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Yang H, Sun L, Li W, Liu G, Tang Y. In Silico Prediction of Chemical Toxicity for Drug Design Using Machine Learning Methods and Structural Alerts. Front Chem 2018. [PMID: 29515993 PMCID: PMC5826228 DOI: 10.3389/fchem.2018.00030] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
During drug development, safety is always the most important issue, including a variety of toxicities and adverse drug effects, which should be evaluated in preclinical and clinical trial phases. This review article at first simply introduced the computational methods used in prediction of chemical toxicity for drug design, including machine learning methods and structural alerts. Machine learning methods have been widely applied in qualitative classification and quantitative regression studies, while structural alerts can be regarded as a complementary tool for lead optimization. The emphasis of this article was put on the recent progress of predictive models built for various toxicities. Available databases and web servers were also provided. Though the methods and models are very helpful for drug design, there are still some challenges and limitations to be improved for drug safety assessment in the future.
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Affiliation(s)
- Hongbin Yang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Lixia Sun
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
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Rezaei Kolahchi A, Khadem Mohtaram N, Pezeshgi Modarres H, Mohammadi MH, Geraili A, Jafari P, Akbari M, Sanati-Nezhad A. Microfluidic-Based Multi-Organ Platforms for Drug Discovery. MICROMACHINES 2016; 7:E162. [PMID: 30404334 PMCID: PMC6189912 DOI: 10.3390/mi7090162] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022]
Abstract
Development of predictive multi-organ models before implementing costly clinical trials is central for screening the toxicity, efficacy, and side effects of new therapeutic agents. Despite significant efforts that have been recently made to develop biomimetic in vitro tissue models, the clinical application of such platforms is still far from reality. Recent advances in physiologically-based pharmacokinetic and pharmacodynamic (PBPK-PD) modeling, micro- and nanotechnology, and in silico modeling have enabled single- and multi-organ platforms for investigation of new chemical agents and tissue-tissue interactions. This review provides an overview of the principles of designing microfluidic-based organ-on-chip models for drug testing and highlights current state-of-the-art in developing predictive multi-organ models for studying the cross-talk of interconnected organs. We further discuss the challenges associated with establishing a predictive body-on-chip (BOC) model such as the scaling, cell types, the common medium, and principles of the study design for characterizing the interaction of drugs with multiple targets.
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Affiliation(s)
- Ahmad Rezaei Kolahchi
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Nima Khadem Mohtaram
- Laboratory for Innovations in MicroEngineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada.
- Division of Medical Sciences, University of Victoria, Victoria, BC V8P 5C2, Canada.
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Hassan Pezeshgi Modarres
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Mohammad Hossein Mohammadi
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Azadi Ave., Tehran 11155-9516, Iran.
| | - Armin Geraili
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Azadi Ave., Tehran 11155-9516, Iran.
| | - Parya Jafari
- Department of Electrical Engineering, Sharif University of Technology, Azadi Ave., Tehran 11155-9516, Iran.
| | - Mohsen Akbari
- Laboratory for Innovations in MicroEngineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada.
- Division of Medical Sciences, University of Victoria, Victoria, BC V8P 5C2, Canada.
| | - Amir Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
- Center for Bioengineering Research and Education, Biomedical Engineering Program, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
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Li X. In vitro toxicity testing of cigarette smoke based on the air-liquid interface exposure: A review. Toxicol In Vitro 2016; 36:105-113. [PMID: 27470133 DOI: 10.1016/j.tiv.2016.07.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/22/2016] [Accepted: 07/25/2016] [Indexed: 02/08/2023]
Abstract
Cigarette smoke is a complex aerosol comprising particulate phase and gaseous vapour phase. The air-liquid interface exposure provides a possible technical means to implement whole smoke exposure for the assessment of tobacco products. In this review, the research progress in the in vitro toxicity testing of cigarette smoke based on the air-liquid interface exposure is summarized. The contents presented involve mainly cytotoxicity, genotoxicity, oxidative stress, inflammation, systems toxicology, 3D culture and cigarette smoke dosimetry related to cigarette smoke, as well as the assessment of electronic cigarette aerosol. Prospect of the application of the air-liquid interface exposure method in assessing the biological effects of tobacco smoke is discussed.
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Affiliation(s)
- Xiang Li
- Key Laboratory of Tobacco Chemistry, Zhengzhou Tobacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou 450001, China.
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Abstract
The exponential growth of the Internet of Things and the global popularity and remarkable decline in cost of the mobile phone is driving the digital transformation of medical practice. The rapidly maturing digital, non-medical world of mobile (wireless) devices, cloud computing and social networking is coalescing with the emerging digital medical world of omics data, biosensors and advanced imaging which offers the increasingly realistic prospect of personalized medicine. Described as a potential “seismic” shift from the current “healthcare” model to a “wellness” paradigm that is predictive, preventative, personalized and participatory, this change is based on the development of increasingly sophisticated biosensors which can track and measure key biochemical variables in people. Additional key drivers in this shift are metabolomic and proteomic signatures, which are increasingly being reported as pre-symptomatic, diagnostic and prognostic of toxicity and disease. These advancements also have profound implications for toxicological evaluation and safety assessment of pharmaceuticals and environmental chemicals. An approach based primarily on human in vivo and high-throughput in vitro human cell-line data is a distinct possibility. This would transform current chemical safety assessment practice which operates in a human “data poor” to a human “data rich” environment. This could also lead to a seismic shift from the current animal-based to an animal-free chemical safety assessment paradigm.
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Affiliation(s)
- George D Loizou
- Health Risks, Health and Safety Laboratory, Health and Safety Executive Buxton, UK
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Raies AB, Bajic VB. In silico toxicology: computational methods for the prediction of chemical toxicity. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2016; 6:147-172. [PMID: 27066112 PMCID: PMC4785608 DOI: 10.1002/wcms.1240] [Citation(s) in RCA: 336] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/27/2015] [Accepted: 11/10/2015] [Indexed: 01/08/2023]
Abstract
Determining the toxicity of chemicals is necessary to identify their harmful effects on humans, animals, plants, or the environment. It is also one of the main steps in drug design. Animal models have been used for a long time for toxicity testing. However, in vivo animal tests are constrained by time, ethical considerations, and financial burden. Therefore, computational methods for estimating the toxicity of chemicals are considered useful. In silico toxicology is one type of toxicity assessment that uses computational methods to analyze, simulate, visualize, or predict the toxicity of chemicals. In silico toxicology aims to complement existing toxicity tests to predict toxicity, prioritize chemicals, guide toxicity tests, and minimize late-stage failures in drugs design. There are various methods for generating models to predict toxicity endpoints. We provide a comprehensive overview, explain, and compare the strengths and weaknesses of the existing modeling methods and algorithms for toxicity prediction with a particular (but not exclusive) emphasis on computational tools that can implement these methods and refer to expert systems that deploy the prediction models. Finally, we briefly review a number of new research directions in in silico toxicology and provide recommendations for designing in silico models. WIREs Comput Mol Sci 2016, 6:147-172. doi: 10.1002/wcms.1240 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Arwa B Raies
- King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Centre (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) Thuwal Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Centre (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) Thuwal Saudi Arabia
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Hunt CA, Kennedy RC, Kim SHJ, Ropella GEP. Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:461-80. [PMID: 23737142 PMCID: PMC3739932 DOI: 10.1002/wsbm.1222] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A crisis continues to brew within the pharmaceutical research and development (R&D) enterprise: productivity continues declining as costs rise, despite ongoing, often dramatic scientific and technical advances. To reverse this trend, we offer various suggestions for both the expansion and broader adoption of modeling and simulation (M&S) methods. We suggest strategies and scenarios intended to enable new M&S use cases that directly engage R&D knowledge generation and build actionable mechanistic insight, thereby opening the door to enhanced productivity. What M&S requirements must be satisfied to access and open the door, and begin reversing the productivity decline? Can current methods and tools fulfill the requirements, or are new methods necessary? We draw on the relevant, recent literature to provide and explore answers. In so doing, we identify essential, key roles for agent-based and other methods. We assemble a list of requirements necessary for M&S to meet the diverse needs distilled from a collection of research, review, and opinion articles. We argue that to realize its full potential, M&S should be actualized within a larger information technology framework—a dynamic knowledge repository—wherein models of various types execute, evolve, and increase in accuracy over time. We offer some details of the issues that must be addressed for such a repository to accrue the capabilities needed to reverse the productivity decline. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- C Anthony Hunt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
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