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Daghighi A, Casanola-Martin GM, Iduoku K, Kusic H, González-Díaz H, Rasulev B. Multi-Endpoint Acute Toxicity Assessment of Organic Compounds Using Large-Scale Machine Learning Modeling. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10116-10127. [PMID: 38797941 DOI: 10.1021/acs.est.4c01017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
In recent years, alternative animal testing methods such as computational and machine learning approaches have become increasingly crucial for toxicity testing. However, the complexity and scarcity of available biomedical data challenge the development of predictive models. Combining nonlinear machine learning together with multicondition descriptors offers a solution for using data from various assays to create a robust model. This work applies multicondition descriptors (MCDs) to develop a QSTR (Quantitative Structure-Toxicity Relationship) model based on a large toxicity data set comprising more than 80,000 compounds and 59 different end points (122,572 data points). The prediction capabilities of developed single-task multi-end point machine learning models as well as a novel data analysis approach with the use of Convolutional Neural Networks (CNN) are discussed. The results show that using MCDs significantly improves the model and using them with CNN-1D yields the best result (R2train = 0.93, R2ext = 0.70). Several structural features showed a high level of contribution to the toxicity, including van der Waals surface area (VSA), number of nitrogen-containing fragments (nN+), presence of S-P fragments, ionization potential, and presence of C-N fragments. The developed models can be very useful tools to predict the toxicity of various compounds under different conditions, enabling quick toxicity assessment of new compounds.
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Affiliation(s)
- Amirreza Daghighi
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58102, United States
- Biomedical Engineering Program, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Gerardo M Casanola-Martin
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Kweeni Iduoku
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58102, United States
- Biomedical Engineering Program, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Hrvoje Kusic
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulicev Trg 19, Zagreb 10000, Croatia
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, Leioa 48940, Spain
- BIOFISIKA, Basque Center for Biophysics CSIC-UPVEH, Leioa 48940, Spain
- IKERBASQUE, Basque Foundation for Science,Bilbao, Biscay 48011, Spain
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58102, United States
- Biomedical Engineering Program, North Dakota State University, Fargo, North Dakota 58102, United States
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Burloiu AM, Manda G, Lupuliasa D, Socoteanu RP, Mihai DP, Neagoe IV, Anghelache LI, Surcel M, Anastasescu M, Olariu L, Gîrd CE, Barbuceanu SF, Ferreira LFV, Boscencu R. Assessment of Some Unsymmetrical Porphyrins as Promising Molecules for Photodynamic Therapy of Cutaneous Disorders. Pharmaceuticals (Basel) 2023; 17:62. [PMID: 38256895 PMCID: PMC10818616 DOI: 10.3390/ph17010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
In order to select for further development novel photosensitizers for photodynamic therapy in cutaneous disorders, three unsymmetrical porphyrins, namely 5-(4-hydroxy-3-methoxyphenyl)-10,15,20-tris-(4-acetoxy-3-methoxyphenyl) porphyrin (P2.2), 5-(2-hydroxy-5-methoxyphenyl)-10,15,20-tris-(4-carboxymethylphenyl) porphyrin (P3.2), and 5-(2,4-dihydroxyphenyl)-10,15,20-tris-(4-acetoxy-3-methoxyphenyl) porphyrin (P4.2), along with their fully symmetrical counterparts 5,10,15,20-tetrakis-(4-acetoxy-3-methoxyphenyl) porphyrin (P2.1) and 5,10,15,20-tetrakis-(4-carboxymethylphenyl) porphyrin (P3.1) were comparatively evaluated. The absorption and fluorescence properties, as well as atomic force microscopy measurements were performed to evaluate the photophysical characteristics as well as morphological and textural properties of the mentioned porphyrins. The cellular uptake of compounds and the effect of photodynamic therapy on the viability, proliferation, and necrosis of human HaCaT keratinocytes, human Hs27 skin fibroblasts, human skin SCL II squamous cell carcinoma, and B16F10 melanoma cells were assessed in vitro, in correlation with the structural and photophysical properties of the investigated porphyrins, and with the predictions regarding diffusion through cell membranes and ADMET properties. All samples were found to be isotropic and self-similar, with slightly different degrees of aggregability, had a relatively low predicted toxicity (class V), and a predicted long half-life after systemic administration. The in vitro study performed on non-malignant and malignant skin-relevant cells highlighted that the asymmetric P2.2 porphyrin qualified among the five investigated porphyrins to be a promising photosensitizer candidate for PDT in skin disorders. P2.2 was shown to accumulate well within cells, and induced by PDT a massive decrease in the number of metabolically active skin cells, partly due to cell death by necrosis. P2.2 had in this respect a better behavior than the symmetric P.2.1 compound and the related asymmetric compound P4.2. The strong action of P2.2-mediated PDT on normal skin cells might be an important drawback for further development of this compound. Meanwhile, the P3.1 and P3.2 compounds were not able to accumulate well in skin cells, and did not elicit significant PDT in vitro. Taken together, our experiments suggest that P2.2 can be a promising candidate for the development of novel photosensitizers for PDT in skin disorders.
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Affiliation(s)
- Andreea Mihaela Burloiu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia St., 020956 Bucharest, Romania; (A.M.B.); (D.L.); (D.P.M.); (C.E.G.); (S.F.B.)
| | - Gina Manda
- “Victor Babeş” National Institute of Pathology, 050096 Bucharest, Romania; (I.V.N.); (L.-I.A.); (M.S.)
| | - Dumitru Lupuliasa
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia St., 020956 Bucharest, Romania; (A.M.B.); (D.L.); (D.P.M.); (C.E.G.); (S.F.B.)
| | - Radu Petre Socoteanu
- “Ilie Murgulescu” Institute of Physical Chemistry, Romanian Academy, 060021 Bucharest, Romania; (R.P.S.); (M.A.)
| | - Dragos Paul Mihai
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia St., 020956 Bucharest, Romania; (A.M.B.); (D.L.); (D.P.M.); (C.E.G.); (S.F.B.)
| | - Ionela Victoria Neagoe
- “Victor Babeş” National Institute of Pathology, 050096 Bucharest, Romania; (I.V.N.); (L.-I.A.); (M.S.)
| | | | - Mihaela Surcel
- “Victor Babeş” National Institute of Pathology, 050096 Bucharest, Romania; (I.V.N.); (L.-I.A.); (M.S.)
| | - Mihai Anastasescu
- “Ilie Murgulescu” Institute of Physical Chemistry, Romanian Academy, 060021 Bucharest, Romania; (R.P.S.); (M.A.)
| | - Laura Olariu
- “SC. Biotehnos SA”, 3-5 Gorunului St., 075100 Bucharest, Romania;
| | - Cerasela Elena Gîrd
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia St., 020956 Bucharest, Romania; (A.M.B.); (D.L.); (D.P.M.); (C.E.G.); (S.F.B.)
| | - Stefania Felicia Barbuceanu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia St., 020956 Bucharest, Romania; (A.M.B.); (D.L.); (D.P.M.); (C.E.G.); (S.F.B.)
| | - Luis Filipe Vieira Ferreira
- BSIRG—Biospectroscopy and Interfaces Research Group, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
| | - Rica Boscencu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia St., 020956 Bucharest, Romania; (A.M.B.); (D.L.); (D.P.M.); (C.E.G.); (S.F.B.)
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Zhu T, Li S, Li L, Tao C. A new perspective on predicting the reaction rate constants of hydrated electrons for organic contaminants: Exploring molecular structure characterization methods and ambient conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166316. [PMID: 37591396 DOI: 10.1016/j.scitotenv.2023.166316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/26/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023]
Abstract
Hydrated electrons (eaq-) exhibit rapid degradation of diverse persistent organic contaminants (OCs) and hold great promise as a formidable reducing agent in water treatment. However, the diverse structures of compounds exert different influences on the second-order rate constant of hydrated electron reactions (keaq-), while the same OCs demonstrate notable discrepancies in keaq- values across different pH levels. This study aims to develop machine learning (ML) models that can effectively simulate the intricate reaction kinetics between eaq- and OCs. Furthermore, the introduction of the pH variable enables a comprehensive investigation into the impact of ambient conditions on this process, thereby improving the practicality of the model. A dataset encompassing 701 keaq- values derived from 351 peer-reviewed publications was compiled. To comprehensively investigate compound properties, this study introduced molecular descriptor (MD), molecular fingerprint (MF), and the integration of both (MD + MF) as model variables. Furthermore, 60 sets of predictive models were established utilizing two variable screening methodologies (MLR and RF) and ten prominent algorithms. Through statistical parameter analysis, it was determined that descriptors combined with MD and MF, the RF screening method, and the symbolism algorithm exhibited the best predictive efficacy. Importantly, the combination of descriptor models exhibited significantly superior performance compared to individual MF and MD models. Notably, the optimal model, denoted as RF - (MF + MD) - LGB, exhibited highly satisfactory predictive results (R2tra = 0.967, Q2tra = 0.840, R2ext = 0.761). The mechanistic explanation study based on Shapley Additive Explanations (SHAP) values further elucidated the crucial influences of polarity, pH, molecular weight, electronegativity, carbon-carbon double bonds, and molecular topology on the degradation of OCs by eaq-. The proposed modeling approach, particularly the integration of MF and MD, alongside the introduction of pH, may furnish innovative ideas for advanced reduction or oxidation processes (ARPs/AOPs) and machine learning applications in other domains.
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Affiliation(s)
- Tengyi Zhu
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China.
| | - Shuyin Li
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | - Lili Li
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | - Cuicui Tao
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
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Kisiel-Nawrot E, Pindjakova D, Latocha M, Bak A, Kozik V, Suwinska K, Cizek A, Jampilek J, Zięba A. Towards Anticancer and Antibacterial Agents: Design and Synthesis of 1,2,3-Triazol-quinobenzothiazine Derivatives. Int J Mol Sci 2023; 24:13250. [PMID: 37686059 PMCID: PMC10487436 DOI: 10.3390/ijms241713250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
In this paper, we describe a new method for synthesizing hybrid combinations of 1,2,3-triazoles with a tetracyclic quinobenzothiazinium system. The developed approach allowed for the production of a series of new azaphenothiazine derivatives with the 1,2,3-triazole system in different positions of the benzene ring. In practice, the methodology consists of the reaction of triazole aniline derivatives with thioquinanthrenediinium bis-chloride. The structure of the products was determined by 1H-NMR, 13C-NMR spectroscopy, and HR-MS spectrometry, respectively. Moreover, the spatial structure of the molecule and the arrangement of molecules in the crystal (unit cell) were determined by X-ray crystallography. The anticancer activity profiles of the synthesized compounds were tested in vitro against human cancer cells of the A549, SNB-19, and T47D lines and the normal NHDF cell line. Additional tests of antibacterial activity against methicillin-sensitive and methicillin-resistant staphylococci, vancomycin-sensitive and vancomycin-resistant enterococci, and two mycobacterial strains were also performed. In fact, the dependence of anticancer and antibacterial activity on the substituent type and its position in the quinobenzothiazinium system was observed. Furthermore, the distance-guided property evaluation was performed using principal component analysis (PCA) and hierarchical clustering analysis (HCA) on the pool of the calculated descriptors. Finally, the theoretically approximated partition coefficients (clogP) were (inter-)correlated with each other and cross-compared with the empirically specified logPTLC parameters.
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Affiliation(s)
- Ewa Kisiel-Nawrot
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Jagiellońska 4, 41-200 Sosnowiec, Poland
| | - Dominika Pindjakova
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Malgorzata Latocha
- Department of Cell Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Jedności 9, 41-200 Sosnowiec, Poland
| | - Andrzej Bak
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Violetta Kozik
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Kinga Suwinska
- Faculty of Mathematics and Natural Sciences, Cardinal Stefan Wyszyński University, K. Woycickiego 1/3, 01-938 Warszawa, Poland
| | - Alois Cizek
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Palackeho tr. 1946/1, 612 42 Brno, Czech Republic
| | - Josef Jampilek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10 Bratislava, Slovakia
| | - Andrzej Zięba
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Jagiellońska 4, 41-200 Sosnowiec, Poland
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Ungureanu AR, Popovici V, Oprean C, Danciu C, Schröder V, Olaru OT, Mihai DP, Popescu L, Luță EA, Chițescu CL, Gîrd CE. Cytotoxicity Analysis and In Silico Studies of Three Plant Extracts with Potential Application in Treatment of Endothelial Dysfunction. Pharmaceutics 2023; 15:2125. [PMID: 37631338 PMCID: PMC10459174 DOI: 10.3390/pharmaceutics15082125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/06/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Endothelial dysfunction is the basis of the physiopathological mechanisms of vascular diseases. In addition to the therapeutic activity of plant extracts, cytotoxicity is significant. This research evaluates the cytotoxicity of three vegetal extracts (Calendulae flos extract-CE, Ginkgo bilobae folium extract-GE, and Sophorae flos extract-SE). In vitro evaluation was performed using an endothelial cell line model (Human Pulmonary Artery Endothelial Cells-HPAEC) when a dose-dependent cytotoxic activity was observed after 72 h. The IC50 values were calculated for all extracts: Calendulae flos extract (IC50 = 91.36 μg/mL), Sophorae flos extract (IC50 = 68.61 μg/mL), and Ginkgo bilobae folium extract (IC50 = 13.08 μg/mL). Therefore, at the level of HPAEC cells, the cytotoxicity of the extracts follows the order GE > SE > CE. The apoptotic mechanism implied in cell death was predicted for several phytocompounds using the PASS algorithm and molecular docking simulations, highlighting potential interactions with caspases-3 and -8. In vivo analysis was performed through brine shrimp lethality assay (BSLA) when lethal, behavioral, and cytological effects were evaluated on Artemia salina larvae. The viability examined after 24 h (assessment of lethal effects) follows the same sequence: CE > SE > GE. In addition, the predicted cell permeability was observed mainly for GE constituents through in silico studies. However, the extracts can be considered nontoxic according to Clarckson's criteria because no BSL% was registered at 1200 µg/mL. The obtained data reveal that all three extracts are safe for human use and suitable for incorporation in further pharmaceutical formulations.
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Affiliation(s)
- Andreea Roxana Ungureanu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Violeta Popovici
- Department of Microbiology and Immunology, Faculty of Dental Medicine, Ovidius University of Constanta, 7 Ilarie Voronca Street, 900684 Constanta, Romania;
| | - Camelia Oprean
- Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania;
- OncoGen Centre, County Hospital’ Pius Branzeu’, Blvd. Liviu Rebreanu 156, 300723 Timisoara, Romania
| | - Corina Danciu
- Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania;
| | - Verginica Schröder
- Department of Cellular and Molecular Biology, Faculty of Pharmacy, Ovidius University of Constanta, 6 Capitan Al. Serbanescu Street, 900001 Constanta, Romania;
| | - Octavian Tudorel Olaru
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Dragoș Paul Mihai
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Liliana Popescu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Emanuela-Alice Luță
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
| | - Carmen Lidia Chițescu
- Faculty of Medicine and Pharmacy, “Dunărea de Jos” University of Galați, A.I. Cuza 35, 800010 Galați, Romania;
| | - Cerasela Elena Gîrd
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.R.U.); (O.T.O.); (L.P.); (E.-A.L.); (C.E.G.)
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6
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Wang Y, Tang W, Xiao Z, Yang W, Peng Y, Chen J, Li J. Novel quantitative structure activity relationship models for predicting hexadecane/air partition coefficients of organic compounds. J Environ Sci (China) 2023; 124:98-104. [PMID: 36182199 DOI: 10.1016/j.jes.2021.10.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 06/16/2023]
Abstract
Predicting the logarithm of hexadecane/air partition coefficient (L) for organic compounds is crucial for understanding the environmental behavior and fate of organic compounds and developing prediction models with polyparameter linear free energy relationships. Herein, two quantitative structure activity relationship (QSAR) models were developed with 1272 L values for the organic compounds by using multiple linear regression (MLR) and support vector machine (SVM) algorithms. On the basis of the OECD principles, the goodness of fit, robustness and predictive ability for the developed models were evaluated. The SVM model was first developed, and the predictive capability for the SVM model is slightly better than that for the MLR model. The applicability domain (AD) of these two models has been extended to include more kinds of emerging pollutants, i.e., oraganosilicon compounds. The developed QSAR models can be used for predicting L values of various organic compounds. The van der Waals interactions between the organic compound and the hexadecane have a significant effect on the L value of the compound. These in silico models developed in current study can provide an alternative to experimental method for high-throughput obtaining L values of organic compounds.
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Affiliation(s)
- Ya Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Weihao Tang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Zijun Xiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Wenhao Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yue Peng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Junhua Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Nascimben M, Rimondini L. Molecular Toxicity Virtual Screening Applying a Quantized Computational SNN-Based Framework. Molecules 2023; 28:molecules28031342. [PMID: 36771009 PMCID: PMC9919191 DOI: 10.3390/molecules28031342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Spiking neural networks are biologically inspired machine learning algorithms attracting researchers' attention for their applicability to alternative energy-efficient hardware other than traditional computers. In the current work, spiking neural networks have been tested in a quantitative structure-activity analysis targeting the toxicity of molecules. Multiple public-domain databases of compounds have been evaluated with spiking neural networks, achieving accuracies compatible with high-quality frameworks presented in the previous literature. The numerical experiments also included an analysis of hyperparameters and tested the spiking neural networks on molecular fingerprints of different lengths. Proposing alternatives to traditional software and hardware for time- and resource-consuming tasks, such as those found in chemoinformatics, may open the door to new research and improvements in the field.
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Affiliation(s)
- Mauro Nascimben
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases CAAD, Università del Piemonte Orientale, 28100 Novara, Italy
- Enginsoft SpA, 35129 Padua, Italy
- Correspondence:
| | - Lia Rimondini
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases CAAD, Università del Piemonte Orientale, 28100 Novara, Italy
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8
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Zhu T, Tao C, Cheng H, Cong H. Versatile in silico modelling of microplastics adsorption capacity in aqueous environment based on molecular descriptor and machine learning. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157455. [PMID: 35863580 DOI: 10.1016/j.scitotenv.2022.157455] [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: 05/25/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
To comprehensively evaluate the hazards of microplastics and their coexisting organic pollutants, the sorption capacity of microplastics is a major issue that is quantified through the microplastic-aqueous sorption coefficient (Kd). Almost all quantitative structure-property relationship (QSPR) models that describe Kd apply only to narrow, relatively homogeneous groups of reactants. Herein, non-hybrid QSPR-based models were developed to predict PE-water (KPE-w), PE-seawater (KPE-sw), PVC-water (KPVC-w) and PP-seawater (KPP-sw) sorption coefficients at different temperatures, with eight machine learning algorithms. Moreover, novel hybrid intelligent models for predicting Kd more accurately were innovatively developed by applying GA, PSO and AdaBoost algorithms to optimize MLP and ELM models. The results indicated that all three optimization algorithms could improve the robustness and predictability of the standalone MLP and ELM models. In all models trained with KPE-w, KPE-sw, KPVC-w and KPP-sw data sets, GBDT-1 and XGBoost-1 models, MLP-GA-2 and MLP-PSO-2 models, MLR-3 and MLR-4 models performed better in terms of goodness of fit (Radj2: 0.907-0.999), robustness (QBOOT2: 0.900-0.937) and predictability (Rext2: 0.889-0.970), respectively. Analyzing the descriptors revealed that temperature, lipophilicity, ionization potential and molecular size were correlated closely with the adsorption capacity of microplastics to organic pollutants. The proposed QSPR models may assist in initial environmental exposure assessments without imposing heavy costs in the early experimental phase.
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Affiliation(s)
- Tengyi Zhu
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | - Cuicui Tao
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | - Haomiao Cheng
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China
| | - Haibing Cong
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, Jiangsu, China.
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9
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Zwickl CM, Graham J, Jolly R, Bassan A, Ahlberg E, Amberg A, Anger LT, Barton-Maclaren T, Beilke L, Bellion P, Brigo A, Cronin MT, Custer L, Devlin A, Burleigh-Flayers H, Fish T, Glover K, Glowienke S, Gromek K, Jones D, Karmaus A, Kemper R, Piparo EL, Madia F, Martin M, Masuda-Herrera M, McAtee B, Mestre J, Milchak L, Moudgal C, Mumtaz M, Muster W, Neilson L, Patlewicz G, Paulino A, Roncaglioni A, Ruiz P, Suarez D, Szabo DT, Valentin JP, Vardakou I, Woolley D, Myatt G. Principles and Procedures for Assessment of Acute Toxicity Incorporating In Silico Methods. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 24:100237. [PMID: 36818760 PMCID: PMC9934006 DOI: 10.1016/j.comtox.2022.100237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acute toxicity in silico models are being used to support an increasing number of application areas including (1) product research and development, (2) product approval and registration as well as (3) the transport, storage and handling of chemicals. The adoption of such models is being hindered, in part, because of a lack of guidance describing how to perform and document an in silico analysis. To address this issue, a framework for an acute toxicity hazard assessment is proposed. This framework combines results from different sources including in silico methods and in vitro or in vivo experiments. In silico methods that can assist the prediction of in vivo outcomes (i.e., LD50) are analyzed concluding that predictions obtained using in silico approaches are now well-suited for reliably supporting assessment of LD50-based acute toxicity for the purpose of GHS classification. A general overview is provided of the endpoints from in vitro studies commonly evaluated for predicting acute toxicity (e.g., cytotoxicity/cytolethality as well as assays targeting specific mechanisms). The increased understanding of pathways and key triggering mechanisms underlying toxicity and the increased availability of in vitro data allow for a shift away from assessments solely based on endpoints such as LD50, to mechanism-based endpoints that can be accurately assessed in vitro or by using in silico prediction models. This paper also highlights the importance of an expert review of all available information using weight-of-evidence considerations and illustrates, using a series of diverse practical use cases, how in silico approaches support the assessment of acute toxicity.
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Affiliation(s)
| | - Jessica Graham
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Robert Jolly
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Arianna Bassan
- Innovatune srl, Via Giulio Zanon 130/D, 35129 Padova, Italy
| | - Ernst Ahlberg
- Universal Prediction AB, Gothenburg, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Alexander Amberg
- Sanofi, R&D Preclinical Safety Frankfurt, Industriepark Hoechst, D-65926 Frankfurt am Main, Germany
| | | | - Tara Barton-Maclaren
- Healthy Environments and Consumer Safety Branch, Health Canada / Government of Canada
| | - Lisa Beilke
- Toxicology Solutions, Inc., 10531 4S Commons Dr. #594, San Diego, CA 92127, USA
| | - Phillip Bellion
- Boehringer Ingelheim Animal Health, Binger Str. 128, 55216 Ingelheim am Rhein, Germany
| | - Alessandro Brigo
- Roche Pharmaceutical Research & Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | | | | | - Amy Devlin
- FDA Center for Drug Evaluation and Research, Silver Spring, MD 20993, USA
| | | | - Trevor Fish
- Nelson Laboratories, Salt Lake City, Utah, USA
| | | | | | | | - David Jones
- MHRA, 10 South Colonnade, Canary Wharf, London E14 4PU
| | - Agnes Karmaus
- Integrated Laboratory Systems, LLC, Morrisville, NC, USA
| | | | - Elena Lo Piparo
- Chemical Food Safety Group, Nestlé Research, Lausanne, Switzerland
| | - Federica Madia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | | | - Jordi Mestre
- IMIM Institut Hospital Del Mar d’Investigacions Mèdiques and Universitat Pompeu Fabra, Doctor Aiguader 88, Parc de Recerca Biomèdica, 08003 Barcelona, Spain
- Chemotargets SL, Baldiri Reixac 4, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | | | | | - Moiz Mumtaz
- Office of the Associate Director for Science, Agency for Toxic Substances and Disease Registry, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Wolfgang Muster
- Roche Pharmaceutical Research & Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | | | - Grace Patlewicz
- Centre for Computational Toxicology and Exposure (CCTE), US Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | - Alessandra Roncaglioni
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Patricia Ruiz
- Centers for Disease Control and Prevention (CDC), Atlanta, GA 30341, USA
| | - Diana Suarez
- FSTox Consulting LTD, 2 Brooks Road Raunds Wellingborough NN9 6NS
| | | | - Jean-Pierre Valentin
- UCB-Biopharma SRL, Development Science, Avenue de l’industrie, Braine l’Alleud, Wallonia, Belgium
| | - Ioanna Vardakou
- British American Tobacco (Investments) Ltd., R&D Centre, Southampton, Hampshire SO15 8TL, UK
| | | | - Glenn Myatt
- Instem, 1393 Dublin Rd, Columbus, OH 43215, USA
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10
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Prediction of aquatic toxicity of energetic materials using genetic function approximation. FIREPHYSCHEM 2022. [DOI: 10.1016/j.fpc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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11
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Abstract
In this chapter, we give a brief overview of the regulatory requirements for acute systemic toxicity information in the European Union, and we review structure-based computational models that are available and potentially useful in the assessment of acute systemic toxicity. Emphasis is placed on quantitative structure-activity relationship (QSAR) models implemented by means of a range of software tools. The most recently published literature models for acute systemic toxicity are also discussed, and perspectives for future developments in this field are offered.
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Affiliation(s)
- Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Antonia Diukendjieva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Andrew P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
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12
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Dzobo K. The Role of Natural Products as Sources of Therapeutic Agents for Innovative Drug Discovery. COMPREHENSIVE PHARMACOLOGY 2022. [PMCID: PMC8016209 DOI: 10.1016/b978-0-12-820472-6.00041-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Emerging threats to human health require a concerted effort in search of both preventive and treatment strategies, placing natural products at the center of efforts to obtain new therapies and reduce disease spread and associated mortality. The therapeutic value of compounds found in plants has been known for ages, resulting in their utilization in homes and in clinics for the treatment of many ailments ranging from common headache to serious conditions such as wounds. Despite the advancement observed in the world, plant based medicines are still being used to treat many pathological conditions or are used as alternatives to modern medicines. In most cases, these natural products or plant-based medicines are used in an un-purified state as extracts. A lot of research is underway to identify and purify the active compounds responsible for the healing process. Some of the current drugs used in clinics have their origins as natural products or came from plant extracts. In addition, several synthetic analogues are natural product-based or plant-based. With the emergence of novel infectious agents such as the SARS-CoV-2 in addition to already burdensome diseases such as diabetes, cancer, tuberculosis and HIV/AIDS, there is need to come up with new drugs that can cure these conditions. Natural products offer an opportunity to discover new compounds that can be converted into drugs given their chemical structure diversity. Advances in analytical processes make drug discovery a multi-dimensional process involving computational designing and testing and eventual laboratory screening of potential drug candidates. Lead compounds will then be evaluated for safety, pharmacokinetics and efficacy. New technologies including Artificial Intelligence, better organ and tissue models such as organoids allow virtual screening, automation and high-throughput screening to be part of drug discovery. The use of bioinformatics and computation means that drug discovery can be a fast and efficient process and enable the use of natural products structures to obtain novel drugs. The removal of potential bottlenecks resulting in minimal false positive leads in drug development has enabled an efficient system of drug discovery. This review describes the biosynthesis and screening of natural products during drug discovery as well as methods used in studying natural products.
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13
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He S, Leanse LG, Feng Y. Artificial intelligence and machine learning assisted drug delivery for effective treatment of infectious diseases. Adv Drug Deliv Rev 2021; 178:113922. [PMID: 34461198 DOI: 10.1016/j.addr.2021.113922] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/14/2021] [Accepted: 08/09/2021] [Indexed: 12/23/2022]
Abstract
In the era of antimicrobial resistance, the prevalence of multidrug-resistant microorganisms that resist conventional antibiotic treatment has steadily increased. Thus, it is now unquestionable that infectious diseases are significant global burdens that urgently require innovative treatment strategies. Emerging studies have demonstrated that artificial intelligence (AI) can transform drug delivery to promote effective treatment of infectious diseases. In this review, we propose to evaluate the significance, essential principles, and popular tools of AI in drug delivery for infectious disease treatment. Specifically, we will focus on the achievements and key findings of current research, as well as the applications of AI on drug delivery throughout the whole antimicrobial treatment process, with an emphasis on drug development, treatment regimen optimization, drug delivery system and administration route design, and drug delivery outcome prediction. To that end, the challenges of AI in drug delivery for infectious disease treatments and their current solutions and future perspective will be presented and discussed.
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Affiliation(s)
- Sheng He
- Boston Children's Hospital, Harvard Medical School, Harvard University, Boston, MA, USA.
| | - Leon G Leanse
- Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Yanfang Feng
- Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA, USA.
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14
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Zarini D, Sangion A, Ferri E, Caruso E, Zucchi S, Orro A, Papa E. Are In Silico Approaches Applicable As a First Step for the Prediction of e-Liquid Toxicity in e-Cigarettes? Chem Res Toxicol 2020; 33:2381-2389. [PMID: 32786541 DOI: 10.1021/acs.chemrestox.0c00136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent studies have raised concerns about e-cigarette liquid inhalation toxicity by reporting the presence of chemicals with European Union CLP toxicity classification. In this scenario, the regulatory context is still developing and is not yet up to date with vaping current reality. Due to the paucity of toxicological studies, robust data regarding which components in e-liquids exhibit potential toxicities, are still inconsistent. In this study we applied computational methods for estimating the toxicity of poorly studied chemicals as a useful tool for predicting the acute toxicity of chemicals contained in e-liquids. The purpose of this study was 3-fold: (a) to provide a lower tier assessment of the potential health concerns associated with e-liquid ingredients, (b) to prioritize e-liquid ingredients by calculating the e-tox index, and (c) to estimate acute toxicity of e-liquid mixtures. QSAR models were generated using QSARINS software to fill the acute toxicity data gap of 264 e-liquid ingredients. As a second step, the potential acute toxicity of e-liquids mixtures was evaluated. Our preliminary data suggest that a computational approach may serve as a roadmap to enable regulatory bodies to better regulate e-liquid composition and to contribute to consumer health protection.
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Affiliation(s)
- Daniele Zarini
- Trusticert SRL, Piazza della scienza 2, 20126 Milano, Italy
| | - Alessandro Sangion
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C1A4, Canada.,QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, Varese 21100, Italy
| | - Emanuele Ferri
- Trusticert SRL, Piazza della scienza 2, 20126 Milano, Italy
| | - Enrico Caruso
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Via J.H. Dunant, 3, Varese, 21100, Italy
| | - Sara Zucchi
- Trusticert SRL, Piazza della scienza 2, 20126 Milano, Italy
| | - Alessandro Orro
- Institute for Biomedical Technologies National Research Council, Via Fratelli Cervi 19, 20133 Segrate, Milano, Italy
| | - Ester Papa
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, Varese 21100, Italy
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15
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Chavan S, Scherbak N, Engwall M, Repsilber D. Predicting Chemical-Induced Liver Toxicity Using High-Content Imaging Phenotypes and Chemical Descriptors: A Random Forest Approach. Chem Res Toxicol 2020; 33:2261-2275. [DOI: 10.1021/acs.chemrestox.9b00459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Swapnil Chavan
- School of Science and Technology, Örebro University, 70112 Örebro, Sweden
| | - Nikolai Scherbak
- School of Science and Technology, Örebro University, 70112 Örebro, Sweden
| | - Magnus Engwall
- School of Science and Technology, Örebro University, 70112 Örebro, Sweden
| | - Dirk Repsilber
- School of Medical Sciences, Örebro University, 70185 Örebro, Sweden
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16
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Watanabe M, Sasaki T, Takeshita JI, Kushida M, Shimizu Y, Oki H, Kitsunai Y, Nakayama H, Saruhashi H, Ogura R, Shizu R, Hosaka T, Yoshinari K. Application of cytochrome P450 reactivity on the characterization of chemical compounds and its association with repeated-dose toxicity. Toxicol Appl Pharmacol 2020; 388:114854. [PMID: 31836524 DOI: 10.1016/j.taap.2019.114854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 11/18/2022]
Abstract
Repeated-dose toxicity (RDT) studies are one of the critical studies to assess chemical safety. There have been some studies attempting to predict RDT endpoints based on chemical substructures, but it remains very difficult to establish such a method, and a more detailed characterization of chemical compounds seems necessary. Cytochrome P450s (P450s) comprise multiple forms with different substrate specificities and play important roles in both the detoxification and metabolic activation of xenobiotics. In this study, we investigated possible use of P450 reactivity of chemical compounds to classify the compounds. A total of 148 compounds with available rat RDT test data were used as test compounds and subjected to inhibition assays against 18 human and rat P450s. Among the tested compounds, 82 compounds inhibited at least one P450 form. Hierarchical clustering analyses using the P450 inhibitory profiles divided the 82 compounds into nine groups, some of which showed characteristic chemical and biological properties. Principal component analyses of the P450 inhibition data in combination with the calculated chemical descriptors demonstrated that P450 inhibition data were plotted differently than most chemical descriptors in the loading plots. Finally, association analyses between P450 inhibition and RDT endpoints showed that some endpoints related to the liver, kidney and hematology were significantly associated with the inhibition of some P450s. Our present results suggest that the P450 reactivity profiles can be used as novel descriptors for characterizing chemical compounds for the investigation of the toxicity mechanism and/or the establishment of a toxicity prediction model.
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Affiliation(s)
- Michiko Watanabe
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Takamitsu Sasaki
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Jun-Ichi Takeshita
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Madoka Kushida
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yuki Shimizu
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hitomi Oki
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yoko Kitsunai
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Haruka Nakayama
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hitomi Saruhashi
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Rui Ogura
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Ryota Shizu
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Takuomi Hosaka
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kouichi Yoshinari
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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17
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Ancuceanu R, Dinu M, Neaga I, Laszlo FG, Boda D. Development of QSAR machine learning-based models to forecast the effect of substances on malignant melanoma cells. Oncol Lett 2019; 17:4188-4196. [PMID: 31007759 PMCID: PMC6466999 DOI: 10.3892/ol.2019.10068] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022] Open
Abstract
SK-MEL-5 is a human melanoma cell line that has been used in various studies to explore new therapies against melanoma in different in vitro experiments. Based on this study we report on the development of quantitative structure-activity relationship (QSAR) models able to predict the cytotoxic effect of diverse chemical compounds on this cancer cell line. The dataset of cytotoxic and inactive compounds were downloaded from the PubChem database. It contains the data for all chemical compounds for which cytotoxicity results expressed by GI50 was recorded. In total 13 blocks of molecular descriptors were computed and used, after appropriate pre-processing in building QSAR models with four machine learning classifiers: Random forest (RF), gradient boosting, support vector machine and random k-nearest neighbors. Among the 186 models reported none had a positive predictive value (PPV) higher than 0.90 in both nested cross-validation and on an external dataset testing, but 7 models had a PPV higher than 0.85 in both evaluations, all seven using the RFs algorithm as a classifier, and topological descriptors, information indices, 2D-autocorrelation descriptors, P-VSA-like descriptors, and edge-adjacency descriptors as sets of features used for classification. The y-scrambling test was associated with considerably worse performance (confirming the non-random character of the models) and the applicability domain was assessed through three different methods.
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Affiliation(s)
- Robert Ancuceanu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, 'Carol Davila' University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Mihaela Dinu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, 'Carol Davila' University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Iana Neaga
- Department of Public Health and Management, Faculty of Medicine, 'Carol Davila' University of Medicine and Pharmacy, 050463 Bucharest, Romania
| | - Fekete Gyula Laszlo
- Department of Dermatology, University of Medicine and Pharmacy of Târgu Mureş, 540142 Târgu Mureş, Romania
| | - Daniel Boda
- Dermatology Research Laboratory, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania
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18
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Thomford NE, Senthebane DA, Rowe A, Munro D, Seele P, Maroyi A, Dzobo K. Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery. Int J Mol Sci 2018; 19:E1578. [PMID: 29799486 PMCID: PMC6032166 DOI: 10.3390/ijms19061578] [Citation(s) in RCA: 547] [Impact Index Per Article: 91.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 12/12/2022] Open
Abstract
The therapeutic properties of plants have been recognised since time immemorial. Many pathological conditions have been treated using plant-derived medicines. These medicines are used as concoctions or concentrated plant extracts without isolation of active compounds. Modern medicine however, requires the isolation and purification of one or two active compounds. There are however a lot of global health challenges with diseases such as cancer, degenerative diseases, HIV/AIDS and diabetes, of which modern medicine is struggling to provide cures. Many times the isolation of "active compound" has made the compound ineffective. Drug discovery is a multidimensional problem requiring several parameters of both natural and synthetic compounds such as safety, pharmacokinetics and efficacy to be evaluated during drug candidate selection. The advent of latest technologies that enhance drug design hypotheses such as Artificial Intelligence, the use of 'organ-on chip' and microfluidics technologies, means that automation has become part of drug discovery. This has resulted in increased speed in drug discovery and evaluation of the safety, pharmacokinetics and efficacy of candidate compounds whilst allowing novel ways of drug design and synthesis based on natural compounds. Recent advances in analytical and computational techniques have opened new avenues to process complex natural products and to use their structures to derive new and innovative drugs. Indeed, we are in the era of computational molecular design, as applied to natural products. Predictive computational softwares have contributed to the discovery of molecular targets of natural products and their derivatives. In future the use of quantum computing, computational softwares and databases in modelling molecular interactions and predicting features and parameters needed for drug development, such as pharmacokinetic and pharmacodynamics, will result in few false positive leads in drug development. This review discusses plant-based natural product drug discovery and how innovative technologies play a role in next-generation drug discovery.
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Affiliation(s)
- Nicholas Ekow Thomford
- Pharmacogenomics and Drug Metabolism Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
- School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana.
| | - Dimakatso Alice Senthebane
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), University of Cape Town Medical Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Arielle Rowe
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), University of Cape Town Medical Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Daniella Munro
- Pharmacogenomics and Drug Metabolism Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Palesa Seele
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
| | - Alfred Maroyi
- Department of Botany, University of Fort Hare, Private Bag, Alice X1314, South Africa.
| | - Kevin Dzobo
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, Wernher and Beit Building (South), University of Cape Town Medical Campus, Anzio Road, Observatory, Cape Town 7925, South Africa.
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa.
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19
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Lo YC, Rensi SE, Torng W, Altman RB. Machine learning in chemoinformatics and drug discovery. Drug Discov Today 2018; 23:1538-1546. [PMID: 29750902 DOI: 10.1016/j.drudis.2018.05.010] [Citation(s) in RCA: 431] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/29/2018] [Accepted: 05/02/2018] [Indexed: 01/03/2023]
Abstract
Chemoinformatics is an established discipline focusing on extracting, processing and extrapolating meaningful data from chemical structures. With the rapid explosion of chemical 'big' data from HTS and combinatorial synthesis, machine learning has become an indispensable tool for drug designers to mine chemical information from large compound databases to design drugs with important biological properties. To process the chemical data, we first reviewed multiple processing layers in the chemoinformatics pipeline followed by the introduction of commonly used machine learning models in drug discovery and QSAR analysis. Here, we present basic principles and recent case studies to demonstrate the utility of machine learning techniques in chemoinformatics analyses; and we discuss limitations and future directions to guide further development in this evolving field.
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Affiliation(s)
- Yu-Chen Lo
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Stefano E Rensi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Wen Torng
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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20
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Evaluating Molecular Properties Involved in Transport of Small Molecules in Stratum Corneum: A Quantitative Structure-Activity Relationship for Skin Permeability. Molecules 2018; 23:molecules23040911. [PMID: 29662033 PMCID: PMC6017021 DOI: 10.3390/molecules23040911] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 11/17/2022] Open
Abstract
The skin permeability (Kp) defines the rate of a chemical penetrating across the stratum corneum. This value is widely used to quantitatively describe the transport of molecules in the outermost layer of epidermal skin and indicate the significance of skin absorption. This study defined a Kp quantitative structure-activity relationship (QSAR) based on 106 chemical substances of Kp measured using human skin and interpreted the molecular interactions underlying transport behavior of small molecules in the stratum corneum. The Kp QSAR developed in this study identified four molecular descriptors that described the molecular cyclicity in the molecule reflecting local geometrical environments, topological distances between pairs of oxygen and chlorine atoms, lipophilicity, and similarity to antineoplastics in molecular properties. This Kp QSAR considered the octanol-water partition coefficient to be a direct influence on transdermal movement of molecules. Moreover, the Kp QSAR identified a sub-domain of molecular properties initially defined to describe the antineoplastic resemblance of a compound as a significant factor in affecting transdermal permeation of solutes. This finding suggests that the influence of molecular size on the chemical’s skin-permeating capability should be interpreted with other relevant physicochemical properties rather than being represented by molecular weight alone.
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21
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Bureau R. Nontest Methods to Predict Acute Toxicity: State of the Art for Applications of In Silico Methods. Methods Mol Biol 2018; 1800:519-534. [PMID: 29934909 DOI: 10.1007/978-1-4939-7899-1_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The assessment of acute toxicity of chemicals by in silico methods is actually done by two methodologies, read-across and QSAR. The two approaches are strongly based on the similarity between the chemical for which a risk assessment is required and the reference chemical(s) for which the experimental data are known. Here, we describe the two methodologies with some main publications as illustrations and the in silico data associated with acute toxicity endpoints (ECHA, REACH) accessible via eChemPortal.
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Affiliation(s)
- Ronan Bureau
- Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Normandie Univ, UNICAEN, Caen, France.
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Hamadache M, Benkortbi O, Hanini S, Amrane A. QSAR modeling in ecotoxicological risk assessment: application to the prediction of acute contact toxicity of pesticides on bees (Apis mellifera L.). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:896-907. [PMID: 29067614 DOI: 10.1007/s11356-017-0498-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
Despite their indisputable importance around the world, the pesticides can be dangerous for a range of species of ecological importance such as honeybees (Apis mellifera L.). Thus, a particular attention should be paid to their protection, not only for their ecological importance by contributing to the maintenance of wild plant diversity, but also for their economic value as honey producers and crop-pollinating agents. For all these reasons, the environmental protection requires the resort of risk assessment of pesticides. The goal of this work was therefore to develop a validated QSAR model to predict contact acute toxicity (LD50) of 111 pesticides to bees because the QSAR models devoted to this species are very scarce. The analysis of the statistical parameters of this model and those published in the literature shows that our model is more efficient. The QSAR model was assessed according to the OECD principles for the validation of QSAR models. The calculated values for the internal and external validation statistic parameters (Q 2 and [Formula: see text] are greater than 0.85. In addition to this validation, a mathematical equation derived from the ANN model was used to predict the LD50 of 20 other pesticides. A good correlation between predicted and experimental values was found (R 2 = 0.97 and RMSE = 0.14). As a result, this equation could be a means of predicting the toxicity of new pesticides.
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Affiliation(s)
- Mabrouk Hamadache
- Département du génie des procédés et environnement, Faculté de technologie, Université de Médéa, 26000, Médéa, Algeria.
| | - Othmane Benkortbi
- Département du génie des procédés et environnement, Faculté de technologie, Université de Médéa, 26000, Médéa, Algeria
| | - Salah Hanini
- Département du génie des procédés et environnement, Faculté de technologie, Université de Médéa, 26000, Médéa, Algeria
| | - Abdeltif Amrane
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, Université de Rennes 1, 11 allée de Beaulieu, 35708, Rennes Cedex 7, CS 50837, France
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23
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Cvetnic M, Juretic Perisic D, Kovacic M, Kusic H, Dermadi J, Horvat S, Bolanca T, Marin V, Karamanis P, Loncaric Bozic A. Prediction of biodegradability of aromatics in water using QSAR modeling. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 139:139-149. [PMID: 28129599 DOI: 10.1016/j.ecoenv.2017.01.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
The study was aimed at developing models for predicting the biodegradability of aromatic water pollutants. For that purpose, 36 single-benzene ring compounds, with different type, number and position of substituents, were used. The biodegradability was estimated according to the ratio of the biochemical (BOD5) and chemical (COD) oxygen demand values determined for parent compounds ((BOD5/COD)0), as well as for their reaction mixtures in half-life achieved by UV-C/H2O2 process ((BOD5/COD)t1/2). The models correlating biodegradability and molecular structure characteristics of studied pollutants were derived using quantitative structure-activity relationship (QSAR) principles and tools. Upon derivation of the models and calibration on the training and subsequent testing on the test set, 3- and 5-variable models were selected as the most predictive for (BOD5/COD)0 and (BOD5/COD)t1/2, respectively, according to the values of statistical parameters R2 and Q2. Hence, 3-variable model predicting (BOD5/COD)0 possessed R2=0.863 and Q2=0.799 for training set, and R2=0.710 for test set, while 5-variable model predicting (BOD5/COD)1/2 possessed R2=0.886 and Q2=0.788 for training set, and R2=0.564 for test set. The selected models are interpretable and transparent, reflecting key structural features that influence targeted biodegradability and can be correlated with the degradation mechanisms of studied compounds by UV-C/H2O2.
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Affiliation(s)
- Matija Cvetnic
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulicev trg 19, Zagreb 10000, Croatia
| | - Daria Juretic Perisic
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulicev trg 19, Zagreb 10000, Croatia
| | - Marin Kovacic
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulicev trg 19, Zagreb 10000, Croatia
| | - Hrvoje Kusic
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulicev trg 19, Zagreb 10000, Croatia.
| | - Jasna Dermadi
- Pliva Croatia Ltd, TAPI Croatia, TAPI R&D, Prilaz baruna Filipovica 25, Zagreb 10000, Croatia
| | - Sanja Horvat
- GKP Komunalac d.o.o., Mosna 15, Koprivnica 48000, Croatia
| | - Tomislav Bolanca
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulicev trg 19, Zagreb 10000, Croatia
| | - Vedrana Marin
- EnCor Biotechnology, 4949 SW 41st Blvd S40, Gainesville, FL 32608, USA
| | - Panaghiotis Karamanis
- Department of Chemistry, Institute of Analytical and Physical Chemistry for the Environment and Materials, 64053 Pau, France
| | - Ana Loncaric Bozic
- Faculty of Chemical Engineering and Technology, University of Zagreb, Marulicev trg 19, Zagreb 10000, Croatia.
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24
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Construction of Metabolism Prediction Models for CYP450 3A4, 2D6, and 2C9 Based on Microsomal Metabolic Reaction System. Int J Mol Sci 2016; 17:ijms17101686. [PMID: 27735849 PMCID: PMC5085718 DOI: 10.3390/ijms17101686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/22/2016] [Accepted: 09/30/2016] [Indexed: 02/04/2023] Open
Abstract
During the past decades, there have been continuous attempts in the prediction of metabolism mediated by cytochrome P450s (CYP450s) 3A4, 2D6, and 2C9. However, it has indeed remained a huge challenge to accurately predict the metabolism of xenobiotics mediated by these enzymes. To address this issue, microsomal metabolic reaction system (MMRS)—a novel concept, which integrates information about site of metabolism (SOM) and enzyme—was introduced. By incorporating the use of multiple feature selection (FS) techniques (ChiSquared (CHI), InfoGain (IG), GainRatio (GR), Relief) and hybrid classification procedures (Kstar, Bayes (BN), K-nearest neighbours (IBK), C4.5 decision tree (J48), RandomForest (RF), Support vector machines (SVM), AdaBoostM1, Bagging), metabolism prediction models were established based on metabolism data released by Sheridan et al. Four major biotransformations, including aliphatic C-hydroxylation, aromatic C-hydroxylation, N-dealkylation and O-dealkylation, were involved. For validation, the overall accuracies of all four biotransformations exceeded 0.95. For receiver operating characteristic (ROC) analysis, each of these models gave a significant area under curve (AUC) value >0.98. In addition, an external test was performed based on dataset published previously. As a result, 87.7% of the potential SOMs were correctly identified by our four models. In summary, four MMRS-based models were established, which can be used to predict the metabolism mediated by CYP3A4, 2D6, and 2C9 with high accuracy.
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25
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He S, Li M, Ye X, Wang H, Yu W, He W, Wang Y, Qiao Y. Site of metabolism prediction for oxidation reactions mediated by oxidoreductases based on chemical bond. Bioinformatics 2016; 33:363-372. [DOI: 10.1093/bioinformatics/btw617] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/22/2016] [Indexed: 12/31/2022] Open
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Burton J, Worth AP, Tsakovska I, Diukendjieva A. In Silico Models for Acute Systemic Toxicity. Methods Mol Biol 2016; 1425:177-200. [PMID: 27311468 DOI: 10.1007/978-1-4939-3609-0_10] [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: 05/12/2023]
Abstract
In this chapter, we give an overview of the regulatory requirements for acute systemic toxicity information in the European Union, and we review the availability of structure-based computational models that are available and potentially useful in the assessment of acute systemic toxicity. The most recently published literature models for acute systemic toxicity are also discussed, and perspectives for future developments in this field are offered.
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Affiliation(s)
- Julien Burton
- Systems Toxicology Unit and EURL ECVAM, Institute for Health and Consumer Protection, Joint Research Centre, European Commission, Ispra, Varese, Italy
| | - Andrew P Worth
- Systems Toxicology Unit and EURL ECVAM, Institute for Health and Consumer Protection, Joint Research Centre, European Commission, Ispra, Varese, Italy.
| | - Ivanka Tsakovska
- Department of QSAR & Molecular Modeling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Antonia Diukendjieva
- Department of QSAR & Molecular Modeling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
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27
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Chavan S, Abdelaziz A, Wiklander JG, Nicholls IA. A k-nearest neighbor classification of hERG K(+) channel blockers. J Comput Aided Mol Des 2016; 30:229-36. [PMID: 26860111 PMCID: PMC4802000 DOI: 10.1007/s10822-016-9898-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/28/2016] [Indexed: 01/08/2023]
Abstract
A series of 172 molecular structures that block the hERG K+ channel were used to develop a classification model where, initially, eight types of PaDEL fingerprints were used for k-nearest neighbor model development. A consensus model constructed using Extended-CDK, PubChem and Substructure count fingerprint-based models was found to be a robust predictor of hERG activity. This consensus model demonstrated sensitivity and specificity values of 0.78 and 0.61 for the internal dataset compounds and 0.63 and 0.54 for the external (PubChem) dataset compounds, respectively. This model has identified the highest number of true positives (i.e. 140) from the PubChem dataset so far, as compared to other published models, and can potentially serve as a basis for the prediction of hERG active compounds. Validating this model against FDA-withdrawn substances indicated that it may even be useful for differentiating between mechanisms underlying QT prolongation.
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Affiliation(s)
- Swapnil Chavan
- Bioorganic and Biophysical Chemistry Laboratory, Department of Chemistry and Biomedical Sciences, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, 391 82, Kalmar, Sweden.
| | - Ahmed Abdelaziz
- eADMET GmbH, Lichtenbergstraße 8, 85748, Garching, Munich, Germany
| | - Jesper G Wiklander
- Bioorganic and Biophysical Chemistry Laboratory, Department of Chemistry and Biomedical Sciences, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, 391 82, Kalmar, Sweden
| | - Ian A Nicholls
- Bioorganic and Biophysical Chemistry Laboratory, Department of Chemistry and Biomedical Sciences, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, 391 82, Kalmar, Sweden. .,Department of Chemistry-BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden.
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28
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Warr WA. Many InChIs and quite some feat. J Comput Aided Mol Des 2015; 29:681-94. [PMID: 26081259 DOI: 10.1007/s10822-015-9854-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/10/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Wendy A Warr
- Wendy Warr & Associates, Holmes Chapel, Crewe, Cheshire, CW4 7HZ, UK,
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29
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Chavan S, Friedman R, Nicholls IA. Acute Toxicity-Supported Chronic Toxicity Prediction: A k-Nearest Neighbor Coupled Read-Across Strategy. Int J Mol Sci 2015; 16:11659-77. [PMID: 26006240 PMCID: PMC4463722 DOI: 10.3390/ijms160511659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/21/2015] [Accepted: 05/08/2015] [Indexed: 11/23/2022] Open
Abstract
A k-nearest neighbor (k-NN) classification model was constructed for 118 RDT NEDO (Repeated Dose Toxicity New Energy and industrial technology Development Organization; currently known as the Hazard Evaluation Support System (HESS)) database chemicals, employing two acute toxicity (LD50)-based classes as a response and using a series of eight PaDEL software-derived fingerprints as predictor variables. A model developed using Estate type fingerprints correctly predicted the LD50 classes for 70 of 94 training set chemicals and 19 of 24 test set chemicals. An individual category was formed for each of the chemicals by extracting its corresponding k-analogs that were identified by k-NN classification. These categories were used to perform the read-across study for prediction of the chronic toxicity, i.e., Lowest Observed Effect Levels (LOEL). We have successfully predicted the LOELs of 54 of 70 training set chemicals (77%) and 14 of 19 test set chemicals (74%) to within an order of magnitude from their experimental LOEL values. Given the success thus far, we conclude that if the k-NN model predicts LD50 classes correctly for a certain chemical, then the k-analogs of such a chemical can be successfully used for data gap filling for the LOEL. This model should support the in silico prediction of repeated dose toxicity.
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Affiliation(s)
- Swapnil Chavan
- Bioorganic and Biophysical Chemistry Laboratory, Department of Chemistry and Biomedical Sciences and Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Ran Friedman
- Computational Chemistry and Biochemistry Group, Department of Chemistry and Biomedical Sciences and Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Ian A Nicholls
- Bioorganic and Biophysical Chemistry Laboratory, Department of Chemistry and Biomedical Sciences and Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-391 82 Kalmar, Sweden.
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden.
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