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Afahanam LE, Louis H, Benjamin I, Gber TE, Ikot IJ, Manicum ALE. Heteroatom (B, N, P, and S)-Doped Cyclodextrin as a Hydroxyurea (HU) Drug Nanocarrier: A Computational Approach. ACS OMEGA 2023; 8:9861-9872. [PMID: 36969463 PMCID: PMC10035006 DOI: 10.1021/acsomega.2c06630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
Theoretical examination of hydroxyurea adsorption capabilities toward the cyclodextrin surface for proper drug delivery systems was carried out utilizing DFT simulations. The study aims to assess the efficacy of doped cyclodextrin (doped with boron, nitrogen, phosphorus, and sulfur atoms) in increasing its stability and efficiency in intermolecular interactions, hence facilitating optimal drug delivery. The adsorption energies were found to follow a decreasing order of B@ACD-HU>N@ACD-HU>P@ACD-HU>S@ACD-HU with energies of -0.046, -0.0326, -0.015, and 0.944 kcal/mol, respectively. The S@ACD-HU complex, unlike previous systems, had a physical adsorption energy. The N@ACD-HU and B@ACD-HU complexes had the shortest bond lengths of 1.42 Å (N122-C15) and 1.54 Å (B126-C15), respectively. The HOMO and LUMO values were also high in identical systems, -6.367 and -2.918 eV (B@ACD-HU) and -6.278 and -1.736 eV (N@ACD-HU), respectively, confirming no chemical interaction. The N@ACD-HU has the largest energy gap of 4.54 eV. For the QTAIM analysis and plots, the maximum electron density and ellipticity index were detected in B@ACD-HU, 0.600 au (H70-N129) and 0.8685 au (H70-N129), respectively, but N@ACD-HU exhibited a high Laplacian energy of 0.7524 a.u (H133-N122). The fragments' TDOS, OPDOS, and PDOS exhibited a strong bond interaction of greater than 1, and they had different Fermi levels, with the highest value of -8.16 eV in the N@ACD-HU complex. Finally, the NCI analysis revealed that the complexes were noncovalent. According to the literature, the van der Waals form of interactions is used in the intermolecular forces of cyclodextrin cavities. The B@ACD-HU and N@ACD-HU systems were more greenish in color with no spatial interaction. These two systems have outperformed other complexes in intermolecular interactions, resulting in more efficient drug delivery. They had the highest negative adsorption energies, the shortest bond length, the highest HOMO/LUMO energies, the highest energy gap, the highest stabilization energy, the strongest bonding effect, the highest electron density, the highest ellipticity index, and a strong van der Waals interaction that binds the drug and the surface together.
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Affiliation(s)
- Lucy E. Afahanam
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar P.M.B 1115, Nigeria
| | - Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar P.M.B 1115, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar P.M.B 1115, Nigeria
| | - Innocent Benjamin
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar P.M.B 1115, Nigeria
- Department
of Microbiology, Faculty of Biological Sciences, University of Calabar, Calabar P.M.B 1115, Nigeria
| | - Terkumbur E. Gber
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar P.M.B 1115, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar P.M.B 1115, Nigeria
| | - Immaculata J. Ikot
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar P.M.B 1115, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar P.M.B 1115, Nigeria
| | - Amanda-Lee E. Manicum
- Department
of Chemistry, Tshwane University of Technology, Pretoria 0183, South Africa
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Jafari G, Raissi H, Shahabi M. Assessment of sulfobutylether-beta-cyclodextrin as a promising Fluorometholone molecule container: DFT, Docking, Molecular dynamics and MM-PBSA free energy calculations. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1996575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Heidar Raissi
- Chemistry Department, University of Birjand, Birjand, Iran
| | - Mahnaz Shahabi
- Chemistry Department, University of Birjand, Birjand, Iran
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Cheriet M, Djemil R, Khellaf A, Khatmi D. Dopamine Family Complexes With β-Cyclodextrin: Molecular Docking Studies. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1970588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mouna Cheriet
- Unité de recherche sur les plantes médicinales (URPM.3000,Laghouat) rattachée au centre de recherche en biotechnologie (CRBt 2500,Constantine), Constantine, Algérie
| | - Rayenne Djemil
- Laboratory of Computational Chemistry and Nanomaterials (LCCN), Guelma, Algeria
| | - Ammar Khellaf
- École Nationale Polytechnique de Constantine, Laboratoire des Mathématiques Appliquées et Modélisation, Guelma, Algérie
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Guendouzi O, Guendouzi A, Ouici HB, Brahim H, Boumediene M, Elkeurti M. A quantum chemical study of encapsulation and stabilization of gallic acid in β-cyclodextrin as a drug delivery system. CAN J CHEM 2020. [DOI: 10.1139/cjc-2019-0464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This research paper describes the study of the inclusion complex formation of a 1:1 stoichiometry ratio of host–guest inclusion complex (X-β-CD) between gallic acid (GA), which is reported to have anti-cancer effects, and β-cyclodextrin (β-CD). The use of β-CD for the encapsulation of bioactive compounds can protect the drugs against conjugation and metabolic inactivation and improve the aqueous solubility for increasing their capacity to functionalize the products. The objective of this study is to give insight on the mechanism of complexation and the capability of β-CD to encapsulate GA compound (X) in gas and solution phases. We examine and compare the performances of different quantum mechanical methods, namely HF/6-31G* and density functional theory (DFT; B97D3/6-31G* functional including dispersion correction), to study the importance of the contribution of the dispersion forces and the hydrogen bonding in the mechanism of interaction. The stability of the optimized geometries of the complex was evaluated with the supermolecule method. Two modes of complexation are taken into consideration. Moreover, the inclusion complex can be confirmed using the frontier molecular orbital (FMO) theory, the global indices of reactivity, the electronic populations condensed natural bond orbital (NBO) analysis, and the molecular docking, which examine the quality and the nature of the hydrophobic interactions during the complexation process.
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Affiliation(s)
- Oukacha Guendouzi
- Department of Physics, Faculty of Sciences, University of Saïda, Saïda, Algeria
- Laboratory of Chemistry, Synthesis, Properties and Applications, University of Saïda, Saïda, Algeria
| | - Abdelkrim Guendouzi
- Laboratory of Chemistry, Synthesis, Properties and Applications, University of Saïda, Saïda, Algeria
- Department of Chemistry, Faculty of Sciences, University of Saïda, Saïda, Algeria
- Laboratory of Applied Thermodynamics and Molecular Modeling, University of Tlemcen, Tlemcen, Algeria
| | - Houari Boumediene Ouici
- Laboratory of Chemistry, Synthesis, Properties and Applications, University of Saïda, Saïda, Algeria
- Department of Chemistry, Faculty of Sciences, University of Saïda, Saïda, Algeria
| | - Houari Brahim
- Laboratory of Chemistry, Synthesis, Properties and Applications, University of Saïda, Saïda, Algeria
- Department of Chemistry, Faculty of Sciences, University of Saïda, Saïda, Algeria
| | - Mostefa Boumediene
- Laboratory of Chemistry, Synthesis, Properties and Applications, University of Saïda, Saïda, Algeria
- Department of Chemistry, Faculty of Sciences, University of Saïda, Saïda, Algeria
| | - Mohammed Elkeurti
- Department of Physics, Faculty of Sciences, University of Saïda, Saïda, Algeria
- Laboratory of Physico-Chemical Studies, University of Saïda, Saïda, Algeria
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Patel P, Wang J, Wilson AK. Prediction of pK a s of Late Transition-Metal Hydrides via a QM/QM Approach. J Comput Chem 2020; 41:171-183. [PMID: 31495951 DOI: 10.1002/jcc.26057] [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: 07/05/2019] [Accepted: 08/04/2019] [Indexed: 11/09/2022]
Abstract
Three implicit solvation models, the conductor-like polarizable continuum model (C-PCM), the conductor-like screening model (COSMO), and universal implicit solvent model (SMD), combined with a hybrid two layer QM/QM approach (ONIOM), were utilized to calculate the pKa values, using a direct thermodynamic scheme, of a set of Group 10 transition metal (TM) hydrides in acetonitrile. To obtain the optimal combination of quantum methods for ONIOM calculations with implicit solvation models, the influence of factors, such as the choice of density functional and basis set, the atomic radii used to build a cavity in the solvent, and the size of the model system in an ONIOM scheme, was examined. Additionally, the impact of Grimme's empirical dispersion correction and exact exchange was also investigated. The results were calibrated by experimental data. This investigation provides insight about effective models for the prediction of thermodynamic properties of TM-containing complexes with bulky ligands. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Prajay Patel
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas, 76203-5017.,Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824-1322
| | - Jiaqi Wang
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas, 76203-5017.,Department of Chemistry, Beijing Forestry University, Beijing, China, 100083
| | - Angela K Wilson
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas, 76203-5017.,Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824-1322
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Unexpected molecular mechanism of trimethylsilyl bromide elimination from 2-(trimethylsilyloxy)-3-bromo-3-methyl-isoxazolidines. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2467-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bezzina B, Djemil R, Bensouilah N. Quantitative and qualitative analyses of intermolecular interactions in neutral/deprotonated aspirin@β-CD inclusion complexes: QTAIM and NBO analyses. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2429-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Kącka‐Zych A, Ríos‐Gutiérrez M, Domingo LR. A molecular electron density theory study of the Lewis acid–catalyzed decomposition reaction of nitroethyl benzoate using aluminum derivatives. J PHYS ORG CHEM 2019. [DOI: 10.1002/poc.3938] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Agnieszka Kącka‐Zych
- Institute of Organic Chemistry and TechnologyCracow University of Technology Cracow Poland
| | | | - Luis R. Domingo
- Departamento de Quimica OrganicaUniversidad de Valencia Burjassot Spain
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Kącka A, Domingo LR, Jasiński R. Does a fluorinated Lewis acid catalyst change the molecular mechanism of the decomposition process of nitroethyl carboxylates? RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-3106-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ghadari R. Nitrogen doped nanographene structures; study on the adsorption of nucleobases, nucleotides, and their triphosphate derivatives using mixed docking, MD, and QM/MM approaches. J Chem Phys 2017; 146:044105. [PMID: 28147537 DOI: 10.1063/1.4974088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The interactions of the nucleobases, nucleotides, and their triphosphate derivatives in both neutral and anionic forms with the nitrogen doped graphenes (NG) were studied using docking and molecular dynamic simulation methods. In docking studies, based on binding energy results, the anionic species and nucleobases were showing the most and the least tendency toward the surface of the NG, respectively. The molecular mechanic/Poisson-Boltzmann surface area results revealed similar results, except for the anionic species; in these studies, the anionic species showed a lesser affinity toward the NG. The time-dependent density functional theory studies were carried out to investigate the effects of the NG on the electronic nature of the investigated ligands; a red-shift in all of the cases was observed. The results of binding energy decomposition and atoms in molecules studies showed that the interactions are van der Waals in nature. The graphitic, pyridinic, and pyrrolic nitrogen atoms which were considered in this study behaved similar to each other.
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Affiliation(s)
- Rahim Ghadari
- Computational Chemistry Laboratory, Department of Organic and Biochemistry, Faculty of Chemistry, University of Tabriz, 5166616471 Tabriz, Iran
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A DFT study of inclusion complexes of the antituberculosis drugs pyrazinamide and isoniazid with cucurbit[7]uril. J INCL PHENOM MACRO 2017. [DOI: 10.1007/s10847-017-0738-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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