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Liggri PGV, Pérez-Garrido A, Tsitsanou KE, Dileep KV, Michaelakis A, Papachristos DP, Pérez-Sánchez H, Zographos SE. 2D finger-printing and molecular docking studies identified potent mosquito repellents targeting odorant binding protein 1. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023:103961. [PMID: 37217081 DOI: 10.1016/j.ibmb.2023.103961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Personal protection measures against the mosquitoes like the use of repellents constitute valuable tools in the effort to prevent the transmission of vector-borne diseases. Therefore, the discovery of novel repellent molecules which will be effective at lower concentrations and provide a longer duration of protection remains an urgent need. Mosquito Odorant-Binding Proteins (OBPs) involved in the initial steps of the olfactory signal transduction cascade have been recognized not only as passive carriers of odors and pheromones but also as the first molecular filter to discriminate semiochemicals, hence serving as molecular targets for the design of novel pest control agents. Among the three-dimensional structures of mosquito OBPs solved in the last decades, the OBP1 complexes with known repellents have been widely used as reference structures in docking analysis and molecular dynamics simulation studies for the structure-based discovery of new molecules with repellent activity. Herein, ten compounds known to be active against mosquitoes and/or displaying a binding affinity for Anopheles gambiae AgamOBP1 were used as queries in an in silico screening of over 96 million chemical samples in order to detect molecules with structural similarity. Further filtering of the acquired hits on the basis of toxicity, vapor pressure, and commercial availability resulted in 120 unique molecules that were subjected to molecular docking studies against OBP1. For seventeen potential OBP1-binders, the free energy of binding (FEB) and mode of interaction with the protein were further estimated by molecular docking simulations leading to the selection of eight molecules exhibiting the highest similarity with their parental compounds and favorable energy values. The in vitro determination of their binding affinity to AgamOBP1 and the evaluation of their repellent activity against female Aedes albopictus mosquitoes revealed that our combined ligand similarity screening and OBP1 structure-based molecular docking successfully detected three molecules with enhanced repellent properties. A novel DEET-like repellent with lower volatility (8.55 × 10-4 mmHg) but a higher binding affinity for OBP1 than DEET (1.35 × 10-3 mmHg). A highly active repellent molecule that is predicted to bind to the secondary Icaridin (sIC)-binding site of OBP1 with higher affinity than to the DEET-site and, therefore, represents a new scaffold to be exploited for the discovery of binders targeting multiple OBP sites. Finally, a third potent repellent exhibiting a high degree of volatility was found to be a strong DEET-site binder of OBP1 that could be used in slow-release formulations.
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Affiliation(s)
- Panagiota G V Liggri
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece; Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece.
| | - Alfonso Pérez-Garrido
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), 30107, Spain
| | - Katerina E Tsitsanou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece
| | - Kalarickal V Dileep
- Laboratory for Computational and Structural Biology, Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala, 680005, India
| | - Antonios Michaelakis
- Benaki Phytopathological Institute, Department of Entomology and Agricultural Zoology, 8 S Delta Str. 14561, Kifissia, Athens, Greece
| | - Dimitrios P Papachristos
- Benaki Phytopathological Institute, Department of Entomology and Agricultural Zoology, 8 S Delta Str. 14561, Kifissia, Athens, Greece
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), 30107, Spain.
| | - Spyros E Zographos
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece.
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Ahmadi S, Mehrabi M, Rezaei S, Mardafkan N. Structure-activity relationship of the radical scavenging activities of some natural antioxidants based on the graph of atomic orbitals. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.04.103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Kar S, Roy K, Leszczynski J. On Applications of QSARs in Food and Agricultural Sciences: History and Critical Review of Recent Developments. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2017. [DOI: 10.1007/978-3-319-56850-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
For more than half a century free radical-induced alterations at cellular and organ levels have
been investigated as a probable underlying mechanism of a number of adverse health conditions. Consequently,
significant research efforts have been spent for discovering more effective and potent antioxidants /
free radical scavengers for treatment of these adverse conditions. Being by far the most used antioxidants
among natural and synthetic compounds, mono- and polyphenols have been the focus of both experimental
and computational research on mechanisms of free radical scavenging. Quantum chemical studies have provided
a significant amount of data on mechanisms of reactions between phenolic compounds and free radicals outlining a
number of properties with a key role for the radical scavenging activity and capacity of phenolics. The obtained quantum
chemical parameters together with other molecular descriptors have been used in quantitative structure-activity relationship
(QSAR) analyses for the design of new more effective phenolic antioxidants and for identification of the most useful
natural antioxidant phenolics. This review aims at presenting the state of the art in quantum chemical and QSAR studies
of phenolic antioxidants and at analysing the trends observed in the field in the last decade.
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Affiliation(s)
- Petko Alov
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences. 105 Acad. G. Bonchev St., 1113 Sofia, Bulgaria.
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Topological sub-structural molecular design (TOPS-MODE): a useful tool to explore key fragments of human $$\mathbf{A}_{3}$$ A 3 adenosine receptor ligands. Mol Divers 2015. [DOI: 10.1007/s11030-015-9617-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Pérez-Garrido A, Rivero-Buceta V, Cano G, Kumar S, Pérez-Sánchez H, Bautista MT. Latest QSAR study of adenosine A $$_{\mathrm{2B}}$$ 2 B receptor affinity of xanthines and deazaxanthines. Mol Divers 2015; 19:975-89. [DOI: 10.1007/s11030-015-9608-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/24/2015] [Indexed: 12/24/2022]
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Casoni D, Sârbu C. Comprehensive evaluation of antioxidant activity: a chemometric approach using principal component analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:343-348. [PMID: 24060480 DOI: 10.1016/j.saa.2013.08.094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/27/2013] [Accepted: 08/24/2013] [Indexed: 06/02/2023]
Abstract
A novel chemometric approach is described for evaluating the radical scavenging activity of biogenic amine related compounds by using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) procedure and principal component analysis (PCA) tool. By a comprehensive chemometric investigation of variations in the radical scavenging profiles provided by the full-range UV-Vis spectra for different test duration and different relative concentrations (different molar ratio - [AH]/[DPPH]) of the investigated compounds, new antioxidant activity evaluation parameters were proposed. The new proposed parameters (PC1, mPC1, maxPC1) are in good agreement with the reference DPPH results (% RSA and IC50 derived from the reference DPPH test), obtained for the investigated amines and reference antioxidants. Much more, the PCA profiles are better patterns for the comprehensive characterization of radical scavenging activity of compounds, allowing visualization of complex information by a simple graphical representation and underlying the (dis)similarity of compounds related both to the reaction kinetics and compounds concentration.
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Affiliation(s)
- Dorina Casoni
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany Janos Str., No. 11, RO-400028 Cluj-Napoca, România.
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Muthu Mareeswaran P, Babu E, Sathish V, Kim B, Woo SI, Rajagopal S. p-Sulfonatocalix[4]arene as a carrier for curcumin. NEW J CHEM 2014. [DOI: 10.1039/c3nj00935a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Fatemi MH, Gholami Rostami E. Prediction of the Radical Scavenging Activities of Some Antioxidant from Their Molecular Structure. Ind Eng Chem Res 2013. [DOI: 10.1021/ie4001426] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohammad H. Fatemi
- Chemometrics Laboratory, Faculty
of Chemistry, University of Mazandaran,
Babolsar, Iran
| | - Elham Gholami Rostami
- Chemometrics Laboratory, Faculty
of Chemistry, University of Mazandaran,
Babolsar, Iran
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Mitra I, Saha A, Roy K. Quantification of contributions of different molecular fragments for antioxidant activity of coumarin derivatives based on QSAR analyses. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0527] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Attempts have been made in the present work using in silico techniques for identification of essential structural features imparting antioxidant potential to naturally available coumarin molecules and their synthetic derivatives. Four different types of modeling tools have been employed for the qualitative and quantitative assessment of the molecular fragments constituting the biological pharmacophore. The descriptor-based quantitative structure–activity relationship (QSAR) and group-based QSAR (G-QSAR) models provide a quantitative estimation of the substituent requirements and the chemical nature of the parent moiety. Subsequently, 3D pharmacophore and hologram QSAR (HQSAR) models enable identification of the key molecular components necessary for the antioxidant potency to the molecules. All of the different models infer the importance of the hydrogen bond acceptor ketonic fragment for interaction of the antioxidant molecules with the neighbouring toxic radicals. Additionally, the phenyl substituent attached to the side chain and the benzene nucleus of the benzopyran moiety also constitute the response pharmacophore for the molecules under study. The models thus developed may serve as an essential query tool for screening of databases for selection of molecules bearing the essential fragments and subsequent prediction of their free radical scavenging potency.
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Affiliation(s)
- Indrani Mitra
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, 92 A P C Road, Kolkata 700009, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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Predictive chemometric modeling of DPPH free radical-scavenging activity of azole derivatives using 2D- and 3D-quantitative structure–activity relationship tools. Future Med Chem 2013; 5:261-80. [DOI: 10.4155/fmc.12.207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background: The endogenous antioxidants often fail to manage the systemic free radical overload resulting from extensive exposure to environmental pollutants and improper diet. Such free-radical burden over a prolonged period leads to oxidative stress, which in turn, promotes an array of fatal diseases. Results: Five different in silico methodologies have been employed here for a series of azole derivatives, which identify the essential structural attributes of the molecules and quantify the contributions of the prime molecular prerequisites for designing compounds with improved antioxidant activity. Conclusion: The importance of the different constituents is quantitatively analyzed using the descriptor-based quantitative structure–activity relationship and group-based quantitative structure–activity relationship models while the pharmacophore, comparative molecular similarity index analysis and hologram quantitative structure–activity relationship models serve as essential query tools for screening of azole compounds in order to select potent antioxidant molecules.
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Mitra I, Saha A, Roy K. Predictive Modeling of Antioxidant Coumarin Derivatives Using Multiple Approaches: Descriptor-Based QSAR, 3D-Pharmacophore Mapping, and HQSAR. Sci Pharm 2012; 81:57-80. [PMID: 23641329 PMCID: PMC3617663 DOI: 10.3797/scipharm.1208-01] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 09/09/2012] [Indexed: 01/26/2023] Open
Abstract
The inability of the systemic antioxidants to alleviate the exacerbation of free radical formation from metabolic outputs and environmental pollutants claims an urgent demand for the identification and design of new chemical entities with potent antioxidant activity. In the present work, different QSAR approaches have been utilized for identifying the essential structural attributes imparting a potential antioxidant activity profile of the coumarin derivatives. The descriptor-based QSAR model provides a quantitative outline regarding the structural prerequisites of the molecules, while 3D pharmacophore and HQSAR models emphasize the favourable spatial arrangement of the various chemical features and the crucial molecular fragments, respectively. All the models infer that the fused benzene ring and the oxygen atom of the pyran ring constituting the parent coumarin nucleus capture the prime pharmacophoric features, imparting superior antioxidant activity to the molecules. The developed models may serve as indispensable query tools for screening untested molecules belonging to the class of coumarin derivatives.
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Affiliation(s)
- Indrani Mitra
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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