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Duda-Seiman C, Duda-Seiman D, Ciubotariu D, Putz MV. QSAR by Minimal Topological Difference[s]: Post-Modern Perspectives. Curr Med Chem 2019; 27:42-53. [PMID: 31272345 DOI: 10.2174/0929867326666190704124857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 06/10/2019] [Accepted: 06/24/2019] [Indexed: 11/22/2022]
Abstract
In the context of reconsidering the Quantitative Structure-Activity Relationship (QSAR) methods at the economical level, namely the optimization rules of OECD, the present review unfolds the key features of Minimal Sterical, Monte-Carlo and Minimal Topological Difference (MTD) methods, developed for quantitative treatment of the relations between biological activity of organic chemical compounds (drugs, pesticides, and so on) and their structures. The initial Minimal Steric Difference (MSD) is completed by the three-dimensional variant of the MTD method, being the last one referred to here, while the main principles of validating and guiding a viable QSAR method verified by the analytical-automated MTD, thus enlarging the perspectives of understanding the chemical-biological interaction at the level of ligand-receptor sites, cavity, and walls, with a true service to the future adaptive molecular design.
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Affiliation(s)
- Corina Duda-Seiman
- Laboratory of Structural and Computational Physical-Chemistry for Nanosciences and QSAR, Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University, Timisoara, Romania
| | - Daniel Duda-Seiman
- Department of Cardiology, Faculty of Medicine, "Victor Babes" University of Medicine and Pharmacy, P-ta Eftimie Murgu No. 2, Timisoara, Romania
| | - Dan Ciubotariu
- Department of Organic Chemistry, Faculty of Pharmacy, "Victor Babes" University of Medicine and Pharmacy, P-ta Eftimie Murgu No. 2, Timisoara, Romania
| | - Mihai V Putz
- Laboratory of Structural and Computational Physical-Chemistry for Nanosciences and QSAR, Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University, Timisoara, Romania.,Laboratory of Renewable Energies-Photovoltaics, R&D National Institute for Electrochemistry and Condensed Matter, Dr. A. Paunescu Podeanu Str. No. 144, RO-300569 Timisoara, Romania
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2
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Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions. Int J Mol Sci 2016; 17:ijms17071087. [PMID: 27399692 PMCID: PMC4964463 DOI: 10.3390/ijms17071087] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 02/07/2023] Open
Abstract
Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions.
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3
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Xie H, Chen L, Zhang J, Xie X, Qiu K, Fu J. A Combined Pharmacophore Modeling, 3D QSAR and Virtual Screening Studies on Imidazopyridines as B-Raf Inhibitors. Int J Mol Sci 2015; 16:12307-23. [PMID: 26035757 PMCID: PMC4490445 DOI: 10.3390/ijms160612307] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 12/11/2022] Open
Abstract
B-Raf kinase is an important target in treatment of cancers. In order to design and find potent B-Raf inhibitors (BRIs), 3D pharmacophore models were created using the Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database (GALAHAD). The best pharmacophore model obtained which was used in effective alignment of the data set contains two acceptor atoms, three donor atoms and three hydrophobes. In succession, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on 39 imidazopyridine BRIs to build three dimensional quantitative structure-activity relationship (3D QSAR) models based on both pharmacophore and docking alignments. The CoMSIA model based on the pharmacophore alignment shows the best result (q2 = 0.621, r2pred = 0.885). This 3D QSAR approach provides significant insights that are useful for designing potent BRIs. In addition, the obtained best pharmacophore model was used for virtual screening against the NCI2000 database. The hit compounds were further filtered with molecular docking, and their biological activities were predicted using the CoMSIA model, and three potential BRIs with new skeletons were obtained.
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Affiliation(s)
- Huiding Xie
- Department of Chemistry, Yunnan University, Kunming 650091, China.
- Department of Chemistry, School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
| | - Lijun Chen
- Department of Chemistry, School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
| | - Jianqiang Zhang
- Department of Chemistry, Yunnan University, Kunming 650091, China.
| | - Xiaoguang Xie
- Department of Chemistry, Yunnan University, Kunming 650091, China.
| | - Kaixiong Qiu
- Department of Chemistry, School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
| | - Jijun Fu
- Department of Chemistry, School of Pharmaceutical Science & Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
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Zayed MEM, El-Shishtawy RM, Elroby SA, Obaid AY, Al-amshany ZM. Experimental and theoretical study of o-substituent effect on the fluorescence of 8-hydroxyquinoline. Int J Mol Sci 2015; 16:3804-19. [PMID: 25674853 PMCID: PMC4346927 DOI: 10.3390/ijms16023804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/29/2015] [Indexed: 11/17/2022] Open
Abstract
The synthesis and characterization of different ether and ester derivatives of 8-hydroxyquinoline have been made. UV-visible and fluorescence spectra of these compounds have revealed spectral dependence on both solvent and O-substituent. The fluorescence intensity of ether derivatives revealed higher intensity for 8-octyloxyquinoline compared with 8-methoxyquinoline, whereas those of ester derivatives had less fluorescence than 8-hydroxyquinoline. Theoretical calculations based on Time-dependent density functional theory (TD-DFT) were carried out for the quinolin-8-yl benzoate (8-OateQ) compound to understand the effect of O-substituent on the electronic absorption of 8-hydroxyquinaline (8-HQ). The calculations revealed comparable results with those obtained from the experimental data. Optimized geometrical structure was calculated with DFT at B3LYP/6-311++G** level of theory. The results indicated that 8-OateQ is not a coplanar structure. The absorption spectra of the compound were computed in gas-phase and solvent using B3LYP and CAM-B3LYP methods with 6-311++G ** basis set. The agreement between calculated and experimental wavelengths was very good at CAM-B3LYP/6-311++G** level of theory.
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Affiliation(s)
- Mohie E M Zayed
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah B.O.208203, Saudi Arabia.
| | - Reda M El-Shishtawy
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah B.O.208203, Saudi Arabia.
- Dyeing, Printing and Textile Auxiliaries Department, Textile Research Division, National Research Center, Dokki, Cairo 12622, Egypt.
| | - Shaaban A Elroby
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah B.O.208203, Saudi Arabia.
- Chemistry Department, Faculty of Science, Beni Suef University, Beni Suef 6251, Egypt.
| | - Abdullah Y Obaid
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah B.O.208203, Saudi Arabia.
| | - Zahra M Al-amshany
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah B.O.208203, Saudi Arabia.
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Lozano NBH, Oliveira RF, Weber KC, Honorio KM, Guido RVC, Andricopulo AD, de Sousa AG, da Silva ABF. Pattern recognition techniques applied to the study of leishmanial glyceraldehyde-3-phosphate dehydrogenase inhibition. Int J Mol Sci 2014; 15:3186-203. [PMID: 24566143 PMCID: PMC3958905 DOI: 10.3390/ijms15023186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 01/21/2014] [Accepted: 01/24/2014] [Indexed: 11/16/2022] Open
Abstract
Chemometric pattern recognition techniques were employed in order to obtain Structure-Activity Relationship (SAR) models relating the structures of a series of adenosine compounds to the affinity for glyceraldehyde 3-phosphate dehydrogenase of Leishmania mexicana (LmGAPDH). A training set of 49 compounds was used to build the models and the best ones were obtained with one geometrical and four electronic descriptors. Classification models were externally validated by predictions for a test set of 14 compounds not used in the model building process. Results of good quality were obtained, as verified by the correct classifications achieved. Moreover, the results are in good agreement with previous SAR studies on these molecules, to such an extent that we can suggest that these findings may help in further investigations on ligands of LmGAPDH capable of improving treatment of leishmaniasis.
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Affiliation(s)
- Norka B H Lozano
- Instituto de Química de São Carlos, USP, São Carlos (SP), 13566-590, Brazil.
| | - Rafael F Oliveira
- Universidade Federal da Paraíba, João Pessoa (PB), 58051-900, Brazil.
| | - Karen C Weber
- Universidade Federal da Paraíba, João Pessoa (PB), 58051-900, Brazil.
| | - Kathia M Honorio
- Escola de Artes Ciências e Humanidades, USP, São Paulo (SP), 03828-000, Brazil.
| | - Rafael V C Guido
- Instituto de Física de São Carlos, USP, São Carlos (SP), 13566-590, Brazil.
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Sun NB, Shi YX, Liu XH, Ma Y, Tan CX, Weng JQ, Jin JZ, Li BJ. Design, synthesis, antifungal activities and 3D-QSAR of new N,N'-diacylhydrazines containing 2,4-dichlorophenoxy moiety. Int J Mol Sci 2013; 14:21741-56. [PMID: 24189221 PMCID: PMC3856032 DOI: 10.3390/ijms141121741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 10/21/2013] [Accepted: 10/23/2013] [Indexed: 11/16/2022] Open
Abstract
A series of new N,N'-diacylhydrazine derivatives were designed and synthesized. Their structures were verified by 1H-NMR, mass spectra (MS) and elemental analysis. The antifungal activities of these N,N'-diacylhydrazines were evaluated. The bioassay results showed that most of these N,N'-diacylhydrazines showed excellent antifungal activities against Cladosporium cucumerinum, Corynespora cassiicola, Sclerotinia sclerotiorum, Erysiphe cichoracearum, and Colletotrichum orbiculare in vivo. The half maximal effective concentration (EC50) of one of the compounds was also determined, and found to be comparable with a commercial drug. To further investigate the structure-activity relationship, comparative molecular field analysis (CoMFA) was performed on the basis of antifungal activity data. Both the steric and electronic field distributions of CoMFA are in good agreement in this study.
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Affiliation(s)
- Na-Bo Sun
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China; E-Mails: (N.-B.S.); (J.-Z.J.)
| | - Yan-Xia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; E-Mail:
| | - Xing-Hai Liu
- College of Chemical Engineering and Materials Science, Zhejiang University of Technology, Hangzhou 310014, China; E-Mails: (C.-X.T.); (J.-Q.W.)
| | - Yi Ma
- State-Key Laboratory of Elemento-Organic Chemistry, National Pesticidal Engineering Centre, Nankai University, Tianjin 300071, China; E-Mail:
| | - Cheng-Xia Tan
- College of Chemical Engineering and Materials Science, Zhejiang University of Technology, Hangzhou 310014, China; E-Mails: (C.-X.T.); (J.-Q.W.)
| | - Jian-Quan Weng
- College of Chemical Engineering and Materials Science, Zhejiang University of Technology, Hangzhou 310014, China; E-Mails: (C.-X.T.); (J.-Q.W.)
| | - Jian-Zhong Jin
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China; E-Mails: (N.-B.S.); (J.-Z.J.)
| | - Bao-Ju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; E-Mail:
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Putz MV, Dudaş NA. Determining chemical reactivity driving biological activity from SMILES transformations: the bonding mechanism of anti-HIV pyrimidines. Molecules 2013; 18:9061-116. [PMID: 23903183 PMCID: PMC6270382 DOI: 10.3390/molecules18089061] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/22/2013] [Accepted: 07/24/2013] [Indexed: 02/08/2023] Open
Abstract
Assessing the molecular mechanism of a chemical-biological interaction and bonding stands as the ultimate goal of any modern quantitative structure-activity relationship (QSAR) study. To this end the present work employs the main chemical reactivity structural descriptors (electronegativity, chemical hardness, chemical power, electrophilicity) to unfold the variational QSAR though their min-max correspondence principles as applied to the Simplified Molecular Input Line Entry System (SMILES) transformation of selected uracil derivatives with anti-HIV potential with the aim of establishing the main stages whereby the given compounds may inhibit HIV infection. The bonding can be completely described by explicitly considering by means of basic indices and chemical reactivity principles two forms of SMILES structures of the pyrimidines, the Longest SMILES Molecular Chain (LoSMoC) and the Branching SMILES (BraS), respectively, as the effective forms involved in the anti-HIV activity mechanism and according to the present work, also necessary intermediates in molecular pathways targeting/docking biological sites of interest.
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Affiliation(s)
- Mihai V Putz
- Laboratory of Computational and Structural Physical Chemistry for Nanosciences and QSAR, Biology-Chemistry Department, West University of Timişoara, Pestalozzi Str. No. 16, Timişoara 300115, Romania.
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Lin YT. A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding. J Cheminform 2013; 5:21. [PMID: 23627990 PMCID: PMC3648400 DOI: 10.1186/1758-2946-5-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 04/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from the bulk of a cell; the second part is the actual detection of the important identities. To identify the key structural modifications around ligand binding, the present study aims to develop a counterpart of tandem technique for cheminformatics. A statistical regression and its outliers act as a computational technique for separation. RESULTS A PPARγ (peroxisome proliferator-activated receptor gamma) agonist cellular system was subjected to such an investigation. Results show that this tandem regression-outlier analysis, or the prioritization of the context equations tagged with features of the outliers, is an effective regression technique of cheminformatics to detect key structural modifications, as well as their tendency of impact to ligand binding. CONCLUSIONS The key structural modifications around ligand binding are effectively extracted or characterized out of cellular reactions. This is because molecular binding is the paramount factor in such ligand cellular system and key structural modifications around ligand binding are expected to create outliers. Therefore, such outliers can be captured by this tandem regression-outlier analysis.
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Affiliation(s)
- Ying-Ting Lin
- Department of Biotechnology, College of Life Sciences, Kaohsiung Medical University, 100, Shih-Chuan 1st Road, San Ming District, 807, Kaohsiung City, Taiwan.
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Assessment of applicability domain for multivariate counter-propagation artificial neural network predictive models by minimum euclidean distance space analysis: a case study. Anal Chim Acta 2012; 759:28-42. [PMID: 23260674 DOI: 10.1016/j.aca.2012.11.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 10/30/2012] [Accepted: 11/02/2012] [Indexed: 11/23/2022]
Abstract
Alongside the validation, the concept of applicability domain (AD) is probably one of the most important aspects which determine the quality as well as reliability of the established quantitative structure-activity relationship (QSAR) models. To date, a variety of approaches for AD estimation have been devised which can be applied to particular type of QSAR models and their practical utilization is extensively elaborated in the literature. The present study introduces a novel, simple, and effective distance-based method for estimation of the AD in case of developed and validated predictive counter-propagation artificial neural network (CP ANN) models through a proficient exploitation of the euclidean distance (ED) metric in the structure-representation vector space. The performance of the method was evaluated and explained in a case study by using a pre-built and validated CP ANN model for prediction of the transport activity of the transmembrane protein bilitranslocase for a diverse set of compounds. The method was tested on two more datasets in order to confirm its performance for evaluation of the applicability domain in CP ANN models. The chemical compounds determined as potential outliers, i.e., outside of the CP ANN model AD, were confirmed in a comparative AD assessment by using the leverage approach. Moreover, the method offers a graphical depiction of the AD for fast and simple determination of the extreme points.
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Toropova AP, Toropov AA, Benfenati E, Gini G, Leszczynska D, Leszczynski J. The average numbers of outliers over groups of various splits into training and test sets: A criterion of the reliability of a QSPR? A case of water solubility. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.05.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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SMILES-based QSPR model for half-wave potentials of 1-phenyl-5-benzyl-sulfanyltetrazoles using CORAL. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.04.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Introducing catastrophe-QSAR. Application on modeling molecular mechanisms of pyridinone derivative-type HIV non-nucleoside reverse transcriptase inhibitors. Int J Mol Sci 2011; 12:9533-69. [PMID: 22272148 PMCID: PMC3257145 DOI: 10.3390/ijms12129533] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 11/28/2011] [Accepted: 12/12/2011] [Indexed: 12/21/2022] Open
Abstract
The classical method of quantitative structure-activity relationships (QSAR) is enriched using non-linear models, as Thom's polynomials allow either uni- or bi-variate structural parameters. In this context, catastrophe QSAR algorithms are applied to the anti-HIV-1 activity of pyridinone derivatives. This requires calculation of the so-called relative statistical power and of its minimum principle in various QSAR models. A new index, known as a statistical relative power, is constructed as an Euclidian measure for the combined ratio of the Pearson correlation to algebraic correlation, with normalized t-Student and the Fisher tests. First and second order inter-model paths are considered for mono-variate catastrophes, whereas for bi-variate catastrophes the direct minimum path is provided, allowing the QSAR models to be tested for predictive purposes. At this stage, the max-to-min hierarchies of the tested models allow the interaction mechanism to be identified using structural parameter succession and the typical catastrophes involved. Minimized differences between these catastrophe models in the common structurally influential domains that span both the trial and tested compounds identify the "optimal molecular structural domains" and the molecules with the best output with respect to the modeled activity, which in this case is human immunodeficiency virus type 1 HIV-1 inhibition. The best molecules are characterized by hydrophobic interactions with the HIV-1 p66 subunit protein, and they concur with those identified in other 3D-QSAR analyses. Moreover, the importance of aromatic ring stacking interactions for increasing the binding affinity of the inhibitor-reverse transcriptase ligand-substrate complex is highlighted.
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Putz MV, Ionaşcu C, Putz AM, Ostafe V. Alert-QSAR. Implications for electrophilic theory of chemical carcinogenesis. Int J Mol Sci 2011; 12:5098-134. [PMID: 21954348 PMCID: PMC3179155 DOI: 10.3390/ijms12085098] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 06/30/2011] [Accepted: 08/03/2011] [Indexed: 12/02/2022] Open
Abstract
Given the modeling and predictive abilities of quantitative structure activity relationships (QSARs) for genotoxic carcinogens or mutagens that directly affect DNA, the present research investigates structural alert (SA) intermediate-predicted correlations A(SA) of electrophilic molecular structures with observed carcinogenic potencies in rats (observed activity, A = Log[1/TD(50)], i.e., [Formula: see text]). The present method includes calculation of the recently developed residual correlation of the structural alert models, i.e., [Formula: see text]. We propose a specific electrophilic ligand-receptor mechanism that combines electronegativity with chemical hardness-associated frontier principles, equality of ligand-reagent electronegativities and ligand maximum chemical hardness for highly diverse toxic molecules against specific receptors in rats. The observed carcinogenic activity is influenced by the induced SA-mutagenic intermediate effect, alongside Hansch indices such as hydrophobicity (LogP), polarizability (POL) and total energy (Etot), which account for molecular membrane diffusion, ionic deformation, and stericity, respectively. A possible QSAR mechanistic interpretation of mutagenicity as the first step in genotoxic carcinogenesis development is discussed using the structural alert chemoinformation and in full accordance with the Organization for Economic Co-operation and Development QSAR guidance principles.
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Affiliation(s)
- Mihai V. Putz
- Laboratory of Computational and Structural Physical Chemistry, Chemistry Department, West University of Timişoara, Pestalozzi Street No.16, Timişoara, RO-300115, Romania; E-Mail: (V.O.)
- “Nicolas Georgescu-Roegen” Forming and Research Center of West University of Timişoara, 4th, Oituz Street, Timişoara, RO-300086, Romania; E-Mail: (C.I.)
| | - Cosmin Ionaşcu
- “Nicolas Georgescu-Roegen” Forming and Research Center of West University of Timişoara, 4th, Oituz Street, Timişoara, RO-300086, Romania; E-Mail: (C.I.)
| | - Ana-Maria Putz
- “Nicolas Georgescu-Roegen” Forming and Research Center of West University of Timişoara, 4th, Oituz Street, Timişoara, RO-300086, Romania; E-Mail: (C.I.)
- Institute of Chemistry Timişoara of the Romanian Academy, 24 Mihai Viteazul Bld., Timişoara, RO-300223, Romania
| | - Vasile Ostafe
- Laboratory of Computational and Structural Physical Chemistry, Chemistry Department, West University of Timişoara, Pestalozzi Street No.16, Timişoara, RO-300115, Romania; E-Mail: (V.O.)
- “Nicolas Georgescu-Roegen” Forming and Research Center of West University of Timişoara, 4th, Oituz Street, Timişoara, RO-300086, Romania; E-Mail: (C.I.)
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Quantitative Structure Inter-Activity Relationship (QSInAR). Cytotoxicity Study of Some Hemisynthetic and Isolated Natural Steroids and Precursors on Human Fibrosarcoma Cells HT1080. Molecules 2011; 16:6603-20. [PMID: 25134765 PMCID: PMC6264182 DOI: 10.3390/molecules16086603] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 01/08/2023] Open
Abstract
Combined experimental and quantitative structure inter-activity relationship (QSIAR) computation methods were advanced in order to establish the structural and mechanistic influences that steroids and triterpenes, either as newly synthesized or naturally isolated products, have on human HT1080 mammalian cancer cells. The main Hansch structural indicators such as hydrophobicity (LogP), polarizability (POL) and total energy (Etot) were considered and both the structure-projected as well as globally computed correlations were reported; while the inter-activity correlation of the global activity with those projected on structural information was revealed as equal to the direct structural-activity one for the trial sets of compounds, the prediction for the testing set of molecules reported even superior performances respecting those characteristic for the calibration set, validating therefore the present QSInAR models; accordingly, it follows that the LogP carries the most part of the cytotoxic signal, while POL has little influence on inhibiting tumor growth—A complementary behavior with their earlier known influence on genotoxic carcinogenesis. Regarding the newly hemisynthetic compounds it was found that stigmasta-4,22-dien-3-one is not adapted for cell membrane diffusion; it is recommended that aminocinnamyl chlorohydrate be further modified in order to acquire better steric influence, while aminocinnamyl-2,3,4,6-O-tétraacétyl-α-D-glucopyranoside was identified as being inhibited in the tumor cell by other molecular mechanisms–here not revealed–although it has a moderate-high anti-cancer structurally predicted activity.
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