - Vittorio Canale
- Department of Medicinal Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688, Krakow, Poland
| | - Katarzyna Grychowska
- Department of Medicinal Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688, Krakow, Poland
| | - Paweł Zajdel
- Department of Medicinal Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688, Krakow, Poland
| | - Elżbieta Pękala
- Department of Pharmaceutical Biochemistry, Jagiellonian University Medical College, 9 Medyczna Street, 30-688, Krakow, Poland.
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Abstract
In recent decades, in silico absorption, distribution, metabolism, excretion (ADME), and toxicity (T) modelling as a tool for rational drug design has received considerable attention from pharmaceutical scientists, and various ADME/T-related prediction models have been reported. The high-throughput and low-cost nature of these models permits a more streamlined drug development process in which the identification of hits or their structural optimization can be guided based on a parallel investigation of bioavailability and safety, along with activity. However, the effectiveness of these tools is highly dependent on their capacity to cope with needs at different stages, e.g. their use in candidate selection has been limited due to their lack of the required predictability. For some events or endpoints involving more complex mechanisms, the current in silico approaches still need further improvement. In this review, we will briefly introduce the development of in silico models for some physicochemical parameters, ADME properties and toxicity evaluation, with an emphasis on the modelling approaches thereof, their application in drug discovery, and the potential merits or deficiencies of these models. Finally, the outlook for future ADME/T modelling based on big data analysis and systems sciences will be discussed.
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Vračko M, Bobst S. Prediction of mutagenicity and carcinogenicity using in silico modelling: A case study of polychlorinated biphenyls. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:667-682. [PMID: 26329919 DOI: 10.1080/1062936x.2015.1080185] [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: 06/27/2015] [Accepted: 08/03/2015] [Indexed: 06/05/2023]
Abstract
In silico modelling is an important alternative method for the evaluation of properties of chemical compounds. Basically, two concepts are used in its applications: QSAR modelling for endpoint predictions, and grouping (categorization) of large groups of chemicals. In the presented report we address both of these concepts. As a case study we present the results on a set of polychlorinated biphenyls (PCBs) and some of their metabolites. Their mutagenicity and carcinogenic potency were evaluated with CAESAR and T.E.S.T. models, which are freely available over the internet. We discuss the value and reliability of the predictions, the applicability domain of models and the ability to create prioritized groupings of PCBs as a category of chemicals.
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Affiliation(s)
- M Vračko
- a Kemijski Inštitut/National Institute of Chemistry , Ljubljana , Slovenia
| | - S Bobst
- b Nexeo Solutions LLC , Texas , USA
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35
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Ring M, Eskofier BM. Data mining in the U.S. National Toxicology Program (NTP) database reveals a potential bias regarding liver tumors in rodents irrespective of the test agent. PLoS One 2015; 10:e0116488. [PMID: 25658102 PMCID: PMC4319901 DOI: 10.1371/journal.pone.0116488] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/08/2014] [Indexed: 11/19/2022] Open
Abstract
Long-term studies in rodents are the benchmark method to assess carcinogenicity of single substances, mixtures, and multi-compounds. In such a study, mice and rats are exposed to a test agent at different dose levels for a period of two years and the incidence of neoplastic lesions is observed. However, this two-year study is also expensive, time-consuming, and burdensome to the experimental animals. Consequently, various alternatives have been proposed in the literature to assess carcinogenicity on basis of short-term studies. In this paper, we investigated if effects on the rodents' liver weight in short-term studies can be exploited to predict the incidence of liver tumors in long-term studies. A set of 138 paired short- and long-term studies was compiled from the database of the U.S. National Toxicology Program (NTP), more precisely, from (long-term) two-year carcinogenicity studies and their preceding (short-term) dose finding studies. In this set, data mining methods revealed patterns that can predict the incidence of liver tumors with accuracies of over 80%. However, the results simultaneously indicated a potential bias regarding liver tumors in two-year NTP studies. The incidence of liver tumors does not only depend on the test agent but also on other confounding factors in the study design, e.g., species, sex, type of substance. We recommend considering this bias if the hazard or risk of a test agent is assessed on basis of a NTP carcinogenicity study.
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Affiliation(s)
- Matthias Ring
- Digital Sports Group, Pattern Recognition Lab, Friedrich-Alexander-Universität, Erlangen-Nürnberg (FAU), Germany
- * E-mail:
| | - Bjoern M. Eskofier
- Digital Sports Group, Pattern Recognition Lab, Friedrich-Alexander-Universität, Erlangen-Nürnberg (FAU), Germany
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36
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Plošnik A, Zupan J, Vračko M. Evaluation of toxic endpoints for a set of cosmetic ingredients with CAESAR models. CHEMOSPHERE 2015; 120:492-499. [PMID: 25278177 DOI: 10.1016/j.chemosphere.2014.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/29/2014] [Accepted: 09/02/2014] [Indexed: 06/03/2023]
Abstract
The randomly selected set of 558 chemicals from Cosmetic inventory was studied with internet accessible program package CAESAR. Four toxic endpoints were considered: mutagenicity, carcinogenicity, developmental toxicity and skin sensitization. The CAESAR program provides beside the predictions comprehensive information on applicability domain and the similarity between the considered compound and the compounds from model's training set. This information was used to implement for clustering and classification of chemicals. As the technique the Self Organizing Maps was applied. This technique also enables us to define to each cluster the cluster indicator, i.e., the characteristic compound, which is considered as a representative for a cluster.
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Affiliation(s)
- Alja Plošnik
- Kemijski institut/National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Jure Zupan
- Kemijski institut/National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Marjan Vračko
- Kemijski institut/National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
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37
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Khalifa NS, Barakat HS, Elhallouty S, Salem D. Do cancer cells in human and meristematic cells in plant exhibit similar responses toward plant extracts with cytotoxic activities? Cytotechnology 2015; 67:123-33. [PMID: 24705601 PMCID: PMC4294835 DOI: 10.1007/s10616-013-9666-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 11/05/2013] [Indexed: 10/25/2022] Open
Abstract
We examined the effect of water extracts of Persea americana fruit, and of the leaves of Tabernamontana divericata, Nerium oleander and Annona cherimolia (positive control) on Vicia faba root cells. We had confirmed in our previously published data the cytotoxicity of these plant extracts on four human cancer cell lines: liver (HepG-2), lung (A549), colon (HT-29) and breast (MCF-7). Vicia faba roots were soaked in plant extracts at dilutions of 100, 1,250, 2,500, 5,000, 10,000, 20,000 ppm for 4 and 24 h. All treatments resulted in a significant reduction in the mitotic index in a dose dependant manner. Root cells treated with T. divericata, N. oleander and A. cherimolia exhibited a decrease in prophase cell percentage, increase in micronuclei and chromosomal abnormalities as concentration increased. The P. americana treatment showed the highest cytotoxic effect on cancer cells, prophase cell percentage increased linearly with the applied concentration and no micronuclei were detected. This study shows that root tip assay of beans can be used in initial screening for new plant extracts to validate their use as candidates for containing active cytotoxic agents against malignant cells. This will greatly help in exploring new plant extracts as drugs for cancer treatment.
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Affiliation(s)
- Noha S Khalifa
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt,
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38
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Gini G, Franchi AM, Manganaro A, Golbamaki A, Benfenati E. ToxRead: a tool to assist in read across and its use to assess mutagenicity of chemicals. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:999-1011. [PMID: 25511972 DOI: 10.1080/1062936x.2014.976267] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/15/2014] [Indexed: 06/04/2023]
Abstract
Life sciences, and toxicology in particular, are heavily impacted by the development of methods for data collection and data analysis; they are moving from an analytical approach to a modelling approach. The scarce availability of experimental data is a known bottleneck in assessing the properties of new chemicals. Even when a model is available, the resulting predictions have to be assessed by close scrutiny of the chemicals and the biological properties of the compounds concerned. To avoid unnecessary testing, a read across strategy is often suggested and used. In this paper we discuss how to improve and standardize read across activity using ad hoc visualization and data search methods which use similarity measures and fragment search to organize in a chart a picture of all the relevant information that the expert needs to make an assessment. We show in particular how to apply our system to the case of mutagenicity.
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Affiliation(s)
- G Gini
- a Dipartimento di Elettronica, Informazione e Bioingegneria , Politecnico di Milano , Milan , Italy
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Allen TEH, Goodman JM, Gutsell S, Russell PJ. Defining Molecular Initiating Events in the Adverse Outcome Pathway Framework for Risk Assessment. Chem Res Toxicol 2014; 27:2100-12. [DOI: 10.1021/tx500345j] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Timothy E. H. Allen
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jonathan M. Goodman
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Steve Gutsell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom
| | - Paul J. Russell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom
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40
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Vedani A, Dobler M, Hu Z, Smieško M. OpenVirtualToxLab--a platform for generating and exchanging in silico toxicity data. Toxicol Lett 2014; 232:519-32. [PMID: 25240273 DOI: 10.1016/j.toxlet.2014.09.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/03/2014] [Indexed: 11/30/2022]
Abstract
The VirtualToxLab is an in silico technology for estimating the toxic potential--endocrine and metabolic disruption, some aspects of carcinogenicity and cardiotoxicity--of drugs, chemicals and natural products. The technology is based on an automated protocol that simulates and quantifies the binding of small molecules towards a series of currently 16 proteins, known or suspected to trigger adverse effects: 10 nuclear receptors (androgen, estrogen α, estrogen β, glucocorticoid, liver X, mineralocorticoid, peroxisome proliferator-activated receptor γ, progesterone, thyroid α, thyroid β), four members of the cytochrome P450 enzyme family (1A2, 2C9, 2D6, 3A4), a cytosolic transcription factor (aryl hydrocarbon receptor) and a potassium ion channel (hERG). The toxic potential of a compound--its ability to trigger adverse effects--is derived from its computed binding affinities toward these very proteins: the computationally demanding simulations are executed in client-server model on a Linux cluster of the University of Basel. The graphical-user interface supports all computer platforms, allows building and uploading molecular structures, inspecting and downloading the results and, most important, rationalizing any prediction at the atomic level by interactively analyzing the binding mode of a compound with its target protein(s) in real-time 3D. Access to the VirtualToxLab is available free of charge for universities, governmental agencies, regulatory bodies and non-profit organizations.
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Affiliation(s)
- Angelo Vedani
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; Foundation Biographics Laboratory 3R, Klingelbergstrasse 50, 4056 Basel, Switzerland.
| | - Max Dobler
- Foundation Biographics Laboratory 3R, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Zhenquan Hu
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Martin Smieško
- Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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41
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Lo Piparo E, Maunz A, Helma C, Vorgrimmler D, Schilter B. Automated and reproducible read-across like models for predicting carcinogenic potency. Regul Toxicol Pharmacol 2014; 70:370-8. [PMID: 25047023 DOI: 10.1016/j.yrtph.2014.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 10/25/2022]
Abstract
Several qualitative (hazard-based) models for chronic toxicity prediction are available through commercial and freely available software, but in the context of risk assessment a quantitative value is mandatory in order to be able to apply a Margin of Exposure (predicted toxicity/exposure estimate) approach to interpret the data. Recently quantitative models for the prediction of the carcinogenic potency have been developed, opening some hopes in this area, but this promising approach is currently limited by the fact that the proposed programs are neither publically nor commercially available. In this article we describe how two models (one for mouse and one for rat) for the carcinogenic potency (TD50) prediction have been developed, using lazar (Lazy Structure Activity Relationships), a procedure similar to read-across, but automated and reproducible. The models obtained have been compared with the recently published ones, resulting in a similar performance. Our aim is also to make the models freely available in the near future thought a user friendly internet web site.
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Affiliation(s)
- Elena Lo Piparo
- Chemical Food Safety Group, Nestlé Research Center, Lausanne, Switzerland.
| | | | | | | | - Benoît Schilter
- Chemical Food Safety Group, Nestlé Research Center, Lausanne, Switzerland
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43
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Schilter B, Benigni R, Boobis A, Chiodini A, Cockburn A, Cronin MTD, Lo Piparo E, Modi S, Thiel A, Worth A. Establishing the level of safety concern for chemicals in food without the need for toxicity testing. Regul Toxicol Pharmacol 2013; 68:275-96. [PMID: 24012706 DOI: 10.1016/j.yrtph.2013.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 10/26/2022]
Abstract
There is demand for methodologies to establish levels of safety concern associated with dietary exposures to chemicals for which no toxicological data are available. In such situations, the application of in silico methods appears promising. To make safety statement requires quantitative predictions of toxicological reference points such as no observed adverse effect level and carcinogenic potency for DNA-reacting chemicals. A decision tree (DT) has been developed to aid integrating exposure information and predicted toxicological reference points obtained with quantitative structure activity relationship ((Q)SAR) software and read across techniques. The predicted toxicological values are compared with exposure to obtain margins of exposure (MoE). The size of the MoE defines the level of safety concern and should account for a number of uncertainties such as the classical interspecies and inter-individual variability as well as others determined on a case by case basis. An analysis of the uncertainties of in silico approaches together with results from case studies suggest that establishing safety concern based on application of the DT is unlikely to be significantly more uncertain than based on experimental data. The DT makes a full use of all data available, ensuring an adequate degree of conservatism. It can be used when fast decision making is required.
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Affiliation(s)
- Benoît Schilter
- Nestlé Research Centre, Vers-Chez-Les-Blanc, Lausanne, Switzerland
| | | | - Alan Boobis
- Imperial College London, London, United Kingdom
| | | | | | | | - Elena Lo Piparo
- Nestlé Research Centre, Vers-Chez-Les-Blanc, Lausanne, Switzerland
| | | | - Anette Thiel
- DSM Nutritional Products, Kaiseraugst, Switzerland
| | - Andrew Worth
- European Commission - Joint Research Centre, Institute for Health & Consumer Protection, Ispra, Italy
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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.
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Affiliation(s)
- K Tanabe
- Neuroscience Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
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Ferrari T, Cattaneo D, Gini G, Golbamaki Bakhtyari N, Manganaro A, Benfenati E. Automatic knowledge extraction from chemical structures: the case of mutagenicity prediction. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:365-83. [PMID: 23710765 DOI: 10.1080/1062936x.2013.773376] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This work proposes a new structure-activity relationship (SAR) approach to mine molecular fragments that act as structural alerts for biological activity. The entire process is designed to fit with human reasoning, not only to make the predictions more reliable but also to permit clear control by the user in order to meet customized requirements. This approach has been tested on the mutagenicity endpoint, showing marked prediction skills and, more interestingly, bringing to the surface much of the knowledge already collected in the literature as well as new evidence.
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Affiliation(s)
- T Ferrari
- Department of Electronics and Information, Politecnico di Milano, Milan, Italy
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46
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Abstract
Use of predictive technologies is an important aspect of many efforts in today's research, development, and regulatory landscapes. Computational methods as predictive tools for supporting drug safety assessments is of widespread interest as the field of in silico assessments rapidly changes with emerging technologies and the large amount of existing data available for modeling. There are challenges associated with application of in silico analyses for drug toxicity predictions and need for strategies and harmonization to enable an acceptable in silico evaluation for prediction of specific toxicity assay outcomes. This chapter will provide an overview focused on computational tools using structure-activity relationships and will highlight initiatives for use of computational assessments and realistic applications for predictive modeling in evaluating potential toxicities of drug-related molecules.
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47
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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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Modi S, Li J, Malcomber S, Moore C, Scott A, White A, Carmichael P. Integrated in silico approaches for the prediction of Ames test mutagenicity. J Comput Aided Mol Des 2012; 26:1017-33. [DOI: 10.1007/s10822-012-9595-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 08/09/2012] [Indexed: 02/04/2023]
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Vedani A, Dobler M, Smieško M. VirtualToxLab - a platform for estimating the toxic potential of drugs, chemicals and natural products. Toxicol Appl Pharmacol 2012; 261:142-53. [PMID: 22521603 DOI: 10.1016/j.taap.2012.03.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 03/26/2012] [Accepted: 03/28/2012] [Indexed: 10/28/2022]
Abstract
The VirtualToxLab is an in silico technology for estimating the toxic potential (endocrine and metabolic disruption, some aspects of carcinogenicity and cardiotoxicity) of drugs, chemicals and natural products. The technology is based on an automated protocol that simulates and quantifies the binding of small molecules towards a series of proteins, known or suspected to trigger adverse effects. The toxic potential, a non-linear function ranging from 0.0 (none) to 1.0 (extreme), is derived from the individual binding affinities of a compound towards currently 16 target proteins: 10 nuclear receptors (androgen, estrogen α, estrogen β, glucocorticoid, liver X, mineralocorticoid, peroxisome proliferator-activated receptor γ, progesterone, thyroid α, and thyroid β), four members of the cytochrome P450 enzyme family (1A2, 2C9, 2D6, and 3A4), a cytosolic transcription factor (aryl hydrocarbon receptor) and a potassium ion channel (hERG). The interface to the technology allows building and uploading molecular structures, viewing and downloading results and, most importantly, rationalizing any prediction at the atomic level by interactively analyzing the binding mode of a compound with its target protein(s) in real-time 3D. The VirtualToxLab has been used to predict the toxic potential for over 2500 compounds: the results are posted on http://www.virtualtoxlab.org. The free platform - the OpenVirtualToxLab - is accessible (in client-server mode) over the Internet. It is free of charge for universities, governmental agencies, regulatory bodies and non-profit organizations.
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Affiliation(s)
- Angelo Vedani
- Biographics Laboratory 3R, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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50
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Kar S, Roy K. First report on development of quantitative interspecies structure-carcinogenicity relationship models and exploring discriminatory features for rodent carcinogenicity of diverse organic chemicals using OECD guidelines. CHEMOSPHERE 2012; 87:339-355. [PMID: 22225702 DOI: 10.1016/j.chemosphere.2011.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 12/08/2011] [Accepted: 12/08/2011] [Indexed: 05/31/2023]
Abstract
Different regulatory agencies in food and drug administration and environmental protection worldwide are employing quantitative structure-activity relationship (QSAR) models to fill the data gaps related with properties of chemicals affecting the environment and human health. Carcinogenicity is a toxicity endpoint of major concern in recent times. Interspecies toxicity correlations may provide a tool for estimating sensitivity towards toxic chemical exposure with known levels of uncertainty for a diversity of wildlife species. In this background, we have developed quantitative interspecies structure-carcinogenicity correlation models for rat and mouse [rodent species according to the Organization for Economic Cooperation and Development (OECD) guidelines] based on the carcinogenic potential of 166 organic chemicals with wide diversity of molecular structures, spanning a large number of chemical classes and biological mechanisms. All the developed models have been assessed according to the OECD principles for the validation of QSAR models. Consensus predictions for carcinogenicity of the individual compounds are presented here for any one species when the data for the other species are available. Informative illustrations of the contributing structural fragments of chemicals which are responsible for specific carcinogenicity endpoints are identified by the developed models. The models have also been used to predict mouse carcinogenicities of 247 organic chemicals (for which rat carcinogenicities are present) and rat carcinogenicities of 150 chemicals (for which mouse carcinogenicities are present). Discriminatory features for rat and mouse carcinogenicity values have also been explored.
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Affiliation(s)
- Supratik Kar
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700 032, India
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