2017 | |
Gajewicz, A., Jagiello, K., Cronin, M. T. D., Leszczynski, J., Puzyn, T. Addressing a bottle neck for regulation of nanomaterials: quantitative read-across (Nano-QRA) algorithm for cases when only limited data is available (Journal Article) Environ. Sci.: Nano, 4 (2), pp. 346–358, 2017, ISSN: 2051-8153. @article{Gajewicz2017, title = {Addressing a bottle neck for regulation of nanomaterials: quantitative read-across (Nano-QRA) algorithm for cases when only limited data is available}, author = {Gajewicz, A. and Jagiello, K. and Cronin, M. T. D. and Leszczynski, J. and Puzyn, T.}, url = {http://xlink.rsc.org/?DOI=C6EN00399K}, doi = {10.1039/C6EN00399K}, issn = {2051-8153}, year = {2017}, date = {2017-01-01}, journal = {Environ. Sci.: Nano}, volume = {4}, number = {2}, pages = {346--358}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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Toropova, A.P., Toropov, A.A., Veselinović, A.M., Veselinović, J.B., Leszczynska, D., Leszczynski, J. Quasi-SMILES as a Novel Tool for Prediction of Nanomaterials′ Endpoints (Incollection) Multi-Scale Approaches in Drug Discovery, pp. 191–221, Elsevier, 2017. @incollection{Toropova2017, title = {Quasi-SMILES as a Novel Tool for Prediction of Nanomaterials′ Endpoints}, author = {Toropova, A.P. and Toropov, A.A. and Veselinovi\'{c}, A.M. and Veselinovi\'{c}, J.B. and Leszczynska, D. and Leszczynski, J.}, url = {http://linkinghub.elsevier.com/retrieve/pii/B9780081011294000084}, doi = {10.1016/B978-0-08-101129-4.00008-4}, year = {2017}, date = {2017-01-01}, booktitle = {Multi-Scale Approaches in Drug Discovery}, pages = {191--221}, publisher = {Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
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Kar, Supratik, Roy, Kunal, Leszczynski, Jerzy On Applications of QSARs in Food and Agricultural Sciences: History and Critical Review of Recent Developments (Incollection) pp. 203–302, 2017. @incollection{Kar2017, title = {On Applications of QSARs in Food and Agricultural Sciences: History and Critical Review of Recent Developments}, author = {Kar, Supratik and Roy, Kunal and Leszczynski, Jerzy}, url = {http://link.springer.com/10.1007/978-3-319-56850-8_7}, doi = {10.1007/978-3-319-56850-8_7}, year = {2017}, date = {2017-01-01}, pages = {203--302}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
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Ahmed, Lucky, Rasulev, Bakhtiyor, Kar, Supratik, Krupa, Paweł, Mozolewska, Magdalena A., Leszczynski, Jerzy Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose (Journal Article) Nanoscale, 9 (29), pp. 10263–10276, 2017, ISSN: 2040-3364. (Abstract | Links | BibTeX | Tags: ) @article{Ahmed2017, title = {Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose}, author = {Ahmed, Lucky and Rasulev, Bakhtiyor and Kar, Supratik and Krupa, Pawe{\l} and Mozolewska, Magdalena A. and Leszczynski, Jerzy}, url = {http://xlink.rsc.org/?DOI=C7NR00770A}, doi = {10.1039/C7NR00770A}, issn = {2040-3364}, year = {2017}, date = {2017-01-01}, journal = {Nanoscale}, volume = {9}, number = {29}, pages = {10263--10276}, abstract = {Fullerene-based nanoparticles have been the subject of vital interest due to their unique properties and potential application in many areas, including medicine.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fullerene-based nanoparticles have been the subject of vital interest due to their unique properties and potential application in many areas, including medicine. |
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Natalia Sizochenko, Danuta Leszczynska, Jerzy Leszczynski Nanomaterials, 7 (10), pp. 330, 2017, ISSN: 2079-4991. (Links | BibTeX | Tags: causality, liquid drop model, Metal oxide nanoparticles, molecular descriptors, QSAR, regression tree, Toxicity, zebrafish) @article{Sizochenko2017b, title = {Modeling of Interactions between the Zebrafish Hatching Enzyme ZHE1 and A Series of Metal Oxide Nanoparticles: Nano-QSAR and Causal Analysis of Inactivation Mechanisms}, author = { Natalia Sizochenko and Danuta Leszczynska and Jerzy Leszczynski}, url = {http://www.mdpi.com/2079-4991/7/10/330}, doi = {10.3390/nano7100330}, issn = {2079-4991}, year = {2017}, date = {2017-01-01}, journal = {Nanomaterials}, volume = {7}, number = {10}, pages = {330}, keywords = {causality, liquid drop model, Metal oxide nanoparticles, molecular descriptors, QSAR, regression tree, Toxicity, zebrafish}, pubstate = {published}, tppubtype = {article} } |
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Natalia Sizochenko, Jerzy Leszczynski Drug-Nanoparticle Composites (Journal Article) Journal of Nanotoxicology and Nanomedicine, 2 (1), pp. 1–10, 2017, ISSN: 2379-7452. (Links | BibTeX | Tags: classifie, descriptors, drug delivery, drug-polymer interactions, molecular docking, plga) @article{Sizochenko2017a, title = {Drug-Nanoparticle Composites}, author = { Natalia Sizochenko and Jerzy Leszczynski}, url = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/JNN.2017010101}, doi = {10.4018/JNN.2017010101}, issn = {2379-7452}, year = {2017}, date = {2017-01-01}, journal = {Journal of Nanotoxicology and Nanomedicine}, volume = {2}, number = {1}, pages = {1--10}, keywords = {classifie, descriptors, drug delivery, drug-polymer interactions, molecular docking, plga}, pubstate = {published}, tppubtype = {article} } |
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Alicja Mikolajczyk, Natalia Sizochenko, Ewa Mulkiewicz, Anna Malankowska, Michal Nischk, Przemyslaw Jurczak, Seishiro Hirano, Grzegorz Nowaczyk, Adriana Zaleska-Medynska, Jerzy Leszczynski, , Agnieszka Gajewicz, Tomasz Puzyn Evaluating the toxicity of TiO2-based nanoparticles to Chinese hamster ovary cells and Escherichia coli: a complementary experimental and computational approach (Journal Article) Nanomaterials, accepted , pp. 2171–2180, 2017, ISSN: 2190-4286. (Links | BibTeX | Tags: 2017, 2171, 2180, 8, au, beilstein j, bimetallic nanoparticles, Nano-QSAR, nanotechnol, nanotoxicity, pd, second-generation nanoparticles, tio 2 photocatalyst) @article{Mikolajczyk2017, title = {Evaluating the toxicity of TiO2-based nanoparticles to Chinese hamster ovary cells and Escherichia coli: a complementary experimental and computational approach}, author = { Alicja Mikolajczyk and Natalia Sizochenko and Ewa Mulkiewicz and Anna Malankowska and Michal Nischk and Przemyslaw Jurczak and Seishiro Hirano and Grzegorz Nowaczyk and Adriana Zaleska-Medynska and Jerzy Leszczynski, and Agnieszka Gajewicz and Tomasz Puzyn}, doi = {10.3762/bjnano.8.216}, issn = {2190-4286}, year = {2017}, date = {2017-01-01}, journal = {Nanomaterials}, volume = {accepted}, pages = {2171--2180}, keywords = {2017, 2171, 2180, 8, au, beilstein j, bimetallic nanoparticles, Nano-QSAR, nanotechnol, nanotoxicity, pd, second-generation nanoparticles, tio 2 photocatalyst}, pubstate = {published}, tppubtype = {article} } |
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A. Gooch, N. Sizochenko, L. Sviatenko, L. Gorb, J. Leszczynski A quantum chemical based toxicity study of estimated reduction potential and hydrophobicity in series of nitroaromatic compounds (Journal Article) SAR and QSAR in Environmental Research, 28 (2), pp. 133–150, 2017, ISSN: 1029046X. (Abstract | Links | BibTeX | Tags: hydrophobicity, LUMO energy, nitroaromatic, QSAR, reduction potential, Toxicity) @article{Gooch2017b, title = {A quantum chemical based toxicity study of estimated reduction potential and hydrophobicity in series of nitroaromatic compounds}, author = { A. Gooch and N. Sizochenko and L. Sviatenko and L. Gorb and J. Leszczynski}, url = {http://dx.doi.org/10.1080/1062936X.2017.1286687}, doi = {10.1080/1062936X.2017.1286687}, issn = {1029046X}, year = {2017}, date = {2017-01-01}, journal = {SAR and QSAR in Environmental Research}, volume = {28}, number = {2}, pages = {133--150}, publisher = {Taylor & Francis}, abstract = {Nitroaromatic compounds and the products of their degradation are toxic to bacteria, cells and animals. Various studies have been carried out to better understand the mechanism of toxicity of aromatic nitrocompounds and their relationship to humans and the environment. Recent data relate cytotoxicity of nitroaromatic compounds to their single- or two-electron enzymatic reduction. However, mechanisms of animal toxicity could be more complex. This work investigates the estimated reduction and oxidation potentials of 34 nitroaromatic compounds using quantum chemical approaches. All geometries were optimized with density functional theory (DFT) using the solvation model based on density (SMD) and polarizable continuum model (PCM) solvent model protocols. Quantitative structure-activity/property (QSAR/QSPR) models were developed using descriptors obtained from quantum chemical optimizations as well as the DRAGON software program. The QSAR/QSPR equations developed consist of two to four descriptors. Correlations have been identified between electron affinity (ELUMO) and hydrophobicity (log P).}, keywords = {hydrophobicity, LUMO energy, nitroaromatic, QSAR, reduction potential, Toxicity}, pubstate = {published}, tppubtype = {article} } Nitroaromatic compounds and the products of their degradation are toxic to bacteria, cells and animals. Various studies have been carried out to better understand the mechanism of toxicity of aromatic nitrocompounds and their relationship to humans and the environment. Recent data relate cytotoxicity of nitroaromatic compounds to their single- or two-electron enzymatic reduction. However, mechanisms of animal toxicity could be more complex. This work investigates the estimated reduction and oxidation potentials of 34 nitroaromatic compounds using quantum chemical approaches. All geometries were optimized with density functional theory (DFT) using the solvation model based on density (SMD) and polarizable continuum model (PCM) solvent model protocols. Quantitative structure-activity/property (QSAR/QSPR) models were developed using descriptors obtained from quantum chemical optimizations as well as the DRAGON software program. The QSAR/QSPR equations developed consist of two to four descriptors. Correlations have been identified between electron affinity (ELUMO) and hydrophobicity (log P). |
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Ali Mirchi, Natalia Sizochenko, Tandabany C. Dinadayalane, Jerzy Leszczynski Binding of alkali metal ions with 1,3,5- Tri(phenyl)benzene and 1,3,5-Tris(naphthyl)benzene: The effect of phenyl and naphthyl rings substitution on cation-$pi$ interactions revealed by DFT study (Journal Article) (Submitted for publication), 2017. (BibTeX | Tags: ) @article{Mirchi2017, title = {Binding of alkali metal ions with 1,3,5- Tri(phenyl)benzene and 1,3,5-Tris(naphthyl)benzene: The effect of phenyl and naphthyl rings substitution on cation-$pi$ interactions revealed by DFT study}, author = { Ali Mirchi and Natalia Sizochenko and Tandabany C. Dinadayalane and Jerzy Leszczynski}, year = {2017}, date = {2017-01-01}, journal = {(Submitted for publication)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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Ali Mirchi, Natalia Sizochenko, Jerzy Leszczynski Fullerene quinazolinone conjugates targeting Mycobacterium tuberculosis: A combination of molecular docking, QSAR and ONIOM approaches (Journal Article) (Submitted for publication), 2017. (BibTeX | Tags: ) @article{Mirchi2017a, title = {Fullerene quinazolinone conjugates targeting Mycobacterium tuberculosis: A combination of molecular docking, QSAR and ONIOM approaches}, author = { Ali Mirchi and Natalia Sizochenko and Jerzy Leszczynski}, year = {2017}, date = {2017-01-01}, journal = {(Submitted for publication)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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2016 | |
Supratik Kar, Natalia Sizochenko, Lucky Ahmed, Victor S. Batista, Jerzy Leszczynski Nano Energy, 26 , pp. 677–691, 2016, ISSN: 22112855. (Abstract | Links | BibTeX | Tags: ) @article{Kar2016b, title = {Quantitative structure-property relationship model leading to virtual screening of fullerene derivatives: Exploring structural attributes critical for photoconversion efficiency of polymer solar cell acceptors}, author = { Supratik Kar and Natalia Sizochenko and Lucky Ahmed and Victor S. Batista and Jerzy Leszczynski}, url = {http://dx.doi.org/10.1016/j.nanoen.2016.06.011 http://linkinghub.elsevier.com/retrieve/pii/S2211285516301914}, doi = {10.1016/j.nanoen.2016.06.011}, issn = {22112855}, year = {2016}, date = {2016-08-01}, journal = {Nano Energy}, volume = {26}, pages = {677--691}, abstract = {The power conversion efficiency (PCE) of pure polymer solar cells (PSCs) remains low, although significantly higher values could be achieved by using PSCs as carrier donors in conjunction with composite fullerene derivative (FD) acceptors. Significant resources, however, are required to experimentally develop and screen FDs that may serve as efficient acceptors in PSCs. Often, the materials are expensive, the methods are time consuming, and the production processes can generate toxic hazards. As an alternative approach, we introduce a quantitative structure-property relationship (QSPR) model for predicting the PCE of 59 FDs, including both C60 and C70 FDs. The QSPR model enables identification of the essential structural attributes necessary for quantifying the molecular prerequisites of diverse FDs, chiefly responsible for high PCE of PSC acceptors in composition with poly(3-hexylthiophene) (P3HT). The identified properties and structural fragments are particularly valuable for guiding future synthetic efforts for development of FDs with improved power conversion efficiency. Furthermore, a large number of FDs are collected to generate a database. Virtual screening of the database employing the developed QSPR model allows for identification of nine FDs with higher PCE than previously studied FDs}, keywords = {}, pubstate = {published}, tppubtype = {article} } The power conversion efficiency (PCE) of pure polymer solar cells (PSCs) remains low, although significantly higher values could be achieved by using PSCs as carrier donors in conjunction with composite fullerene derivative (FD) acceptors. Significant resources, however, are required to experimentally develop and screen FDs that may serve as efficient acceptors in PSCs. Often, the materials are expensive, the methods are time consuming, and the production processes can generate toxic hazards. As an alternative approach, we introduce a quantitative structure-property relationship (QSPR) model for predicting the PCE of 59 FDs, including both C60 and C70 FDs. The QSPR model enables identification of the essential structural attributes necessary for quantifying the molecular prerequisites of diverse FDs, chiefly responsible for high PCE of PSC acceptors in composition with poly(3-hexylthiophene) (P3HT). The identified properties and structural fragments are particularly valuable for guiding future synthetic efforts for development of FDs with improved power conversion efficiency. Furthermore, a large number of FDs are collected to generate a database. Virtual screening of the database employing the developed QSPR model allows for identification of nine FDs with higher PCE than previously studied FDs |
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Wojciech Kolodziejczyk, Supratik Kar, Glake A. Hill, Jerzy Leszczynski A comprehensive computational analysis of cathinone and its metabolites using quantum mechanical approaches and docking studies (Journal Article) Structural Chemistry, 27 (4), pp. 1291–1302, 2016, ISSN: 1040-0400. (Abstract | Links | BibTeX | Tags: ) @article{Kolodziejczyk2016, title = {A comprehensive computational analysis of cathinone and its metabolites using quantum mechanical approaches and docking studies}, author = { Wojciech Kolodziejczyk and Supratik Kar and Glake A. Hill and Jerzy Leszczynski}, url = {http://link.springer.com/10.1007/s11224-016-0779-9}, doi = {10.1007/s11224-016-0779-9}, issn = {1040-0400}, year = {2016}, date = {2016-08-01}, journal = {Structural Chemistry}, volume = {27}, number = {4}, pages = {1291--1302}, abstract = {Conformers of the psychoactive compound of the Khat plant cathinone along with its amino alcohol metabolites norephedrine and norpseudoephedrine have been calculated using DFT (M062X/B3LYP) and MP2 levels of theory for gas and solution phases. Gas-phase studies revealed that cathinone has two, norephedrine has four and norpseudoephedrine has three low-energy conformations with all conformers connected by rotational transition states. To understand the solvent effect to the energetic profiles of the studied species, the conductor-like screening model is employed within aqueous medium. It explains lowering of energy of all studied conformers in solution. The molecular electrostatic potential surface data for each molecule revealed likely reaction sites for the studied molecules. The computed IR spectra for cathinone and its metabolites have been compared with experimental data and rotational transition states connecting all conformers have been reported. The natural bond orbital analyses for only ligands and separately for their complexes with amino acid residues in protein pockets from the docking results are also performed to corroborate the results obtained from the MP2 and DFT calculations. The comprehensive computational study explore important amino acid residues}, keywords = {}, pubstate = {published}, tppubtype = {article} } Conformers of the psychoactive compound of the Khat plant cathinone along with its amino alcohol metabolites norephedrine and norpseudoephedrine have been calculated using DFT (M062X/B3LYP) and MP2 levels of theory for gas and solution phases. Gas-phase studies revealed that cathinone has two, norephedrine has four and norpseudoephedrine has three low-energy conformations with all conformers connected by rotational transition states. To understand the solvent effect to the energetic profiles of the studied species, the conductor-like screening model is employed within aqueous medium. It explains lowering of energy of all studied conformers in solution. The molecular electrostatic potential surface data for each molecule revealed likely reaction sites for the studied molecules. The computed IR spectra for cathinone and its metabolites have been compared with experimental data and rotational transition states connecting all conformers have been reported. The natural bond orbital analyses for only ligands and separately for their complexes with amino acid residues in protein pockets from the docking results are also performed to corroborate the results obtained from the MP2 and DFT calculations. The comprehensive computational study explore important amino acid residues |
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Alla P. Toropova, Andrey A. Toropov, Aleksandar M. Veselinović, Jovana B. Veselinović, Danuta Leszczynska, Jerzy Leszczynski Monte Carlo-based quantitative structure-activity relationship models for toxicity of organic chemicals to Daphnia magna (Journal Article) Environmental Toxicology and Chemistry, 2016, ISSN: 07307268. (Abstract | Links | BibTeX | Tags: ) @article{Toropova2016b, title = {Monte Carlo-based quantitative structure-activity relationship models for toxicity of organic chemicals to Daphnia magna}, author = { Alla P. Toropova and Andrey A. Toropov and Aleksandar M. Veselinovi\'{c} and Jovana B. Veselinovi\'{c} and Danuta Leszczynska and Jerzy Leszczynski}, url = {http://doi.wiley.com/10.1002/etc.3466}, doi = {10.1002/etc.3466}, issn = {07307268}, year = {2016}, date = {2016-07-01}, journal = {Environmental Toxicology and Chemistry}, abstract = {Quantitative structure{\textendash}activity relationships (QSARs) for toxicity of a large set of 758 organic compounds to Daphnia magna were built up. The simplified molecular input-line entry system (SMILES) was used to represent the molecular structure. The Correlation and Logic (CORAL) software was utilized as a tool to develop the QSAR models. These models are built up using the Monte Carlo method and according to the principle “QSAR is a random event” if one checks a group of random distributions in the visible training set and the invisible validation set. Three distributions of the data into the visible training, calibration, and invisible validation sets are examined. The predictive potentials (i.e., statistical characteristics for the invisible validation set of the best model) are as follows: n ¼ 87, r 2 ¼ 0.8377, root mean square error ¼ 0.564. The mechanistic interpretations and the domain of applicability of built models are suggested and discussed}, keywords = {}, pubstate = {published}, tppubtype = {article} } Quantitative structure–activity relationships (QSARs) for toxicity of a large set of 758 organic compounds to Daphnia magna were built up. The simplified molecular input-line entry system (SMILES) was used to represent the molecular structure. The Correlation and Logic (CORAL) software was utilized as a tool to develop the QSAR models. These models are built up using the Monte Carlo method and according to the principle “QSAR is a random event” if one checks a group of random distributions in the visible training set and the invisible validation set. Three distributions of the data into the visible training, calibration, and invisible validation sets are examined. The predictive potentials (i.e., statistical characteristics for the invisible validation set of the best model) are as follows: n ¼ 87, r 2 ¼ 0.8377, root mean square error ¼ 0.564. The mechanistic interpretations and the domain of applicability of built models are suggested and discussed |
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Supratik Kar, Rudra Narayan Das, Kunal Roy, Jerzy Leszczynski Can Toxicity for Different Species be Correlated? (Journal Article) International Journal of Quantitative Structure-Property Relationships, 1 (2), pp. 23–51, 2016, ISSN: 2379-7487. (Abstract | Links | BibTeX | Tags: Extrapolation, i-QSTR, Interspecies Correlation, Mode of Action, QSAR, REACH, Toxicity, US EPA) @article{Kar2016, title = {Can Toxicity for Different Species be Correlated?}, author = { Supratik Kar and Rudra Narayan Das and Kunal Roy and Jerzy Leszczynski}, url = {http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/IJQSPR.2016070102}, doi = {10.4018/IJQSPR.2016070102}, issn = {2379-7487}, year = {2016}, date = {2016-06-01}, journal = {International Journal of Quantitative Structure-Property Relationships}, volume = {1}, number = {2}, pages = {23--51}, abstract = {Experimental evaluation of the toxicity of a compound is an expensive practice, and it requires sacrifice of a large number of animals. As a consequence, in silico techniques for predictive toxicology are taking the central stage of attention of the scientific community. Interspecies quantitative structuretoxicity relationship (i-QSTR) modeling provides a tool for estimation of contaminant's sensitivity with known levels of uncertainty for a diverse pool of species. It is capable of extrapolating data for one toxicity endpoint to another toxicity endpoint when the data for the second species are unavailable. The emerging i-QSTR approach can overcome the cost of multiple toxicity tests, improve the understanding of the mechanism of toxic action (MOA) of chemicals for different organisms and endpoints and is very useful in order to fill the data gaps where toxicity value for a particular compound is absent for a specific endpoint.}, keywords = {Extrapolation, i-QSTR, Interspecies Correlation, Mode of Action, QSAR, REACH, Toxicity, US EPA}, pubstate = {published}, tppubtype = {article} } Experimental evaluation of the toxicity of a compound is an expensive practice, and it requires sacrifice of a large number of animals. As a consequence, in silico techniques for predictive toxicology are taking the central stage of attention of the scientific community. Interspecies quantitative structuretoxicity relationship (i-QSTR) modeling provides a tool for estimation of contaminant's sensitivity with known levels of uncertainty for a diverse pool of species. It is capable of extrapolating data for one toxicity endpoint to another toxicity endpoint when the data for the second species are unavailable. The emerging i-QSTR approach can overcome the cost of multiple toxicity tests, improve the understanding of the mechanism of toxic action (MOA) of chemicals for different organisms and endpoints and is very useful in order to fill the data gaps where toxicity value for a particular compound is absent for a specific endpoint. |
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Hayriye Yilmaz, Lucky Ahmed, Bakhtiyor Rasulev, Jerzy Leszczynski Application of ligand- and receptor-based approaches for prediction of the HIV-RT inhibitory activity of fullerene derivatives (Journal Article) Journal of Nanoparticle Research, 18 (5), pp. 123, 2016, ISSN: 1388-0764. (Abstract | Links | BibTeX | Tags: ) @article{Yilmaz2016, title = {Application of ligand- and receptor-based approaches for prediction of the HIV-RT inhibitory activity of fullerene derivatives}, author = { Hayriye Yilmaz and Lucky Ahmed and Bakhtiyor Rasulev and Jerzy Leszczynski}, url = {http://link.springer.com/10.1007/s11051-016-3429-7}, doi = {10.1007/s11051-016-3429-7}, issn = {1388-0764}, year = {2016}, date = {2016-05-01}, journal = {Journal of Nanoparticle Research}, volume = {18}, number = {5}, pages = {123}, abstract = {Fullerene and its derivatives have potential to be utilized in many biomedical applications. In the present study, we investigated the role of fullerene derivatives as inhibitors of HIV-RT by combined protein{\textendash}ligand docking approach and QSAR methods. The study shows the best predictive QSAR model that represents a two-variable model. It has a good ratio of the number of descriptors and predictive ability. The main contributions to the inhibitory activity are provided by signal JhetZ descriptor and l (dipole moment, as a measure of the polarity of a compound). The developed GA-MLRA-based model demonstrates a good performance, confirmed by statistics R2 training ¼ 0:867; Q2 ¼ 0:788; R2 test ¼ 0:902 : The structure{\textendash}activity analysis of these fullerene analogues allowed us to design and suggest for synthesis a set of new potentially active fullerenes. Finally, the molecular docking analysis was carried out to understand the details of interactions between HIV-RT and fullerene-C60 derivatives.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fullerene and its derivatives have potential to be utilized in many biomedical applications. In the present study, we investigated the role of fullerene derivatives as inhibitors of HIV-RT by combined protein–ligand docking approach and QSAR methods. The study shows the best predictive QSAR model that represents a two-variable model. It has a good ratio of the number of descriptors and predictive ability. The main contributions to the inhibitory activity are provided by signal JhetZ descriptor and l (dipole moment, as a measure of the polarity of a compound). The developed GA-MLRA-based model demonstrates a good performance, confirmed by statistics R2 training ¼ 0:867; Q2 ¼ 0:788; R2 test ¼ 0:902 : The structure–activity analysis of these fullerene analogues allowed us to design and suggest for synthesis a set of new potentially active fullerenes. Finally, the molecular docking analysis was carried out to understand the details of interactions between HIV-RT and fullerene-C60 derivatives. |
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Books & Articles
2017 | |
Addressing a bottle neck for regulation of nanomaterials: quantitative read-across (Nano-QRA) algorithm for cases when only limited data is available (Journal Article) Environ. Sci.: Nano, 4 (2), pp. 346–358, 2017, ISSN: 2051-8153. |
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Quasi-SMILES as a Novel Tool for Prediction of Nanomaterials′ Endpoints (Incollection) Multi-Scale Approaches in Drug Discovery, pp. 191–221, Elsevier, 2017. |
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On Applications of QSARs in Food and Agricultural Sciences: History and Critical Review of Recent Developments (Incollection) pp. 203–302, 2017. |
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Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose (Journal Article) Nanoscale, 9 (29), pp. 10263–10276, 2017, ISSN: 2040-3364. |
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Nanomaterials, 7 (10), pp. 330, 2017, ISSN: 2079-4991. |
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Drug-Nanoparticle Composites (Journal Article) Journal of Nanotoxicology and Nanomedicine, 2 (1), pp. 1–10, 2017, ISSN: 2379-7452. |
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Evaluating the toxicity of TiO2-based nanoparticles to Chinese hamster ovary cells and Escherichia coli: a complementary experimental and computational approach (Journal Article) Nanomaterials, accepted , pp. 2171–2180, 2017, ISSN: 2190-4286. |
|
A quantum chemical based toxicity study of estimated reduction potential and hydrophobicity in series of nitroaromatic compounds (Journal Article) SAR and QSAR in Environmental Research, 28 (2), pp. 133–150, 2017, ISSN: 1029046X. |
|
Binding of alkali metal ions with 1,3,5- Tri(phenyl)benzene and 1,3,5-Tris(naphthyl)benzene: The effect of phenyl and naphthyl rings substitution on cation-$pi$ interactions revealed by DFT study (Journal Article) (Submitted for publication), 2017. |
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Fullerene quinazolinone conjugates targeting Mycobacterium tuberculosis: A combination of molecular docking, QSAR and ONIOM approaches (Journal Article) (Submitted for publication), 2017. |
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2016 | |
Nano Energy, 26 , pp. 677–691, 2016, ISSN: 22112855. |
|
A comprehensive computational analysis of cathinone and its metabolites using quantum mechanical approaches and docking studies (Journal Article) Structural Chemistry, 27 (4), pp. 1291–1302, 2016, ISSN: 1040-0400. |
|
Monte Carlo-based quantitative structure-activity relationship models for toxicity of organic chemicals to Daphnia magna (Journal Article) Environmental Toxicology and Chemistry, 2016, ISSN: 07307268. |
|
Can Toxicity for Different Species be Correlated? (Journal Article) International Journal of Quantitative Structure-Property Relationships, 1 (2), pp. 23–51, 2016, ISSN: 2379-7487. |
|
Application of ligand- and receptor-based approaches for prediction of the HIV-RT inhibitory activity of fullerene derivatives (Journal Article) Journal of Nanoparticle Research, 18 (5), pp. 123, 2016, ISSN: 1388-0764. |
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