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Speck-Planche A, Kleandrova VV. Multi-Condition QSAR Model for the Virtual Design of Chemicals with Dual Pan-Antiviral and Anti-Cytokine Storm Profiles. ACS OMEGA 2022; 7:32119-32130. [PMID: 36120024 PMCID: PMC9476185 DOI: 10.1021/acsomega.2c03363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Respiratory viruses are infectious agents, which can cause pandemics. Although nowadays the danger associated with respiratory viruses continues to be evidenced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the virus responsible for the current COVID-19 pandemic, other viruses such as SARS-CoV-1, the influenza A and B viruses (IAV and IBV, respectively), and the respiratory syncytial virus (RSV) can lead to globally spread viral diseases. Also, from a biological point of view, most of these viruses can cause an organ-damaging hyperinflammatory response known as the cytokine storm (CS). Computational approaches constitute an essential component of modern drug development campaigns, and therefore, they have the potential to accelerate the discovery of chemicals able to simultaneously inhibit multiple molecular and nonmolecular targets. We report here the first multicondition model based on quantitative structure-activity relationships and an artificial neural network (mtc-QSAR-ANN) for the virtual design and prediction of molecules with dual pan-antiviral and anti-CS profiles. Our mtc-QSAR-ANN model exhibited an accuracy higher than 80%. By interpreting the different descriptors present in the mtc-QSAR-ANN model, we could retrieve several molecular fragments whose assembly led to new molecules with drug-like properties and predicted pan-antiviral and anti-CS activities.
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Affiliation(s)
- Alejandro Speck-Planche
- Grupo
de Química Computacional y Teórica (QCT-USFQ), Departamento
de Ingeniería Química, Universidad
San Francisco de Quito, Diego de Robles y vía Interoceánica, Quito 170901, Ecuador
| | - Valeria V. Kleandrova
- Laboratory
of Fundamental and Applied Research of Quality and Technology of Food
Production, Moscow State University of Food
Production, Volokolamskoe
shosse 11, 125080, Moscow, Russian Federation
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2
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PTML Modeling for Pancreatic Cancer Research: In Silico Design of Simultaneous Multi-Protein and Multi-Cell Inhibitors. Biomedicines 2022; 10:biomedicines10020491. [PMID: 35203699 PMCID: PMC8962338 DOI: 10.3390/biomedicines10020491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 02/07/2023] Open
Abstract
Pancreatic cancer (PANC) is a dangerous type of cancer that is a major cause of mortality worldwide and exhibits a remarkably poor prognosis. To date, discovering anti-PANC agents remains a very complex and expensive process. Computational approaches can accelerate the search for anti-PANC agents. We report for the first time two models that combined perturbation theory with machine learning via a multilayer perceptron network (PTML-MLP) to perform the virtual design and prediction of molecules that can simultaneously inhibit multiple PANC cell lines and PANC-related proteins, such as caspase-1, tumor necrosis factor-alpha (TNF-alpha), and the insulin-like growth factor 1 receptor (IGF1R). Both PTML-MLP models exhibited accuracies higher than 78%. Using the interpretation from one of the PTML-MLP models as a guideline, we extracted different molecular fragments desirable for the inhibition of the PANC cell lines and the aforementioned PANC-related proteins and then assembled some of those fragments to form three new molecules. The two PTML-MLP models predicted the designed molecules as potentially versatile anti-PANC agents through inhibition of the three PANC-related proteins and multiple PANC cell lines. Conclusions: This work opens new horizons for the application of the PTML modeling methodology to anticancer research.
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3
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In Silico Model for Chemical-Induced Chromosomal Damages Elucidates Mode of Action and Irrelevant Positives. Genes (Basel) 2020; 11:genes11101181. [PMID: 33050664 PMCID: PMC7650694 DOI: 10.3390/genes11101181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 11/17/2022] Open
Abstract
In silico tools to predict genotoxicity have become important for high-throughput screening of chemical substances. However, current in silico tools to evaluate chromosomal damage do not discriminate in vitro-specific positives that can be followed by in vivo tests. Herein, we establish an in silico model for chromosomal damages with the following approaches: (1) re-categorizing a previous data set into three groups (positives, negatives, and misleading positives) according to current reports that use weight-of-evidence approaches and expert judgments; (2) utilizing a generalized linear model (Elastic Net) that uses partial structures of chemicals (organic functional groups) as explanatory variables of the statistical model; and (3) interpreting mode of action in terms of chemical structures identified. The accuracy of our model was 85.6%, 80.3%, and 87.9% for positive, negative, and misleading positive predictions, respectively. Selected organic functional groups in the models for positive prediction were reported to induce genotoxicity via various modes of actions (e.g., DNA adduct formation), whereas those for misleading positives were not clearly related to genotoxicity (e.g., low pH, cytotoxicity induction). Therefore, the present model may contribute to high-throughput screening in material design or drug discovery to verify the relevance of estimated positives considering their mechanisms of action.
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Hsu CW, Hewes KP, Stavitskaya L, Kruhlak NL. Construction and application of (Q)SAR models to predict chemical-induced in vitro chromosome aberrations. Regul Toxicol Pharmacol 2018; 99:274-288. [PMID: 30278198 DOI: 10.1016/j.yrtph.2018.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 12/23/2022]
Abstract
In drug development, genetic toxicology studies are conducted using in vitro and in vivo assays to identify potential mutagenic and clastogenic effects, as outlined in the International Council for Harmonisation (ICH) S2 regulatory guideline. (Quantitative) structure-activity relationship ((Q)SAR) models that predict assay outcomes can be used as an early screen to prioritize pharmaceutical candidates, or later during product development to evaluate safety when experimental data are unavailable or inconclusive. In the current study, two commercial QSAR platforms were used to build models for in vitro chromosomal aberrations in Chinese hamster lung (CHL) and Chinese hamster ovary (CHO) cells. Cross-validated CHL model predictive performance showed sensitivity of 80 and 82%, and negative predictivity of 75 and 76% based on 875 training set compounds. For CHO, sensitivity of 61 and 67% and negative predictivity of 68 and 74% was achieved based on 817 training set compounds. The predictive performance of structural alerts in a commercial expert rule-based SAR software was also investigated and showed positive predictivity of 48-100% for selected alerts. Case studies examining incorrectly-predicted compounds, non-DNA-reactive clastogens, and recently-approved pharmaceuticals are presented, exploring how an investigational approach using similarity searching and expert knowledge can improve upon individual (Q)SAR predictions of the clastogenicity of drugs.
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Affiliation(s)
- Chia-Wen Hsu
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, USA
| | - Kurt P Hewes
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, USA
| | - Lidiya Stavitskaya
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, USA
| | - Naomi L Kruhlak
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD, USA.
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Toropov AA, Toropova AP, Raitano G, Benfenati E. CORAL: Building up QSAR models for the chromosome aberration test. Saudi J Biol Sci 2018; 26:1101-1106. [PMID: 31516335 PMCID: PMC6734133 DOI: 10.1016/j.sjbs.2018.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 04/23/2018] [Accepted: 05/06/2018] [Indexed: 12/13/2022] Open
Abstract
A high level of chromosomal aberrations in peripheral blood lymphocytes may be an early marker of cancer risk, but data on risk of specific cancers and types of chromosomal aberrations are limited. Consequently, the development of predictive models for chromosomal aberrations test is important task. Majority of models for chromosomal aberrations test are so-called knowledge-based rules system. The CORAL software (http://www.insilico.eu/coral, abbreviation of “CORrelation And Logic”) is an alternative for knowledge-based rules system. In contrast to knowledge-based rules system, the CORAL software gives possibility to estimate the influence upon the predictive potential of a model of different molecular alerts as well as different splits into the training set and validation set. This possibility is not available for the approaches based on the knowledge-based rules system. Quantitative Structure–Activity Relationships (QSAR) for chromosome aberration test are established for five random splits into the training, calibration, and validation sets. The QSAR approach is based on representation of the molecular structure by simplified molecular input-line entry system (SMILES) without data on physicochemical and/or biochemical parameters. In spite of this limitation, the statistical quality of these models is quite good.
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Affiliation(s)
| | - Alla P. Toropova
- Corresponding author at: Laboratory of Environmental Chemistry and Toxicology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy.
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Guardado Yordi E, Matos MJ, Pérez Martínez A, Tornes AC, Santana L, Molina E, Uriarte E. In silico genotoxicity of coumarins: application of the Phenol-Explorer food database to functional food science. Food Funct 2017; 8:2958-2966. [PMID: 28745361 DOI: 10.1039/c7fo00402h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coumarins are a group of phytochemicals that may be beneficial or harmful to health depending on their type and dosage and the matrix that contains them. Some of these compounds have been proven to display pro-oxidant and clastogenic activities. Therefore, in the current work, we have studied the coumarins that are present in food sources extracted from the Phenol-Explorer database in order to predict their clastogenic activity and identify the structure-activity relationships and genotoxic structural alerts using alternative methods in the field of computational toxicology. It was necessary to compile information on the type and amount of coumarins in different food sources through the analysis of databases of food composition available online. A virtual screening using a clastogenic model and different software, such as MODESLAB, ChemDraw and STATISTIC, was performed. As a result, a table of food composition was prepared and qualitative information from this data was extracted. The virtual screening showed that the esterified substituents inactivate molecules, while the methoxyl and hydroxyl substituents contribute to their activity and constitute, together with the basic structures of the studied subclasses, clastogenic structural alerts. Chemical subclasses of simple coumarins and furocoumarins were classified as active (xanthotoxin, isopimpinellin, esculin, scopoletin, scopolin and bergapten). In silico genotoxicity was mainly predicted for coumarins found in beer, sherry, dried parsley, fresh parsley and raw celery stalks. The results obtained can be interesting for the future design of functional foods and dietary supplements. These studies constitute a reference for the genotoxic chemoinformatic analysis of bioactive compounds present in databases of food composition.
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Affiliation(s)
- E Guardado Yordi
- Universidad de Camagüey Ignacio Agramonte Loynaz, Facultad de Ciencias Aplicadas, Cincunvalación Norte Km 5 1/2, Camagüey, Cuba. and Universidad de Santiago de Compostela, Facultad de Farmacia, Campus vida, 15782 Santiago de Compostela, Spain
| | - M J Matos
- Universidad de Santiago de Compostela, Facultad de Farmacia, Campus vida, 15782 Santiago de Compostela, Spain
| | - A Pérez Martínez
- Universidad de Camagüey Ignacio Agramonte Loynaz, Facultad de Ciencias Aplicadas, Cincunvalación Norte Km 5 1/2, Camagüey, Cuba. and Universidad Estatal Amazónica, Facultad de Ciencias de la Tierra, Km 2 1/2 vía Puyo a Tena (Paso Lateral), Puyo, Ecuador
| | - A C Tornes
- Universidad de Camagüey Ignacio Agramonte Loynaz, Facultad de Ciencias Aplicadas, Cincunvalación Norte Km 5 1/2, Camagüey, Cuba.
| | - L Santana
- Universidad de Santiago de Compostela, Facultad de Farmacia, Campus vida, 15782 Santiago de Compostela, Spain
| | - E Molina
- Universidad de Camagüey Ignacio Agramonte Loynaz, Facultad de Ciencias Aplicadas, Cincunvalación Norte Km 5 1/2, Camagüey, Cuba. and Universidad de Santiago de Compostela, Facultad de Farmacia, Campus vida, 15782 Santiago de Compostela, Spain
| | - E Uriarte
- Universidad de Santiago de Compostela, Facultad de Farmacia, Campus vida, 15782 Santiago de Compostela, Spain and Instituto de Química Aplicada, Universidad Autónoma de Chile, Pedro de Valdivia 425, 7500912 Santiago, Chile
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7
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Yordi EG, Matos MJ, Pupo RC, Santana L, Uriarte E, Pérez EM. In silico clastogenic activity of dietary phenolic acids. Lebensm Wiss Technol 2015. [DOI: 10.1016/j.lwt.2014.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Miltojević AB, Radulović NS. Structural elucidation of thermolysis products of methyl N-methyl-N-nitrosoanthranilate. RSC Adv 2015. [DOI: 10.1039/c5ra07612a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MethylN-methyl-N-nitrosoanthranilate thermolysis in the vapor and condensed phases gave different coupling products, dimethyl 2,2′-(1,2-dimethylhydrazine-1,2-diyl)dibenzoate and methyl 5-methyl-6-oxo-(5H)-phenanthridine-4-carboxylate, respectively.
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Affiliation(s)
- Ana B. Miltojević
- Department of Chemistry
- Faculty of Science and Mathematics
- University of Niš
- 18000 Niš
- Serbia
| | - Niko S. Radulović
- Department of Chemistry
- Faculty of Science and Mathematics
- University of Niš
- 18000 Niš
- Serbia
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9
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Pérez-Garrido A, Girón-Rodríguez F, Morales Helguera A, Borges F, Combes RD. Topological structural alerts modulations of mammalian cell mutagenicity for halogenated derivatives. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 25:17-33. [PMID: 24283490 DOI: 10.1080/1062936x.2013.820791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Genotoxicity is a key toxicity endpoint for current regulatory requirements regarding new and existing chemicals. However, genotoxicity testing is time-consuming and costly, and involves the use of laboratory animals. This has motivated the development of computational approaches, designed to predict genotoxicity without the need to conduct laboratory tests. Currently, many existing computational methods, like quantitative structure-activity relationship (QSAR) models, provide limited information about the possible mechanisms involved in mutagenicity or predictions based on structural alerts (SAs) do not take statistical models into account. This paper describes an attempt to address this problem by using the TOPological Substructural MOlecular Design (TOPS-MODE) approach to develop and validate improved QSAR models for predicting the mutagenicity of a range of halogenated derivatives. Our most predictive model has an accuracy of 94.12%, exhibits excellent cross-validation and external set statistics. A reasonable interpretation of the model in term of SAs was achieved by means of bond contributions to activity. The results obtained led to the following conclusions: primary halogenated derivatives are more mutagenic than secondary ones; and substitution of chlorine by bromine increases mutagenicity while polyhalogenation decreases activity. The paper demonstrates the potential of the TOPS-MODE approach in developing QSAR models for identifying structural alerts for mutagenicity, combining high predictivity with relevant mechanistic interpretation.
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Affiliation(s)
- A Pérez-Garrido
- a Cátedra de Ingeniería y Toxicología Ambiental, Universidad Católica de San Antonio , Guadalupe , Murcia , Spain
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Speck-Planche A, Kleandrova VV, Cordeiro MND. New insights toward the discovery of antibacterial agents: Multi-tasking QSBER model for the simultaneous prediction of anti-tuberculosis activity and toxicological profiles of drugs. Eur J Pharm Sci 2013; 48:812-8. [DOI: 10.1016/j.ejps.2013.01.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/05/2013] [Accepted: 01/23/2013] [Indexed: 01/11/2023]
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11
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Pérez-Garrido A, Helguera AM, Morillas Ruiz JM, Zafrilla Rentero P. Topological sub-structural molecular design approach: Radical scavenging activity. Eur J Med Chem 2012; 49:86-94. [DOI: 10.1016/j.ejmech.2011.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 12/14/2011] [Accepted: 12/20/2011] [Indexed: 12/01/2022]
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12
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Pérez-Garrido A, Helguera AM, Borges F, Cordeiro MNDS, Rivero V, Escudero AG. Two new parameters based on distances in a receiver operating characteristic chart for the selection of classification models. J Chem Inf Model 2011; 51:2746-59. [PMID: 21923162 DOI: 10.1021/ci2003076] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There are several indices that provide an indication of different types on the performance of QSAR classification models, being the area under a Receiver Operating Characteristic (ROC) curve still the most powerful test to overall assess such performance. All ROC related parameters can be calculated for both the training and test sets, but, nevertheless, neither of them constitutes an absolute indicator of the classification performance by themselves. Moreover, one of the biggest drawbacks is the computing time needed to obtain the area under the ROC curve, which naturally slows down any calculation algorithm. The present study proposes two new parameters based on distances in a ROC curve for the selection of classification models with an appropriate balance in both training and test sets, namely the following: the ROC graph Euclidean distance (ROCED) and the ROC graph Euclidean distance corrected with Fitness Function (FIT(λ)) (ROCFIT). The behavior of these indices was observed through the study on the mutagenicity for four genotoxicity end points of a number of nonaromatic halogenated derivatives. It was found that the ROCED parameter gets a better balance between sensitivity and specificity for both the training and prediction sets than other indices such as the Matthews correlation coefficient, the Wilk's lambda, or parameters like the area under the ROC curve. However, when the ROCED parameter was used, the follow-on linear discriminant models showed the lower statistical significance. But the other parameter, ROCFIT, maintains the ROCED capabilities while improving the significance of the models due to the inclusion of FIT(λ).
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Affiliation(s)
- Alfonso Pérez-Garrido
- Cátedra de Ingeniería y Toxicología Ambiental, Universidad Cátolica San Antonio, Guadalupe, Murcia, Spain
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13
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Yordi EG, Pérez EM, Matos MJ, Villares EU. Structural alerts for predicting clastogenic activity of pro-oxidant flavonoid compounds: quantitative structure-activity relationship study. ACTA ACUST UNITED AC 2011; 17:216-24. [PMID: 21940715 DOI: 10.1177/1087057111421623] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Flavonoids have been reported to exert multiple biological effects that include acting as pro-oxidants at very high doses. The authors determined a structural alert to identify the clastogenic activity of a series of flavonoids with pro-oxidant activity. The methodology was based on a quantitative structure-activity relationship (QSAR) study. Specifically, the authors developed a virtual screening method for a clastogenic model using the topological substructural molecular design (TOPS-MODE) approach. It represents a useful platform for the automatic generation of structural alerts, based on the calculation of spectral moments of molecular bond matrices appropriately weighted, taking into account the hydrophobic, electronic, and steric molecular features. Therefore, it was possible to establish the structural criteria for maximal clastogenicity of pro-oxidant flavonoids: the presence of a 3-hydroxyl group and a 4-carbonyl group in ring C, the maximal number of hydroxyl groups in ring B, the presence of methoxyl and phenyl groups, the absence of a 2,3-double bond in ring C, and the presence of 5,7 hydroxyl groups in ring A. The presented clastogenic model may be useful for screening new pro-oxidant compounds. This alert could help in the design of new and efficient flavonoids, which could be used as bioactive compounds in nutraceuticals and functional food.
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Affiliation(s)
- Estela Guardado Yordi
- Department of Food Science and Technology, Faculty of Chemistry, University of Camaguey, Camaguey, Cuba.
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14
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García I, Fall Y, García-Mera X, Prado-Prado F. Theoretical study of GSK−3α: neural networks QSAR studies for the design of new inhibitors using 2D descriptors. Mol Divers 2011; 15:947-55. [DOI: 10.1007/s11030-011-9325-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/20/2011] [Indexed: 10/18/2022]
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Schwöbel JAH, Koleva YK, Enoch SJ, Bajot F, Hewitt M, Madden JC, Roberts DW, Schultz TW, Cronin MTD. Measurement and Estimation of Electrophilic Reactivity for Predictive Toxicology. Chem Rev 2011; 111:2562-96. [DOI: 10.1021/cr100098n] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Johannes A. H. Schwöbel
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Yana K. Koleva
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Steven J. Enoch
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Fania Bajot
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Mark Hewitt
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Judith C. Madden
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - David W. Roberts
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
| | - Terry W. Schultz
- College of Veterinary Medicine, Department of Comparative Medicine, The University of Tennessee, 2407 River Drive, Knoxville, Tennessee 37996-4543, United States
| | - Mark T. D. Cronin
- School of Pharmacy and Chemistry, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, England
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Naven RT, Louise-May S, Greene N. The computational prediction of genotoxicity. Expert Opin Drug Metab Toxicol 2010; 6:797-807. [DOI: 10.1517/17425255.2010.495118] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Multi-target spectral moment QSAR versus ANN for antiparasitic drugs against different parasite species. Bioorg Med Chem 2010; 18:2225-2231. [PMID: 20185316 DOI: 10.1016/j.bmc.2010.01.068] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 01/22/2010] [Accepted: 01/29/2010] [Indexed: 11/23/2022]
Abstract
There are many of pathogen parasite species with different susceptibility profile to antiparasitic drugs. Unfortunately, almost QSAR models predict the biological activity of drugs against only one parasite species. Consequently, predicting the probability with which a drug is active against different species with a single unify model is a goal of the major importance. In so doing, we use Markov Chains theory to calculate new multi-target spectral moments to fit a QSAR model that predict by the first time a mt-QSAR model for 500 drugs tested in the literature against 16 parasite species and other 207 drugs no tested in the literature using spectral moments. The data was processed by linear discriminant analysis (LDA) classifying drugs as active or non-active against the different tested parasite species. The model correctly classifies 311 out of 358 active compounds (86.9%) and 2328 out of 2577 non-active compounds (90.3%) in training series. Overall training performance was 89.9%. Validation of the model was carried out by means of external predicting series. In these series the model classified correctly 157 out 190, 82.6% of antiparasitic compounds and 1151 out of 1277 non-active compounds (90.1%). Overall predictability performance was 89.2%. In addition we developed four types of non Linear Artificial neural networks (ANN) and we compared with the mt-QSAR model. The improved ANN model had an overall training performance was 87%. The present work report the first attempts to calculate within a unify framework probabilities of antiparasitic action of drugs against different parasite species based on spectral moment analysis.
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Pérez-Garrido A, Helguera AM, López GC, Cordeiro MNDS, Escudero AG. A topological substructural molecular design approach for predicting mutagenesis end-points of alpha, beta-unsaturated carbonyl compounds. Toxicology 2009; 268:64-77. [PMID: 20004227 DOI: 10.1016/j.tox.2009.11.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 11/29/2009] [Accepted: 11/30/2009] [Indexed: 11/18/2022]
Abstract
Chemically reactive, alpha, beta-unsaturated carbonyl compounds are common environmental pollutants able to produce a wide range of adverse effects, including, e.g. mutagenicity. This toxic property can often be related to chemical structure, in particular to specific molecular substructures or fragments (alerts), which can then be used in specialized software or expert systems for predictive purposes. In the past, there have been many attempts to predict the mutagenicity of alpha, beta-unsaturated carbonyl compounds through quantitative structure activity relationships (QSAR) but considering only one exclusive endpoint: the Ames test. Besides, even though those studies give a comprehensive understanding of the phenomenon, they do not provide substructural information that could be useful forward improving expert systems based on structural alerts (SAs). This work reports an evaluation of classification models to probe the mutagenic activity of alpha, beta-unsaturated carbonyl compounds over two endpoints--the Ames and mammalian cell gene mutation tests--based on linear discriminant analysis along with the topological Substructure molecular design (TOPS-MODE) approach. The obtained results showed the better ability of the TOPS-MODE approach in flagging structural alerts for the mutagenicity of these compounds compared to the expert system TOXTREE. Thus, the application of the present QSAR models can aid toxicologists in risk assessment and in prioritizing testing, as well as in the improvement of expert systems, such as the TOXTREE software, where SAs are implemented.
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Affiliation(s)
- Alfonso Pérez-Garrido
- Enviromental Engineering and Toxicology Dpt., Catholic University of San Antonio, Guadalupe, Murcia, C.P. 30107, Spain.
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Pérez-Garrido A, Helguera AM, Cordeiro MND, Escudero AG. QSPR modelling with the topological substructural molecular design approach: β-cyclodextrin complexation. J Pharm Sci 2009; 98:4557-76. [DOI: 10.1002/jps.21747] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Estrada E. Quantum-Chemical Foundations of the Topological Substructural Molecular Design. J Phys Chem A 2008; 112:5208-17. [DOI: 10.1021/jp8010712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ernesto Estrada
- Complex Systems Research Group, RIAIDT & Department of Organic Chemistry, Faculty of Pharmacy, Edificio CACTUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Pérez-Garrido A, González MP, Escudero AG. Halogenated derivatives QSAR model using spectral moments to predict haloacetic acids (HAA) mutagenicity. Bioorg Med Chem 2008; 16:5720-32. [DOI: 10.1016/j.bmc.2008.03.070] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 02/29/2008] [Accepted: 03/25/2008] [Indexed: 10/22/2022]
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Morales Helguera A, Pérez González M, Dias Soeiro Cordeiro MN, Cabrera Pérez MÁ. Quantitative Structure−Carcinogenicity Relationship for Detecting Structural Alerts in Nitroso Compounds: Species, Rat; Sex, Female; Route of Administration, Gavage. Chem Res Toxicol 2008; 21:633-42. [DOI: 10.1021/tx700336n] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Aliuska Morales Helguera
- Department of Chemistry and Molecular Simulation and Drug Design Group, Chemical Bioactive Center, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba, and REQUIMTE, Chemistry Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Maykel Pérez González
- Department of Chemistry and Molecular Simulation and Drug Design Group, Chemical Bioactive Center, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba, and REQUIMTE, Chemistry Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Maria Natália Dias Soeiro Cordeiro
- Department of Chemistry and Molecular Simulation and Drug Design Group, Chemical Bioactive Center, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba, and REQUIMTE, Chemistry Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Miguel Ángel Cabrera Pérez
- Department of Chemistry and Molecular Simulation and Drug Design Group, Chemical Bioactive Center, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba, and REQUIMTE, Chemistry Department, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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How to confirm identified toxicants in effect-directed analysis. Anal Bioanal Chem 2008; 390:1959-73. [DOI: 10.1007/s00216-007-1808-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 12/10/2007] [Accepted: 12/12/2007] [Indexed: 10/22/2022]
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Mekenyan O, Todorov M, Serafimova R, Stoeva S, Aptula A, Finking R, Jacob E. Identifying the Structural Requirements for Chromosomal Aberration by Incorporating Molecular Flexibility and Metabolic Activation of Chemicals. Chem Res Toxicol 2007; 20:1927-41. [DOI: 10.1021/tx700249q] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ovanes Mekenyan
- Laboratory of Mathematical Chemistry, Bourgas As. Zlatarov University, 8010 Bourgas, Bulgaria, Safety Environmental Assurance Centre (SEAC), Unilever Colworth, Colworth House, Sharnbrook, Bedford MK44 1LQ, U.K., and Department of Product Safety, Regulations, Toxicology and Ecology, BASF Aktiengesellschaft, D-67056 Ludwigshafen, Germany
| | - Milen Todorov
- Laboratory of Mathematical Chemistry, Bourgas As. Zlatarov University, 8010 Bourgas, Bulgaria, Safety Environmental Assurance Centre (SEAC), Unilever Colworth, Colworth House, Sharnbrook, Bedford MK44 1LQ, U.K., and Department of Product Safety, Regulations, Toxicology and Ecology, BASF Aktiengesellschaft, D-67056 Ludwigshafen, Germany
| | - Rossitsa Serafimova
- Laboratory of Mathematical Chemistry, Bourgas As. Zlatarov University, 8010 Bourgas, Bulgaria, Safety Environmental Assurance Centre (SEAC), Unilever Colworth, Colworth House, Sharnbrook, Bedford MK44 1LQ, U.K., and Department of Product Safety, Regulations, Toxicology and Ecology, BASF Aktiengesellschaft, D-67056 Ludwigshafen, Germany
| | - Stoyanka Stoeva
- Laboratory of Mathematical Chemistry, Bourgas As. Zlatarov University, 8010 Bourgas, Bulgaria, Safety Environmental Assurance Centre (SEAC), Unilever Colworth, Colworth House, Sharnbrook, Bedford MK44 1LQ, U.K., and Department of Product Safety, Regulations, Toxicology and Ecology, BASF Aktiengesellschaft, D-67056 Ludwigshafen, Germany
| | - Aynur Aptula
- Laboratory of Mathematical Chemistry, Bourgas As. Zlatarov University, 8010 Bourgas, Bulgaria, Safety Environmental Assurance Centre (SEAC), Unilever Colworth, Colworth House, Sharnbrook, Bedford MK44 1LQ, U.K., and Department of Product Safety, Regulations, Toxicology and Ecology, BASF Aktiengesellschaft, D-67056 Ludwigshafen, Germany
| | - Robert Finking
- Laboratory of Mathematical Chemistry, Bourgas As. Zlatarov University, 8010 Bourgas, Bulgaria, Safety Environmental Assurance Centre (SEAC), Unilever Colworth, Colworth House, Sharnbrook, Bedford MK44 1LQ, U.K., and Department of Product Safety, Regulations, Toxicology and Ecology, BASF Aktiengesellschaft, D-67056 Ludwigshafen, Germany
| | - Elard Jacob
- Laboratory of Mathematical Chemistry, Bourgas As. Zlatarov University, 8010 Bourgas, Bulgaria, Safety Environmental Assurance Centre (SEAC), Unilever Colworth, Colworth House, Sharnbrook, Bedford MK44 1LQ, U.K., and Department of Product Safety, Regulations, Toxicology and Ecology, BASF Aktiengesellschaft, D-67056 Ludwigshafen, Germany
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25
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Helguera AM, González MP, D S Cordeiro MN, Pérez MAC. Quantitative structure carcinogenicity relationship for detecting structural alerts in nitroso-compounds. Toxicol Appl Pharmacol 2007; 221:189-202. [PMID: 17477948 DOI: 10.1016/j.taap.2007.02.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 02/16/2007] [Accepted: 02/21/2007] [Indexed: 02/01/2023]
Abstract
Prevention of environmentally induced cancers is a major health problem of which solutions depend on the rapid and accurate screening of potential chemical hazards. Lately, theoretical approaches such as the one proposed here - Quantitative Structure-Activity Relationship (QSAR) - are increasingly used for assessing the risks of environmental chemicals, since they can markedly reduce costs, avoid animal testing, and speed up policy decisions. This paper reports a QSAR study based on the Topological Substructural Molecular Design (TOPS-MODE) approach, aiming at predicting the rodent carcinogenicity of a set of nitroso-compounds selected from the Carcinogenic Potency Data Base (CPDB). The set comprises nitrosoureas (14 chemicals), N-nitrosamines (18 chemicals) C-nitroso-compounds (1 chemical), nitrosourethane (1 chemical) and nitrosoguanidine (1 chemical), which have been bioassayed in male rat using gavage as the route of administration. Here we are especially concerned in gathering the role of both parameters on the carcinogenic activity of this family of compounds. First, the regression model was derived, upon removal of one identified nitrosamine outlier, and was able to account for more than 84% of the variance in the experimental activity. Second, the TOPS-MODE approach afforded the bond contributions -- expressed as fragment contributions to the carcinogenic activity -- that can be interpreted and provide tools for better understanding the mechanisms of carcinogenesis. Finally, and most importantly, we demonstrate the potentialities of this approach towards the recognition of structural alerts for carcinogenicity predictions.
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Affiliation(s)
- Aliuska Morales Helguera
- Department of Chemistry, Faculty of Chemistry and Pharmacy, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba
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Estrada E, Uriarte E, Molina E, Simón-Manso Y, Milne GWA. An Integrated in Silico Analysis of Drug-Binding to Human Serum Albumin. J Chem Inf Model 2006; 46:2709-24. [PMID: 17125211 DOI: 10.1021/ci600274f] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Approaches such as quantitative structure-activity relationships (QSAR) and molecular modeling are integrated with the study of complex networks to understand drug binding to human serum albumin (HSA). A robust QSAR model using the topological substructural molecular descriptors/design (TOPS-MODE) approach has been derived and shows good predictability and interpretability in terms of structural contribution to drug binding to HSA. A perfect agreement exists between the group/fragment contributions found by TOPS-MODE and the specific interactions of drugs with HSA. These results indicate a preponderant contribution of hydrophobic regions of drugs to the specific binding to drug-binding sites 1 and 2 in HSA and specific roles of polar groups which anchor drugs to HSA binding sites. The occurrence of fragments contributing to drug binding to HSA can be represented by complex networks. The fragment-to-fragment complex network displays "small-world" and "scale-free" characteristics and in this way is similar to other complex networks including biological, social, and technological networks. A small number of fragments appear very frequently in most drugs. These molecular "empathic" fragments are good candidates for guiding future drug discovery research.
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Affiliation(s)
- Ernesto Estrada
- Complex Systems Research Group, X-rays Unit, Edificio CACTUS, Santiago de Compostela 15982, Spain.
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