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Abstract
In this chapter, we give a brief overview of the regulatory requirements for acute systemic toxicity information in the European Union, and we review structure-based computational models that are available and potentially useful in the assessment of acute systemic toxicity. Emphasis is placed on quantitative structure-activity relationship (QSAR) models implemented by means of a range of software tools. The most recently published literature models for acute systemic toxicity are also discussed, and perspectives for future developments in this field are offered.
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Affiliation(s)
- Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Antonia Diukendjieva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Andrew P Worth
- European Commission, Joint Research Centre (JRC), Ispra, Italy
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Al Sharif M, Alov P, Vitcheva V, Diukendjieva A, Aluani D, Tzankova V, Pajeva I. Development of a Protocol for Virtual Screening of PPARγ Weak Partial Agonists and Their Metabolites: Case Study on Naturally-derived Oleanane Triterpenoids. Int J Bioautomation 2021. [DOI: 10.7546/ijba.2021.25.2.000792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Triterpenoids are well known metabolic syndrome (MetS) modulators. One of the suggested molecular mechanisms of action involves peroxisome proliferator-activated receptor gamma (PPARγ) activation. In this study we aimed to: (i) develop a virtual screening (VS) protocol for PPARγ weak partial agonists, (ii) predict potential metabolic transformations of naturally-derived triterpenoids, and (iii) perform VS of the triterpenoids and their metabolites. The NIH PubMed system was searched for publications about naturally-derived oleanane triterpenoids which are agonists or up-regulators of PPARγ. Structure- and ligand-based methods were combined in the development of the VS protocol. Metabolites were predicted using Meteor Nexus expert system (Lhasa Limited). Two in-house virtual libraries of PPARγ weak partial agonists and naturally-derived triterpenoids with their predicted metabolites were compiled. The pharmacophore-based docking protocol was applied for VS of the collected triterpenoids. Most of the docking poses reproduced the binding mode of caulophyllogenin (a weak partial agonist) in a complex with PPARγ (PDB ID 5F9B). Our results contribute to the mechanistic explanation of the effects of triterpenoids suggesting possible weak partial agonistic activity toward PPARγ. This research can direct further studies on triterpenoids’ role in MetS modulation. The developed protocol can be applied for VS of any PPARγ weak partial agonists.
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Diukendjieva A, Tsakovska I, Alov P, Pencheva T, Pajeva I, Worth AP, Madden JC, Cronin MT. Advances in the prediction of gastrointestinal absorption: Quantitative Structure-Activity Relationship (QSAR) modelling of PAMPA permeability. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.comtox.2018.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Diukendjieva A, Alov P, Tsakovska I, Pencheva T, Richarz A, Kren V, Cronin MTD, Pajeva I. In vitro and in silico studies of the membrane permeability of natural flavonoids from Silybum marianum (L.) Gaertn. and their derivatives. Phytomedicine 2019; 53:79-85. [PMID: 30668415 DOI: 10.1016/j.phymed.2018.09.001] [Citation(s) in RCA: 10] [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: 02/28/2018] [Revised: 07/04/2018] [Accepted: 09/03/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND In recent years the number of natural products used as pharmaceuticals, components of dietary supplements and cosmetics has increased tremendously requiring more extensive evaluation of their pharmacokinetic properties. PURPOSE This study aims at combining in vitro and in silico methods to evaluate the gastrointestinal absorption (GIA) of natural flavonolignans from milk thistle (Silybum marianum (L.) Gaertn.) and their derivatives. METHODS A parallel artificial membrane permeability assay (PAMPA) was used to evaluate the transcellular permeability of the plant main components. A dataset of 269 compounds with measured PAMPA values and specialized software tools for calculating molecular descriptors were utilized to develop a quantitative structure-activity relationship (QSAR) model to predict PAMPA permeability. RESULTS The PAMPA permeabilities of 7 compounds constituting the main components of the milk thistle were measured and their GIA was evaluated. A freely-available and easy to use QSAR model predicting PAMPA permeability from calculated physico-chemical molecular descriptors was derived and validated on an external dataset of 783 compounds with known GIA. The predicted permeability values correlated well with obtained in vitro results. The QSAR model was further applied to predict the GIA of 31 experimentally untested flavonolignans. CONCLUSIONS According to both in vitro and in silico results most flavonolignans are highly permeable in the gastrointestinal tract, which is a prerequisite for sufficient bioavailability and use as lead structures in drug development. The combined in vitro/in silico approach can be used for the preliminary evaluation of GIA and to guide further laboratory experiments on pharmacokinetic characterization of bioactive compounds, including natural products.
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Affiliation(s)
- Antonia Diukendjieva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Block 105, 1113 Sofia, Bulgaria
| | - Petko Alov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Block 105, 1113 Sofia, Bulgaria
| | - Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Block 105, 1113 Sofia, Bulgaria
| | - Tania Pencheva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Block 105, 1113 Sofia, Bulgaria
| | - Andrea Richarz
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England, United Kingdom
| | - Vladimir Kren
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, CZ 14220 Prague, Czech Republic
| | - Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England, United Kingdom
| | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Block 105, 1113 Sofia, Bulgaria.
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Al Sharif M, Diukendjieva A, Alov P, Tsakovska I, Pajeva I. Optimized Structure-based Methodology for Studying PPARγ Partial Agonists. Int J Bioautomation 2018. [DOI: 10.7546/ijba.2018.22.1.65-72] [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: 11/27/2022] Open
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Al Sharif M, Alov P, Diukendjieva A, Vitcheva V, Simeonova R, Krasteva I, Shkondrov A, Tsakovska I, Pajeva I. Molecular determinants of PPARγ partial agonism and related in silico/in vivo studies of natural saponins as potential type 2 diabetes modulators. Food Chem Toxicol 2017; 112:47-59. [PMID: 29247773 DOI: 10.1016/j.fct.2017.12.009] [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: 10/01/2017] [Revised: 12/04/2017] [Accepted: 12/07/2017] [Indexed: 12/29/2022]
Abstract
The metabolic syndrome, which includes hypertension, type 2 diabetes (T2D) and obesity, has reached an epidemic-like scale. Saponins and sapogenins are considered as valuable natural products for ameliorating this pathology, possibly through the nuclear receptor PPARγ activation. The aims of this study were: to look for in vivo antidiabetic effects of a purified saponins' mixture (PSM) from Astragalus corniculatus Bieb; to reveal by in silico methods the molecular determinants of PPARγ partial agonism, and to investigate the potential PPARγ participation in the PSM effects. In the in vivo experiments spontaneously hypertensive rats (SHRs) with induced T2D were treated with PSM or pioglitazone as a referent PPARγ full agonist, and pathology-relevant biochemical markers were analysed. The results provided details on the PSM modulation of the glucose homeostasis and its potential mechanism. The in silico studies focused on analysis of the protein-ligand interactions in crystal structures of human PPARγ-partial agonist complexes, pharmacophore modelling and molecular docking. They outlined key pharmacophoric features, typical for the PPARγ partial agonists, which were used for pharmacophore-based docking of the main PSM sapogenin. The in silico studies, strongly suggest possible involvement of PPARγ-mediated mechanisms in the in vivo antidiabetic and antioxidant effects of PSM from A. corniculatus.
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Affiliation(s)
- Merilin Al Sharif
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 105, 1113 Sofia, Bulgaria.
| | - Petko Alov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 105, 1113 Sofia, Bulgaria.
| | - Antonia Diukendjieva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 105, 1113 Sofia, Bulgaria.
| | - Vessela Vitcheva
- Faculty of Pharmacy, Medical University of Sofia, Dunav 2 Str., 1000 Sofia, Bulgaria.
| | - Rumyana Simeonova
- Faculty of Pharmacy, Medical University of Sofia, Dunav 2 Str., 1000 Sofia, Bulgaria.
| | - Ilina Krasteva
- Faculty of Pharmacy, Medical University of Sofia, Dunav 2 Str., 1000 Sofia, Bulgaria.
| | - Aleksandar Shkondrov
- Faculty of Pharmacy, Medical University of Sofia, Dunav 2 Str., 1000 Sofia, Bulgaria.
| | - Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 105, 1113 Sofia, Bulgaria.
| | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 105, 1113 Sofia, Bulgaria.
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Diukendjieva A, Sharif MA, Alov P, Pencheva T, Tsakovska I, Pajeva I. ADME/Tox Properties and Biochemical Interactions of Silybin Congeners: In silico Study. Nat Prod Commun 2017. [DOI: 10.1177/1934578x1701200208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Silymarin, the active constituent of Silybum marianum (milk thistle), and its main component, silybin, are products with well-known hepatoprotective, cytoprotective, antioxidant, and chemopreventative properties. Despite substantial in vitro and in vivo investigations of these flavonolignans, their mechanisms of action and potential toxic effects are not fully defined. In this study we explored important ADME/Tox properties and biochemical interactions of selected flavonolignans using in silico methods. A quantitative structure–activity relationship (QSAR) model based on data from a parallel artificial membrane permeability assay (PAMPA) was used to estimate bioavailability after oral administration. Toxic effects and metabolic transformations were predicted using the knowledge-based expert systems Derek Nexus and Meteor Nexus (Lhasa Ltd). Potential estrogenic activity of the studied silybin congeners was outlined. To address further the stereospecificity of this effect the stereoisomeric forms of silybin were docked into the ligand-binding domain of the human estrogen receptor alpha (ERα) (MOE software, CCG). According to our results both stereoisomers can be accommodated into the ERα active site, but different poses and interactions were observed for silybin A and silybin B.
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Affiliation(s)
- Antonia Diukendjieva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 105, 1113 Sofia, Bulgaria
| | - Merilin Al Sharif
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 105, 1113 Sofia, Bulgaria
| | - Petko Alov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 105, 1113 Sofia, Bulgaria
| | - Tania Pencheva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 105, 1113 Sofia, Bulgaria
| | - Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 105, 1113 Sofia, Bulgaria
| | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 105, 1113 Sofia, Bulgaria
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Diukendjieva A, Al Sharif M, Alov P, Pencheva T, Tsakovska I, Pajeva I. ADME/Tox Properties and Biochemical Interactions of Silybin Congeners: In silico Study. Nat Prod Commun 2017; 12:175-178. [PMID: 30428204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Silymarin, the active constituent of Silybum marianum (milk thistle), and its main component, silybin, are products with well-known hepatoprotective, cytoprotective, antioxidant, and chemopreventative properties. Despite substantial in vitro and in vivo investigations of these flavonolignans, their mechanisms of action and potential toxic effects are not fully defined. In this study we explored important ADME/Tox properties and biochemical interactions of selected flavonolignans using in silico methods. A quantitative structure-activity relationship (QSAR) model based on data from a parallel artificial membrane permeability assay (PAMPA) was used to estimate bioavailability after oral administration. Toxic effects and metabolic transformations were predicted using the knowledge-based expert systems Derek Nexus and Meteor Nexus (Lhasa Ltd). Potential estrogenic activity of the studied silybin congeners was outlined. To address further the stereospecificity of this effect the stereoisomeric forms of silybin were docked into the ligand-binding domain of the human estrogen receptor alpha (ERa) (MOE software, CCG). According to our results both stereoisomers can be accommodated into the ERa active site, but different poses and interactions were observed for silybin A and silybin B.
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Burton J, Worth AP, Tsakovska I, Diukendjieva A. In Silico Models for Acute Systemic Toxicity. Methods Mol Biol 2016; 1425:177-200. [PMID: 27311468 DOI: 10.1007/978-1-4939-3609-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In this chapter, we give an overview of the regulatory requirements for acute systemic toxicity information in the European Union, and we review the availability of structure-based computational models that are available and potentially useful in the assessment of acute systemic toxicity. The most recently published literature models for acute systemic toxicity are also discussed, and perspectives for future developments in this field are offered.
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Affiliation(s)
- Julien Burton
- Systems Toxicology Unit and EURL ECVAM, Institute for Health and Consumer Protection, Joint Research Centre, European Commission, Ispra, Varese, Italy
| | - Andrew P Worth
- Systems Toxicology Unit and EURL ECVAM, Institute for Health and Consumer Protection, Joint Research Centre, European Commission, Ispra, Varese, Italy.
| | - Ivanka Tsakovska
- Department of QSAR & Molecular Modeling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Antonia Diukendjieva
- Department of QSAR & Molecular Modeling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Tsakovska I, Al Sharif M, Alov P, Diukendjieva A, Fioravanzo E, Cronin MTD, Pajeva I. Molecular modelling study of the PPARγ receptor in relation to the mode of action/adverse outcome pathway framework for liver steatosis. Int J Mol Sci 2014; 15:7651-66. [PMID: 24857909 PMCID: PMC4057697 DOI: 10.3390/ijms15057651] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 03/30/2014] [Revised: 04/18/2014] [Accepted: 04/21/2014] [Indexed: 12/14/2022] Open
Abstract
The comprehensive understanding of the precise mode of action and/or adverse outcome pathway (MoA/AOP) of chemicals has become a key step toward the development of a new generation of predictive toxicology tools. One of the challenges of this process is to test the feasibility of the molecular modelling approaches to explore key molecular initiating events (MIE) within the integrated strategy of MoA/AOP characterisation. The description of MoAs leading to toxicity and liver damage has been the focus of much interest. Growing evidence underlines liver PPARγ ligand-dependent activation as a key MIE in the elicitation of liver steatosis. Synthetic PPARγ full agonists are of special concern, since they may trigger a number of adverse effects not observed with partial agonists. In this study, molecular modelling was performed based on the PPARγ complexes with full agonists extracted from the Protein Data Bank. The receptor binding pocket was analysed, and the specific ligand-receptor interactions were identified for the most active ligands. A pharmacophore model was derived, and the most important pharmacophore features were outlined and characterised in relation to their specific role for PPARγ activation. The results are useful for the characterisation of the chemical space of PPARγ full agonists and could facilitate the development of preliminary filtering rules for the effective virtual ligand screening of compounds with PPARγ full agonistic activity.
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Affiliation(s)
- Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
| | - Merilin Al Sharif
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
| | - Petko Alov
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
| | - Antonia Diukendjieva
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
| | - Elena Fioravanzo
- Soluzioni Informatiche srl, Via Ferrari 14, Vicenza 36100, Italy.
| | - Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK.
| | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering-BAS, Acad. G. Bonchev Str., Bl.105, Sofia 1113, Bulgaria.
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