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Kotli M, Piir G, Maran U. Pesticide effect on earthworm lethality via interpretable machine learning. J Hazard Mater 2024; 461:132577. [PMID: 37793249 DOI: 10.1016/j.jhazmat.2023.132577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 10/06/2023]
Abstract
Earthworms are among the most important animals (invertebrates) for soil health. Many chemical substances released into nature for agricultural development, such as pesticides, may have unwanted effects on those organisms. However, it is essential to understand the extent of the impact of chemicals on soil health first and then make the proper decisions for regulatory or commercial purposes. We hypothesize that there is an expressible quantitative structure-activity relationship (QSAR) between the structure of pesticide compounds and the acute toxicity effect of earthworm species Eisenia fetida. The description of this relationship allows for a better assessment of the impact of chemicals on the said earthworm. To describe this relationship, a dataset of chemicals was collected from open-access sources to develop a mathematical model. A novel approach, combining genetic algorithm and Bayesian optimization, was used to select structural features into the model and to optimize model parameters. The final QSAR classification model was created with the Random Forest algorithm and exhibited good prediction Accuracy of 0.78 on training set and 0.80 on test set. The model representation follows FAIR principles and is available on QsarDB.org.
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Affiliation(s)
- Mihkel Kotli
- University of Tartu, Institute of Chemistry, Tartu, Estonia
| | - Geven Piir
- University of Tartu, Institute of Chemistry, Tartu, Estonia
| | - Uko Maran
- University of Tartu, Institute of Chemistry, Tartu, Estonia.
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2
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Piir G, Sild S, Maran U. Interpretable machine learning for the identification of estrogen receptor agonists, antagonists, and binders. Chemosphere 2024; 347:140671. [PMID: 37951393 DOI: 10.1016/j.chemosphere.2023.140671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
An abnormal hormonal activity or exposure to endocrine-disrupting chemicals (EDCs) can cause endocrine system malfunction. Among the many interactions EDCs can affect is the disruption of estrogen signalling, which can lead to adverse health effects such as cancer, osteoporosis, neurodegenerative diseases, cardiovascular disease, insulin resistance, and obesity. Knowing which chemical can act as an EDC is a significant advantage and a practical necessity. New Approach Methodologies (NAM) computational models offer a quick and cost-effective solution for preliminary hazard assessment of chemicals without animal testing. Therefore, a machine learning approach was used to investigate the relationships between estrogen receptor (ER) activity and chemical structure to identify chemicals that can interact with ER. For this purpose, the consolidated in vitro assay data from ToxCast/Tox21 projects was used for developing Random Forest classification models for ER binding, agonists, and antagonists. The overall classification prediction accuracy reaches up to 82%, depending on whether the model predicted agonists, antagonists, or compounds that bind to the active site. Given the imbalance in endocrine disruption data, the derived models are good candidates for deprioritising chemicals and reducing animal testing. The interpretation of theoretical molecular descriptors of the models was consistent with the molecular interactions known in the ligand binding pocket. The estimated class probabilities enabled the analysis of the applicability domain of the developed models and the assessment of the predictions' reliability, followed by the guidelines for interpreting prediction results. The models are openly accessible and useable at QsarDB.org (http://dx.doi.org/10.15152/QDB.259) according to the FAIR (Findable, Accessible, Interoperable, Reusable) principles.
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Affiliation(s)
- Geven Piir
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu, 50411, Estonia
| | - Sulev Sild
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu, 50411, Estonia
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu, 50411, Estonia.
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3
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Martens M, Stierum R, Schymanski EL, Evelo CT, Aalizadeh R, Aladjov H, Arturi K, Audouze K, Babica P, Berka K, Bessems J, Blaha L, Bolton EE, Cases M, Damalas DΕ, Dave K, Dilger M, Exner T, Geerke DP, Grafström R, Gray A, Hancock JM, Hollert H, Jeliazkova N, Jennen D, Jourdan F, Kahlem P, Klanova J, Kleinjans J, Kondic T, Kone B, Lynch I, Maran U, Martinez Cuesta S, Ménager H, Neumann S, Nymark P, Oberacher H, Ramirez N, Remy S, Rocca-Serra P, Salek RM, Sallach B, Sansone SA, Sanz F, Sarimveis H, Sarntivijai S, Schulze T, Slobodnik J, Spjuth O, Tedds J, Thomaidis N, Weber RJ, van Westen GJ, Wheelock CE, Williams AJ, Witters H, Zdrazil B, Županič A, Willighagen EL. ELIXIR and Toxicology: a community in development. F1000Res 2023; 10:ELIXIR-1129. [PMID: 37842337 PMCID: PMC10568213 DOI: 10.12688/f1000research.74502.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.
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Affiliation(s)
- Marvin Martens
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Rob Stierum
- Risk Analysis for Products In Development (RAPID), Netherlands Organisation for applied scientific research TNO, Utrecht, 3584 CB, The Netherlands
| | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 EN, The Netherlands
| | - Reza Aalizadeh
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Hristo Aladjov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Kasia Arturi
- Department Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, 8600, Switzerland
| | | | - Pavel Babica
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Palacky University Olomouc, Olomouc, 77146, Czech Republic
| | | | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Evan E. Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Dimitrios Ε. Damalas
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Kirtan Dave
- School of Science, GSFC University, Gujarat, 391750, India
| | - Marco Dilger
- Forschungs- und Beratungsinstitut Gefahrstoffe (FoBiG) GmbH, Freiburg im Breisgau, 79106, Germany
| | | | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology, Vrije Universiteit, Amsterdam, 1081 HZ, The Netherlands
| | - Roland Grafström
- Department of Toxicology, Misvik Biology, Turku, 20520, Finland
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden
| | - Alasdair Gray
- Department of Computer Science, Heriot-Watt University, Edinburgh, UK
| | | | - Henner Hollert
- Department Evolutionary Ecology & Environmental Toxicology (E3T), Goethe-University, Frankfurt, D-60438, Germany
| | | | - Danyel Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Fabien Jourdan
- MetaboHUB, French metabolomics infrastructure in Metabolomics and Fluxomics, Toulouse, France
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | - Pascal Kahlem
- Scientific Network Management SL, Barcelona, 08015, Spain
| | - Jana Klanova
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Todor Kondic
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Boï Kone
- Faculty of Pharmacy, Malaria Research and Training Center, Bamako, BP:1805, Mali
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, 50411, Estonia
| | | | - Hervé Ménager
- Institut Français de Bioinformatique, Evry, F-91000, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, F-75015, France
| | - Steffen Neumann
- Research group Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, A-6020, Austria
| | - Noelia Ramirez
- Institut d'Investigacio Sanitaria Pere Virgili-Universitat Rovira i Virgili, Tarragona, 43007, Spain
| | | | - Philippe Rocca-Serra
- Data Readiness Group, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Reza M. Salek
- International Agency for Research on Cancer, World Health Organisation, Lyon, 69372, France
| | - Brett Sallach
- Department of Environment and Geography, University of York, UK, York, YO10 5NG, UK
| | | | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, 08003, Spain
| | | | | | - Tobias Schulze
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, 04318, Germany
| | | | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, SE-75124, Sweden
| | - Jonathan Tedds
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Ralf J.M. Weber
- School of Biosciences, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Gerard J.P. van Westen
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research, Leiden, 2333 CC, The Netherlands
| | - Craig E. Wheelock
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm SE-141-86, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Antony J. Williams
- Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | | | - Barbara Zdrazil
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | - Anže Županič
- Department Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
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Oja M, Sild S, Piir G, Maran U. Intrinsic Aqueous Solubility: Mechanistically Transparent Data-Driven Modeling of Drug Substances. Pharmaceutics 2022; 14:pharmaceutics14102248. [PMID: 36297685 PMCID: PMC9611068 DOI: 10.3390/pharmaceutics14102248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022] Open
Abstract
Intrinsic aqueous solubility is a foundational property for understanding the chemical, technological, pharmaceutical, and environmental behavior of drug substances. Despite years of solubility research, molecular structure-based prediction of the intrinsic aqueous solubility of drug substances is still under active investigation. This paper describes the authors’ systematic data-driven modelling in which two fit-for-purpose training data sets for intrinsic aqueous solubility were collected and curated, and three quantitative structure–property relationships were derived to make predictions for the most recent solubility challenge. All three models perform well individually, while being mechanistically transparent and easy to understand. Molecular descriptors involved in the models are related to the following key steps in the solubility process: dissociation of the molecule from the crystal, formation of a cavity in the solvent, and insertion of the molecule into the solvent. A consensus modeling approach with these models remarkably improved prediction capability and reduced the number of strong outliers by more than two times. The performance and outliers of the second solubility challenge predictions were analyzed retrospectively. All developed models have been published in the QsarDB.org repository according to FAIR principles and can be used without restrictions for exploring, downloading, and making predictions.
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Affiliation(s)
| | | | | | - Uko Maran
- Correspondence: ; Tel.: +372-7-375-254; Fax: +372-7-375-264
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5
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Toots KM, Sild S, Leis J, Acree WE, Maran U. Machine Learning Quantitative Structure–Property Relationships as a Function of Ionic Liquid Cations for the Gas-Ionic Liquid Partition Coefficient of Hydrocarbons. Int J Mol Sci 2022; 23:ijms23147534. [PMID: 35886881 PMCID: PMC9323540 DOI: 10.3390/ijms23147534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 02/01/2023] Open
Abstract
Ionic liquids (ILs) are known for their unique characteristics as solvents and electrolytes. Therefore, new ILs are being developed and adapted as innovative chemical environments for different applications in which their properties need to be understood on a molecular level. Computational data-driven methods provide means for understanding of properties at molecular level, and quantitative structure–property relationships (QSPRs) provide the framework for this. This framework is commonly used to study the properties of molecules in ILs as an environment. The opposite situation where the property is considered as a function of the ionic liquid does not exist. The aim of the present study was to supplement this perspective with new knowledge and to develop QSPRs that would allow the understanding of molecular interactions in ionic liquids based on the structure of the cationic moiety. A wide range of applications in electrochemistry, separation and extraction chemistry depends on the partitioning of solutes between the ionic liquid and the surrounding environment that is characterized by the gas-ionic liquid partition coefficient. To model this property as a function of the structure of a cationic counterpart, a series of ionic liquids was selected with a common bis-(trifluoromethylsulfonyl)-imide anion, [Tf2N]−, for benzene, hexane and cyclohexane. MLR, SVR and GPR machine learning approaches were used to derive data-driven models and their performance was compared. The cross-validation coefficients of determination in the range 0.71–0.93 along with other performance statistics indicated a strong accuracy of models for all data series and machine learning methods. The analysis and interpretation of descriptors revealed that generally higher lipophilicity and dispersion interaction capability, and lower polarity in the cations induces a higher partition coefficient for benzene, hexane, cyclohexane and hydrocarbons in general. The applicability domain analysis of models concluded that there were no highly influential outliers and the models are applicable to a wide selection of cation families with variable size, polarity and aliphatic or aromatic nature.
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Affiliation(s)
- Karl Marti Toots
- Department of Chemistry, University of Tartu, 14a Ravila Street, 50411 Tartu, Estonia; (K.M.T.); (S.S.); (J.L.)
| | - Sulev Sild
- Department of Chemistry, University of Tartu, 14a Ravila Street, 50411 Tartu, Estonia; (K.M.T.); (S.S.); (J.L.)
| | - Jaan Leis
- Department of Chemistry, University of Tartu, 14a Ravila Street, 50411 Tartu, Estonia; (K.M.T.); (S.S.); (J.L.)
| | - William E. Acree
- Department of Chemistry, University of North Texas, 1155 Union Circle Drive #305070, Denton, TX 76203, USA;
| | - Uko Maran
- Department of Chemistry, University of Tartu, 14a Ravila Street, 50411 Tartu, Estonia; (K.M.T.); (S.S.); (J.L.)
- Correspondence:
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6
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Hunt KE, García-Sosa AT, Shalima T, Maran U, Vilu R, Kanger T. Synthesis of 6'-galactosyllactose, a deviant human milk oligosaccharide, with the aid of Candida antarctica lipase-B. Org Biomol Chem 2022; 20:4724-4735. [PMID: 35612321 DOI: 10.1039/d2ob00550f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Research on human milk oligosaccharides (HMOs) has increased over the past decade showing great interest in their beneficial effects. Here we describe a method for the selective deacetylation using immobilised Candida antarctica lipase-B, Novozyme N435 (N435), of pyranose saccharides in organic media with the aim of simplifying and improving the pathways for the synthesis of HMOs. By first studying in depth the deacetylation reaction of peracetylated D-glucose two reaction conditions were found, which were used on different HMO building blocks, peracetylated saccharides and thioglycosides. D-Glucose based saccharides showed selectivity towards the fourth and the sixth position deacetylation. While α-anomer of peracetylated D-galactose remained unreactive and β-anomer favoured the first position deacetylation. Peracetylated L-fucose, on the other hand, had no selectivity as the main product was fully unprotected L-fucose. Taking the peracetylated D-glucose deacetylation reaction product and selectively protecting the primary hydroxyl group in the sixth position left only the fourth position open for the glycosylation. Meanwhile, the deacetylation product of D-galactose thioglycoside, with the sixth position deacetylated, had both acceptor and donor capabilities. Using the two aforementioned products derived from the N435 deacetylation reactions a deviant HMO, 6'-galactosyllactose (6'-GL) was synthesised.
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Affiliation(s)
- Kaarel Erik Hunt
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia. .,Centre of Food and Fermentation Technologies, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Alfonso T García-Sosa
- Department of Chemistry, University of Tartu, Ravila Street 14a, 50411 Tartu, Estonia
| | - Tatsiana Shalima
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Uko Maran
- Department of Chemistry, University of Tartu, Ravila Street 14a, 50411 Tartu, Estonia
| | - Raivo Vilu
- Centre of Food and Fermentation Technologies, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Tõnis Kanger
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
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Toots KM, Sild S, Leis J, Acree Jr. WE, Maran U. The quantitative structure-property relationships for the gas-ionic liquid partition coefficient of a large variety of organic compounds in three ionic liquids. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Rice M, Wong B, Oja M, Samuels K, Williams AK, Fong J, Sapse AM, Maran U, Korobkova EA. A role of flavonoids in cytochrome c-cardiolipin interactions. Bioorg Med Chem 2021; 33:116043. [PMID: 33530021 DOI: 10.1016/j.bmc.2021.116043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 11/26/2022]
Abstract
The processes preceding the detachment of cytochrome c (cyt c) from the inner mitochondrial membrane in intrinsic apoptosis involve peroxidation of cardiolipin (CL) catalyzed by cyt c-CL complex. In the present work, we studied the effect of 17 dietary flavonoids on the peroxidase activity of cyt c bound to liposomes. Specifically, we explored the relationship between peroxidase activity and flavonoids' (1) potential to modulate cyt c unfolding, (2) effect on the oxidation state of heme iron, (3) membrane permeability, (4) membrane binding energy, and (5) structure. The measurements revealed that flavones, flavonols, and flavanols were the strongest, while isoflavones were the weakest inhibitors of the oxidation. Flavonoids' peroxidase inhibition activity correlated positively with their potential to suppress Trp-59 fluorescence in cyt c as well as the number of OH groups. Hydrophilic flavonoids, such as catechin, having the lowest membrane permeability and the strongest binding with phosphocholine (PC) based on the quantum chemical calculations exhibited the strongest inhibition of Amplex Red (AR) peroxidation, suggesting a membrane-protective function of flavonoids at the surface. The results of the present research specify basic principles for the design of molecules that will control the catalytic oxidation of lipids in mitochondrial membranes. These principles take into account the number of hydroxyl groups and hydrophilicity of flavonoids.
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Affiliation(s)
- Malaysha Rice
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Bokey Wong
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Mare Oja
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia
| | - Kelley Samuels
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Alicia K Williams
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Jenny Fong
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA
| | - Anne-Marie Sapse
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA; The Graduate Center at the City University of New York, 365 5th Ave, New York, NY 10016, USA
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia
| | - Ekaterina A Korobkova
- Department of Sciences, John Jay College of Criminal Justice, City University of New York, 524 W 59th St., NY 10019, USA.
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9
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Piir G, Sild S, Maran U. Binary and multi-class classification for androgen receptor agonists, antagonists and binders. Chemosphere 2021; 262:128313. [PMID: 33182081 DOI: 10.1016/j.chemosphere.2020.128313] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/24/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
Androgens and androgen receptor regulate a variety of biological effects in the human body. The impaired functioning of androgen receptor may have different adverse health effects from cancer to infertility. Therefore, it is important to determine whether new chemicals have any binding activity and act as androgen agonists or antagonists before commercial use. Due to the large number of chemicals that require experimental testing, the computational methods are a viable alternative. Therefore, the aim of the present study was to develop predictive QSAR models for classifying compounds according to their activity at the androgen receptor. A large data set of chemicals from the CoMPARA project was used for this purpose and random forest classification models have been developed for androgen binding, agonistic, and antagonistic activity. In addition, a unique effort has been made for multi-class approach that discriminates between inactive compounds, agonists and antagonists simultaneously. For the evaluation set, the classification models predicted agonists with 80% of accuracy and for the antagonists' and binders' the respective metrics were 72% and 78%. Combining agonists, antagonists and inactive compounds into a multi-class approach added complexity to the modelling task and resulted to 64% prediction accuracy for the evaluation set. Considering the size of the training data sets and their imbalance, the achieved evaluation accuracy is very good. The final classification models are available for exploring and predicting at QsarDB repository (https://doi.org/10.15152/QDB.236).
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Affiliation(s)
- Geven Piir
- University of Tartu, Institute of Chemistry, Ravila 14A, Tartu, 50411, Estonia
| | - Sulev Sild
- University of Tartu, Institute of Chemistry, Ravila 14A, Tartu, 50411, Estonia
| | - Uko Maran
- University of Tartu, Institute of Chemistry, Ravila 14A, Tartu, 50411, Estonia.
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10
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Zukić S, Maran U. Modelling of antiproliferative activity measured in HeLa cervical cancer cells in a series of xanthene derivatives. SAR QSAR Environ Res 2020; 31:905-921. [PMID: 33236957 DOI: 10.1080/1062936x.2020.1839131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Cancer remains one of the leading causes of death in humans, and new drug substances are therefore being developed. Thus, the anti-cancer activity of xanthene derivatives has become an important topic in the development of new and potent anti-cancer drug substances. Previously published novel series of xanthen-3-one and xanthen-1,8-dione derivatives have been synthesized in one of our laboratories and showed anti-proliferative activity in HeLa cancer cell lines. This series serves as a good basis to develop quantitative structure-activity relationship (QSAR), to study the relations between anti-proliferative activity and chemical structures. A QSAR model has been derived that relies only on two-dimensional molecular descriptors, providing mechanistic insight into the anti-proliferative activity of xanthene derivatives. The model is validated internally and externally and additionally with the set of inactive compounds of the original data, confirming model applicability for the design and discovery of novel xanthene derivatives. The QSAR model is available at the QsarDB repository (http://dx.doi.10.15152/QDB.237).
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Affiliation(s)
- S Zukić
- Department of Pharmaceutical Chemistry, University of Sarajevo , Sarajevo, Bosnia and Herzegovina
| | - U Maran
- Department of Chemistry, University of Tartu , Tartu, Estonia
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11
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Mansouri K, Kleinstreuer N, Abdelaziz AM, Alberga D, Alves VM, Andersson PL, Andrade CH, Bai F, Balabin I, Ballabio D, Benfenati E, Bhhatarai B, Boyer S, Chen J, Consonni V, Farag S, Fourches D, García-Sosa AT, Gramatica P, Grisoni F, Grulke CM, Hong H, Horvath D, Hu X, Huang R, Jeliazkova N, Li J, Li X, Liu H, Manganelli S, Mangiatordi GF, Maran U, Marcou G, Martin T, Muratov E, Nguyen DT, Nicolotti O, Nikolov NG, Norinder U, Papa E, Petitjean M, Piir G, Pogodin P, Poroikov V, Qiao X, Richard AM, Roncaglioni A, Ruiz P, Rupakheti C, Sakkiah S, Sangion A, Schramm KW, Selvaraj C, Shah I, Sild S, Sun L, Taboureau O, Tang Y, Tetko IV, Todeschini R, Tong W, Trisciuzzi D, Tropsha A, Van Den Driessche G, Varnek A, Wang Z, Wedebye EB, Williams AJ, Xie H, Zakharov AV, Zheng Z, Judson RS. CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. Environ Health Perspect 2020; 128:27002. [PMID: 32074470 DOI: 10.23645/epacomptox.5176876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
BACKGROUND Endocrine disrupting chemicals (EDCs) are xenobiotics that mimic the interaction of natural hormones and alter synthesis, transport, or metabolic pathways. The prospect of EDCs causing adverse health effects in humans and wildlife has led to the development of scientific and regulatory approaches for evaluating bioactivity. This need is being addressed using high-throughput screening (HTS) in vitro approaches and computational modeling. OBJECTIVES In support of the Endocrine Disruptor Screening Program, the U.S. Environmental Protection Agency (EPA) led two worldwide consortiums to virtually screen chemicals for their potential estrogenic and androgenic activities. Here, we describe the Collaborative Modeling Project for Androgen Receptor Activity (CoMPARA) efforts, which follows the steps of the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP). METHODS The CoMPARA list of screened chemicals built on CERAPP's list of 32,464 chemicals to include additional chemicals of interest, as well as simulated ToxCast™ metabolites, totaling 55,450 chemical structures. Computational toxicology scientists from 25 international groups contributed 91 predictive models for binding, agonist, and antagonist activity predictions. Models were underpinned by a common training set of 1,746 chemicals compiled from a combined data set of 11 ToxCast™/Tox21 HTS in vitro assays. RESULTS The resulting models were evaluated using curated literature data extracted from different sources. To overcome the limitations of single-model approaches, CoMPARA predictions were combined into consensus models that provided averaged predictive accuracy of approximately 80% for the evaluation set. DISCUSSION The strengths and limitations of the consensus predictions were discussed with example chemicals; then, the models were implemented into the free and open-source OPERA application to enable screening of new chemicals with a defined applicability domain and accuracy assessment. This implementation was used to screen the entire EPA DSSTox database of ∼875,000 chemicals, and their predicted AR activities have been made available on the EPA CompTox Chemicals dashboard and National Toxicology Program's Integrated Chemical Environment. https://doi.org/10.1289/EHP5580.
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Affiliation(s)
- Kamel Mansouri
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
- ScitoVation LLC, Research Triangle Park, North Carolina, USA
- Integrated Laboratory Systems, Inc., Morrisville, North Carolina, USA
| | - Nicole Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Ahmed M Abdelaziz
- Technische Universität München, Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt, Department für Biowissenschaftliche Grundlagen, Weihenstephaner Steig 23, 85350 Freising, Germany
| | - Domenico Alberga
- Department of Pharmacy-Drug Sciences, University of Bari, Bari, Italy
| | - Vinicius M Alves
- Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
- Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Carolina H Andrade
- Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Fang Bai
- School of Pharmacy, Lanzhou University, China
| | - Ilya Balabin
- Information Systems & Global Solutions (IS&GS), Lockheed Martin, USA
| | - Davide Ballabio
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Emilio Benfenati
- Istituto di Ricerche Farmacologiche "Mario Negri", IRCCS, Milan, Italy
| | - Barun Bhhatarai
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Scott Boyer
- Swedish Toxicology Sciences Research Center, Karolinska Institutet, Södertälje, Sweden
| | - Jingwen Chen
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Viviana Consonni
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Sherif Farag
- Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Denis Fourches
- Department of Chemistry, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Paola Gramatica
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Francesca Grisoni
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Chris M Grulke
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Dragos Horvath
- Laboratoire de Chémoinformatique-UMR7140, University of Strasbourg/CNRS, Strasbourg, France
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Jiazhong Li
- School of Pharmacy, Lanzhou University, China
| | - Xuehua Li
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | | | - Serena Manganelli
- Istituto di Ricerche Farmacologiche "Mario Negri", IRCCS, Milan, Italy
| | | | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Gilles Marcou
- Laboratoire de Chémoinformatique-UMR7140, University of Strasbourg/CNRS, Strasbourg, France
| | - Todd Martin
- National Risk Management Research Laboratory, U.S. EPA, Cincinnati, Ohio, USA
| | - Eugene Muratov
- Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Orazio Nicolotti
- Department of Pharmacy-Drug Sciences, University of Bari, Bari, Italy
| | - Nikolai G Nikolov
- Division of Risk Assessment and Nutrition, National Food Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Ulf Norinder
- Swedish Toxicology Sciences Research Center, Karolinska Institutet, Södertälje, Sweden
| | - Ester Papa
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Michel Petitjean
- Computational Modeling of Protein-Ligand Interactions (CMPLI)-INSERM UMR 8251, INSERM ERL U1133, Functional and Adaptative Biology (BFA), Universite de Paris, Paris, France
| | - Geven Piir
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Pavel Pogodin
- Institute of Biomedical Chemistry IBMC, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry IBMC, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia
| | - Xianliang Qiao
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Ann M Richard
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | | | - Patricia Ruiz
- Computational Toxicology and Methods Development Laboratory, Division of Toxicology and Human Health Sciences, Agency for Toxic Substances and Disease Registry, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Chetan Rupakheti
- National Risk Management Research Laboratory, U.S. EPA, Cincinnati, Ohio, USA
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, Illinois, USA
| | - Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Alessandro Sangion
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Karl-Werner Schramm
- Technische Universität München, Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt, Department für Biowissenschaftliche Grundlagen, Weihenstephaner Steig 23, 85350 Freising, Germany
| | - Chandrabose Selvaraj
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | - Sulev Sild
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Lixia Sun
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Olivier Taboureau
- Computational Modeling of Protein-Ligand Interactions (CMPLI)-INSERM UMR 8251, INSERM ERL U1133, Functional and Adaptative Biology (BFA), Universite de Paris, Paris, France
| | - Yun Tang
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Igor V Tetko
- BIGCHEM GmbH, Neuherberg, Germany
- Helmholtz Zentrum Muenchen - German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Roberto Todeschini
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alexander Tropsha
- Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - George Van Den Driessche
- Department of Chemistry, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Alexandre Varnek
- Laboratoire de Chémoinformatique-UMR7140, University of Strasbourg/CNRS, Strasbourg, France
| | - Zhongyu Wang
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Eva B Wedebye
- Division of Risk Assessment and Nutrition, National Food Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Antony J Williams
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | - Hongbin Xie
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ziye Zheng
- Chemistry Department, Umeå University, Umeå, Sweden
| | - Richard S Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
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12
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Mansouri K, Kleinstreuer N, Abdelaziz AM, Alberga D, Alves VM, Andersson PL, Andrade CH, Bai F, Balabin I, Ballabio D, Benfenati E, Bhhatarai B, Boyer S, Chen J, Consonni V, Farag S, Fourches D, García-Sosa AT, Gramatica P, Grisoni F, Grulke CM, Hong H, Horvath D, Hu X, Huang R, Jeliazkova N, Li J, Li X, Liu H, Manganelli S, Mangiatordi GF, Maran U, Marcou G, Martin T, Muratov E, Nguyen DT, Nicolotti O, Nikolov NG, Norinder U, Papa E, Petitjean M, Piir G, Pogodin P, Poroikov V, Qiao X, Richard AM, Roncaglioni A, Ruiz P, Rupakheti C, Sakkiah S, Sangion A, Schramm KW, Selvaraj C, Shah I, Sild S, Sun L, Taboureau O, Tang Y, Tetko IV, Todeschini R, Tong W, Trisciuzzi D, Tropsha A, Van Den Driessche G, Varnek A, Wang Z, Wedebye EB, Williams AJ, Xie H, Zakharov AV, Zheng Z, Judson RS. CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. Environ Health Perspect 2020; 128:27002. [PMID: 32074470 PMCID: PMC7064318 DOI: 10.1289/ehp5580] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 11/27/2019] [Accepted: 12/05/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Endocrine disrupting chemicals (EDCs) are xenobiotics that mimic the interaction of natural hormones and alter synthesis, transport, or metabolic pathways. The prospect of EDCs causing adverse health effects in humans and wildlife has led to the development of scientific and regulatory approaches for evaluating bioactivity. This need is being addressed using high-throughput screening (HTS) in vitro approaches and computational modeling. OBJECTIVES In support of the Endocrine Disruptor Screening Program, the U.S. Environmental Protection Agency (EPA) led two worldwide consortiums to virtually screen chemicals for their potential estrogenic and androgenic activities. Here, we describe the Collaborative Modeling Project for Androgen Receptor Activity (CoMPARA) efforts, which follows the steps of the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP). METHODS The CoMPARA list of screened chemicals built on CERAPP's list of 32,464 chemicals to include additional chemicals of interest, as well as simulated ToxCast™ metabolites, totaling 55,450 chemical structures. Computational toxicology scientists from 25 international groups contributed 91 predictive models for binding, agonist, and antagonist activity predictions. Models were underpinned by a common training set of 1,746 chemicals compiled from a combined data set of 11 ToxCast™/Tox21 HTS in vitro assays. RESULTS The resulting models were evaluated using curated literature data extracted from different sources. To overcome the limitations of single-model approaches, CoMPARA predictions were combined into consensus models that provided averaged predictive accuracy of approximately 80% for the evaluation set. DISCUSSION The strengths and limitations of the consensus predictions were discussed with example chemicals; then, the models were implemented into the free and open-source OPERA application to enable screening of new chemicals with a defined applicability domain and accuracy assessment. This implementation was used to screen the entire EPA DSSTox database of ∼ 875,000 chemicals, and their predicted AR activities have been made available on the EPA CompTox Chemicals dashboard and National Toxicology Program's Integrated Chemical Environment. https://doi.org/10.1289/EHP5580.
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Affiliation(s)
- Kamel Mansouri
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
- ScitoVation LLC, Research Triangle Park, North Carolina, USA
- Integrated Laboratory Systems, Inc., Morrisville, North Carolina, USA
| | - Nicole Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Ahmed M. Abdelaziz
- Technische Universität München, Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt, Department für Biowissenschaftliche Grundlagen, Weihenstephaner Steig 23, 85350 Freising, Germany
| | - Domenico Alberga
- Department of Pharmacy-Drug Sciences, University of Bari, Bari, Italy
| | - Vinicius M. Alves
- Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
- Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Carolina H. Andrade
- Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Fang Bai
- School of Pharmacy, Lanzhou University, China
| | - Ilya Balabin
- Information Systems & Global Solutions (IS&GS), Lockheed Martin, USA
| | - Davide Ballabio
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Emilio Benfenati
- Istituto di Ricerche Farmacologiche “Mario Negri”, IRCCS, Milan, Italy
| | - Barun Bhhatarai
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Scott Boyer
- Swedish Toxicology Sciences Research Center, Karolinska Institutet, Södertälje, Sweden
| | - Jingwen Chen
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Viviana Consonni
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Sherif Farag
- Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Denis Fourches
- Department of Chemistry, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Paola Gramatica
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Francesca Grisoni
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Chris M. Grulke
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Dragos Horvath
- Laboratoire de Chémoinformatique—UMR7140, University of Strasbourg/CNRS, Strasbourg, France
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Jiazhong Li
- School of Pharmacy, Lanzhou University, China
| | - Xuehua Li
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | | | - Serena Manganelli
- Istituto di Ricerche Farmacologiche “Mario Negri”, IRCCS, Milan, Italy
| | | | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Gilles Marcou
- Laboratoire de Chémoinformatique—UMR7140, University of Strasbourg/CNRS, Strasbourg, France
| | - Todd Martin
- National Risk Management Research Laboratory, U.S. EPA, Cincinnati, Ohio, USA
| | - Eugene Muratov
- Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Orazio Nicolotti
- Department of Pharmacy-Drug Sciences, University of Bari, Bari, Italy
| | - Nikolai G. Nikolov
- Division of Risk Assessment and Nutrition, National Food Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Ulf Norinder
- Swedish Toxicology Sciences Research Center, Karolinska Institutet, Södertälje, Sweden
| | - Ester Papa
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Michel Petitjean
- Computational Modeling of Protein-Ligand Interactions (CMPLI)–INSERM UMR 8251, INSERM ERL U1133, Functional and Adaptative Biology (BFA), Universite de Paris, Paris, France
| | - Geven Piir
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Pavel Pogodin
- Institute of Biomedical Chemistry IBMC, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry IBMC, 10 Building 8, Pogodinskaya st., Moscow 119121, Russia
| | - Xianliang Qiao
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Ann M. Richard
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | | | - Patricia Ruiz
- Computational Toxicology and Methods Development Laboratory, Division of Toxicology and Human Health Sciences, Agency for Toxic Substances and Disease Registry, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Chetan Rupakheti
- National Risk Management Research Laboratory, U.S. EPA, Cincinnati, Ohio, USA
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, Illinois, USA
| | - Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Alessandro Sangion
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Karl-Werner Schramm
- Technische Universität München, Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt, Department für Biowissenschaftliche Grundlagen, Weihenstephaner Steig 23, 85350 Freising, Germany
| | - Chandrabose Selvaraj
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | - Sulev Sild
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Lixia Sun
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Olivier Taboureau
- Computational Modeling of Protein-Ligand Interactions (CMPLI)–INSERM UMR 8251, INSERM ERL U1133, Functional and Adaptative Biology (BFA), Universite de Paris, Paris, France
| | - Yun Tang
- Department of Pharmaceutical Sciences, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Igor V. Tetko
- BIGCHEM GmbH, Neuherberg, Germany
- Helmholtz Zentrum Muenchen – German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Roberto Todeschini
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicology Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Alexander Tropsha
- Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - George Van Den Driessche
- Department of Chemistry, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Alexandre Varnek
- Laboratoire de Chémoinformatique—UMR7140, University of Strasbourg/CNRS, Strasbourg, France
| | - Zhongyu Wang
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Eva B. Wedebye
- Division of Risk Assessment and Nutrition, National Food Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Antony J. Williams
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
| | - Hongbin Xie
- School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ziye Zheng
- Chemistry Department, Umeå University, Umeå, Sweden
| | - Richard S. Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA
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13
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Kahn I, Maran U, Benfenati E, Netzeva TI, Schultz TW, Cronin MTD. Comparative Quantitative Structure–Activity–Activity Relationships for Toxicity to Tetrahymena pyriformis and Pimephales promelas. Altern Lab Anim 2019; 35:15-24. [PMID: 17411347 DOI: 10.1177/026119290703500112] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
An approach for predicting acute aquatic toxicity, in the form of a quantitative structure–activity–activity relationship (QSAAR), is described. This study assessed relative toxic effects to a fish, Pimephales promelas, and a ciliate, Tetrahymena pyriformis, and attempted to form relationships between them. A good agreement between toxic potencies ( R2 = 0.754) was found for a chemically diverse dataset of 364 compounds, when using toxicity to the ciliate as a surrogate to that for fish. This relationship was extended by adding three theoretical structural descriptors of the molecules. The inclusion of these descriptors improved the relationship further ( R2 = 0.824). The structural features that were found to improve the extrapolation between the toxicity to the two different species were related to the electron distribution of the carbon skeleton of the toxicant, its hydrogen-bonding ability, and its relative nitrogen content. Such a QSAAR approach provides a potential tool for predicting the toxicities of chemicals for environmental risk assessment and thus for reducing animal tests.
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Affiliation(s)
- Iiris Kahn
- Department of Chemistry, University of Tartu, Tartu, Estonia
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14
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Oja M, Sild S, Maran U. Logistic Classification Models for pH–Permeability Profile: Predicting Permeability Classes for the Biopharmaceutical Classification System. J Chem Inf Model 2019; 59:2442-2455. [DOI: 10.1021/acs.jcim.8b00833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mare Oja
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia
| | - Sulev Sild
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia
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15
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Sild S, Piir G, Neagu D, Maran U. CHAPTER 6. Storing and Using Qualitative and Quantitative Structure–Activity Relationships in the Era of Toxicological and Chemical Data Expansion. Issues in Toxicology 2019. [DOI: 10.1039/9781782623656-00185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Piir G, Kahn I, García-Sosa AT, Sild S, Ahte P, Maran U. Best Practices for QSAR Model Reporting: Physical and Chemical Properties, Ecotoxicity, Environmental Fate, Human Health, and Toxicokinetics Endpoints. Environ Health Perspect 2018; 126:126001. [PMID: 30561225 PMCID: PMC6371683 DOI: 10.1289/ehp3264] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 10/19/2018] [Accepted: 11/07/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Quantitative and qualitative structure–activity relationships (QSARs) have been used to understand chemical behavior for almost a century. The main source of QSAR models is the scientific literature, but the open question is how well these models are documented. OBJECTIVES The main aim of this study was to critically analyze the publication practices of QSARs with regard to transparency, potential reproducibility, and independent verification. The focus was on the level of technical completeness of the published QSARs. METHODS A total of 1,533 QSAR articles reporting 79 individual endpoints, mostly in environmental and health science, were reviewed. The QSAR parameters required for technical completeness were grouped into five categories: chemical structures, experimental endpoint values, descriptor values, mathematical representation of the model, and predicted endpoint values. The data were summarized and discussed using Circos plots. RESULTS Altogether, 42.5% of the reviewed articles were found to be potentially reproducible. The potential reproducibility for different endpoint groups varied; the respective rates were 39% for physical and chemical properties, 52% for ecotoxicity, 56% for environmental fate, 30% for human health, and 32% for toxicokinetics. The reproducibility of QSARs is discussed and placed in the context of the reproducibility of the experimental methods. Included are 65 references to open QSAR datasets as examples of models restored from scientific articles. DISCUSSION Strikingly poor documentation of QSARs was observed, which reduces the transparency, availability, and consequently, the application of research results in scientific, industrial, and regulatory areas. A list of the components needed to ensure the best practices for QSAR reporting is provided, allowing long-term use and preservation of the models. This list also allows an assessment of the reproducibility of models by interested parties such as journal editors, reviewers, regulators, evaluators, and potential users. https://doi.org/10.1289/EHP3264.
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Affiliation(s)
- Geven Piir
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Iiris Kahn
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | | | - Sulev Sild
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Priit Ahte
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, Estonia
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Pisponen A, Mootse H, Poikalainen V, Kaart T, Maran U, Karus A. Corrigendum to “Effects of temperature and concentration on particle size in a lactose solution using dynamic light scattering analysis” [International Dairy Journal 61 (2016) 205–210]. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2017.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Viira B, García-Sosa AT, Maran U. Chemical structure and correlation analysis of HIV-1 NNRT and NRT inhibitors and database-curated, published inhibition constants with chemical structure in diverse datasets. J Mol Graph Model 2017; 76:205-223. [PMID: 28738270 DOI: 10.1016/j.jmgm.2017.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/18/2017] [Accepted: 06/19/2017] [Indexed: 01/26/2023]
Abstract
Human immunodeficiency virus (HIV-1) reverse transcriptase is a major target for designing anti-HIV drugs. Developed inhibitors are divided into non-nucleoside analog reverse-transcriptase inhibitors (NNRTIs) and nucleoside analog reverse-transcriptase inhibitors (NRTIs) depending on their mechanism. Given that many inhibitors have been studied and for many of them binding affinity constants have been calculated, it is beneficial to analyze the chemical landscape of these families of inhibitors and correlate these inhibition constants with molecular structure descriptors. For this, the HIV-1 RT data was retrieved from the ChEMBL database, carefully curated, and original literature verified, grouped into NRTIs and NNRTIs, analyzed using a hierarchical scaffold classification method and modelled with best multi-linear regression approach. Analysis of the HIV-1 NNRTIs subset results in ten different common structural parent types of oxazepanone, piperazinone, pyrazine, oxazinanone, diazinanone, pyridine, pyrrole, diazepanone, thiazole, and triazine. The same analysis for HIV-1 NRTIs groups structures into four different parent types of uracil, pyrimide, pyrimidione, and imidazole. Each scaffold tree corresponding to the parent types has been carefully analyzed and examined, and changes in chemical structure favorable to potency and stability are highlighted. For both subsets, descriptive and predictive QSAR models are derived, discussed and externally validated, revealing general trends in relationships between molecular structure and binding affinity constants in structurally diverse datasets. Data and QSAR models are available at the QsarDB repository (http://dx.doi.org/10.15152/QDB.202).
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Affiliation(s)
- Birgit Viira
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia
| | | | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia.
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Jakobson L, Vaahtera L, Tõldsepp K, Nuhkat M, Wang C, Wang YS, Hõrak H, Valk E, Pechter P, Sindarovska Y, Tang J, Xiao C, Xu Y, Gerst Talas U, García-Sosa AT, Kangasjärvi S, Maran U, Remm M, Roelfsema MRG, Hu H, Kangasjärvi J, Loog M, Schroeder JI, Kollist H, Brosché M. Natural Variation in Arabidopsis Cvi-0 Accession Reveals an Important Role of MPK12 in Guard Cell CO2 Signaling. PLoS Biol 2016; 14:e2000322. [PMID: 27923039 PMCID: PMC5147794 DOI: 10.1371/journal.pbio.2000322] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/03/2016] [Indexed: 12/20/2022] Open
Abstract
Plant gas exchange is regulated by guard cells that form stomatal pores. Stomatal adjustments are crucial for plant survival; they regulate uptake of CO2 for photosynthesis, loss of water, and entrance of air pollutants such as ozone. We mapped ozone hypersensitivity, more open stomata, and stomatal CO2-insensitivity phenotypes of the Arabidopsis thaliana accession Cvi-0 to a single amino acid substitution in MITOGEN-ACTIVATED PROTEIN (MAP) KINASE 12 (MPK12). In parallel, we showed that stomatal CO2-insensitivity phenotypes of a mutant cis (CO2-insensitive) were caused by a deletion of MPK12. Lack of MPK12 impaired bicarbonate-induced activation of S-type anion channels. We demonstrated that MPK12 interacted with the protein kinase HIGH LEAF TEMPERATURE 1 (HT1)-a central node in guard cell CO2 signaling-and that MPK12 functions as an inhibitor of HT1. These data provide a new function for plant MPKs as protein kinase inhibitors and suggest a mechanism through which guard cell CO2 signaling controls plant water management.
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Affiliation(s)
- Liina Jakobson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Lauri Vaahtera
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Kadri Tõldsepp
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Maris Nuhkat
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Cun Wang
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, La Jolla, California, United States of America
| | - Yuh-Shuh Wang
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Hanna Hõrak
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ervin Valk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Priit Pechter
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | - Jing Tang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chuanlei Xiao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Xu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ulvi Gerst Talas
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Saijaliisa Kangasjärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - M. Rob G. Roelfsema
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, University of Würzburg, Würzburg, Germany
| | - Honghong Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jaakko Kangasjärvi
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Distinguished Scientist Fellowship Program, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Julian I. Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California, San Diego, La Jolla, California, United States of America
| | - Hannes Kollist
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mikael Brosché
- Institute of Technology, University of Tartu, Tartu, Estonia
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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Tetko IV, Maran U, Tropsha A. Public (Q)SAR Services, Integrated Modeling Environments, and Model Repositories on the Web: State of the Art and Perspectives for Future Development. Mol Inform 2016; 36. [PMID: 27778468 DOI: 10.1002/minf.201600082] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/03/2016] [Indexed: 01/08/2023]
Abstract
Thousands of (Quantitative) Structure-Activity Relationships (Q)SAR models have been described in peer-reviewed publications; however, this way of sharing seldom makes models available for the use by the research community outside of the developer's laboratory. Conversely, on-line models allow broad dissemination and application representing the most effective way of sharing the scientific knowledge. Approaches for sharing and providing on-line access to models range from web services created by individual users and laboratories to integrated modeling environments and model repositories. This emerging transition from the descriptive and informative, but "static", and for the most part, non-executable print format to interactive, transparent and functional delivery of "living" models is expected to have a transformative effect on modern experimental research in areas of scientific and regulatory use of (Q)SAR models.
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Affiliation(s)
- Igor V Tetko
- Institute of Structural Biology, Helmholtz Zentrum München -, German Research Center for Environmental Health (GmbH), Institute of Structural Biology, Ingolstädter Landstraße 1, D-, 85764, Neuherberg, Germany.,BigChem GmbH, Ingolstädter Landstraße 1, b. 60w, D-, 85764, Neuherberg, Germany
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu, 50411, Estonia
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.,Butlerov Institute of Chemistry, Kazan Federal University, Kremlyovskaya St. 18, 420008, Kazan, Russia
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Oja M, Maran U. Quantitative structure-permeability relationships at various pH values for neutral and amphoteric drugs and drug-like compounds. SAR QSAR Environ Res 2016; 27:813-832. [PMID: 27748631 DOI: 10.1080/1062936x.2016.1238408] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
Human intestinal absorption is a key property for orally administered drugs and is dependent on pH. This study focuses on neutral and amphoteric compounds and their membrane permeabilities across the range of pH values found in the human intestine. The membrane permeability values for 15 neutral and 60 amphoteric compounds at pH 3, 5, 7.4 and 9 were measured using the parallel artificial membrane permeability assay (PAMPA). For each data series the quantitative structure-permeability relationships were developed and analysed. The results show that the membrane permeability of neutral compounds is attributed to a single structural characteristic, the hydrogen bond donor ability. Amphoteric compounds are more complex because of their chemical constitution, and therefore require three-parameter models to describe and predict membrane permeability. Analysis of the models for amphoteric compounds reveals that membrane permeability depends on multiple structural characteristics: the partition coefficient, hydrogen bond properties and the shape of the molecules. In addition to conventional validation strategies, two external compounds (isradipine and omeprazole) were tested and revealed very good agreement of pH profiles between experimental and predicted membrane permeability for all of the developed models. Selected QSAR models are available at the QsarDB repository (http://dx.doi.org/10.15152/QDB.184).
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Affiliation(s)
- Mare Oja
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, Estonia
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Viira B, Selyutina A, García-Sosa AT, Karonen M, Sinkkonen J, Merits A, Maran U. Design, discovery, modelling, synthesis, and biological evaluation of novel and small, low toxicity s-triazine derivatives as HIV-1 non-nucleoside reverse transcriptase inhibitors. Bioorg Med Chem 2016; 24:2519-2529. [PMID: 27108399 DOI: 10.1016/j.bmc.2016.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/10/2016] [Accepted: 04/08/2016] [Indexed: 11/15/2022]
Abstract
A set of top-ranked compounds from a multi-objective in silico screen was experimentally tested for toxicity and the ability to inhibit the activity of HIV-1 reverse transcriptase (RT) in cell-free assay and in cell-based assay using HIV-1 based virus-like particles. Detailed analysis of a commercial sample that indicated specific inhibition of HIV-1 reverse transcription revealed that a minor component that was structurally similar to that of the main compound was responsible for the strongest inhibition. As a result, novel s-triazine derivatives were proposed, modelled, discovered, and synthesised, and their antiviral activity and cellular toxicity were tested. Compounds 18a and 18b were found to be efficient HIV-1 RT inhibitors, with an IC50 of 5.6±1.1μM and 0.16±0.05μM in a cell-based assay using infectious HIV-1, respectively. Compound 18b also had no detectable toxicity for different human cell lines. Their binding mode and interactions with the RT suggest that there was strong and adaptable binding in a tight (NNRTI) hydrophobic pocket. In summary, this iterative study produced structural clues and led to a group of non-toxic, novel compounds to inhibit HIV-RT with up to nanomolar potency.
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Affiliation(s)
- Birgit Viira
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia
| | | | | | - Maarit Karonen
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Jari Sinkkonen
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu 50411, Estonia.
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia.
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Oja M, Maran U. Quantitative structure-permeability relationships at various pH values for acidic and basic drugs and drug-like compounds. SAR QSAR Environ Res 2015; 26:701-719. [PMID: 26383235 DOI: 10.1080/1062936x.2015.1085896] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/19/2015] [Indexed: 06/05/2023]
Abstract
Absorption in gastrointestinal tract compartments varies and is largely influenced by pH. Therefore, considering pH in studies and analyses of membrane permeability provides an opportunity to gain a better understanding of the behaviour of compounds and to obtain good permeability estimates for prediction purposes. This study concentrates on relationships between the chemical structure and membrane permeability of acidic and basic drugs and drug-like compounds. The membrane permeability of 36 acidic and 61 basic compounds was measured using the parallel artificial membrane permeability assay (PAMPA) at pH 3, 5, 7.4 and 9. Descriptive and/or predictive single-parameter quantitative structure-permeability relationships were derived for all pH values. For acidic compounds, membrane permeability is mainly influenced by hydrogen bond donor properties, as revealed by models with r(2) > 0.8 for pH 3 and pH 5. For basic compounds, the best (r(2) > 0.7) structure-permeability relationships are obtained with the octanol-water distribution coefficient for pH 7.4 and pH 9, indicating the importance of partition properties. In addition to the validation set, the prediction quality of the developed models was tested with folic acid and astemizole, showing good matches between experimental and calculated membrane permeabilities at key pHs. Selected QSAR models are available at the QsarDB repository ( http://dx.doi.org/10.15152/QDB.166 ).
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Affiliation(s)
- M Oja
- a Institute of Chemistry , University of Tartu , Ravila 14A, Tartu 50411 , Estonia
| | - U Maran
- a Institute of Chemistry , University of Tartu , Ravila 14A, Tartu 50411 , Estonia
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Ruusmann V, Sild S, Maran U. QSAR DataBank repository: open and linked qualitative and quantitative structure-activity relationship models. J Cheminform 2015; 7:32. [PMID: 26110025 PMCID: PMC4479250 DOI: 10.1186/s13321-015-0082-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/08/2015] [Indexed: 11/29/2022] Open
Abstract
Background Structure–activity relationship models have been used to gain insight into chemical and physical processes in biomedicine, toxicology, biotechnology, etc. for almost a century. They have been recognized as valuable tools in decision support workflows for qualitative and quantitative predictions. The main obstacle preventing broader adoption of quantitative structure–activity relationships [(Q)SARs] is that published models are still relatively difficult to discover, retrieve and redeploy in a modern computer-oriented environment. This publication describes a digital repository that makes in silico (Q)SAR-type descriptive and predictive models archivable, citable and usable in a novel way for most common research and applied science purposes. Description The QSAR DataBank (QsarDB) repository aims to make the processes and outcomes of in silico modelling work transparent, reproducible and accessible. Briefly, the models are represented in the QsarDB data format and stored in a content-aware repository (a.k.a. smart repository). Content awareness has two dimensions. First, models are organized into collections and then into collection hierarchies based on their metadata. Second, the repository is not only an environment for browsing and downloading models (the QDB archive) but also offers integrated services, such as model analysis and visualization and prediction making. Conclusions The QsarDB repository unlocks the potential of descriptive and predictive in silico (Q)SAR-type models by allowing new and different types of collaboration between model developers and model users. The key enabling factor is the representation of (Q)SAR models in the QsarDB data format, which makes it easy to preserve and share all relevant data, information and knowledge. Model developers can become more productive by effectively reusing prior art. Model users can make more confident decisions by relying on supporting information that is larger and more diverse than before. Furthermore, the smart repository automates most of the mundane work (e.g., collecting, systematizing, and reporting data), thereby reducing the time to decision. Graphical abstract ![]()
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Affiliation(s)
- V Ruusmann
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - S Sild
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - U Maran
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
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Oja M, Maran U. The Permeability of an Artificial Membrane for Wide Range of pH in Human Gastrointestinal Tract: Experimental Measurements and Quantitative StructureActivity Relationship. Mol Inform 2015; 34:493-506. [PMID: 27490393 DOI: 10.1002/minf.201400147] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 05/06/2015] [Indexed: 11/08/2022]
Abstract
In silico models for membrane permeability have been based on values measured for single pH. Depending on the diet (fasted/fed state) and part of human intestine the range of pH varies approximately from 2.4 to 8.0. This motivated to study and model the membrane permeability of chemicals considering the whole range of pH in the human intestine. For this, effective membrane permeability values were measured for 65 drugs and drug-like compounds using PAMPA method at four pHs (3, 5, 7.4, 9) over 48 h, introducing technological innovations for the time-dependence measurement. The highest permeability value of a compound from four pHs was used to derive QSAR analyzing a large pool of molecular descriptors and introducing new descriptor. Using stepwise forward selection approach a significant QSAR model was derived that included only two mechanistically relevant descriptors, the logarithmic octanol-water partition coefficient and hydrogen bonding surface area. Prediction confidence of the model was blind tested with a true external validation set of 15 compounds. The resulting QSAR model shows potential to combine permeability values from various pH-s into one descriptive and predictive model for estimating maximum permeability in human gastrointestinal tract. The QSAR model and data are available through the QsarDB repository (http://dx.doi.org/10.15152/QDB.137).
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Affiliation(s)
- Mare Oja
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia phone +372 7 375 254, fax +372 7 375 264
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia phone +372 7 375 254, fax +372 7 375 264.
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Piir G, Sild S, Maran U. Classifying bio-concentration factor with random forest algorithm, influence of the bio-accumulative vs. non-bio-accumulative compound ratio to modelling result, and applicability domain for random forest model. SAR QSAR Environ Res 2014; 25:967-81. [PMID: 25482723 DOI: 10.1080/1062936x.2014.969310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/03/2014] [Indexed: 05/27/2023]
Abstract
In environmental risk assessment, the bio-concentration factor (BCF) is a widely used parameter in the estimation of the bio-accumulation potential of chemicals. BCF data often have an uneven distribution of classes (bio-accumulative vs. non-bio-accumulative), which could severely bias the classification results towards the prevailing class. The present study focuses on the influence of uneven distribution of the classes in training phase of Random Forest (RF) classification models. Three different training set designs were used and descriptors selected to the models based on the occurrence frequency in RF trees and considering the mechanistic aspects they reflect. Models were compared and their classification performance was analysed, indicating good predictive characteristics (sensitivity = 0.90 and specificity = 0.83) for the balanced set; also imbalanced sets have their strengths in certain application scenarios. The confidence of classifications was assessed with a new schema for the applicability domain that makes use of the RF proximity matrix by analysing the similarity between the predicted compound and the training set of the model. All developed models were made available in the transparent, accessible and reproducible way in QsarDB repository (http://dx.doi.org/10.15152/QDB.116).
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Affiliation(s)
- G Piir
- a Institute of Chemistry , University of Tartu , Tartu , Estonia
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García-Sosa AT, Maran U. Improving the use of ranking in virtual screening against HIV-1 integrase with triangular numbers and including ligand profiling with antitargets. J Chem Inf Model 2014; 54:3172-85. [PMID: 25303089 DOI: 10.1021/ci500300u] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A delicate balance exists between a drug molecule's toxicity and its activity. Indeed, efficacy, toxicity, and side effect problems are a common cause for the termination of drug candidate compounds and development projects. To address this, an antitarget interaction profile is built and combined with virtual screening and cross docking for new inhibitors of HIV-1 integrase, in order to consider possible off-target interactions as early as possible in a drug or hit discovery program. New ranking techniques using triangular numbers improve ranking information on the compounds and recovery of known inhibitors into the top compounds using different docking programs. This improved ranking arises from using consensus of ranks between docking programs and ligand efficiencies to derive a new rank, instead of using absolute score values, or average of ranks. The triangular number rerank also allowed the objective combination of results from several protein targets or screen conditions and several programs. Triangular number reranking conserves more information than other reranking methods such as average of scores or averages of ranks. In addition, the use of triangular numbers for reranking makes possible the use of thresholds with a justified leeway based on the number of available known inhibitors, so that the majority of the compounds above the threshold in ranks compare to the compounds that have known experimentally determined biological activity. The battery of anti- or off-targets can be tailored to specific molecular or drug design challenges. In silico filters can thus be deployed in successive stages, for prefiltering, activity profiling, and for further analysis and triaging of libraries of compounds.
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Ruusmann V, Sild S, Maran U. QSAR DataBank - an approach for the digital organization and archiving of QSAR model information. J Cheminform 2014; 6:25. [PMID: 24910716 PMCID: PMC4047268 DOI: 10.1186/1758-2946-6-25] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 03/11/2014] [Indexed: 12/02/2022] Open
Abstract
Background Research efforts in the field of descriptive and predictive Quantitative Structure-Activity Relationships or Quantitative Structure–Property Relationships produce around one thousand scientific publications annually. All the materials and results are mainly communicated using printed media. The printed media in its present form have obvious limitations when they come to effectively representing mathematical models, including complex and non-linear, and large bodies of associated numerical chemical data. It is not supportive of secondary information extraction or reuse efforts while in silico studies poses additional requirements for accessibility, transparency and reproducibility of the research. This gap can and should be bridged by introducing domain-specific digital data exchange standards and tools. The current publication presents a formal specification of the quantitative structure-activity relationship data organization and archival format called the QSAR DataBank (QsarDB for shorter, or QDB for shortest). Results The article describes QsarDB data schema, which formalizes QSAR concepts (objects and relationships between them) and QsarDB data format, which formalizes their presentation for computer systems. The utility and benefits of QsarDB have been thoroughly tested by solving everyday QSAR and predictive modeling problems, with examples in the field of predictive toxicology, and can be applied for a wide variety of other endpoints. The work is accompanied with open source reference implementation and tools. Conclusions The proposed open data, open source, and open standards design is open to public and proprietary extensions on many levels. Selected use cases exemplify the benefits of the proposed QsarDB data format. General ideas for future development are discussed.
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Affiliation(s)
- Villu Ruusmann
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Sulev Sild
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
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Aruoja V, Moosus M, Kahru A, Sihtmäe M, Maran U. Measurement of baseline toxicity and QSAR analysis of 50 non-polar and 58 polar narcotic chemicals for the alga Pseudokirchneriella subcapitata. Chemosphere 2014; 96:23-32. [PMID: 23895738 DOI: 10.1016/j.chemosphere.2013.06.088] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/28/2013] [Accepted: 06/30/2013] [Indexed: 06/02/2023]
Abstract
In this paper a set of homogenous experimental algal toxicity data was measured for 50 non-polar narcotic chemicals using the alga Pseudokirchneriella subcapitata in a closed test with a growth rate endpoint. Most of the tested compounds are high volume industrial chemicals that so far lacked published REACH-compliant algal growth inhibition values. The test protocol fulfilled the criteria set forth in the OECD guideline 201 and had the same sensitivity as the open test which allowed direct comparison of toxicity values. Baseline QSAR model for non-polar narcotic compounds was established and compared with previous analogous models. Multi-linear QSAR model was derived for the non-polar and 58 previously tested polar (anilines and phenols) narcotic compounds modulating hydrophobicity, molecular size, electronic and molecular stability effects coded in the molecular descriptors. Descriptors in the model were analyzed and applicability domain was assessed providing further guidelines for the in silico prediction purposes in decision support while performing risk assessment. QSAR models in the manuscript are available on-line through QsarDB repository for exploring and prediction services (http://hdl.handle.net/10967/106).
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Affiliation(s)
- Villem Aruoja
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, Tallinn 12618, Estonia.
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Ruusmann V, Maran U. From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions. J Comput Aided Mol Des 2013; 27:583-603. [PMID: 23884706 DOI: 10.1007/s10822-013-9664-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 07/02/2013] [Indexed: 01/23/2023]
Abstract
The scientific literature is important source of experimental and chemical structure data. Very often this data has been harvested into smaller or bigger data collections leaving the data quality and curation issues on shoulders of users. The current research presents a systematic and reproducible workflow for collecting series of data points from scientific literature and assembling a database that is suitable for the purposes of high quality modelling and decision support. The quality assurance aspect of the workflow is concerned with the curation of both chemical structures and associated toxicity values at (1) single data point level and (2) collection of data points level. The assembly of a database employs a novel "timeline" approach. The workflow is implemented as a software solution and its applicability is demonstrated on the example of the Tetrahymena pyriformis acute aquatic toxicity endpoint. A literature collection of 86 primary publications for T. pyriformis was found to contain 2,072 chemical compounds and 2,498 unique toxicity values, which divide into 2,440 numerical and 58 textual values. Every chemical compound was assigned to a preferred toxicity value. Examples for most common chemical and toxicological data curation scenarios are discussed.
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Affiliation(s)
- Villu Ruusmann
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu, Estonia
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Moosus M, Hiob R, Maran U. Quantitative relationship between rate constants and molecular structure descriptors for the gas phase hydrogen abstraction reactions. SAR QSAR Environ Res 2013; 24:501-518. [PMID: 23724929 DOI: 10.1080/1062936x.2013.792869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The abstraction of hydrogen by general radicals has a wide role in environmental and also in technological processes because it results in reactive free radicals that play a vital role in atmospheric chemistry and also in biochemical processes. In addition to experimental studies, the theoretical modelling of this elementary reaction has been important for understanding and predicting respective rate constants. In this paper, molecular descriptors in the context of a QSAR approach are used to codify the relationship between molecular structure and rate constants. Unique experimental data is collected from the literature for the reaction R(i)• + R(j)H → R(i)H + R(j)•, where R(i)• = H• and R(j)• are diverse radicals. The four-parameter QSAR model (n = 34, r(2) = 0.81, r(2)(CV) = 0.74, r(2)(scr) = 0.12, s(2) = 0.19) is presented for the bimolecular rate constants, accompanied with model diagnostics and analysis of descriptors in the model.
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Affiliation(s)
- Maikki Moosus
- Institute of Chemistry, University of Tartu, Tartu, Estonia
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Abstract
Important understanding can be gained from using molecular biology-based and chemistry-based techniques together. Bayesian classifiers have thus been developed in the present work using several statistically significant molecular properties of compiled datasets of drugs and non-drugs, including their disease category or organ. The results show they provide a useful classification and simplicity of several different ligand efficiencies and molecular properties. Early recall of drugs among non-drugs using the classifiers as a ranking tool is also provided. As the chemical space of compounds is addressed together with their anatomical characterization, chemical libraries can be improved to select for specific organ or disease. Eventually, by including even finer detail, the method may help in designing libraries with specific pharmacological or toxicological target chemical space. Alternatively, a lack of statistically significant differences in property density distributions may help in further describing compounds with possibility of activity on several organs or disease groups, and given their very similar or considerably overlapping chemical space, therefore wanted or unwanted side-effects. The overlaps between densities for several properties of organs or disease categories were calculated by integrating the area under the curves where they intersect. The naïve Bayesian classifiers are readily built, fast to score, and easily interpretable.
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Affiliation(s)
- A T García-Sosa
- Institute of Chemistry, University of Tartu, Tartu, Estonia.
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Piir G, Sild S, Maran U. Comparative analysis of local and consensus quantitative structure-activity relationship approaches for the prediction of bioconcentration factor. SAR QSAR Environ Res 2013; 24:175-199. [PMID: 23410132 DOI: 10.1080/1062936x.2012.762426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Quantitative structure-activity relationships (QSARs) are broadly classified as global or local, depending on their molecular constitution. Global models use large and diverse training sets covering a wide range of chemical space. Local models focus on smaller structurally or chemically similar subsets that are conventionally selected by human experts or alternatively using clustering analysis. The current study focuses on the comparative analysis of different clustering algorithms (expectation-maximization, K-means and hierarchical) for seven different descriptor sets as structural characteristics and two rule-based approaches to select subsets for designing local QSAR models. A total of 111 local QSAR models are developed for predicting bioconcentration factor. Predictions from local models were compared with corresponding predictions from the global model. The comparison of coefficients of determination (r(2)) and standard deviations for local models with similar subsets from the global model show improved prediction quality in 97% of cases. The descriptor content of derived QSARs is discussed and analyzed. Local QSAR models were further consolidated within the framework of consensus approach. All different consensus approaches increased performance over the global and local models. The consensus approach reduced the number of strongly deviating predictions by evening out prediction errors, which were produced by some local QSARs.
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Affiliation(s)
- G Piir
- Institute of Chemistry, University of Tartu, Tartu, Estonia
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García-Sosa AT, Oja M, Hetényi C, Maran U. DrugLogit: logistic discrimination between drugs and nondrugs including disease-specificity by assigning probabilities based on molecular properties. J Chem Inf Model 2012; 52:2165-80. [PMID: 22830445 DOI: 10.1021/ci200587h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The increasing knowledge of both structure and activity of compounds provides a good basis for enhancing the pharmacological characterization of chemical libraries. In addition, pharmacology can be seen as incorporating both advances from molecular biology as well as chemical sciences, with innovative insight provided from studying target-ligand data from a ligand molecular point of view. Predictions and profiling of libraries of drug candidates have previously focused mainly on certain cases of oral bioavailability. Inclusion of other administration routes and disease-specificity would improve the precision of drug profiling. In this work, recent data are extended, and a probability-based approach is introduced for quantitative and gradual classification of compounds into categories of drugs/nondrugs, as well as for disease- or organ-specificity. Using experimental data of over 1067 compounds and multivariate logistic regressions, the classification shows good performance in training and independent test cases. The regressions have high statistical significance in terms of the robustness of coefficients and 95% confidence intervals provided by a 1000-fold bootstrapping resampling. Besides their good predictive power, the classification functions remain chemically interpretable, containing only one to five variables in total, and the physicochemical terms involved can be easily calculated. The present approach is useful for an improved description and filtering of compound libraries. It can also be applied sequentially or in combinations of filters, as well as adapted to particular use cases. The scores and equations may be able to suggest possible routes for compound or library modification. The data is made available for reuse by others, and the equations are freely accessible at http://hermes.chem.ut.ee/~alfx/druglogit.html.
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García-Sosa AT, Oja M, Hetényi C, Maran U. Disease-Specific Differentiation Between Drugs and Non-Drugs Using Principal Component Analysis of Their Molecular Descriptor Space. Mol Inform 2012; 31:369-83. [DOI: 10.1002/minf.201100094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 01/25/2012] [Indexed: 01/04/2023]
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T. Garcia-Sosa A, Maran U, Hetenyi C. Molecular Property Filters Describing Pharmacokinetics and Drug Binding. Curr Med Chem 2012; 19:1646-62. [DOI: 10.2174/092986712799945021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 01/26/2012] [Accepted: 01/27/2012] [Indexed: 11/22/2022]
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Moosus M, Maran U. Quantitative structure-activity relationship analysis of acute toxicity of diverse chemicals to Daphnia magna with whole molecule descriptors. SAR QSAR Environ Res 2011; 22:757-774. [PMID: 21999753 DOI: 10.1080/1062936x.2011.623317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Quantitative structure-activity relationship analysis and estimation of toxicological effects at lower-mid trophic levels provide first aid means to understand the toxicity of chemicals. Daphnia magna serves as a good starting point for such toxicity studies and is also recognized for regulatory use in estimating the risk of chemicals. The ECOTOX database was queried and analysed for available data and a homogenous subset of 253 compounds for the endpoint LC50 48 h was established. A four-parameter quantitative structure-activity relationship was derived (coefficient of determination, r (2) = 0.740) for half of the compounds and internally validated (leave-one-out cross-validated coefficient of determination, [Formula: see text] = 0.714; leave-many-out coefficient of determination, [Formula: see text] = 0.738). External validation was carried out with the remaining half of the compounds (coefficient of determination for external validation, [Formula: see text] = 0.634). Two of the descriptors in the model (log P, average bonding information content) capture the structural characteristics describing penetration through bio-membranes. Another two descriptors (energy of highest occupied molecular orbital, weighted partial negative surface area) capture the electronic structural characteristics describing the interaction between the chemical and its hypothetic target in the cell. The applicability domain was subsequently analysed and discussed.
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Affiliation(s)
- M Moosus
- Institute of Chemistry, University of Tartu, Estonia
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García-Sosa AT, Sild S, Takkis K, Maran U. Combined Approach Using Ligand Efficiency, Cross-Docking, and Antitarget Hits for Wild-Type and Drug-Resistant Y181C HIV-1 Reverse Transcriptase. J Chem Inf Model 2011; 51:2595-611. [DOI: 10.1021/ci200203h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Sulev Sild
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Kalev Takkis
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
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Piir G, Sild S, Roncaglioni A, Benfenati E, Maran U. QSAR model for the prediction of bio-concentration factor using aqueous solubility and descriptors considering various electronic effects. SAR QSAR Environ Res 2010; 21:711-729. [PMID: 21120758 DOI: 10.1080/1062936x.2010.528596] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The in silico modelling of bio-concentration factor (BCF) is of considerable interest in environmental sciences, because it is an accepted indicator for the accumulation potential of chemicals in organisms. Numerous QSAR models have been developed for the BCF, and the majority utilize the octanol/water partition coefficient (log P) to account for the penetration characteristics of the chemicals. The present work used descriptors from a variety of software packages for the development of a multi-linear regression model to estimate BCF. The modelled data set of 473 diverse compounds covers a wide range of log BCF values. In the proposed QSAR model, most of the variation is described by the calculated solubility in water. Other contributing descriptors describe, for instance, hydrophobic surface area, hydrogen bonding and other electronic effects. The model was validated internally by using a variety of statistical approaches. Two external validations were also performed. For the former validation, a subset from the same data source was used. The 2nd external validation was based on an independent data set collected from different resources. All validations showed the consistency of the model. The applicability domain of the model was discussed and described and a thorough outlier analysis was performed.
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Affiliation(s)
- G Piir
- Institute of Chemistry, University of Tartu, Tartu, Estonia
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Tulp I, Dobchev DA, Katritzky AR, Acree W, Maran U. A General Treatment of Solubility 4. Description and Analysis of a PCA Model for Ostwald Solubility Coefficients. J Chem Inf Model 2010; 50:1275-83. [DOI: 10.1021/ci1000828] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Indrek Tulp
- Institute of Chemistry, University of Tartu, 14A Ravila, Tartu 50411, Estonia, Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida, 32611, Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia, and Department of Chemistry, University of North Texas, Denton, Texas 76203-5070
| | - Dimitar A. Dobchev
- Institute of Chemistry, University of Tartu, 14A Ravila, Tartu 50411, Estonia, Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida, 32611, Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia, and Department of Chemistry, University of North Texas, Denton, Texas 76203-5070
| | - Alan R. Katritzky
- Institute of Chemistry, University of Tartu, 14A Ravila, Tartu 50411, Estonia, Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida, 32611, Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia, and Department of Chemistry, University of North Texas, Denton, Texas 76203-5070
| | - William Acree
- Institute of Chemistry, University of Tartu, 14A Ravila, Tartu 50411, Estonia, Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida, 32611, Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia, and Department of Chemistry, University of North Texas, Denton, Texas 76203-5070
| | - Uko Maran
- Institute of Chemistry, University of Tartu, 14A Ravila, Tartu 50411, Estonia, Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida, 32611, Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia, and Department of Chemistry, University of North Texas, Denton, Texas 76203-5070
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Abstract
A dataset of protein-drug complexes with experimental binding energy and crystal structure were analyzed and the performance of different docking engines and scoring functions (as well as components of these) for predicting the free energy of binding and several ligand efficiency indices were compared. The aim was not to evaluate the best docking method, but to determine the effect of different efficiency indices on the experimental and predicted free energy. Some ligand efficiency indices, such as DeltaG/W (Wiener index), DeltaG/NoC (number of carbons), and DeltaG/P (partition coefficient), improve the correlation between experimental and calculated values. This effect was shown to be valid across the different scoring functions and docking programs. It also removes the common bias of scoring functions in favor of larger ligands. For all scoring functions, the efficiency indices effectively normalize the free energy derived indices, to give values closer to experiment. Compound collection filtering can be done prior or after docking, using pharmacokinetic as well as pharmacodynamic profiles. Achieving these better correlations with experiment can improve the ability of docking scoring functions to predict active molecules in virtual screening.
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Maran U, Sild S, Tulp I, Takkis K, Moosus M. Chapter 6. Molecular Descriptors from Two-Dimensional Chemical Structure. In Silico Toxicology 2010. [DOI: 10.1039/9781849732093-00148] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Tulp I, Sild S, Maran U. Relationship Between Structure and Permeability in Artificial Membranes: Theoretical Whole Molecule Descriptors in Development of QSAR Models. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200860160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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García-Sosa AT, Sild S, Maran U. Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivir-resistant H274Y variant. J Chem Inf Model 2008; 48:2074-80. [PMID: 18847186 DOI: 10.1021/ci800242z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The binding sites of wild-type avian influenza A H5N1 neuraminidase, as well as those of the Tamiflu (oseltamivir)-resistant H274Y variant, were explored computationally to design inhibitors that target simultaneously several adjacent binding sites of the open conformation of the virus protein. The compounds with the best computed free energies of binding, in agreement by two docking methods, consensus scoring, and ligand efficiency values, suggest that mimicking a polysaccharide, beta-lactam, and other structures, including known drugs, could be routes for multibinding site inhibitor design. This new virtual screening method based on consensus scoring and ligand efficiency indices is introduced, which allows the combination of pharmacodynamic and pharmacokinetic properties into unique measures.
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Colombo A, Benfenati E, Karelson M, Maran U. The proposal of architecture for chemical splitting to optimize QSAR models for aquatic toxicity. Chemosphere 2008; 72:772-780. [PMID: 18471854 DOI: 10.1016/j.chemosphere.2008.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 02/20/2008] [Accepted: 03/11/2008] [Indexed: 05/26/2023]
Abstract
One of the challenges in the field of quantitative structure-activity relationship (QSAR) analysis is the correct classification of a chemical compound to an appropriate model for the prediction of activity. Thus, in previous studies, compounds have been divided into distinct groups according to their mode of action or chemical class. In the current study, theoretical molecular descriptors were used to divide 568 organic substances into subsets with toxicity measured for the 96-h lethal median concentration for the Fathead minnow (Pimephales promelas). Simple constitutional descriptors such as the number of aliphatic and aromatic rings and a quantum chemical descriptor, maximum bond order of a carbon atom divide compounds into nine subsets. For each subset of compounds the automatic forward selection of descriptors was applied to construct QSAR models. Significant correlations were achieved for each subset of chemicals and all models were validated with the leave-one-out internal validation procedure (R(2)(cv) approximately 0.80). The results encourage to consider this alternative way for the prediction of toxicity using QSAR subset models without direct reference to the mechanism of toxic action or the traditional chemical classification.
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Affiliation(s)
- Andrea Colombo
- Institute of Chemistry, University of Tartu, Tartu, Estonia
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Org T, Chignola F, Hetényi C, Gaetani M, Rebane A, Liiv I, Maran U, Mollica L, Bottomley MJ, Musco G, Peterson P. The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression. EMBO Rep 2008; 9:370-6. [PMID: 18292755 PMCID: PMC2261226 DOI: 10.1038/sj.embor.2008.11] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 12/07/2007] [Accepted: 01/09/2008] [Indexed: 12/28/2022] Open
Abstract
Mutations in the gene autoimmune regulator (AIRE) cause autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. AIRE is expressed in thymic medullary epithelial cells, where it promotes the expression of tissue-restricted antigens. By the combined use of biochemical and biophysical methods, we show that AIRE selectively interacts with histone H3 through its first plant homeodomain (PHD) finger (AIRE-PHD1) and preferentially binds to non-methylated H3K4 (H3K4me0). Accordingly, in vivo AIRE binds to and activates promoters containing low levels of H3K4me3 in human embryonic kidney 293 cells. We conclude that AIRE-PHD1 is an important member of a newly identified class of PHD fingers that specifically recognize H3K4me0, thus providing a new link between the status of histone modifications and the regulation of tissue-restricted antigen expression in thymus.
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Affiliation(s)
- Tõnis Org
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
| | - Francesca Chignola
- Biomolecular NMR Laboratory, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Csaba Hetényi
- Institute of Chemical Physics, University of Tartu, Tartu 51010, Estonia
| | - Massimiliano Gaetani
- Biomolecular NMR Laboratory, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Ana Rebane
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
| | - Ingrid Liiv
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
| | - Uko Maran
- Institute of Chemical Physics, University of Tartu, Tartu 51010, Estonia
| | - Luca Mollica
- Biomolecular NMR Laboratory, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Matthew J Bottomley
- Istituto di Ricerche di Biologia Molecolare, via Pontina km 30.600, Pomezia (Rome), 00040, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Pärt Peterson
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
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Org T, Chignola F, Hetényi C, Gaetani M, Rebane A, Liiv I, Maran U, Mollica L, Bottomley MJ, Musco G, Peterson P. The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression. EMBO Rep 2008. [PMID: 18292755 PMCID: PMC2261226 DOI: 10.1038/embor.2008.11] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mutations in the gene autoimmune regulator (AIRE) cause autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. AIRE is expressed in thymic medullary epithelial cells, where it promotes the expression of tissue-restricted antigens. By the combined use of biochemical and biophysical methods, we show that AIRE selectively interacts with histone H3 through its first plant homeodomain (PHD) finger (AIRE–PHD1) and preferentially binds to non-methylated H3K4 (H3K4me0). Accordingly, in vivo AIRE binds to and activates promoters containing low levels of H3K4me3 in human embryonic kidney 293 cells. We conclude that AIRE–PHD1 is an important member of a newly identified class of PHD fingers that specifically recognize H3K4me0, thus providing a new link between the status of histone modifications and the regulation of tissue-restricted antigen expression in thymus.
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Affiliation(s)
- Tõnis Org
- Molecular Pathology, University of Tartu, Tartu 50411, Estonia
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Schuller B, Demuth B, Mix H, Rasch K, Romberg M, Sild S, Maran U, Bała P, del Grosso E, Casalegno M, Piclin N, Pintore M, Sudholt W, Baldridge KK. Chemomentum - UNICORE 6 Based Infrastructure for Complex Applications in Science and Technology. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-3-540-78474-6_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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