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Chabane S, Boudjelal A, Bouaziz-Terrachet S, Spinozzi E, Maggi F, Petrelli R, Tail G. Analgesic effect of Centaurium erythraea and molecular docking investigation of the major component swertiamarin. Nat Prod Res 2023:1-7. [PMID: 37948163 DOI: 10.1080/14786419.2023.2278160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
Abstract
Centaurium erythraea Rafn is employed in Algerian traditional medicine for treating pain. The analgesic activity of the ethanolic extract (EE) from the flowering aerial parts of this plant was examined, and molecular docking of the main bioactive compound was performed. The EE, characterised by the iridoid swertiamarin, was administered to Wistar albino rats in pain models. Peripheral analgesic activity was evaluated using the acetic acid-induced writhing test, and a hot plate test was performed for central antinociceptive activity evaluation. Treatment with EE significantly decreased rats' writhing induced by acetic acid suggesting peripheral analgesic activity. Furthermore, the elevation of mean basal reaction time in the hot plate method indicated central analgesic activity. Molecular docking studies showed good docking energy with acceptable binding interactions of swertiamarin with cyclooxygenase-2 protein. This supports the analgesic activity of C. erythraea EE, justifying the traditional use of the plant as an analgesic herbal remedy.
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Affiliation(s)
- Sarra Chabane
- Department of Life and Nature Science, Faculty of Sciences, University of M'Sila, M'Sila, Algeria
- Laboratory of Biology: Applications in Health and Environment, University of M'Sila, M'Sila, Algeria
| | - Amel Boudjelal
- Laboratory of Biology: Applications in Health and Environment, University of M'Sila, M'Sila, Algeria
- Department of Microbiology and Biochemistry, Faculty of Sciences, University of M'Sila, M'Sila, Algeria
| | - Souhila Bouaziz-Terrachet
- Applied Chemistry and Materials Laboratory (LabCAM), Faculty of Sciences, University of Mohamed Bouguerra, Boumerdes, Algeria
- Laboratory of Theoretical Physico-Chemistry and Computer Chemistry, Faculty of Chemistry, University of Science and Technology Houari Boumédiène, Bab Ezzouar, Algeria
| | - Eleonora Spinozzi
- Chemistry Interdisciplinary Project (ChIP) Research Center, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Filippo Maggi
- Chemistry Interdisciplinary Project (ChIP) Research Center, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Riccardo Petrelli
- Chemistry Interdisciplinary Project (ChIP) Research Center, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Ghania Tail
- Department of Biology, University of Blida 1, Blida, Algeria
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Bourouai MA, Si Larbi K, Bouchoucha A, Terrachet-Bouaziz S, Djebbar S. New Ni(II) and Pd(II) complexes bearing derived sulfa drug ligands: synthesis, characterization, DFT calculations, and in silico and in vitro biological activity studies. Biometals 2023; 36:153-188. [PMID: 36427181 DOI: 10.1007/s10534-022-00469-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022]
Abstract
In the present study, the synthesis of six new Ni(II) and Pd(II) complexes with three derived sulfamethoxazole drug ligands is reported. The coordination mode, geometry, and chemical formula of all the synthesized compounds have been determined by elemental analysis, mass spectrometry, emission atomic spectroscopy, conductivity measurements, magnetic susceptibility, FTIR, TGA, 1H-NMR, electronic absorption spectroscopy, SEM-EDX along with DFT calculations. The Schiff Base ligands were found to be bidentate and coordinated to the metal ions through sulfonamidic nitrogen and oxazolic nitrogen atoms leading to a square planar geometry for palladium (II) while a distorted octahedral geometry around Nickel (II) ion was suggested. Biological applications of the new complexes including in vitro antimicrobial, antioxidant and anticancer properties were investigated. The results showed that the new metal (II) compounds exhibit remarkable antibacterial inhibition activity against both Gram-positive and Gram-negative bacteria, in addition to noticeable DPPH free radical scavenging activity. The in vitro cytotoxicity assay of the complexes against cell lines of chronic myelogenous leukaemia (K562) showed promising potential for the application of the coordination compounds in antitumor therapy. Subsequently, to evaluate the pharmaceutical potential of the metal-containing compounds, pharmacokinetics and toxicity were studied by ADMET simulations while interactions between the complexes and bacterial proteins were evaluated by molecular docking.
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Affiliation(s)
- Mohamed Amine Bourouai
- Hydrometallurgy and Molecular Inorganic Chemistry Laboratory, Faculty of Chemistry, University of Science and Technology Houari Boumediene, BP 32 El Alia, 16111, Algiers, Algeria
| | - Karima Si Larbi
- Hydrometallurgy and Molecular Inorganic Chemistry Laboratory, Faculty of Chemistry, University of Science and Technology Houari Boumediene, BP 32 El Alia, 16111, Algiers, Algeria
| | - Afaf Bouchoucha
- Hydrometallurgy and Molecular Inorganic Chemistry Laboratory, Faculty of Chemistry, University of Science and Technology Houari Boumediene, BP 32 El Alia, 16111, Algiers, Algeria.
| | | | - Safia Djebbar
- Hydrometallurgy and Molecular Inorganic Chemistry Laboratory, Faculty of Chemistry, University of Science and Technology Houari Boumediene, BP 32 El Alia, 16111, Algiers, Algeria
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Design, Synthesis, Biological evaluation of Isonicotinoyl-pyrazolyl-coumarin derivatives and computational study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133487] [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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4
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Sodium dodecyl benzene sulfonate-catalyzed reaction for green synthesis of biologically active benzylpyrazolyl-coumarin derivatives, mechanism studies, theoretical calculations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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5
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Coordination of new palladium (II) complexes with derived furopyran-3,4‑dione ligands: Synthesis, characterization, redox behaviour, DFT, antimicrobial activity, molecular docking and ADMET studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Ould Lamara K, Makhloufi-Chebli M, Benazzouz-Touami A, Terrachet-Bouaziz S, Robert A, Machado-Rodrigues C, Behr JB. Synthesis, biological activities of chalcones and novel 4-acetylpyridine oximes, molecular docking of the synthesized products as acetylcholinesterase ligands. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Benazzouz-Touami A, Chouh A, Halit S, Terrachet-Bouaziz S, Makhloufi-Chebli M, Ighil-Ahriz K, Silva AM. New Coumarin-Pyrazole hybrids: Synthesis, Docking studies and Biological evaluation as potential cholinesterase inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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8
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Kerflani A, Si Larbi K, Rabahi A, Bouchoucha A, Zaater S, Terrachet-Bouaziz S. Novel palladium (II) complexes with iminocoumarin ligands: Synthesis, characterisation, electrochemical behaviour, DFT calculations and biological activities, ADMET study and molecular docking. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120659] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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Lamara KO, Makhloufi-Chebli M, Benazzouz-Touami A, Terrachet-Bouaziz S, Hamdi N, Silva AM, Behr JB. Selectivity control in the reaction between 2-hydroxyarylaldehydes and 4-hydroxycoumarin. Antioxidant activities and computational studies of the formed products. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Hadhoum N, Zohra Hadjadj-Aoul F, Hocine S, Bouaziz-Terrachet S, Seklaoui N, Boubrit F, Abderrahim W, Redouane Mekacher L. Design and One-Pot Synthesis of Some New [3,5-Di(4’,5’-diphenyl-2’-substituted)-1H-imidazol-1-yl)]-1H-1,2,4-triazole Derivatives: in silico ADMET and Docking Study, Antibacterial and Antifungal Activities Evaluation. HETEROCYCLES 2021. [DOI: 10.3987/com-21-14503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Hammad S, Bouaziz-Terrachet S, Meghnem R, Meziane D. Pharmacophore development, drug-likeness analysis, molecular docking, and molecular dynamics simulations for identification of new CK2 inhibitors. J Mol Model 2020; 26:160. [PMID: 32472293 DOI: 10.1007/s00894-020-04408-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Protein kinase 2 (CK2), an essential serine/threonine casein kinase, is considered an interesting target for cancer treatments. Different molecular modeling approaches such as pharmacophore modeling, molecular docking, and molecular dynamics simulations have been used to develop new CK2 inhibitors. This study presents a pharmacophore model that was generated by combining and merging the structure-based and ligand-based pharmacophore features and validated using receiver operating characteristic (ROC). Based on validation results revealing good predictive ability, this pharmacophore model was used as a three-dimensional query in a virtual screening simulation. Several compounds with different chemical scaffolds were retrieved as hits, which were further analyzed and refined using several molecular property filters. The obtained compounds were then filtered and compared to the crystallographic ligand on the basis of their predicted docking energies, binding mode, and interactions with CK2 active site residues. This step resulted in a compound with a high pharmacophore fit value and better docking energy. Molecular dynamics simulation indicated stable binding of the predicted compound to CK2 protein, characterized by root mean square deviation (RMSD) and root mean square fluctuation (RMSF) and hydrogen bond. Graphical abstract.
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Affiliation(s)
- Sara Hammad
- Department of Chemistry, Faculty of Sciences, University of Mouloud Maamri, Tizi Ouzou, Algeria.,Laboratory of Theoretical Physico-Chemistry and Computer Chemistry, Faculty of Chemistry, University of Science and Technology Houari Boumédiène, Algiers, Algeria
| | - Souhila Bouaziz-Terrachet
- Laboratory of Theoretical Physico-Chemistry and Computer Chemistry, Faculty of Chemistry, University of Science and Technology Houari Boumédiène, Algiers, Algeria. .,Department of Chemistry, Faculty of Sciences, University of Mohamed Bouguerra, Boumerdes, Algeria.
| | - Rosa Meghnem
- Department of Chemistry, Faculty of Sciences, University of Mouloud Maamri, Tizi Ouzou, Algeria.,Laboratory of Theoretical Physico-Chemistry and Computer Chemistry, Faculty of Chemistry, University of Science and Technology Houari Boumédiène, Algiers, Algeria
| | - Dalila Meziane
- Department of Chemistry, Faculty of Sciences, University of Mouloud Maamri, Tizi Ouzou, Algeria
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12
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Coy-Barrera E. Discrimination of Naturally-Occurring 2-Arylbenzofurans as Cyclooxygenase-2 Inhibitors: Insights into the Binding Mode and Enzymatic Inhibitory Activity. Biomolecules 2020; 10:biom10020176. [PMID: 31979339 PMCID: PMC7072606 DOI: 10.3390/biom10020176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/12/2020] [Accepted: 01/20/2020] [Indexed: 01/04/2023] Open
Abstract
2-arylbenzofuran-containing compounds are chemical entities that can be naturally produced by several organisms. A wide-range of activities is described for several compounds of this kind and they are, therefore, valuable moieties for a lead finding from nature. Although there are in-vitro data about the activity of 2-arylbenzofuran-related compounds against cyclooxygenase (COX) enzymes, the molecular level of these COX-inhibiting constituents had not been deeply explored. Thus, 58 2-arylbenzofurans were initially screened through molecular docking within the active site of nine COX-2 crystal structures. The resulting docking scores were statistically analyzed and good reproducibility and convergence were found to discriminate the best-docked compounds. Discriminated compounds exhibited the best performance in molecular dynamics simulations as well as the most-favorable binding energies and the lowest in-vitro IC50 values for COX-2 inhibition. A three-dimensional quantitative activity-structure relationship (3D-QSAR) was also demonstrated, which showed some crucial structural requirements for enhanced enzyme inhibition. Therefore, four hits are proposed as lead structures for the development of COX-2 inhibitors based on 2-arylbenzofurans in further studies.
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Affiliation(s)
- Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
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13
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Ounissi M, Kameli A, Tigrine C, Rachedi FZ. Computer-aided identification of natural lead compounds as cyclooxygenase-2 inhibitors using virtual screening and molecular dynamic simulation. Comput Biol Chem 2018; 77:1-16. [DOI: 10.1016/j.compbiolchem.2018.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 11/28/2022]
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14
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Molecular-Docking Study of the Interaction of Anti-Inflammatory N-Aroyl-Substituted Halo(H)Anthranilic Acid Amides and Hydrazides with Cyclooxygenase 1. Pharm Chem J 2018. [DOI: 10.1007/s11094-018-1832-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Tu M, Cheng S, Lu W, Du M. Advancement and prospects of bioinformatics analysis for studying bioactive peptides from food-derived protein: Sequence, structure, and functions. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.04.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Kendur U, Chimmalagi GH, Patil SM, Gudasi KB, Frampton CS. Synthesis, structural characterization and biological evaluation of mononuclear transition metal complexes of zwitterionic dehydroacetic acid N
-aroylhydrazone ligand. Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Umashri Kendur
- Department of Studies in Chemistry; Karnatak University; Dharwad 580003 Karnataka India
| | - Geeta H. Chimmalagi
- Department of Studies in Chemistry; Karnatak University; Dharwad 580003 Karnataka India
| | - Sunil M. Patil
- Department of Studies in Chemistry; Karnatak University; Dharwad 580003 Karnataka India
| | - Kalagouda B. Gudasi
- Department of Studies in Chemistry; Karnatak University; Dharwad 580003 Karnataka India
| | - Christopher S. Frampton
- Institute of Materials & Manufacturing, Wolfson Centre for Materials Processing; Brunel University; London Uxbridge UK
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Chaudhary N, Aparoy P. Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies. J Biomol Struct Dyn 2016; 35:868-882. [PMID: 26982261 DOI: 10.1080/07391102.2016.1165736] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
COX-2 is a well-known drug target in inflammatory disorders. COX-1/COX-2 selectivity of NSAIDs is crucial in assessing the gastrointestinal side effects associated with COX-1 inhibition. Celecoxib, rofecoxib, and valdecoxib are well-known specific COX-2 inhibiting drugs. Recently, polmacoxib, a COX-2/CA-II dual inhibitor has been approved by the Korean FDA. These COXIBs have similar structure with diverse activity range. Present study focuses on unraveling the mechanism behind the 10-fold difference in the activities of these sulfonamide-containing COXIBs. In order to obtain insights into their binding with COX-2 at molecular level, molecular dynamics simulations studies, and MM-PBSA approaches were employed. Further, per-residue decomposition of these energies led to the identification of crucial amino acids and interactions contributing to the differential binding of COXIBs. The results clearly indicated that Leu338, Ser339, Arg499, Ile503, Phe504, Val509, and Ser516 (Leu352, Ser353, Arg513, Ile517, Phe518, Val523, and Ser530 in PGHS-1 numbering) were imperative in determining the activity of these COXIBs. The binding energies and energy contribution of various residues were similar in all the three simulations. The results suggest that hydrogen bond interaction between the hydroxyl group of Ser516 and five-membered ring of diarylheterocycles augments the affinity in COXIBs. The SAR of the inhibitors studied and the per-residue energy decomposition values suggested the importance of Ser516. Additionally, the positive binding energy obtained with Arg106 explains the binding of COXIBs in hydrophobic channel deep in the COX-2 active site. The findings of the present work would aid in the development of potent COX-2 inhibitors.
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Affiliation(s)
- Neha Chaudhary
- a Centre for Computational Biology and Bioinformatics, School of Life Sciences , Central University of Himachal Pradesh , Dharamshala , Himachal Pradesh 176215 , India
| | - Polamarasetty Aparoy
- a Centre for Computational Biology and Bioinformatics, School of Life Sciences , Central University of Himachal Pradesh , Dharamshala , Himachal Pradesh 176215 , India
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Trombetta D, Giofrè SV, Tomaino A, Raciti R, Saija A, Cristani M, Romeo R, Siracusa L, Ruberto G. Selective COX-2 Inhibitory Properties of Dihydrostilbenes from Liquorice Leaves–In Vitro Assays and Structure/Activity Relationship Study. Nat Prod Commun 2014. [DOI: 10.1177/1934578x1400901226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Three dihydrostilbenes belonging to the polyphenol pool characterized in the leaves of Sicilian liquorice ( Glycyrrhiza glabra L.) have been tested for their antioxidant and anti-inflammatory activity. The three dihydrostilbenes (PA-82, GA-23, DO-07) were in vitro tested to evaluate their capability to scavenge the stable radical 1,1-diphenyl-2-picrylhydrazyl (DPPH), and to decrease thromboxane B2 (TxB2) and prostaglandin E2 (PGE2) release in human whole blood samples. On the basis of the observed capability of these compounds to affect the cell COX-1/COX-2 pathway, a molecular docking study was carried out in order to understand in detail the ability of these compounds to bind to COX-1 and COX-2. The results show that the liquorice dihydrostilbenes are preferred ligands for COX-2 rather than for COX-1, providing a good rational for the observed selectivity in ex vivo experiments. Therefore, they appear to be good candidates for employment in human therapy against inflammation-related pathological conditions.
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Affiliation(s)
- Domenico Trombetta
- Dipartimento Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina, Contrada Annunziata, I-98168 Messina, Italy
| | - Salvatore V. Giofrè
- Dipartimento Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina, Contrada Annunziata, I-98168 Messina, Italy
| | - Antonio Tomaino
- Dipartimento Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina, Contrada Annunziata, I-98168 Messina, Italy
| | - Roberto Raciti
- Dipartimento Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina, Contrada Annunziata, I-98168 Messina, Italy
| | - Antonella Saija
- Dipartimento Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina, Contrada Annunziata, I-98168 Messina, Italy
| | - Mariateresa Cristani
- Dipartimento Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina, Contrada Annunziata, I-98168 Messina, Italy
| | - Roberto Romeo
- Dipartimento Scienze del Farmaco e dei Prodotti per la Salute, Università di Messina, Contrada Annunziata, I-98168 Messina, Italy
| | - Laura Siracusa
- Istituto del C.N.R. di Chimica Biomolecolare, Via Paolo Gaifami, 18 I-95126 Catania, Italy
| | - Giuseppe Ruberto
- Istituto del C.N.R. di Chimica Biomolecolare, Via Paolo Gaifami, 18 I-95126 Catania, Italy
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Gundogdu-Hizliates C, Alyuruk H, Gocmenturk M, Ergun Y, Cavas L. Synthesis of new ibuprofen derivatives with their in silico and in vitro cyclooxygenase-2 inhibitions. Bioorg Chem 2014; 52:8-15. [DOI: 10.1016/j.bioorg.2013.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 10/23/2013] [Accepted: 10/28/2013] [Indexed: 11/25/2022]
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Kumar V, Gupta GK, Kaur K, Singh R. 4-Fluorophenylhydrazones as potential COX-2 inhibitors: a novel, efficient, one pot solid phase synthesis, docking study and pharmacological evaluation. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0566-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Bouaziz-Terrachet S, Terrachet R, Taïri-Kellou S. Receptor and ligand-based 3D-QSAR study on a series of nonsteroidal anti-inflammatory drugs. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0174-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Anand S, Mohanty D. Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide synthases: a docking and molecular dynamics study. BMC STRUCTURAL BIOLOGY 2012; 12:10. [PMID: 22639887 PMCID: PMC3422181 DOI: 10.1186/1472-6807-12-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 05/28/2012] [Indexed: 12/13/2022]
Abstract
Background Modular polyketide synthases are multifunctional megasynthases which biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH), ketoreductase (KR) and enoyl-reductase (ER) domains. During the catalysis of various reductive steps these domains act on a substrate moiety which is covalently attached to the phosphopantetheine (P-pant) group of the holo-Acyl Carrier Protein (holo-ACP) domain, thus necessitating the formation of holo-ACP:DH and holo-ACP:KR complexes. Even though three dimensional structures are available for DH, KR and ACP domains, no structures are available for DH or KR domains in complex with ACP or substrate moieties. Since Ser of holo-ACP is covalently attached to a large phosphopantetheine group, obtaining complexes involving holo-ACP by standard protein-protein docking has been a difficult task. Results We have modeled the holo-ACP:DH and holo-ACP:KR complexes for identifying specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. A novel combination of protein-protein and protein-ligand docking has been used to first model complexes involving apo-ACP and then dock the phosphopantetheine and substrate moieties using covalent connectivity between ACP, phosphopantetheine and substrate moiety as constraints. The holo-ACP:DH and holo-ACP:KR complexes obtained from docking have been further refined by restraint free explicit solvent MD simulations to incorporate effects of ligand and receptor flexibilities. The results from 50 ns MD simulations reveal that substrate enters into a deep tunnel in DH domain while in case of KR domain the substrate binds a shallow surface exposed cavity. Interestingly, in case of DH domain the predicted binding site overlapped with the binding site in the inhibitor bound crystal structure of FabZ, the DH domain from E.Coli FAS. In case of KR domain, the substrate binding site identified by our simulations was in proximity of the known stereo-specificity determining residues. Conclusions We have modeled the holo-ACP:DH and holo-ACP:KR complexes and identified the specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. Analysis of the conservation profile of binding pocket residues in homologous sequences of DH and KR domains indicated that, these results can also be extrapolated to reductive domains of other modular PKS clusters.
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Affiliation(s)
- Swadha Anand
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Krishna A, Yadav A. Lead compound design for TPR/COX dual inhibition. J Mol Model 2012; 18:4397-408. [PMID: 22588583 DOI: 10.1007/s00894-012-1435-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/17/2012] [Indexed: 11/24/2022]
Abstract
The modes of action of TxA2 antagonists and COX-2 inhibitors were studied utilizing flexible ligand docking with postdocking minimization and ab initio interaction energy calculations. The resulting increased understanding of their binding interactions led to the design of a lead compound with chemical moieties that allowed efficient binding to both the thromboxane receptor and the COX-2 enzyme. This compound is derived from allicin, a natural component of garlic, and is a good starting point for the development of anti-inflammatory drugs with fewer side effects or improved cardiovascular drugs.
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Affiliation(s)
- Abhay Krishna
- Department of Chemistry, University Institute of Engineering and Technology, CSJM University, Kanpur, 208024, India.
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