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Cui GY, Zou JW, Chen J, Hu GX, Jiang YJ, Huang M. QSPR study on Hydrophobicity of Pt(II) complexes with surface electrostatic potential-based descriptors. J Mol Graph Model 2022; 116:108256. [PMID: 35764021 DOI: 10.1016/j.jmgm.2022.108256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 12/14/2022]
Abstract
Pt(II) complexes play an important role in bioinorganic chemistry due to their antitumor activities. In the present study, we focused on building predictive models for the hydrophobicity of Pt(II) complexes. A five-parameter model, integrating frontier orbital energies (EHOMO, ELUMO) and descriptors derived from electrostatic potentials on molecular surface, was firstly constructed by using multiple linear regression (MLR) method. Mechanistic interpretations of the introduced descriptors were elucidated in terms of intermolecular interactions in the n-octanol/water partition system. Then, four up-to-date modeling methods, including support vector machine (SVM), least-squares support vector machine (LSSVM), random forest (RF) and Gaussian process (GP), were utilized to build the nonlinear models. Systematical validations including leave-one-out cross-validation, the validation for test set, as well as a very rigorous Monte Carlo cross-validation (MCCV) were performed to verify the reliability of the constructed models. The peak, median and integralRext2 values of the best GP model are 0.88, 0.86 and 0.84, respectively. The root mean squared errors for the test set (RMSEP) of the MLR, SVM, LSSVM and GP models fall in the range of 0.62-0.71. Although they are not superior to prior models built with the use of a number of descriptors, the results are satisfactory. Applicability domain of the model was evaluated.
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Affiliation(s)
- Guang-Yang Cui
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, 315100, China; College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jian-Wei Zou
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, 315100, China.
| | - Jia Chen
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, 315100, China
| | - Gui-Xiang Hu
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, 315100, China
| | - Yong-Jun Jiang
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, 315100, China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
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Prediction of pEC50(M) and molecular docking study for the selective inhibition of arachidonate 5-lipoxygenase. UKRAINIAN BIOCHEMICAL JOURNAL 2021. [DOI: 10.15407/ubj93.06.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Lotfi S, Ahmadi S, Kumar P. A hybrid descriptor based QSPR model to predict the thermal decomposition temperature of imidazolium ionic liquids using Monte Carlo approach. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116465] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Song P, Xiao S, Zhang Y, Xie J, Cui X. Mechanism of the Intestinal Absorption of Six Flavonoids from Zizyphi Spinosi Semen Across Caco-2 Cell Monolayer Model. Curr Drug Metab 2021; 21:633-645. [PMID: 32664838 DOI: 10.2174/1389200221666200714100455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/17/2020] [Accepted: 05/18/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Flavonoid compounds are one kind of active ingredients isolated from a traditional Chinese herb Zizyphi spinosae semen (ZSS). Studies have shown that ZSS flavonoids have significant antioxidant effects. METHODS In this study, the Caco-2 cell monolayer model was constructed to investigate the intestinal absorption characteristics and mechanism of Isovitexin (IV), Swertisin (ST), Isovitexin-2''-O-β-D-glucopyranoside (IVG), Spinosin (S), 6'''-p-coumaroylspinosin (6-CS) and 6'''-feruloylspinosin (6-FS). RESULTS The results of the bidirectional transport assay showed that the six flavonoids have good intestinal absorption in a near-neutral and 37°C environment, and the absorbability in descending order was 6-FS>6- CS>IVG>S>IV>ST. The results of carrier inhibition experiments and transport kinetics indicated that the absorption mechanism of six flavonoids was energy-dependent monocarboxylate transporter (MCT)-mediated active transport. In particular, the para-cellular pathway also participated in the transport of IV, ST, IVG and S. Furthermore, the efflux process of six flavonoids was mediated by P-glycoprotein (P-gp) and multidrug resistance protein (MRP), which may result in a decrease of bioavailability. CONCLUSION Our findings provide significant information for revealing the relationship between the intestinal absorption mechanism of flavonoids and its structure as well as laying a basis for the research of flavonoid preparations.
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Affiliation(s)
- Panpan Song
- College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Sa Xiao
- College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Yanqing Zhang
- College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Junbo Xie
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Xusheng Cui
- Shijiazhuang Yiling pharmaceutical Co. Ltd, Hebei, 050035, China
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Evaluation of molecular structure based descriptors for the prediction of pEC50(M) for the selective adenosine A2A Receptor. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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The predictive model for band gap prediction of metal oxide nanoparticles based on quasi-SMILES. Struct Chem 2021. [DOI: 10.1007/s11224-021-01748-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Zou JW, Cui GY, Huang M, Hu GX, Jiang YJ. Prediction of the hydrophobicity of platinum(IV) complexes based on molecular surface properties. J Inorg Biochem 2021; 217:111373. [PMID: 33578249 DOI: 10.1016/j.jinorgbio.2021.111373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/10/2021] [Accepted: 01/21/2021] [Indexed: 11/27/2022]
Abstract
A quantitative structure-property relationship (QSPR) study was performed for predicting the hydrophobicity of Pt(IV) complexes. Two four-parameter equations, one based solely on structural descriptors derived from electrostatic potentials (ESPs) on molecular surface, and the other integrated ESP descriptors with molecular surface area (AS), were firstly constructed. Mechanistic interpretations of the structural descriptors introduced were elucidated in terms of solute-solvent intermolecular interactions. Subsequently, several up-to-date modeling techniques, including support vector machine (SVM), least-squares support vector machine (LSSVM), random forest (RF) and Gaussian process (GP), were utilized to build the nonlinear models. Systematical validations including leave-one-out cross-validation, the validation for test set, as well as a more rigorous Monte Carlo cross-validation were performed to verify the reliability of the constructed models. The predictive performances of the four different nonlinear modeling methods follow the order of LSSVM≈GP > RF > SVM. The pure-ESP-based models are generally inferior to the AS-integrated ones. Comparisons with previous results were made.
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Affiliation(s)
- Jian-Wei Zou
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, China.
| | - Guang-Yang Cui
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK
| | - Gui-Xiang Hu
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, China
| | - Yong-Jun Jiang
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315100, China
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Toropov AA, Toropova AP. The Monte Carlo Method as a Tool to Build up Predictive QSPR/QSAR. Curr Comput Aided Drug Des 2020; 16:197-206. [DOI: 10.2174/1573409915666190328123112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/15/2019] [Accepted: 03/19/2019] [Indexed: 11/22/2022]
Abstract
Background:
The Monte Carlo method has a wide application in various scientific researches.
For the development of predictive models in a form of the quantitative structure-property / activity relationships
(QSPRs/QSARs), the Monte Carlo approach also can be useful. The CORAL software provides the
Monte Carlo calculations aimed to build up QSPR/QSAR models for different endpoints.
Methods:
Molecular descriptors are a mathematical function of so-called correlation weights of various
molecular features. The numerical values of the correlation weights give the maximal value of a target
function. The target function leads to a correlation between endpoint and optimal descriptor for the visible
training set. The predictive potential of the model is estimated with the validation set, i.e. compounds that
are not involved in the process of building up the model.
Results:
The approach gave quite good models for a large number of various physicochemical, biochemical,
ecological, and medicinal endpoints. Bibliography and basic statistical characteristics of several CORAL
models are collected in the present review. In addition, the extended version of the approach for more
complex systems (nanomaterials and peptides), where behaviour of systems is defined by a group of conditions
besides the molecular structure is demonstrated.
Conclusion:
The Monte Carlo technique available via the CORAL software can be a useful and convenient
tool for the QSPR/QSAR analysis.
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Affiliation(s)
- Andrey A. Toropov
- Laboratory of Environmental Chemistry and Toxicology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156 Milan, Italy
| | - Alla P. Toropova
- Laboratory of Environmental Chemistry and Toxicology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156 Milan, Italy
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Toropova AP, Toropov AA. Whether the Validation of the Predictive Potential of Toxicity Models is a Solved Task? Curr Top Med Chem 2019; 19:2643-2657. [PMID: 31702504 DOI: 10.2174/1568026619666191105111817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/23/2022]
Abstract
Different kinds of biological activities are defined by complex biochemical interactions, which are termed as a "mathematical function" not only of the molecular structure but also for some additional circumstances, such as physicochemical conditions, interactions via energy and information effects between a substance and organisms, organs, cells. These circumstances lead to the great complexity of prediction for biochemical endpoints, since all "details" of corresponding phenomena are practically unavailable for the accurate registration and analysis. Researchers have not a possibility to carry out and analyse all possible ways of the biochemical interactions, which define toxicological or therapeutically attractive effects via direct experiment. Consequently, a compromise, i.e. the development of predictive models of the above phenomena, becomes necessary. However, the estimation of the predictive potential of these models remains a task that is solved only partially. This mini-review presents a collection of attempts to be used for the above-mentioned task, two special statistical indices are proposed, which may be a measure of the predictive potential of models. These indices are (i) Index of Ideality of Correlation; and (ii) Correlation Contradiction Index.
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Affiliation(s)
- Alla P Toropova
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156 Milano, Italy
| | - Andrey A Toropov
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156 Milano, Italy
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Achary P, Toropova A, Toropov A. Combinations of graph invariants and attributes of simplified molecular input-line entry system (SMILES) to build up models for sweetness. Food Res Int 2019; 122:40-46. [DOI: 10.1016/j.foodres.2019.03.067] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/09/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022]
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“Ideal correlations” for biological activity of peptides. Biosystems 2019; 181:51-57. [DOI: 10.1016/j.biosystems.2019.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/18/2019] [Accepted: 04/12/2019] [Indexed: 02/08/2023]
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Toropova MA, Raškova M, Raška I, Toropova AP. The Index of Ideality of Correlation (IIC): model for sweetness. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-2368-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Toropova AP, Toropov AA. Does the Index of Ideality of Correlation Detect the Better Model Correctly? Mol Inform 2019; 38:e1800157. [DOI: 10.1002/minf.201800157] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/18/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Alla P. Toropova
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS Via La Masa 19 20156 Milan Italy
| | - Andrey A. Toropov
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS Via La Masa 19 20156 Milan Italy
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Toropova AP, Toropov AA. Use of the index of ideality of correlation to improve models of eco-toxicity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:31771-31775. [PMID: 30255265 DOI: 10.1007/s11356-018-3291-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Persistent organic pollutants are compounds used for various everyday purposes, such as personal care products, food, pesticides, and pharmaceuticals. Decomposition of considerable part of the above pollutants is a long-time process. Under such circumstances, estimation of toxicity for large arrays of organic substances corresponding to the above category of pollutants is a necessary component of theoretical chemistry. The CORAL software is a tool to establish quantitative structure-activity relationships (QSARs). The index of ideality of correlation (IIC) was suggested as a criterion of predictive potential of QSAR. The statistical quality of models for eco-toxicity of organic pollutants, which are built up, with use of the IIC is better than statistical quality of models, which are built up without use of data on the IIC.
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Affiliation(s)
- Alla P Toropova
- Laboratory of Environmental Chemistry and Toxicology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156, Milan, Italy.
| | - Andrey A Toropov
- Laboratory of Environmental Chemistry and Toxicology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20156, Milan, Italy
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