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Arzine A, Abchir O, Chalkha M, Chebbac K, Rhazi Y, Barghady N, Yamari I, El Moussaoui A, Nakkabi A, Akhazzane M, Bakhouch M, Chtita S, El Yazidi M. Design, synthesis, In-vitro, In-silico and DFT studies of novel functionalized isoxazoles as antibacterial and antioxidant agents. Comput Biol Chem 2024; 108:107993. [PMID: 38071761 DOI: 10.1016/j.compbiolchem.2023.107993] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 01/22/2024]
Abstract
A series of new isoxazolederivatives incorporating the sulfonate ester function has been synthesized from 2-benzylidenebenzofuran-3(2 H)-one, known as aurone. The synthesis of the target compounds was carried out following an efficient methodology that allows access to the desired products in a reproducible way and with good yield. The structures of the synthesized compounds were established using NMR (1H and 13C) spectroscopy and mass spectrometry. A theoretical study was performed to optimize the geometrical structures and to calculate the structural and electronic parameters of the synthesized compounds. The calculations were also carried out to understand the influence and the effect of substitutions on the chemical reactivity of the studied compounds. The synthesized isoxazoles were screened for their antioxidant and antibacterial activities. The findings demonstrate that the studied compounds exhibit good to moderate antibacterial activity against the tested bacteria (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli). Moreover, a number of the tested isoxazole derivatives exhibit high effectiveness against DPPH free radicals. Besides that, molecular docking studies were carried out to predict binding affinity and identify the most likely binding interactions between the active molecules and the target microorganisms' proteins. A 100 ns molecular dynamics study was then conducted to examine the dynamic behavior and stability of the highly potent isoxazole 4e in complex with the target bacterial proteins. Finally, the ADMET analyses suggest that all the synthesized isoxazoles have good pharmacokinetic profiles and non-toxicity and non-carcinogenicity in biological systems.
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Affiliation(s)
- Aziz Arzine
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Faculty of Sciences Dhar EL Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796 Atlas, Fez 30000, Morocco
| | - Oussama Abchir
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca B.P 7955, Morocco
| | - Mohammed Chalkha
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Faculty of Sciences Dhar EL Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796 Atlas, Fez 30000, Morocco.
| | - Khalid Chebbac
- Laboratory of Biotechnology Conservation and Valorisation of Natural Resources, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdallah University, Fez 30000, Morocco
| | - Yassine Rhazi
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Faculty of Sciences Dhar EL Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796 Atlas, Fez 30000, Morocco
| | - Najoua Barghady
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca B.P 7955, Morocco
| | - Imane Yamari
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca B.P 7955, Morocco
| | - Abdelfattah El Moussaoui
- Laboratory of Biotechnology, Environment, Agri-Food and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco
| | - Asmae Nakkabi
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Faculty of Sciences Dhar EL Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796 Atlas, Fez 30000, Morocco
| | - Mohamed Akhazzane
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Faculty of Sciences Dhar EL Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796 Atlas, Fez 30000, Morocco; Cité de l'innovation, Université Sidi Mohamed Ben Abdellah, Route Immouzer, P.O. Box 2626, Fez 30000, Morocco
| | - Mohamed Bakhouch
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Faculty of Sciences Dhar EL Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796 Atlas, Fez 30000, Morocco; Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, P.O. Box 24, El Jadida 24000, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca B.P 7955, Morocco
| | - Mohamed El Yazidi
- Engineering Laboratory of Organometallic, Molecular Materials and Environment, Faculty of Sciences Dhar EL Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796 Atlas, Fez 30000, Morocco.
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Kuz’min V, Artemenko A, Ognichenko L, Hromov A, Kosinskaya A, Stelmakh S, Sessions ZL, Muratov EN. Simplex representation of molecular structure as universal QSAR/QSPR tool. Struct Chem 2021; 32:1365-1392. [PMID: 34177203 PMCID: PMC8218296 DOI: 10.1007/s11224-021-01793-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/07/2021] [Indexed: 10/24/2022]
Abstract
We review the development and application of the Simplex approach for the solution of various QSAR/QSPR problems. The general concept of the simplex method and its varieties are described. The advantages of utilizing this methodology, especially for the interpretation of QSAR/QSPR models, are presented in comparison to other fragmentary methods of molecular structure representation. The utility of SiRMS is demonstrated not only in the standard QSAR/QSPR applications, but also for mixtures, polymers, materials, and other complex systems. In addition to many different types of biological activity (antiviral, antimicrobial, antitumor, psychotropic, analgesic, etc.), toxicity and bioavailability, the review examines the simulation of important properties, such as water solubility, lipophilicity, as well as luminescence, and thermodynamic properties (melting and boiling temperatures, critical parameters, etc.). This review focuses on the stereochemical description of molecules within the simplex approach and details the possibilities of universal molecular stereo-analysis and stereochemical configuration description, along with stereo-isomerization mechanism and molecular fragment "topography" identification.
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Affiliation(s)
- Victor Kuz’min
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Anatoly Artemenko
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Luidmyla Ognichenko
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Alexander Hromov
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Anna Kosinskaya
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
- Department of Medical Chemistry, Odessa National Medical University, Odessa, 65082 Ukraine
| | - Sergij Stelmakh
- Department of Molecular Structures and Chemoinformatics, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080 Ukraine
| | - Zoe L. Sessions
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Eugene N. Muratov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 USA
- Department of Pharmaceutical Sciences, Federal University of Paraiba, Joao Pessoa, PB 58059 Brazil
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Khanna M, Gautam A, Rajput R, Sharma L. Natural Products as a Paradigm for the Treatment of Coxsackievirus - induced Myocarditis. Curr Top Med Chem 2020; 20:607-616. [PMID: 31995007 DOI: 10.2174/1568026620666200129094516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/22/2019] [Accepted: 10/22/2019] [Indexed: 11/22/2022]
Abstract
Coxsackievirus B3 (CVB3), a member of the Picornaviridae family, is considered to be one of the most important infectious agents to cause virus-induced myocarditis. Despite improvements in studying viral pathology, structure and molecular biology, as well as diagnosis of this disease, there is still no virus-specific drug in clinical use. Structural and nonstructural proteins produced during the coxsackievirus life cycle have been identified as potential targets for blocking viral replication at the step of attachment, entry, uncoating, RNA and protein synthesis by synthetic or natural compounds. Moreover, WIN (for Winthrop) compounds and application of nucleic-acid based strategies were shown to target viral capsid, entry and viral proteases, but have not reached to the clinical trials as a successful antiviral agent. There is an urgent need for diverse molecular libraries for phenotype-selective and high-throughput screening.
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Affiliation(s)
- Madhu Khanna
- Department of Microbiology (Virology Unit), Vallabhbhai Patel Chest Institute, University of Delhi, Delhi-110007, India
| | - Anju Gautam
- Department of Microbiology (Virology Unit), Vallabhbhai Patel Chest Institute, University of Delhi, Delhi-110007, India
| | - Roopali Rajput
- Department of Microbiology (Virology Unit), Vallabhbhai Patel Chest Institute, University of Delhi, Delhi-110007, India
| | - Latika Sharma
- Department of Microbiology (Virology Unit), Vallabhbhai Patel Chest Institute, University of Delhi, Delhi-110007, India
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Korn D, Pervitsky V, Bobrowski T, Alves VM, Schmitt C, Bizon C, Baker N, Chirkova R, Cherkasov A, Muratov E, Tropsha A. COVID-19 Knowledge Extractor (COKE): A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:13289222. [PMID: 33269341 PMCID: PMC7709174 DOI: 10.26434/chemrxiv.13289222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Revised: 11/26/2020] [Indexed: 12/02/2022]
Abstract
Objective: The COVID-19 pandemic has catalyzed a widespread effort to identify drug candidates and biological targets of relevance to SARS-COV-2 infection, which resulted in large numbers of publications on this subject. We have built the COVID-19 Knowledge Extractor (COKE), a web application to extract, curate, and annotate essential drug-target relationships from the research literature on COVID-19 to assist drug repurposing efforts. Materials and Methods: SciBiteAI ontological tagging of the COVID Open Research Dataset (CORD-19), a repository of COVID-19 scientific publications, was employed to identify drug-target relationships. Entity identifiers were resolved through lookup routines using UniProt and DrugBank. A custom algorithm was used to identify co-occurrences of protein and drug terms, and confidence scores were calculated for each entity pair. Results: COKE processing of the current CORD-19 database identified about 3,000 drug-protein pairs, including 29 unique proteins and 500 investigational, experimental, and approved drugs. Some of these drugs are presently undergoing clinical trials for COVID-19. Discussion: The rapidly evolving situation concerning the COVID-19 pandemic has resulted in a dramatic growth of publications on this subject in a short period. These circumstances call for methods that can condense the literature into the key concepts and relationships necessary for insights into SARS-CoV-2 drug repurposing. Conclusion: The COKE repository and web application deliver key drug - target protein relationships to researchers studying SARS-CoV-2. COKE portal may provide comprehensive and critical information on studies concerning drug repurposing against COVID-19. COKE is freely available at https://coke.mml.unc.edu/ and the code is available at https://github.com/DnlRKorn/CoKE.
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Affiliation(s)
- Daniel Korn
- Department of Computer Science, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Vera Pervitsky
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Vinicius M. Alves
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Charles Schmitt
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Chris Bizon
- Renaissance Computing Institute, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7568, USA
| | - Nancy Baker
- ParlezChem, 123 W Union Street, Hillsborough, NC, 27278, USA
| | - Rada Chirkova
- Department of Computer Science, North Carolina State University, Raleigh, NC, 27606-5550
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Egorova A, Ekins S, Schmidtke M, Makarov V. Back to the future: Advances in development of broad-spectrum capsid-binding inhibitors of enteroviruses. Eur J Med Chem 2019; 178:606-622. [PMID: 31226653 PMCID: PMC8194503 DOI: 10.1016/j.ejmech.2019.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 01/16/2023]
Abstract
The hydrophobic pocket within viral capsid protein 1 is a target to combat the rhino- and enteroviruses (RV and EV) using small molecules. The highly conserved amino acids lining this pocket enable the development of antivirals with broad-spectrum of activity against numerous RVs and EVs. Inhibitor binding blocks: the attachment of the virion to the host cell membrane, viral uncoating, and/or production of infectious virus particles. Syntheses and biological studies of the most well-known antipicornaviral capsid binders have been reviewed and we propose next steps in this research.
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Affiliation(s)
- Anna Egorova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow, 119071, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC27606, USA
| | - Michaela Schmidtke
- Jena University Hospital, Department of Medical Microbiology, Section Experimental Virology, Hans-Knöll-Str. 2, 07745, Jena, Germany
| | - Vadim Makarov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prospekt 33-2, Moscow, 119071, Russia.
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Chavan AP, Deshpande RR, Borade NA, Shinde A, Mhaske PC, Sarkar D, Bobade VD. Synthesis of new 1,3,4-oxadiazole and benzothiazolylthioether derivatives of 4-arylmethylidene-3-substituted-isoxazol-5(4H)-one as potential antimycobacterial agents. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02420-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Alves V, Muratov E, Capuzzi S, Politi R, Low Y, Braga R, Zakharov AV, Sedykh A, Mokshyna E, Farag S, Andrade C, Kuz'min V, Fourches D, Tropsha A. Alarms about structural alerts. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2016; 18:4348-4360. [PMID: 28503093 PMCID: PMC5423727 DOI: 10.1039/c6gc01492e] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Structural alerts are widely accepted in chemical toxicology and regulatory decision support as a simple and transparent means to flag potential chemical hazards or group compounds into categories for read-across. However, there has been a growing concern that alerts disproportionally flag too many chemicals as toxic, which questions their reliability as toxicity markers. Conversely, the rigorously developed and properly validated statistical QSAR models can accurately and reliably predict the toxicity of a chemical; however, their use in regulatory toxicology has been hampered by the lack of transparency and interpretability. We demonstrate that contrary to the common perception of QSAR models as "black boxes" they can be used to identify statistically significant chemical substructures (QSAR-based alerts) that influence toxicity. We show through several case studies, however, that the mere presence of structural alerts in a chemical, irrespective of the derivation method (expert-based or QSAR-based), should be perceived only as hypotheses of possible toxicological effect. We propose a new approach that synergistically integrates structural alerts and rigorously validated QSAR models for a more transparent and accurate safety assessment of new chemicals.
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Affiliation(s)
- Vinicius Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
- Laboratory for Molecular Modeling and Design, Department of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Chemical Technology, Odessa National Polytechnic University, Odessa, 65000, Ukraine
| | - Stephen Capuzzi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Regina Politi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yen Low
- Netflix, San Francisco, CA 94123, USA
| | - Rodolpho Braga
- Laboratory for Molecular Modeling and Design, Department of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD 20850, USA
| | | | - Elena Mokshyna
- Laboratory of Theoretical Chemistry, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080, Ukraine
| | - Sherif Farag
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Carolina Andrade
- Laboratory for Molecular Modeling and Design, Department of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Victor Kuz'min
- Laboratory of Theoretical Chemistry, A.V. Bogatsky Physical-Chemical Institute NAS of Ukraine, Odessa, 65080, Ukraine
| | - Denis Fourches
- Department of Chemistry and Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
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Cherkasov A, Muratov EN, Fourches D, Varnek A, Baskin II, Cronin M, Dearden J, Gramatica P, Martin YC, Todeschini R, Consonni V, Kuz'min VE, Cramer R, Benigni R, Yang C, Rathman J, Terfloth L, Gasteiger J, Richard A, Tropsha A. QSAR modeling: where have you been? Where are you going to? J Med Chem 2014; 57:4977-5010. [PMID: 24351051 PMCID: PMC4074254 DOI: 10.1021/jm4004285] [Citation(s) in RCA: 1023] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quantitative structure-activity relationship modeling is one of the major computational tools employed in medicinal chemistry. However, throughout its entire history it has drawn both praise and criticism concerning its reliability, limitations, successes, and failures. In this paper, we discuss (i) the development and evolution of QSAR; (ii) the current trends, unsolved problems, and pressing challenges; and (iii) several novel and emerging applications of QSAR modeling. Throughout this discussion, we provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive QSAR models. We hope that this Perspective will help communications between computational and experimental chemists toward collaborative development and use of QSAR models. We also believe that the guidelines presented here will help journal editors and reviewers apply more stringent scientific standards to manuscripts reporting new QSAR studies, as well as encourage the use of high quality, validated QSARs for regulatory decision making.
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Affiliation(s)
- Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, V6H3Z6, Canada
| | - Eugene N. Muratov
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Molecular Structure and Cheminformatics, A.V. Bogatsky Physical-Chemical Institute National Academy of Sciences of Ukraine, Odessa, 65080, Ukraine
| | - Denis Fourches
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Alexandre Varnek
- Department of Chemistry, L. Pasteur University of Strasbourg, Strasbourg, 67000, France
| | - Igor I. Baskin
- Department of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Mark Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L33AF, UK
| | - John Dearden
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L33AF, UK
| | - Paola Gramatica
- Department of Structural and Functional Biology, University of Insubria, Varese, 21100, Italy
| | | | - Roberto Todeschini
- Milano Chemometrics and QSAR Research Group, University of Milano-Bicocca, Milan, 20126, Italy
| | - Viviana Consonni
- Milano Chemometrics and QSAR Research Group, University of Milano-Bicocca, Milan, 20126, Italy
| | - Victor E. Kuz'min
- Department of Molecular Structure and Cheminformatics, A.V. Bogatsky Physical-Chemical Institute National Academy of Sciences of Ukraine, Odessa, 65080, Ukraine
| | | | - Romualdo Benigni
- Environment and Health Department, Istituto Superiore di Sanita’, Rome, 00161, Italy
| | | | - James Rathman
- Altamira LLC, Columbus OH 43235, USA
- Department of Chemical and Biomolecular Engineering, the Ohio State University, Columbus, OH 43215, USA
| | | | | | - Ann Richard
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27519, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
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10
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Oprisiu I, Varlamova E, Muratov E, Artemenko A, Marcou G, Polishchuk P, Kuz'min V, Varnek A. QSPR Approach to Predict Nonadditive Properties of Mixtures. Application to Bubble Point Temperatures of Binary Mixtures of Liquids. Mol Inform 2012; 31:491-502. [DOI: 10.1002/minf.201200006] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 04/23/2012] [Indexed: 11/11/2022]
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11
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Muratov EN, Varlamova EV, Artemenko AG, Polishchuk PG, Kuz'min VE. Existing and Developing Approaches for QSAR Analysis of Mixtures. Mol Inform 2012; 31:202-21. [PMID: 27477092 DOI: 10.1002/minf.201100129] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 02/04/2012] [Indexed: 11/10/2022]
Abstract
This review is devoted to the critical analysis of advantages and disadvantages of existing mixture descriptors and their usage in various QSAR/QSPR tasks. We describe good practices for the QSAR modeling of mixtures, data sources for mixtures, a discussion of various mixture descriptors and their application, recommendations about proper external validation specific for mixture QSAR modeling, and future perspectives of this field. The biggest problem in QSAR of mixtures is the lack of reliable data about the mixtures' properties. Various mixture descriptors are used for the modeling of different endpoints. However, these descriptors have certain disadvantages, such as applicability only to 1 : 1 binary mixtures, and additive nature. The field of QSAR of mixtures is still under development, and existing efforts could be considered as a foundation for future approaches and studies. The usage of non-additive mixture descriptors, which are sensitive to interaction effects, in combination with best practices of QSAR model development (e.g., thorough data collection and curation, rigorous external validation, etc.) will significantly improve the quality of QSAR studies of mixtures.
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Affiliation(s)
- Eugene N Muratov
- Laboratory of Theoretical Chemistry, Department of Molecular Structure, A. V. Bogatsky Physical Chemical Institute, National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa 65080, Ukraine tel: +380487662394, fax: +380487662394. , .,Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina, Beard Hall 301, CB#7568, Chapel Hill, NC, 27599, USA tel: +19199663459, fax: +19199660204. ,
| | - Ekaterina V Varlamova
- Laboratory of Theoretical Chemistry, Department of Molecular Structure, A. V. Bogatsky Physical Chemical Institute, National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa 65080, Ukraine tel: +380487662394, fax: +380487662394
| | - Anatoly G Artemenko
- Laboratory of Theoretical Chemistry, Department of Molecular Structure, A. V. Bogatsky Physical Chemical Institute, National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa 65080, Ukraine tel: +380487662394, fax: +380487662394
| | - Pavel G Polishchuk
- Laboratory of Theoretical Chemistry, Department of Molecular Structure, A. V. Bogatsky Physical Chemical Institute, National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa 65080, Ukraine tel: +380487662394, fax: +380487662394
| | - Victor E Kuz'min
- Laboratory of Theoretical Chemistry, Department of Molecular Structure, A. V. Bogatsky Physical Chemical Institute, National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa 65080, Ukraine tel: +380487662394, fax: +380487662394
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Artemenko A, Muratov EN, Kuz’min V, Muratov N, Varlamova E, Kuz'mina A, Gorb LG, Golius A, Hill F, Leszczynski J, Tropsha A. QSAR analysis of the toxicity of nitroaromatics in Tetrahymena pyriformis: structural factors and possible modes of action. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2011; 22:575-601. [PMID: 21714735 PMCID: PMC3442116 DOI: 10.1080/1062936x.2011.569950] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The Hierarchical Technology for Quantitative Structure-Activity Relationships (HiT QSAR) was applied to 95 diverse nitroaromatic compounds (including some widely known explosives) tested for their toxicity (50% inhibition growth concentration, IGC₅₀) against the ciliate Tetrahymena pyriformis. The dataset was divided into subsets according to putative mechanisms of toxicity. The Classification and Regression Trees (CART) approach implemented within HiT QSAR has been used for prediction of mechanism of toxicity for new compounds. The resulting models were shown to have ~80% accuracy for external datasets indicating that the mechanistic dataset division was sensible. The Partial Least Squares (PLS) statistical approach was then used to develop 2D QSAR models. Validated PLS models were explored to: (1) elucidate the effects of different substituents in nitroaromatic compounds on toxicity; (2) differentiate compounds by probable mechanisms of toxicity based on their structural descriptors; and (3) analyse the role of various physical-chemical factors responsible for compounds' toxicity. Models were interpreted in terms of molecular fragments promoting or interfering with toxicity. It was also shown that mutual influence of substituents in benzene ring plays the determining role in toxicity variation. Although chemical mechanism based models were statistically significant and externally predictive (r²(ext) = 0.64 for the external set of 63 nitroaromatics identified after all calculations have been completed), they were also shown to have limited coverage (57% for modelling and 76% for external set).
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Affiliation(s)
- A.G. Artemenko
- A.V. Bogatsky Physical-Chemical Institute National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa 65080, Ukraine
- Interdisciplinary Nanotoxicity Center, Jackson State University, 1400 J.R. Lynch Str., Jackson, Mississippi, 39217 USA
| | - E. N. Muratov
- A.V. Bogatsky Physical-Chemical Institute National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa 65080, Ukraine
- Interdisciplinary Nanotoxicity Center, Jackson State University, 1400 J.R. Lynch Str., Jackson, Mississippi, 39217 USA
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - V.E. Kuz’min
- A.V. Bogatsky Physical-Chemical Institute National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa 65080, Ukraine
- Interdisciplinary Nanotoxicity Center, Jackson State University, 1400 J.R. Lynch Str., Jackson, Mississippi, 39217 USA
| | - N.N. Muratov
- Odessa National Polytechnic University, 1 Shevchenko Ave., Odessa, 65000, Ukraine
| | - E.V. Varlamova
- A.V. Bogatsky Physical-Chemical Institute National Academy of Sciences of Ukraine, Lustdorfskaya Doroga 86, Odessa 65080, Ukraine
| | - A.V. Kuz'mina
- Odessa National Medicinal University, 2 Ol'gievskaya Str, Odessa, 65000, Ukraine
| | - L. G. Gorb
- Badger Technical Services, LLC, Vicksburg, Mississippi, USA
| | - A. Golius
- Kharkiv National V.N. Karazin University, Department of Radophysics, Karkiv, 61077, Ukraine
| | - F.C. Hill
- US Army ERDC, 3532 Manor Dr, Vicksburg, Mississippi, 39180, USA
| | - J. Leszczynski
- Interdisciplinary Nanotoxicity Center, Jackson State University, 1400 J.R. Lynch Str., Jackson, Mississippi, 39217 USA
| | - A. Tropsha
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
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