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Quantitative structure–activity relationship study on prolonged anticonvulsant activity of terpene derivatives in pentylenetetrazole test. OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Quantitative structure–activity relationship (QSAR) study has been conducted on 36 terpene derivatives with anticonvulsant activity in timed pentylenetetrazole (PTZ) infusion test. QSAR models for anticonvulsant activity prediction of hydrazones and esters of some monocyclic/bicyclic terpenoids were developed using simplex representation of molecular structure (SiRMS; informational field [IF]) approach based on the SiRMS and the IF of molecule. Four 2D partial least squares QSAR consensus models were developed with the coefficient of determination for test sets
R
test
2
>
0.62
{R}_{\text{test}}^{2}\gt 0.62
. Based on the established QSAR models, we found that carvone and verbenone cores possess the most significant contribution to antiseizure action examined on the model of PTZ-induced convulsions at 3 and 24 h after oral administration of terpene derivatives. Moreover, carbonyl and hydroxy group substitution in terpenoid molecules followed by hydrazones and esters formation leads to enhancement and prolongation of antiseizure action due to the contribution of additional molecular fragments. The presented QSAR models might be utilized to predict anticonvulsant effect among terpene derivatives for their oral administration against onset seizures.
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Kuz’min V, Artemenko A, Ognichenko L, Hromov A, Kosinskaya A, Stelmakh S, Sessions ZL, Muratov EN. Simplex representation of molecular structure as universal QSAR/QSPR tool. Struct Chem 2021; 32:1365-1392. [PMID: 34177203 PMCID: PMC8218296 DOI: 10.1007/s11224-021-01793-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/07/2021] [Indexed: 10/24/2022]
Abstract
We review the development and application of the Simplex approach for the solution of various QSAR/QSPR problems. The general concept of the simplex method and its varieties are described. The advantages of utilizing this methodology, especially for the interpretation of QSAR/QSPR models, are presented in comparison to other fragmentary methods of molecular structure representation. The utility of SiRMS is demonstrated not only in the standard QSAR/QSPR applications, but also for mixtures, polymers, materials, and other complex systems. In addition to many different types of biological activity (antiviral, antimicrobial, antitumor, psychotropic, analgesic, etc.), toxicity and bioavailability, the review examines the simulation of important properties, such as water solubility, lipophilicity, as well as luminescence, and thermodynamic properties (melting and boiling temperatures, critical parameters, etc.). This review focuses on the stereochemical description of molecules within the simplex approach and details the possibilities of universal molecular stereo-analysis and stereochemical configuration description, along with stereo-isomerization mechanism and molecular fragment "topography" identification.
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Affiliation(s)
- Victor Kuz’min
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Anatoly Artemenko
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Luidmyla Ognichenko
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Alexander Hromov
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Anna Kosinskaya
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
- Department of Medical Chemistry, Odessa National Medical University, Odessa, 65082 Ukraine
| | - Sergij Stelmakh
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Zoe L. Sessions
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Eugene N. Muratov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 USA
- Department of Pharmaceutical Sciences, Federal University of Paraiba, Joao Pessoa, PB 58059 Brazil
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Development of Quantitative Structure-Property Relationship (QSPR) Models of Aspartyl-Derivatives Based on Eigenvalues (EVA) of Calculated Vibrational Spectra. FOOD BIOPHYS 2019. [DOI: 10.1007/s11483-019-09577-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Yilmaz H, Sizochenko N, Rasulev B, Toropov A, Guzel Y, Kuz'min V, Leszczynska D, Leszczynski J. Amino substituted nitrogen heterocycle ureas as kinase insert domain containing receptor (KDR) inhibitors: Performance of structure–activity relationship approaches. J Food Drug Anal 2015; 23:168-175. [PMID: 28911371 PMCID: PMC9351780 DOI: 10.1016/j.jfda.2015.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A quantitative structure–activity relationship (QSAR) study was performed on a set of amino-substituted nitrogen heterocyclic urea derivatives. Two novel approaches were applied: (1) the simplified molecular input-line entry systems (SMILES) based optimal descriptors approach; and (2) the fragment-based simplex representation of molecular structure (SiRMS) approach. Comparison with the classic scheme of building up the model and balance of correlation (BC) for optimal descriptors approach shows that the BC scheme provides more robust predictions than the classic scheme for the considered pIC50 of the heterocyclic urea derivatives. Comparison of the SMILES-based optimal descriptors and SiRMS approaches has confirmed good performance of both techniques in prediction of kinase insert domain containing receptor (KDR) inhibitory activity, expressed as a logarithm of inhibitory concentration (pIC50) of studied compounds.
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Affiliation(s)
- Hayriye Yilmaz
- Kayseri Vocational School, Biomedical Devices and Technologies, Erciyes University, 38039, Kayseri, Turkey; Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA
| | - Natalia Sizochenko
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA; Odessa I.I. Mechnikov National University, Department of Chemistry, Dvoryanskaya Street, 2, 65082, Odessa, Ukraine
| | - Bakhtiyor Rasulev
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA
| | - Andrey Toropov
- Laboratory of Environmental Chemistry and Toxicology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156, Via La Masa 19, Milano, Italy
| | - Yahya Guzel
- Department of Chemistry, Faculty of Science, Erciyes University, 38039, Kayseri, Turkey
| | - Viktor Kuz'min
- Odessa I.I. Mechnikov National University, Department of Chemistry, Dvoryanskaya Street, 2, 65082, Odessa, Ukraine
| | - Danuta Leszczynska
- Department of Civil and Environmental Engineering, Jackson State University, Jackson, MS, 39217, USA
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA.
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