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de Oliveira LHD, Cruz JN, Dos Santos CBR, de Melo EB. Multivariate QSAR, similarity search and ADMET studies based in a set of methylamine derivatives described as dopamine transporter inhibitors. Mol Divers 2023:10.1007/s11030-023-10724-5. [PMID: 37670118 DOI: 10.1007/s11030-023-10724-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/27/2023] [Indexed: 09/07/2023]
Abstract
The dopamine transporter (DAT), responsible for the regulation of dopaminergic neurotransmission, is implicated in the etiology of several neuropsychiatric disorders which, in turn, have contributed to high rates of disability and numerous deaths in recent years, significantly impacting the global health system. Although the research for new drugs for the treatment of neuropsychiatric disorders has evolved in recent years, the availability of DAT-selective drugs that do not generate the same psychostimulant effects observed in drugs of abuse remains scarce. Therefore, we performed a QSAR study based on a dataset of 36 methylamine derivatives described as DAT inhibitors. The model was obtained based only in descriptors derived from 2D structures, and it was validated and generated satisfactory results considering the metrics used for internal and external validation. Subsequently, a virtual screening step also based on 2D similarity was performed, where it was possible to identify a total of 1157 compounds. After a series of reductions of the set using toxicity filters, applicability domain evaluation, and pharmacokinetic properties in silico assessment, seven hit compounds were selected as the most promising to be used, in future studies, as new scaffolds for the development of new DAT inhibitors.
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Affiliation(s)
- Luiz Henrique Dias de Oliveira
- Theorical Medicinal and Environmental Chemistry Laboratory (LQMAT), Department of Pharmacy, Western Paraná State University (UNIOESTE), 2069 Universitária St., Cascavel, PR, 85819-110, Brazil
| | - Jorddy Neves Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, AP, 68902-280, Brazil
| | - Cleydson Breno Rodrigues Dos Santos
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, AP, 68902-280, Brazil
| | - Eduardo Borges de Melo
- Theorical Medicinal and Environmental Chemistry Laboratory (LQMAT), Department of Pharmacy, Western Paraná State University (UNIOESTE), 2069 Universitária St., Cascavel, PR, 85819-110, Brazil.
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2
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Pan M, Cheng L, Wang Y, Lyu C, Hou C, Zhang Q. Exploration of 2D and 3D-QSAR analysis and docking studies for novel dihydropteridone derivatives as promising therapeutic agents targeting glioblastoma. Front Pharmacol 2023; 14:1249041. [PMID: 37719847 PMCID: PMC10501407 DOI: 10.3389/fphar.2023.1249041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/21/2023] [Indexed: 09/19/2023] Open
Abstract
Background: Dihydropteridone derivatives represent a novel class of PLK1 inhibitors, exhibiting promising anticancer activity and potential as chemotherapeutic drugs for glioblastoma. Objective: The aim of this study is to develop 2D and 3D-QSAR models to validate the anticancer activity of dihydropteridone derivatives and identify optimal structural characteristics for the design of new therapeutic agents. Methods: The Heuristic method (HM) was employed to construct a 2D-linear QSAR model, while the gene expression programming (GEP) algorithm was utilized to develop a 2D-nonlinear QSAR model. Additionally, the CoMSIA approach was introduced to investigate the impact of drug structure on activity. A total of 200 novel anti-glioma dihydropteridone compounds were designed, and their activity levels were predicted using chemical descriptors and molecular field maps. The compounds with the highest activity were subjected to molecular docking to confirm their binding affinity. Results: Within the analytical purview, the coefficient of determination (R2) for the HM linear model is elucidated at 0.6682, accompanied by an R2 cv of 0.5669 and a residual sum of squares (S2) of 0.0199. The GEP nonlinear model delineates coefficients of determination for the training and validation sets at 0.79 and 0.76, respectively. Empirical modeling outcomes underscore the preeminence of the 3D-QSAR model, succeeded by the GEP nonlinear model, whilst the HM linear model manifested suboptimal efficacy. The 3D paradigm evinced an exemplary fit, characterized by formidable Q2 (0.628) and R2 (0.928) values, complemented by an impressive F-value (12.194) and a minimized standard error of estimate (SEE) at 0.160. The most significant molecular descriptor in the 2D model, which included six descriptors, was identified as "Min exchange energy for a C-N bond" (MECN). By combining the MECN descriptor with the hydrophobic field, suggestions for the creation of novel medications were generated. This led to the identification of compound 21E.153, a novel dihydropteridone derivative, which exhibited outstanding antitumor properties and docking capabilities. Conclusion: The development of 2D and 3D-QSAR models, along with the innovative integration of contour maps and molecular descriptors, offer novel concepts and techniques for the design of glioblastoma chemotherapeutic agents.
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Affiliation(s)
- Meichen Pan
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lingxue Cheng
- Department of Gastroenterology, 960th Hospital of the Chinese People’s Liberation Army, Jinan, China
| | - Yiguo Wang
- Medical Laboratory Center, Chinese Academy of Traditional Chinese Medicine, Beijing, China
| | - Chunyi Lyu
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chao Hou
- Department of Gastroenterology, 960th Hospital of the Chinese People’s Liberation Army, Jinan, China
| | - Qiming Zhang
- Medical Laboratory Center, Chinese Academy of Traditional Chinese Medicine, Beijing, China
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3
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Fernandes PDO, Martins JPA, de Melo EB, de Oliveira RB, Kronenberger T, Maltarollo VG. Quantitative structure-activity relationship and machine learning studies of 2-thiazolylhydrazone derivatives with anti- Cryptococcus neoformans activity. J Biomol Struct Dyn 2022; 40:9789-9800. [PMID: 34121616 DOI: 10.1080/07391102.2021.1935321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cryptococcus neoformans is a fungus responsible for infections in humans with a significant number of cases in immunosuppressed patients, mainly in underdeveloped countries. In this context, the thiazolylhydrazones are a promising class of compounds with activity against C. neoformans. The understanding of the structure-activity relationship of these derivatives could lead to the design of robust compounds that could be promising drug candidates for fungal infections. Specifically, modern techniques such as 4D-QSAR and machine learning methods were employed in this work to generate two QSAR models (one 2D and one 4D) with high predictive power (r2 for the test set equals to 0.934 and 0.831, respectively), and one random forest classification model was reported with Matthews correlation coefficient equals to 1 and 0.62 for internal and external validations, respectively. The physicochemical interpretation of selected models, indicated the importance of aliphatic substituents at the hydrazone moiety to antifungal activity, corroborating experimental data.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Philipe de Oliveira Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - João Paulo A Martins
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo B de Melo
- Laboratório de Química Medicinal e Ambiental Teórica, Universidade Estadual do Oeste do Paraná, Cascavel, Paraná, Brazil
| | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thales Kronenberger
- Department of Pneumonology and Oncology, Internal Medicine VIII, University Hospital of Tübingen, Tübingen, Baden-Württemberg, Germany
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Tabti K, Elmchichi L, Sbai A, Maghat H, Bouachrine M, Lakhlifi T. Molecular modelling of antiproliferative inhibitors based on SMILES descriptors using Monte-Carlo method, docking, MD simulations and ADME/Tox studies. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2110246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Kamal Tabti
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Larbi Elmchichi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Hamid Maghat
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
- High School of Technology Khenifra, Sultan Moulay Sliman University, Benimellal, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
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5
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Target based structural optimization of substituted pyrazolopyrimidine analogues as inhibitor for IRAK4 by 3D-QSAR and molecular simulation. Struct Chem 2022. [DOI: 10.1007/s11224-022-01907-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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A critical evaluation of novel demulsifying agents based on acrylic terpolymers for Mexican heavy crude oils dehydration. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2021.119878] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Dabade SJ, Mandloi D, Bajaj A. Molecular Docking and QSAR Studies of Coumarin Derivatives as NMT Inhibitors: Simple Structural Features as Potential Modulators of Antifungal Activity. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200617105711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Background:
Treatments of fungal diseases, including Candidiasis, remain not up to
scratch in spite of the mounting catalog of synthetic antifungal agents. These have served as the
impetus for investigating new antifungal agents based on natural products. Consequently, genetic
algorithm-multiple linear regression (GA-MLR) based QSAR (Quantitative Structure-Activity Relationship)
studies of coumarin analogues along with molecular docking were carried out.
Methods:
Coumarin analogues with their MIC values were used to generate the training and test
sets of compounds for QSAR models development; the analogues were also docked into the binding
pocket of NMT (MyristoylCoA: protein N-myristoyltransferase).
Results and Discussion:
The statistical parameters for internal and external validation of QSAR
analysis (R2 = 0.830, Q2 = 0.758, R2Pred = 0.610 and R2m overall = 0.683 ), Y Randomization, Ridge
trace, VIF, tolerance and model criteria of Golbraikh and Tropsha data illustrate the robustness of
the best proposed QSAR model. Most of the analogues bind to the electrostatic, hydrophobic
clamp and display hydrogen bonding with amino acid residues of NMT. Interestingly, the most
active coumarin analogue (MolDock score of -189.257) was docked deeply within the binding
pocket of NMT, thereby displaying hydrogen bonding with Tyr107, Leu451, Leu450, Gln226,
Cys393 and Leu394 amino acid residues.
Conclusion:
The combinations of descriptors from various descriptor subsets in QSAR analysis
have highlighted the role of atomic properties such as polarizability and atomic van der Waals volume
to explain the inhibitory activity. The models and related information may pave the way for
important insight into the designing of putative NMT inhibitors for Candida albicans.
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Affiliation(s)
- Sapna Jain Dabade
- Department of Applied Science, SAGE University, Indore & Research Scholar at School of Chemical Sciences, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Dheeraj Mandloi
- Institute of Engineering and Technology, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Amritlal Bajaj
- School of Chemical Sciences, Devi Ahilya Vishwavidyalaya, Indore, India
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8
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Zivkovic M, Zlatanovic M, Zlatanovic N, Golubović M, Veselinović AM. The Application of the Combination of Monte Carlo Optimization Method based QSAR Modeling and Molecular Docking in Drug Design and Development. Mini Rev Med Chem 2020; 20:1389-1402. [DOI: 10.2174/1389557520666200212111428] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 01/18/2023]
Abstract
In recent years, one of the promising approaches in the QSAR modeling Monte Carlo optimization
approach as conformation independent method, has emerged. Monte Carlo optimization has
proven to be a valuable tool in chemoinformatics, and this review presents its application in drug discovery
and design. In this review, the basic principles and important features of these methods are discussed
as well as the advantages of conformation independent optimal descriptors developed from the
molecular graph and the Simplified Molecular Input Line Entry System (SMILES) notation compared
to commonly used descriptors in QSAR modeling. This review presents the summary of obtained results
from Monte Carlo optimization-based QSAR modeling with the further addition of molecular
docking studies applied for various pharmacologically important endpoints. SMILES notation based
optimal descriptors, defined as molecular fragments, identified as main contributors to the increase/
decrease of biological activity, which are used further to design compounds with targeted activity
based on computer calculation, are presented. In this mini-review, research papers in which molecular
docking was applied as an additional method to design molecules to validate their activity further,
are summarized. These papers present a very good correlation among results obtained from Monte
Carlo optimization modeling and molecular docking studies.
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Affiliation(s)
| | | | | | - Mladjan Golubović
- Clinic for Anesthesiology and Intensive Care, Clinical Center Nis, Nis, Serbia
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9
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Lončarić M, Strelec I, Pavić V, Šubarić D, Rastija V, Molnar M. Lipoxygenase Inhibition Activity of Coumarin Derivatives-QSAR and Molecular Docking Study. Pharmaceuticals (Basel) 2020; 13:ph13070154. [PMID: 32709129 PMCID: PMC7408124 DOI: 10.3390/ph13070154] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/10/2023] Open
Abstract
Lipoxygenases (LOXs) are a family of enzymes found in plants, mammals, and microorganisms. In animals and plants, the enzyme has the capability for the peroxidation of unsaturated fatty acids. Although LOXs participate in the plant defense system, the enzyme’s metabolites can have numerous negative effects on human health. Therefore, many types of research are searching for compounds that can inhibit LOXs. The best quantitative structure–activity relationship (QSAR) model was obtained using a Genetic Algorithm (GA). Molecular docking was performed with iGEMDOCK. The inhibition of lipoxygenase was in the range of 7.1 to 96.6%, and the inhibition of lipid peroxidation was 7.0–91.0%. Among the synthesized compounds, the strongest inhibitor of soybean LOX-3 (96.6%) was found to be 3-benzoyl-7-(benzyloxy)-2H-chromen-2-one. A lipid peroxidation inhibition of 91.0% was achieved with ethyl 7-methoxy-2-oxo-2H-chromene-3-carboxylate. The docking scores for the soybean LOX-3 and human 5-LOX also indicated that this compound has the best affinity for these LOX enzymes. The best multiple linear QSAR model contains the atom-centered fragment descriptors C-06, RDF035p, and HATS8p. QSAR and molecular docking studies elucidated the structural features important for the enhanced inhibitory activity of the most active compounds, such as the presence of the benzoyl ring at the 3-position of coumarin’s core. Compounds with benzoyl substituents are promising candidates as potent lipoxygenase inhibitors.
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Affiliation(s)
- Melita Lončarić
- Faculty of Food Faculty Osijek, Josip Juraj Strossmayer University, 31000 Osijek, Croatia; (M.L.); (I.S.)
| | - Ivica Strelec
- Faculty of Food Faculty Osijek, Josip Juraj Strossmayer University, 31000 Osijek, Croatia; (M.L.); (I.S.)
| | - Valentina Pavić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia;
| | - Domagoj Šubarić
- Department of Agroecology and Environmental Protection, Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.Š.); (V.R.)
| | - Vesna Rastija
- Department of Agroecology and Environmental Protection, Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.Š.); (V.R.)
| | - Maja Molnar
- Faculty of Food Faculty Osijek, Josip Juraj Strossmayer University, 31000 Osijek, Croatia; (M.L.); (I.S.)
- Correspondence: ; Tel.: +385-31-224-342
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10
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Santos VHJM, Pontin D, Rambo RS, Seferin M. The Application of Quantitative Structure–Property Relationship Modeling and Exploratory Analysis to Screen Catalysts for the Synthesis of Oleochemical Carbonates from
CO
2
and Bio‐Based Epoxides. J AM OIL CHEM SOC 2020. [DOI: 10.1002/aocs.12361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Victor Hugo Jacks Mendes Santos
- School of TechnologyPUCRS—Pontifical Catholic University of Rio Grande do Sul 6681 Ipiranga Avenue—Building 12 Porto Alegre 90619‐900 Brazil
- Engineering and Materials Technology Graduate ProgramPontifical Catholic University of Rio Grande do Sul 6681 Ipiranga Avenue—Building 32 Porto Alegre 90619‐900 Brazil
- Institute of Petroleum and Natural ResourcesPontifical Catholic University of Rio Grande do Sul 6681 Ipiranga Avenue—Building 96J Porto Alegre 90619‐900 Brazil
| | - Darlan Pontin
- School of TechnologyPUCRS—Pontifical Catholic University of Rio Grande do Sul 6681 Ipiranga Avenue—Building 12 Porto Alegre 90619‐900 Brazil
| | - Raoní Scheibler Rambo
- Institute of Petroleum and Natural ResourcesPontifical Catholic University of Rio Grande do Sul 6681 Ipiranga Avenue—Building 96J Porto Alegre 90619‐900 Brazil
| | - Marcus Seferin
- School of TechnologyPUCRS—Pontifical Catholic University of Rio Grande do Sul 6681 Ipiranga Avenue—Building 12 Porto Alegre 90619‐900 Brazil
- Engineering and Materials Technology Graduate ProgramPontifical Catholic University of Rio Grande do Sul 6681 Ipiranga Avenue—Building 32 Porto Alegre 90619‐900 Brazil
- Institute of Petroleum and Natural ResourcesPontifical Catholic University of Rio Grande do Sul 6681 Ipiranga Avenue—Building 96J Porto Alegre 90619‐900 Brazil
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11
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Janežič D, Jäntschi L, Bolboacă SD. Sugars and Sweeteners: Structure, Properties and In Silico Modeling. Curr Med Chem 2020; 27:5-22. [PMID: 30259809 DOI: 10.2174/0929867325666180926144401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/15/2018] [Accepted: 03/09/2018] [Indexed: 11/22/2022]
Abstract
Several studies report the effects of excessive use of sugars and sweeteners in the diet. These include obesity, cardiac diseases, diabetes, and even lymphomas, leukemias, cancers of the bladder and brain, chronic fatigue syndrome, Parkinson's disease, Alzheimer's disease, multiple sclerosis, autism, and systemic lupus. On the other hand, each sugar and sweetener has a distinct metabolic assimilation process, and its chemical structure plays an important role in this process. Several scientific papers present the biological effects of the sugars and sweeteners in relation to their chemical structure. One important issue dealing with the sugars is the degree of similarity in their structures, focusing mostly on optical isomerism. Finding and developing new sugars and sweeteners with desired properties is an emerging research area, in which in silico approaches play an important role.
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Affiliation(s)
- Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Lorentz Jäntschi
- Department of Physics and Chemistry, Technical University of Cluj-Napoca, Cluj-Napoca, Romania.,Chemistry Doctoral School, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Sorana D Bolboacă
- Department of Medical Informatics and Biostatistics, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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12
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Chtita S, Aouidate A, Belhassan A, Ousaa A, Taourati AI, Elidrissi B, Ghamali M, Bouachrine M, Lakhlifi T. QSAR study of N-substituted oseltamivir derivatives as potent avian influenza virus H5N1 inhibitors using quantum chemical descriptors and statistical methods. NEW J CHEM 2020. [DOI: 10.1039/c9nj04909f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In silico modelling studies were executed on thirty two N-substituted oseltamivir derivatives as inhibitors of influenza virus H5N1.
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Affiliation(s)
- Samir Chtita
- Laboratory Physical Chemistry of Materials
- Faculty of Sciences Ben M’Sik
- Hassan II University of Casablanca
- Casablanca
- Morocco
| | - Adnane Aouidate
- Computer-Aided Drug Discovery Research Center
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen City
- China
| | - Assia Belhassan
- Molecular Chemistry and Natural Substances Laboratory
- Department of chemistry
- Faculty of Sciences
- University Moulay Ismail
- Meknes
| | - Abdellah Ousaa
- Molecular Chemistry and Natural Substances Laboratory
- Department of chemistry
- Faculty of Sciences
- University Moulay Ismail
- Meknes
| | - Abdelali Idrissi Taourati
- Molecular Chemistry and Natural Substances Laboratory
- Department of chemistry
- Faculty of Sciences
- University Moulay Ismail
- Meknes
| | - Bouhya Elidrissi
- Molecular Chemistry and Natural Substances Laboratory
- Department of chemistry
- Faculty of Sciences
- University Moulay Ismail
- Meknes
| | - Mounir Ghamali
- Molecular Chemistry and Natural Substances Laboratory
- Department of chemistry
- Faculty of Sciences
- University Moulay Ismail
- Meknes
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory
- Department of chemistry
- Faculty of Sciences
- University Moulay Ismail
- Meknes
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory
- Department of chemistry
- Faculty of Sciences
- University Moulay Ismail
- Meknes
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13
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Balupuri A, Balasubramanian PK, Cho SJ. 3D-QSAR, docking, molecular dynamics simulation and free energy calculation studies of some pyrimidine derivatives as novel JAK3 inhibitors. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2017.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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14
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Bora A, Suzuki T, Funar-Timofei S. Neonicotinoid insecticide design: molecular docking, multiple chemometric approaches, and toxicity relationship with Cowpea aphids. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:14547-14561. [PMID: 30877540 DOI: 10.1007/s11356-019-04662-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Neonicotinoids are the fastest-growing class of insecticides successfully applied in plant protection, human and animal health care. The significant resistance increases led to the urgent need for alternative new neonicotinoids, with improved insecticidal activity. We performed molecular docking to describe a common binding mode of neonicotinoids into the nicotinic acetylcholine receptor, and to select the appropriate conformations to derive models. These were further used in a QSAR study employing both linear and nonlinear approaches to model the inhibitory activity against the Cowpea aphids. Linear modeling was performed by multiple linear regression and partial least squares and nonlinear modeling by artificial neural networks and support vector machine methods. The OECD principles were considered for QSAR models validation. Robust models with predictive power were found for neonicotinoid diverse structures. Based on our QSAR and docking outcomes, five new insecticides were predicted, according to the model applicability domain, the ligand efficiencies, and the binding mode. Therefore, the developed models can be confidently used for the prediction of the insecticidal activity of new chemicals, saving a substantial amount of time and money and, also, contributing to the chemical risk assessment.
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Affiliation(s)
- Alina Bora
- Institute of Chemistry Timisoara of the Romanian Academy, 24 Mihai Viteazul Av., 300223, Timisoara, Romania
| | - Takahiro Suzuki
- Natural Science Laboratory, Toyo University, 5-28-20 Hakusan, Bunkyo-ku, Tokyo, 112-8606, Japan
| | - Simona Funar-Timofei
- Institute of Chemistry Timisoara of the Romanian Academy, 24 Mihai Viteazul Av., 300223, Timisoara, Romania.
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15
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Crisan L, Borota A, Suzuki T, Funar-Timofei S. An Approach to Identify New Insecticides Against Myzus Persicae. In silico Study Based on Linear and Non-linear Regression Techniques. Mol Inform 2019; 38:e1800119. [PMID: 30632677 DOI: 10.1002/minf.201800119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/04/2018] [Indexed: 11/11/2022]
Abstract
Neonicotinoids are known to have high insecticidal potency, low mammalian toxicity and relatively tough activity for the development of resistance against aphids. A series of guadipyr insecticides, active against Myzus persicae was engaged in silico studies, based on Multiple Linear Regression (MLR), Partial Least Squares regression (PLS), Artificial Neural Networks (ANN), Support Vector Machine (SVM) and Pharmacophore modeling. Robust and predictive models were built using correlations between the insecticidal profile, expressed by experimental pLC50 values, and molecular descriptors, calculated from the energy optimized structures. Four new potential insecticides active against Myzus persicae and their predicted pLC50 toxicity values were reported for the first time. The models presented here can be used as an approach in the screening and prioritization of chemicals in a scientific and regulatory frame and for toxicity prediction.
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Affiliation(s)
- Luminita Crisan
- Computational Chemistry Department, Institute of Chemistry Timisoara of the Romanian Academy, B-dul Mihai Viteazu 24, RO-300223, Timisoara, Romania
| | - Ana Borota
- Computational Chemistry Department, Institute of Chemistry Timisoara of the Romanian Academy, B-dul Mihai Viteazu 24, RO-300223, Timisoara, Romania
| | - Takahiro Suzuki
- Natural Science Laboratory, Toyo University, 5-28-20 Hakusan, Bunkyo-ku, Tokyo, 112-8606, Japan
| | - Simona Funar-Timofei
- Computational Chemistry Department, Institute of Chemistry Timisoara of the Romanian Academy, B-dul Mihai Viteazu 24, RO-300223, Timisoara, Romania
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Ribeiro TPP, Manarin FG, Borges de Melo E. In silico study toward the identification of new and safe potential inhibitors of photosynthetic electron transport. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 153:175-180. [PMID: 29428593 DOI: 10.1016/j.ecoenv.2018.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
To address the rising global demand for food, it is necessary to search for new herbicides that can control resistant weeds. We performed a 2D-quantitative structure-activity relationship (QSAR) study to predict compounds with photosynthesis-inhibitory activity. A data set of 44 compounds (quinolines and naphthalenes), which are described as photosynthetic electron transport (PET) inhibitors, was used. The obtained model was approved in internal and external validation tests. 2D Similarity-based virtual screening was performed and 64 compounds were selected from the ZINC database. By using the VEGA QSAR software, 48 compounds were shown to have potential toxic effects (mutagenicity and carcinogenicity). Therefore, the model was also tested using a set of 16 molecules obtained by a similarity search of the ZINC database. Six compounds showed good predicted inhibition of PET. The obtained model shows potential utility in the design of new PET inhibitors, and the hit compounds found by virtual screening are novel bicyclic scaffolds of this class.
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Deep Eutectic Solvents as Convenient Media for Synthesis of Novel Coumarinyl Schiff Bases and Their QSAR Studies. Molecules 2017; 22:molecules22091482. [PMID: 28872604 PMCID: PMC6151826 DOI: 10.3390/molecules22091482] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/29/2017] [Accepted: 09/02/2017] [Indexed: 11/17/2022] Open
Abstract
Deep eutectic solvents, as green and environmentally friendly media, were utilized in the synthesis of novel coumarinyl Schiff bases. Novel derivatives were synthesized from 2-((4-methyl-2-oxo-2H-chromen-7-yl)oxy)acetohydrazide and corresponding aldehyde in choline chloride:malonic acid (1:1) based deep eutectic solvent. In these reactions, deep eutectic solvent acted as a solvent and catalyst as well. Novel Schiff bases were synthesized in high yields (65–75%) with no need for further purification, and their structures were confirmed by mass spectra, 1H and 13C NMR. Furthermore, their antioxidant activity was determined and compared to antioxidant activity of previously synthesized derivatives, thus investigating their structure–activity relationship utilizing quantitative structure-activity relationship QSAR studies. Calculation of molecular descriptors has been performed by DRAGON software. The best QSAR model (Rtr = 0.636; Rext = 0.709) obtained with three descriptors (MATS3m, Mor22u, Hy) implies that the pairs of atoms higher mass at the path length 3, three-dimensional arrangement of atoms at scattering parameter s = 21 Å−1, and higher number of hydrophilic groups (-OH, -NH) enhanced antioxidant activity. Electrostatic potential surface of the most active compounds showed possible regions for donation of electrons to 1,1-diphenyl-2-picryhydrazyl (DPPH) radicals.
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de Campos LJ, de Melo EB. A QSAR study of integrase strand transfer inhibitors based on a large set of pyrimidine, pyrimidone, and pyridopyrazine carboxamide derivatives. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Funar-Timofei S, Borota A, Crisan L. Combined molecular docking and QSAR study of fused heterocyclic herbicide inhibitors of D1 protein in photosystem II of plants. Mol Divers 2017; 21:437-454. [DOI: 10.1007/s11030-017-9735-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 02/20/2017] [Indexed: 10/20/2022]
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20
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Determination of structural requirements of Mer kinase inhibitors and binding interaction analysis using in silico approaches. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1722-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Santoro AL, Carrilho E, Lanças FM, Montanari CA. Quantitative structure–retention relationships of flavonoids unraveled by immobilized artificial membrane chromatography. Eur J Pharm Sci 2016; 88:147-57. [DOI: 10.1016/j.ejps.2015.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/09/2015] [Accepted: 12/06/2015] [Indexed: 01/27/2023]
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22
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Nesměrák K, Toropov AA, Toropova AP. Model for electrochemical parameters for 4-(benzylsulfanyl)pyridines calculated from the molecular structure. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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de Melo EB, Martins JPA, Miranda EH, Ferreira MMC. A best comprehension about the toxicity of phenylsulfonyl carboxylates in Vibrio fischeri using quantitative structure activity/property relationship methods. JOURNAL OF HAZARDOUS MATERIALS 2016; 304:233-241. [PMID: 26551227 DOI: 10.1016/j.jhazmat.2015.10.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/17/2015] [Accepted: 10/22/2015] [Indexed: 06/05/2023]
Abstract
Aromatic sulfones comprise a class of chemicals used in agrochemical and pharmaceutical industries and as floatation and extractant agents in petrochemical and metallurgy industries. In this study, new QSA(P)R studies were carried out to predict the toxicity against Vibrio fischeri of a set of 52 aromatic sulfones. The same approach was used to evaluate the relationship between these endpoint and the water solubility, another important environmental endpoint. The study resulted in models of good statistical quality and mechanistic interpretation with a possible correlation between the two endpoints, but the toxic effect is also likely to depend on other physicochemical properties. The use of the PLS2, a method not commonly used in QSA(P)R studies, also produced models of greater reliability, and the relationship between the two endpoints was reinforced to some degree. These results are useful for better understanding the process by which these compounds exert their environmental toxicity, thus aiding in the development of industrially useful compounds with less potential environmental damage.
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Bhayye SS, Roy K, Saha A. Pharmacophore generation, atom-based 3D-QSAR, HQSAR and activity cliff analyses of benzothiazine and deazaxanthine derivatives as dual A 2A antagonists/MAO‑B inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:183-202. [PMID: 26873265 DOI: 10.1080/1062936x.2015.1136840] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dual inhibition of A2A and MAO-B is an emerging strategy in neurodegenerative diseases, such as Alzheimer's disease (AD) and Parkinson's disease (PD). In this study, atom-based three-dimensional quantitative structure-activity relationship (3D-QSAR) and hologram quantitative structure-activity relationship (HQSAR) models were generated with benzothiazine and deazaxanthine derivatives. Based on activity against A2A and MAO-B, two statistically significant 3D-QSAR models (r2 = 0.96, q2 = 0.76 and r2 = 0.91, q2 = 0.63) and HQSAR models (r2 = 0.93, q2 = 0.68 and r2 = 0.97, q2 = 0.58) were developed. In an activity cliff analysis, structural outliers were identified by calculating the Mahalanobis distance for a pair of compounds with A2A and MAO-B inhibitory activities. The generated 3D-QSAR and HQSAR models, activity cliff analysis, molecular docking and dynamic studies for dual target protein inhibitors provide key structural scaffolds that serve as building blocks in designing drug-like molecules for neurodegenerative diseases.
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Affiliation(s)
- S S Bhayye
- a Department of Chemical Technology , University of Calcutta , Kolkata , West Bengal , India
| | - K Roy
- b Department of Pharmaceutical Technology , Jadavpur University , Kolkata , West Bengal , India
| | - A Saha
- a Department of Chemical Technology , University of Calcutta , Kolkata , West Bengal , India
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Toropova AP, Toropov AA, Benfenati E, Leszczynska D, Leszczynski J. QSAR model as a random event: A case of rat toxicity. Bioorg Med Chem 2015; 23:1223-30. [DOI: 10.1016/j.bmc.2015.01.055] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 01/12/2023]
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Neves BJ, Andrade CH, Cravo PVL. Natural products as leads in schistosome drug discovery. Molecules 2015; 20:1872-903. [PMID: 25625682 PMCID: PMC6272663 DOI: 10.3390/molecules20021872] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 12/31/2014] [Accepted: 01/14/2015] [Indexed: 11/16/2022] Open
Abstract
Schistosomiasis is a neglected parasitic tropical disease that claims around 200,000 human lives every year. Praziquantel (PZQ), the only drug recommended by the World Health Organization for the treatment and control of human schistosomiasis, is now facing the threat of drug resistance, indicating the urgent need for new effective compounds to treat this disease. Therefore, globally, there is renewed interest in natural products (NPs) as a starting point for drug discovery and development for schistosomiasis. Recent advances in genomics, proteomics, bioinformatics, and cheminformatics have brought about unprecedented opportunities for the rapid and more cost-effective discovery of new bioactive compounds against neglected tropical diseases. This review highlights the main contributions that NP drug discovery and development have made in the treatment of schistosomiasis and it discusses how integration with virtual screening (VS) strategies may contribute to accelerating the development of new schistosomidal leads, especially through the identification of unexplored, biologically active chemical scaffolds and structural optimization of NPs with previously established activity.
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Affiliation(s)
- Bruno J Neves
- LabMol-Laboratory for Drug Design and Molecular Modeling, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia 74605-170, Brazil.
| | - Carolina H Andrade
- LabMol-Laboratory for Drug Design and Molecular Modeling, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia 74605-170, Brazil.
| | - Pedro V L Cravo
- GenoBio-Laboratory of Genomics and Biotechnology, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia 74605-050, Brazil.
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de Campos LJ, de Melo EB. Modeling structure–activity relationships of prodiginines with antimalarial activity using GA/MLR and OPS/PLS. J Mol Graph Model 2014; 54:19-31. [DOI: 10.1016/j.jmgm.2014.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 08/02/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
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Effect of information leakage and method of splitting (rational and random) on external predictive ability and behavior of different statistical parameters of QSAR model. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1193-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Martis EA, Chandarana RC, Shaikh MS, Ambre PK, D’Souza JS, Iyer KR, Coutinho EC, Nandan SR, Pissurlenkar RR. Quantifying ligand–receptor interactions for gorge-spanning acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease. J Biomol Struct Dyn 2014; 33:1107-25. [DOI: 10.1080/07391102.2014.931824] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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SMILES-based quantitative structure–property relationships for half-wave potential of N-benzylsalicylthioamides. Eur J Med Chem 2013; 67:111-4. [DOI: 10.1016/j.ejmech.2013.05.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 01/17/2023]
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Tong J, Xu X, Liu S, Che T, Li Y, Hu Z, Meng Y. Prediction of glass transition temperature of polyacrylate using a quantitative structure property relationship model. POLYMER SCIENCE SERIES A 2013. [DOI: 10.1134/s0965545x13080075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Nesmerak K, Toropov AA, Toropova AP. SMILES-based quantitative structure–retention relationships for RP HPLC of 1-phenyl-5-benzylsulfanyltetrazoles. Struct Chem 2013. [DOI: 10.1007/s11224-013-0293-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Insight into the binding mode and the structural features of the pyrimidine derivatives as human A2A adenosine receptor antagonists. Biosystems 2013; 115:13-22. [PMID: 23665268 DOI: 10.1016/j.biosystems.2013.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/07/2013] [Accepted: 04/24/2013] [Indexed: 12/12/2022]
Abstract
The interaction of 278 monocyclic and bicyclic pyrimidine derivatives with human A2A adenosine receptor (AR) was investigated by employing molecular dynamics, thermodynamic analysis and three-dimensional quantitative structure-activity relationship (3D-QSAR) approaches. The binding analysis reveals that the pyrimidine derivatives are anchored in TM2, 3, 5, 6 and 7 of A2A AR by the aromatic stacking and hydrogen bonding interactions. The key residues involving Phe168, Glu169, and Asn253 stabilize the monocyclic and bicyclic cores of inhibitors. The thermodynamic analysis by molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) approach also confirms the reasonableness of the binding modes. In addition, the ligand-/receptor-based comparative molecular similarity indices analysis (CoMSIA) models of high statistical significance were generated and the resulting contour maps correlate well with the structural features of the antagonists essential for high A2A AR affinity. A minor/bulky group with negative charge at C2/C6 of pyrimidine ring respectively enhances the activity for all these pyrimidine derivatives. Particularly, the higher electron density of the ring in the bicyclic derivatives, the more potent the antagonists. The obatined results might be helpful in rational design of novel candidate of A2A adenosine receptor antagonist for treatment of Parkinson's disease.
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Das RN, Sanderson H, Mwambo AE, Roy K. Preliminary studies on model development for rodent toxicity and its interspecies correlation with aquatic toxicities of pharmaceuticals. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2013; 90:375-381. [PMID: 23238824 DOI: 10.1007/s00128-012-0921-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/01/2012] [Indexed: 06/01/2023]
Abstract
Environmental toxicity due to pharmaceuticals has been an issue of serious concern for long time. Development of chemometric models with reliable predictive power has been considered as an effective tool for the design of new drug agents with reduced or without ecotoxic potential. Considering a higher degree of similarity in genetic homology towards drug receptor with mammals, we have used a dataset of 194 compounds with reported rodent, fish, daphnia and algae toxicity data for extrapolation of their toxicity towards humans. Allowing for rodents as the most surrogate to human physiology, attempts have also been made to develop interspecies correlation models keeping rodent toxicity as dependent variable so that any drug without reported rodent toxicity can be predicted using fish, daphnia or algae toxicity data which can be consequently extrapolated to human toxicity. The developed models have been subjected to multiple validation strategies. Acceptable results have been obtained in both cases of direct and interspecies extrapolation quantitative structure-activity relationship models.
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Affiliation(s)
- Rudra Narayan Das
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur Univeristy, Kolkata, 700 032, India
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Toropov AA, Toropova AP, Benfenati E, Gini G, Leszczynska D, Leszczynski J, De Nucci G. QSAR models for inhibitors of physiological impact of Escherichia coli that leads to diarrhea. Biochem Biophys Res Commun 2013; 432:214-25. [PMID: 23402755 DOI: 10.1016/j.bbrc.2013.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 02/01/2013] [Indexed: 11/15/2022]
Abstract
Quantitative structure - activity relationships (QSARs) developed to evaluate percentage of inhibition of STa-stimulated (Escherichia coli) cGMP accumulation in T84 cells are calculated by the Monte Carlo method. This endpoint represents a measure of biological activity of a substance against diarrhea. Statistical quality of the developed models is quite good. The approach is tested using three random splits of data into the training and test sets. The statistical characteristics for three splits are the following: (1) n=20, r(2)=0.7208, q(2)=0.6583, s=16.9, F=46 (training set); n=11, r(2)=0.8986, s=14.6 (test set); (2) n=19, r(2)=0.6689, q(2)=0.5683, s=17.6, F=34 (training set); n=12, r(2)=0.8998, s=12.1 (test set); and (3) n=20, r(2)=0.7141, q(2)=0.6525, s=14.7, F=45 (training set); n=11, r(2)=0.8858, s=19.5 (test set). Based on the proposed here models hypothetical compounds which can be useful agents against diarrhea are suggested.
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Affiliation(s)
- Andrey A Toropov
- Istituto di Ricerche Farmacologiche Mario Negri, Laboratory of Environmental Chemistry and Toxicology, Via La Masa 19, 20156 Milano, Italy.
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Roy K, Chakraborty P, Mitra I, Ojha PK, Kar S, Das RN. Some case studies on application of “rm2” metrics for judging quality of quantitative structure-activity relationship predictions: Emphasis on scaling of response data. J Comput Chem 2013; 34:1071-82. [DOI: 10.1002/jcc.23231] [Citation(s) in RCA: 309] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 12/08/2012] [Accepted: 12/16/2012] [Indexed: 12/24/2022]
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38
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The definition of the molecular structure for potential anti-malaria agents by the Monte Carlo method. Struct Chem 2012. [DOI: 10.1007/s11224-012-0180-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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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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