1
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Zhang Y, Yu D, Zhao R, Hu F, Li Z, Dong B, Lu P, Song Z, Wang H, Zhang F, Chen W, Liu W, Li H. Enhanced stability and biocompatibility of HIPEs stabilized by cyclodextrin-metal organic frameworks with inclusion of resveratrol and soy protein isolate for β-carotene delivery. Int J Biol Macromol 2024; 274:133431. [PMID: 38936573 DOI: 10.1016/j.ijbiomac.2024.133431] [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: 12/06/2023] [Revised: 06/19/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
High internal phase Pickering emulsions (HIPEs) constitute a significant research domain within colloid interface chemistry, addressing the demand for robust emulsion systems across various applications. An innovative nanoparticle, synthesized from a cyclodextrin metal-organic framework encapsulated with a composite of resveratrol and soy isolate protein (RCS), was employed to fortify a high internal phase emulsion. The emulsion's three-dimensional printing capabilities, alongside the encapsulated delivery efficacy for β-carotene, were thoroughly examined. Cyclodextrin metal-organic frameworks (CD-MOFs), facilitated by cellulose nanofibrils, were synthesized to yield particles at the nanoscale, maintaining a remarkable 97.67 % cellular viability at an elevated concentration of 1000 μg/ml. The RCS nanoparticles demonstrated thermal stability and antioxidant capacities surpassing those of CD-MOF. The integration of soybean isolate protein augmented both the hydrophobicity (from 21.95 ± 0.64° to 59.15 ± 0.78°) and the interfacial tension (from 14.36 ± 0.46 mN/m to 5.34 ± 0.81 mN/m) of the CD-MOF encapsulated with resveratrol, thereby enhancing the RCS nanoparticles' adsorption at the oil-water interface with greater stability. The durability of the RCS-stabilized high internal phase emulsions was contingent upon the RCS concentration. Emulsions stabilized with 5 wt%-RCS exhibited optimal physical and chemical robustness, demonstrating superior performance in emulsion 3D printing and β-carotene encapsulation delivery. This investigation furnishes a novel perspective on the amalgamation of food customization and precision nutrition.
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Affiliation(s)
- Yannan Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong Province 250353, China
| | - Dehai Yu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong Province 250353, China; Shandong Huatai Paper Co., Ltd. & Shandong Yellow Triangle Biotechnology Industry Research Institute Co. Ltd., Dongying, Shandong Province 257335, China.
| | - Rui Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong Province 250353, China
| | - Feihong Hu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong Province 250353, China
| | - Zhuo Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong Province 250353, China
| | - Baoting Dong
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong Province 250353, China
| | - Peng Lu
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Zhaoping Song
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong Province 250353, China; Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Huili Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong Province 250353, China
| | - Fengshan Zhang
- Shandong Huatai Paper Co., Ltd. & Shandong Yellow Triangle Biotechnology Industry Research Institute Co. Ltd., Dongying, Shandong Province 257335, China
| | - Wei Chen
- College of Engineering, Qufu Normal University, Rizhao 276826, China
| | - Wenxia Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong Province 250353, China
| | - Huihui Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong Province 250012, China.
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Mikaelian G, Megariotis G, Theodorou DN. Interactions of a Novel Anthracycline with Oligonucleotide DNA and Cyclodextrins in an Aqueous Environment. J Phys Chem B 2024; 128:6291-6307. [PMID: 38899795 PMCID: PMC11228990 DOI: 10.1021/acs.jpcb.4c02213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Berubicin, a chemotherapy medication belonging to the class of anthracyclines, is simulated in double-stranded DNA sequences and cyclodextrins in an aqueous environment via full-atom molecular dynamics simulations on the time scale of microseconds. The drug is studied in both the neutral and protonated states so as to better comprehend the role of its charge in the formed complexes. The noncovalent berubicin-DNA and berubicin-cyclodextrin complexes are investigated in detail, paying special attention to their thermodynamic description by employing the double decoupling method, the solvent balance method, the weighted solvent accessible surface model, and the linear interaction energy method. A novel approach for extracting the desolvation thermodynamics of the binding process is also presented. Both the binding and desolvation Gibbs energies are decomposed into entropic and enthalpic contributions so as to elucidate the nature of complexation and its driving forces. Selected structural and geometrical properties of all the complexes, which are all stable, are analyzed. Both cyclodextrins under consideration are widely utilized for drug delivery purposes, and a comparative investigation between their bound states with berubicin is carried out.
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Affiliation(s)
- Georgios Mikaelian
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
| | - Grigorios Megariotis
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
- School
of Engineering, Department of Mineral Resources Engineering, University of Western Macedonia, 50100 Kozani, Greece
| | - Doros N. Theodorou
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
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Busch J, Paschek D. Computing Accurate True Self-Diffusion Coefficients and Shear Viscosities Using the OrthoBoXY Approach. J Phys Chem B 2024; 128:1040-1052. [PMID: 38240259 DOI: 10.1021/acs.jpcb.3c07540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
In a recent paper [Busch, J.; Paschek, D. J. Phys. Chem. B 2023, 127, 7983-7987], we have shown that for molecular dynamics (MD) simulations using orthorhombic periodic boundary conditions with "magic" box length ratios of Lz/Lx = Lz/Ly = 2.7933596497, the self-diffusion coefficients Dx and Dy in x- and y-directions are independent of the system size. They both represent the true self-diffusion coefficient D0 = (Dx + Dy)/2, while the shear viscosity can be calculated from diffusion coefficients in x-, y-, and z-directions, using η = kBT·8.1711245653/[3πLz(Dx + Dy - 2Dz)]. In this contribution, we test this "OrthoBoXY" approach by its application to a variety of different systems: liquid water, dimethyl ether, methanol, triglyme, water/methanol mixtures, water/triglyme mixtures, and imidazolium-based ionic liquids. The chosen systems range from small-sized molecular liquids to complex mixtures and ionic liquids, while spanning a viscosity range of almost 3 orders of magnitude. We assess the efficiency of the method for computing true self-diffusion and viscosity data and provide simple formulas for estimating the required MD simulation lengths and sizes for delivering reliable data with targeted uncertainty levels. Our analysis of the system size dependence of statistical uncertainties for both the viscosity and the self-diffusion coefficient leads us to the conclusion that it is preferable to extend the simulation length instead of increasing the system size. MD simulations consisting of 768 molecules or ion pairs seem to be perfectly adequate.
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Affiliation(s)
- Johanna Busch
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
| | - Dietmar Paschek
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
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4
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Busch J, Paschek D. An OrthoBoXY-method for various alternative box geometries. Phys Chem Chem Phys 2024; 26:2907-2914. [PMID: 38086638 DOI: 10.1039/d3cp04916g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
We have shown in a recent contribution [Busch and Paschek, J. Phys. Chem. B, 2023 127, 7983-7987] that for molecular dynamics (MD) simulations of isotropic fluids based on orthorhombic periodic boundary conditions with "magical" box length ratios of Lz/Lx = Lz/Ly = 2.7933596497, the computed self-diffusion coefficients Dx and Dy in x- and y-direction become system size independent. They thus represent the true self-diffusion coefficient D0 = (Dx + Dy)/2, while the shear viscosity can be determined from diffusion coefficients in x-, y-, and z-direction, using the expression η = kBT·8.1711245653/[3πLz(Dx + Dy - 2Dz)]. Here we present a more generalized version of this "OrthoBoXY"-approach, which can be applied to any orthorhombic MD box of any shape. In particular, we would like to test, how the efficiency is affected by using a shape more akin to the cubic form, albeit with different box length ratios Lx/Lz ≠ Ly/Lz and Lx < Ly < Lz. We use NVT and NpT simulations of systems of 1536 TIP4P/2005 water molecules as a benchmark and explore different box geometries to determine the influence of the box shape on the computed statistical uncertainties for D0 and η. Moreover, another "magical" set of box length ratios is discovered with Ly/Lz = 0.57804765578 and Lx/Lz = 0.33413909235, where the self-diffusion coefficient in x-direction becomes system size independent, such that D0 = Dx.
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Affiliation(s)
- Johanna Busch
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Straße 27, D-18059 Rostock, Germany.
| | - Dietmar Paschek
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Straße 27, D-18059 Rostock, Germany.
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5
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Pinelli F, Ponti M, Delleani S, Pizzetti F, Vanoli V, Vangosa FB, Castiglione F, Haugen H, Nogueira LP, Rossetti A, Rossi F, Sacchetti A. β-Cyclodextrin functionalized agarose-based hydrogels for multiple controlled drug delivery of ibuprofen. Int J Biol Macromol 2023; 252:126284. [PMID: 37572821 DOI: 10.1016/j.ijbiomac.2023.126284] [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: 06/26/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
Agarose hydrogels are three-dimensional hydrophilic polymeric frameworks characterised by high water content, viscoelastic properties, and excellent ability as cell and drug delivery systems. However, their hydrophilicity as gel systems makes loading of hydrophobic drugs difficult and often ineffective. The incorporation of amphiphilic molecules (e.g. cyclodextrins) into hydrogels as hosts able to form inclusion complexes with hydrophobic drugs could be a possible solution. However, if not properly confined, the host compounds can get out of the network resulting in uncontrolled release. Therefore, in this work, β-cyclodextrins-based host-guest supramolecular hydrogel systems were synthesised, with β-cyclodextrins (β-CD) covalently bound to the polymeric network, preventing leakage of the host molecules. Hydrogels were prepared at two different β-CD-functionalized polyvinyl alcohol (PVA)/agarose ratios, and characterised chemically and physically. Then ibuprofen, a drug often used as a gold standard in studies involving β-CD both in its hydrophilic and hydrophobic forms, was selected to investigate the release behavior of the synthesised hydrogels and the influence of β-CD on the release. The presence of β-CD linked to the polymeric 3D network ensured a higher and prolonged release profile for the hydrophobic drug and also seemed to have some influence on the hydrophilic one.
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Affiliation(s)
- Filippo Pinelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Maddalena Ponti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Sara Delleani
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Fabio Pizzetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Valeria Vanoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Francesco Briatico Vangosa
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Franca Castiglione
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Havard Haugen
- Department of Biomaterials, Institute for Clinical Dentistry, University of Oslo, PO Box 1109, Blindern, NO-0317 Oslo, Norway
| | - Liebert P Nogueira
- Oral Research Laboratory, Institute for Clinical Dentistry, University of Oslo, PO Box 1109, Blindern, NO-0317 Oslo, Norway
| | - Arianna Rossetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Filippo Rossi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Alessandro Sacchetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
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Karthikeyan M, Dhinesh Kumar M, Kaniraja G, Karunakaran C. Theoretical investigations of free energy of binding and chiral recognition studies of (R)- and (S)-Noradrenaline towards β-cyclodextrin. J Mol Graph Model 2023; 124:108552. [PMID: 37379759 DOI: 10.1016/j.jmgm.2023.108552] [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: 03/29/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/30/2023]
Abstract
Noradrenaline (NA), one of the important excitatory catecholamine neurotransmitters, is used as a medication for Parkinson's Disease (PD). The β-cyclodextrin (β-CD) is one of the most effective drug carrier & also used in chiral separation. So, in this theoretical investigation, the R/S-Noradrenaline (R/S-NA) forms binding & chiral recognition mechanisms and energies with β-CD were explored. Using the AutoDock, R/S forms were first docked into the cavity of β-CD giving host-guest complexes with the free energy of binding for S-NA (-4.81 kcal/mol) larger than R-NA (-4.53 kcal/mol). The host-guest inclusion 1:1 complexes between R/S-NA and β-CD have been also modeled and optimized with ONIOM2 (B3LYP/6-31g++DP: PM6) method by using the Gaussian software. Further, frequency calculations were carried out to obtain the free energies. In comparison to the R-NA (-54.59 kcal/mol), it was observed that the S-NA (-56.48 kcal/mol) with β-CD is more stable. Furthermore, the H-bond results from molecular dynamics simulation revealed that S-NA/β-CD was more stable than R-NA/β-CD. In addition, the thermodynamic properties, vibrational analysis (IR), HOMO-LUMO band gap energy, inter molecular hydrogen bond interactions, and conformational analysis were investigated for both the R/S forms to support & compare the stability of the inclusion complex. These inclusion & high stability of S-NA/β-CD and in turn its theoretical chiral recognition behavior observed agreeing well with the reported NMR experimental data have implications in drug delivery and chiral separation research.
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Affiliation(s)
- Murugesan Karthikeyan
- Biomedical Research Laboratory, Department of Chemistry, Virudhunagar Hindu Nadars' Senthikumara Nadar College (Autonomous & Affiliated to Madurai Kamaraj University), Virudhunagar- 626 001, Tamil Nadu, India
| | - Marimuthu Dhinesh Kumar
- Biomedical Research Laboratory, Department of Chemistry, Virudhunagar Hindu Nadars' Senthikumara Nadar College (Autonomous & Affiliated to Madurai Kamaraj University), Virudhunagar- 626 001, Tamil Nadu, India
| | - Ganesan Kaniraja
- Biomedical Research Laboratory, Department of Chemistry, Virudhunagar Hindu Nadars' Senthikumara Nadar College (Autonomous & Affiliated to Madurai Kamaraj University), Virudhunagar- 626 001, Tamil Nadu, India
| | - Chandran Karunakaran
- Biomedical Research Laboratory, Department of Chemistry, Virudhunagar Hindu Nadars' Senthikumara Nadar College (Autonomous & Affiliated to Madurai Kamaraj University), Virudhunagar- 626 001, Tamil Nadu, India.
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7
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Bhardwaj VK, Purohit R. A comparative study on inclusion complex formation between formononetin and β-cyclodextrin derivatives through multiscale classical and umbrella sampling simulations. Carbohydr Polym 2023; 310:120729. [PMID: 36925262 DOI: 10.1016/j.carbpol.2023.120729] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/31/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023]
Abstract
Formononetin, a naturally occurring isoflavone exhibits a wide range of therapeutic applications including antioxidant, anti-tumor, antiviral, anti-diabetic and neuroprotective activities. However, the low hydro-solubility of formononetin has limited its prospective use in cosmetic, neutraceutical and pharmaceutical industries. Cyclodextrins (CDs), especially β-CD and its derivatives have emerged as promising agents to improve the water solubility of poorly hydrosoluble compounds by the formation of inclusion complexes. We employed multiscale (1000 ns) explicit solvent and umbrella sampling molecular dynamics (MD) simulations to study the interactions and thermodynamic parameters of inclusion complex formation between formononetin and five most commonly used β-CD derivatives. Classical MD simulations revealed two possible binding conformations of formononetin inside the central cavity of hydroxypropyl-β-CD (HP-β-CD), randomly methylated-β-CD (ME-β-CD), and sulfobutylether-β-CD (SBE-β-CD). The binding conformation with the benzopyrone ring of formononetin inside the central cavity of β-CD derivatives was more frequent than the phenyl group occupying the hydrophobic cavity. These interactions were supported by a variety of non-bonded contacts including hydrogen bonds, pi-lone pair, pi-sigma, and pi-alkyl interactions. Formononetin showed favorable end-state MD-driven thermodynamic binding free energies with all the selected β-CD derivatives, except succinyl-β-CD (S-β-CD). Furthermore, umbrella sampling simulations were used to investigate the interactions and thermodynamic parameters of the host-guest inclusion complexes. The SBE-β-CD/formononetin inclusion complex showed the lowest binding energy signifying the highest affinity among all the selected host-guest inclusion complexes. Our study could be used as a standard for analyzing and comparing the ability of different β-CD derivatives to enhance the hydro-solubility of poorly soluble molecules.
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Affiliation(s)
- Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
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8
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Sakai S, Hirano Y, Kobayashi Y, Arai N. Effect of temperature on the structure and drug-release behaviour of inclusion complex of β-cyclodextrin with cyclophosphamide: a molecular dynamics study. SOFT MATTER 2023; 19:2902-2907. [PMID: 36987748 DOI: 10.1039/d2sm01542k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cyclodextrins (CDs) are suitable drug carriers because of their doughnut-shaped cavities with hydrophilic outer and hydrophobic inner surfaces. Temperature-responsive CD-based drug carriers are expected to be one of the most promising candidates for drug delivery systems. In this study, we performed molecular dynamics simulations of the inclusion complex of β-CD with cyclophosphamide (CP) at temperatures from 300 K to 400 K to investigate the temperature dependency of the release behaviour of CP and structural changes of β-CD in an aqueous solution. We analysed the distance between the centres of mass of β-CD and CP and the radius of gyration of β-CD. The CP molecule was released from the β-CD cavity at 400 K, whereas two different inclusion complexes, partially and completely, were observed at T < 400 K. β-CD encapsulating a CP molecule had a more spherical shape and rigidity than β-CD without a CP, and the rigidity of their inclusion complex decreased with increasing temperature. Our findings provide fundamental insights into the behaviours of the β-CD/CP complex and drug release at the molecular level and can facilitate the development of new temperature-responsive drug delivery systems with CD nanocarriers triggered by localised temperature increases using focused ultrasound.
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Affiliation(s)
- Seiga Sakai
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Yoshinori Hirano
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Yusei Kobayashi
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Noriyoshi Arai
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan.
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9
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Tsai YC, Chen WY, Chiu CC. Molecular effects of site-specific phosphate-methylated primer on the structure and motions of Taq DNA polymerase. Comput Struct Biotechnol J 2023; 21:1820-1827. [PMID: 36923470 PMCID: PMC10009445 DOI: 10.1016/j.csbj.2023.02.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Polymerase chain reaction (PCR) is a powerful molecular biology assay for gene detection and quantification. Conventional DNA primers for PCR often suffer from poor sensitivity in specific gene detection. Recently, oligonucleotides containing methyl phosphotriester (MPTE-DNA) have been developed with enhanced DNA hybridization and improved gene detection sensitivity. Yet, site-specific MPTE-modifications on DNA primers have been reported to affect PCR amplification efficiencies while the detailed mechanism remains elusive. Here, we utilized molecular dynamics (MD) simulation to examine the effects of site-specific MPTE-modified primers on the structure and motions of DNA/Taq polymerase complexes. All tested MPTE-DNA/Taq complexes exhibited RMSD values below 2 Å, indicating insignificant effects of all methylation sites on the complex stability. The energetic and hydrogen-bonding analyses suggest minor effects of methylation at t-3, t-4, t-6, and t-7 positions on the DNA-Taq interaction. Principal component analyses further reveal that only t-3, and t-7 methylations preserve the motions of the Taq thumb domain. The site-specific methylation affects the interaction between DNA and the surrounding protein residues, resulting in allosteric-like effects on the DNA/Taq complex. The MD data complement the best experimentally observed PCR efficacies for the t-3 and t-7 positions among all tested MPTE-primers. The unveiled molecular insights can benefit the design of novel PCR primers for improving genetic testing platforms.
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Affiliation(s)
- Yi-Chen Tsai
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Chi-Cheng Chiu
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.,Hierarchical Green-Energy Materials (Hi-GEM) Research Center, National Cheng Kung University, Tainan 701, Taiwan
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10
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Thermodynamics and Transport Properties of CBD and Δ9-THC: A first attempt using Molecular Dynamics. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Megariotis G, Mikaelian G, Avramopoulos A, Romanos N, Theodorou DN. Molecular simulations of fluoxetine in hydrated lipid bilayers, as well as in aqueous solutions containing β-cyclodextrin. J Mol Graph Model 2022; 117:108305. [PMID: 35987186 DOI: 10.1016/j.jmgm.2022.108305] [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: 05/09/2022] [Revised: 07/25/2022] [Accepted: 08/06/2022] [Indexed: 01/14/2023]
Abstract
Fluoxetine, which is a well-known antidepressant drug, is studied in hydrated cholesterol-free and cholesterol-containing lipid bilayers through unbiased and biased atomistic molecular dynamics simulations. The latter are conducted for the calculation of the potential of mean force (PMF) of fluoxetine along an axis perpendicular to the two leaflets of the bilayer. The PMF indicates that the drug prefers to reside inside the lipid phase and allows us to calculate important thermodynamic properties, such as the Gibbs energy difference of partitioning from the water to the lipid phase and the Gibbs energy barrier for hopping events between the two leaflets of the bilayer. The results from the biased simulations are in accord with the mass density profiles calculated from the unbiased simulations. Moreover, we estimate the effect of fluoxetine mole fraction on the order parameters of the lipid alkyl chains and on the area per lipid. It is also found that fluoxetine forms a hydrogen bond network with lipids and water molecules penetrating into the lipid phase. In addition, fluoxoetine is studied in detail in aqueous solutions containing β-cyclodextrin. It is observed from unbiased molecular dynamics simulations that the two aforementioned molecules form a noncovalent complex spontaneously and the calculated binding free energy is in agreement with the literature.
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Affiliation(s)
- Grigorios Megariotis
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece.
| | - Georgios Mikaelian
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece
| | - Aggelos Avramopoulos
- Department of Physics, University of Thessaly, 3rd Km Old National Road Lamia Athens, Lamia, GR, 35100, Greece
| | - Nikolaos Romanos
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece
| | - Doros N Theodorou
- School of Chemical Engineering, National Technical University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, Athens, GR, 15780, Greece
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12
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Deshchenya V, Kondratyuk N, Lankin A, Norman G. Molecular dynamics study of sucrose aqueous solutions: from solution structure to transport coefficients. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Qiao L, Deng F, Hu X, Huang T, An J, Pan D, Yan J, Liang G, He J. Dual sustained-release PTMC/PCL porous microspheres for lipid-soluble drugs. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Dawass N, Langeveld J, Ramdin M, Pérez-Gallent E, Villanueva AA, Giling EJM, Langerak J, van den Broeke LJP, Vlugt TJH, Moultos OA. Solubilities and Transport Properties of CO 2, Oxalic Acid, and Formic Acid in Mixed Solvents Composed of Deep Eutectic Solvents, Methanol, and Propylene Carbonate. J Phys Chem B 2022; 126:3572-3584. [PMID: 35507866 PMCID: PMC9125562 DOI: 10.1021/acs.jpcb.2c01425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Recently, deep eutectic
solvents (DES) have been considered as
possible electrolytes for the electrochemical reduction of CO2 to value-added products such as formic and oxalic acids.
The applicability of pure DES as electrolytes is hindered by high
viscosities. Mixtures of DES with organic solvents can be a promising
way of designing superior electrolytes by exploiting the advantages
of each solvent type. In this study, densities, viscosities, diffusivities,
and ionic conductivities of mixed solvents comprising DES (i.e., reline
and ethaline), methanol, and propylene carbonate were computed using
molecular simulations. To provide a quantitative assessment of the
affinity and mass transport of CO2 and oxalic and formic
acids in the mixed solvents, the solubilities and self-diffusivities
of these solutes were also computed. Our results show that the addition
of DES to the organic solvents enhances the solubilities of oxalic
and formic acids, while the solubility of CO2 in the ethaline-containing
mixtures are in the same order of magnitude with the respective pure
organic components. A monotonic increase in the densities and viscosities
of the mixed solvents is observed as the mole fraction of DES in the
mixture increases, with the exception of the density of ethaline-propylene
carbonate which shows the opposite behavior due to the high viscosity
of the pure organic component. The self-diffusivities of all species
in the mixtures significantly decrease as the mole fraction of DES
approaches unity. Similarly, the self-diffusivities of the dissolved
CO2 and the oxalic and formic acids also decrease by at
least 1 order of magnitude as the composition of the mixture shifts
from the pure organic component to pure DES. The computed ionic conductivities
of all mixed solvents show a maximum value for mole fractions of DES
in the range from 0.2 to 0.6 and decrease as more DES is added to
the mixtures. Since for most mixtures studied here no prior experimental
measurements exist, our findings can serve as a first data set based
on which further investigation of DES-containing electrolyte solutions
can be performed for the electrochemical reduction of CO2 to useful chemicals.
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Affiliation(s)
- Noura Dawass
- Chemical Engineering Program, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
| | - Jilles Langeveld
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Mahinder Ramdin
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Elena Pérez-Gallent
- Department of Sustainable Process and Energy Systems, TNO, Delft, Zuid-Holland 2628CA, The Netherlands
| | - Angel A Villanueva
- Department of Sustainable Process and Energy Systems, TNO, Delft, Zuid-Holland 2628CA, The Netherlands
| | - Erwin J M Giling
- Department of Sustainable Process and Energy Systems, TNO, Delft, Zuid-Holland 2628CA, The Netherlands
| | - Jort Langerak
- Research and Development Department, DMT Environmental Technology, Yndustrywei 3, 8501SN Joure, The Netherlands
| | - Leo J P van den Broeke
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Thijs J H Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Othonas A Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
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15
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Roussey NM, Dickson A. Local Ion Densities can Influence Transition Paths of Molecular Binding. Front Mol Biosci 2022; 9:858316. [PMID: 35558558 PMCID: PMC9086317 DOI: 10.3389/fmolb.2022.858316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/01/2022] [Indexed: 11/22/2022] Open
Abstract
Improper reaction coordinates can pose significant problems for path-based binding free energy calculations. Particularly, omission of long timescale motions can lead to over-estimation of the energetic barriers between the bound and unbound states. Many methods exist to construct the optimal reaction coordinate using a pre-defined basis set of features. Although simulations are typically conducted in explicit solvent, the solvent atoms are often excluded by these feature sets—resulting in little being known about their role in reaction coordinates, and ultimately, their role in determining (un)binding rates and free energies. In this work, analysis is done on an extensive set of host-guest unbinding trajectories, working to characterize differences between high and low probability unbinding trajectories with a focus on solvent-based features, including host-ion interactions, guest-ion interactions and location-dependent ion densities. We find that differences in ion densities as well as guest-ion interactions strongly correlate with differences in the probabilities of reactive paths that are used to determine free energies of (un)binding and play a significant role in the unbinding process.
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Affiliation(s)
- Nicole M. Roussey
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Alex Dickson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, United States
- *Correspondence: Alex Dickson,
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16
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Bahiraei M, Derakhshandeh K, Mahjub R. Hydrophobic ion pairing with cationic derivatives of α-, ß and γ- cyclodextrin as a novel approch for development of a Self Nano-Emulsifying Drug Delivey System (SNEDDS) for oral delivery of Heparin. Drug Dev Ind Pharm 2022; 47:1809-1823. [DOI: 10.1080/03639045.2022.2064485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Masoomeh Bahiraei
- Department of Pharmaceutics, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Katayoun Derakhshandeh
- Department of Pharmaceutics, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
- Medicinal Plant and Natural Product Research Center, Hamadan, University of Medical Sciences, Hamadan, Iran
| | - Reza Mahjub
- Department of Pharmaceutics, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
- Medicinal Plant and Natural Product Research Center, Hamadan, University of Medical Sciences, Hamadan, Iran
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17
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Wang Y, Feng Z, Sun Y, Zhu L, Xia D. Chiral induction in a novel self-assembled supramolecular system composed of α-cyclodextrin porous liquids, chiral silver nanoparticles and planar conjugated molecules. SOFT MATTER 2022; 18:975-982. [PMID: 35014653 DOI: 10.1039/d1sm01248g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The newly developed porous liquids known as liquids with permanent microporosity, have considerable application potential in many unknown areas. Herein, a supramolecular system composed of α-cyclodextrin porous liquid, chiral silver nanoparticles and planar conjugated molecules (methylene blue and indigo carmine) was designed and the induced chirality of the system was observed. It was found that the induced chirality can be easily tuned by changing the pH value of the mixture solution. The induced chiral signal of methylene blue in the developed self-assembled supramolecular system occurred when the pH was between 8 and 10, and furthermore the induced chirality of indigo carmine was found when the pH was between 6.5 and 7.5. The intensity of induced chirality decreases upon increasing temperatures and ionic strength. This study may offer a new approach for the creation of a chiral supramolecular system based on host-guest and electrostatic interaction and make cyclodextrin porous liquids promising candidates for applications in chiral induction.
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Affiliation(s)
- Yan Wang
- College of Chemical Engineering, State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China.
- Oil & Gas Technology Research Institute, Changqing Oilfield Company, Xi'an 710018, China
| | - Zhen Feng
- College of Chemical Engineering, State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China.
| | - Yawei Sun
- College of Chemical Engineering, State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China.
| | - Lijun Zhu
- College of Chemical Engineering, State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China.
| | - Daohong Xia
- College of Chemical Engineering, State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao 266580, China.
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18
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Deng C, Cao C, Zhang Y, Hu J, Gong Y, Zheng M, Zhou Y. Formation and stabilization mechanism of β-cyclodextrin inclusion complex with C10 aroma molecules. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107013] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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19
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Gabriel de Lima P, Giordano Viegas R, Vital de Oliveira O. Computational studies of the encapsulation of ibuprofen and paracetamol into cucurbit[7]uril. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113465] [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]
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20
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Celebi AT, Dawass N, Moultos OA, Vlugt TJH. How sensitive are physical properties of choline chloride-urea mixtures to composition changes: Molecular dynamics simulations and Kirkwood-Buff theory. J Chem Phys 2021; 154:184502. [PMID: 34241035 DOI: 10.1063/5.0049064] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Deep eutectic solvents (DESs) have emerged as a cheaper and greener alternative to conventional organic solvents. Choline chloride (ChCl) mixed with urea at a molar ratio of 1:2 is one of the most common DESs for a wide range of applications such as electrochemistry, material science, and biochemistry. In this study, molecular dynamics simulations are performed to study the effect of urea content on the thermodynamic and transport properties of ChCl and urea mixtures. With increased mole fraction of urea, the number of hydrogen bonds (HBs) between cation-anion and ion-urea decreases, while the number of HBs between urea-urea increases. Radial distribution functions (RDFs) for ChCl-urea and ChCl-ChCl pairs shows a significant decrease as the mole fraction of urea increases. Using the computed RDFs, Kirkwood-Buff Integrals (KBIs) are computed. KBIs show that interactions of urea-urea become stronger, while interactions of urea-ChCl and ChCl-ChCl pairs become slightly weaker with increasing mole fraction of urea. All thermodynamic factors are found larger than one, indicating a non-ideal mixture. Our results also show that self- and collective diffusivities increase, while viscosities decrease with increasing urea content. This is mainly due to the weaker interactions between ions and urea, resulting in enhanced mobilities. Ionic conductivities exhibit a non-monotonic behavior. Up to a mole fraction of 0.5, the ionic conductivities increase with increasing urea content and then reach a plateau.
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Affiliation(s)
- Alper T Celebi
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Noura Dawass
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Othonas A Moultos
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
| | - Thijs J H Vlugt
- Engineering Thermodynamics, Process and Energy Department, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
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21
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Yan X, Wang Y, Meng T, Yan H. Computational Insights Into the Influence of Substitution Groups on the Inclusion Complexation of β-Cyclodextrin. Front Chem 2021; 9:668400. [PMID: 34095084 PMCID: PMC8176092 DOI: 10.3389/fchem.2021.668400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/03/2021] [Indexed: 11/21/2022] Open
Abstract
Cyclodextrins (CDs) and their derivatives have good prospects in soil remediation application due to their ability to enhance the stability and solubility of low water-soluble compounds by inclusion performance. To investigate the effect of different structural properties of cyclodextrin and its derivatives on the inclusion complexation, molecular dynamic (MD) simulations were performed on the inclusion complexes formed by three kinds of CDs with polycyclic aromatic hydrocarbons (PAHs). Based on neutral β-CD, the other two CDs were modified by introducing substitutional groups, including 2-hydroxypropyl and sulfonated butyl (SBE) functional groups in the ring structure, called HP-CD and SBE-CD. MD results show that PAH can merely enter into the cavity of SBE–β-CD from its wide rim. The substitutional groups significantly affect the structure of CDs, which may also cause the flipping of the glucose units. However, the substitutional groups can also enlarge the volume of the hydrophobic cavity, resulting in a tight combination with the guest molecules.
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Affiliation(s)
- Xianghua Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China.,School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Yue Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Tong Meng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
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22
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Chen M, Lu X, Ma X, Xiao Y, Wang Y. Click preparation of multiple-thioether bridged cyclodextrin chiral materials for efficient enantioseparation in high-performance liquid chromatography. Analyst 2021; 146:3025-3033. [PMID: 33949420 DOI: 10.1039/d1an00145k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly efficient covalent immobilization procedure is considered as an essential tool for obtaining stable and reliable cyclodextrin (CD) chiral stationary phases (CSPs). This work reports the "thiolene" click immobilization of heptakis(6-mercapto-6-deoxy)-β-CD-CSP onto alkene functional silica to afford novel multiple-thioether bridged CD CSPs by controlling the surface CD concentration. Solid-state NMR, FTIR, TGA and X-ray photoelectron diffraction spectroscopy (XPS) results proved the successful preparation of the desired CSPs with different surface CD loadings. The surface CD concentrations were calculated to be 0.49 and 0.68 μmol m-2 according to the elemental analysis results. More than 60 chiral enantiomers including isoxazolines, chiral lactides, chiral ketones, dansyl amino acids, small molecule acids and alkalis as well as some flavonoids were resolved or partially separated in the reversed-phase HPLC mode. Compared with the previously prepared single thiolene bridged CD-CSP, the current multiple-thioether CD-CSP afforded much better enantioseparation ability due to the existence of the thiol moiety and a confined structure.
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Affiliation(s)
- Ming Chen
- School of Science, Tianjin Key Laboratory of Molecular Optoelectronic Science, Department of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, P. R. China.
| | - Xinling Lu
- School of Science, Tianjin Key Laboratory of Molecular Optoelectronic Science, Department of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, P. R. China.
| | - Xiaofei Ma
- School of Science, Tianjin Key Laboratory of Molecular Optoelectronic Science, Department of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, P. R. China.
| | - Yin Xiao
- School of Chemical Engineering and Technology, Tianjin Engineering Research Center of Functional Fine Chemicals, Tianjin University, Tianjin 300072, P. R. China
| | - Yong Wang
- School of Science, Tianjin Key Laboratory of Molecular Optoelectronic Science, Department of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, P. R. China.
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23
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Çınaroğlu SS, Biggin PC. Evaluating the Performance of Water Models with Host-Guest Force Fields in Binding Enthalpy Calculations for Cucurbit[7]uril-Guest Systems. J Phys Chem B 2021; 125:1558-1567. [PMID: 33538161 DOI: 10.1021/acs.jpcb.0c11383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational prediction of thermodynamic components with computational methods has become increasingly routine in computer-aided drug design. Although there has been significant recent effort and improvements in the calculation of free energy, the prediction of enthalpy (and entropy) remains underexplored. Furthermore, there has been relatively little work reported so far that attempts to comparatively assess how well different force fields and water models perform in conjunction with each other. Here, we report a comprehensive assessment of force fields and water models using host-guest systems that mimic many features of protein-ligand systems. These systems are computationally inexpensive, possibly because of their small size compared to protein-ligand systems. We present absolute enthalpy calculations using the multibox approach on a set of 25 cucurbit[7]uril-guest pairs. Eight water models were considered (TIP3P, TIP4P, TIP4P-Ew, SPC, SPC/E, OPC, TIP5P, Bind3P), along with five force fields commonly used in the literature (GAFFv1, GAFFv2, CGenFF, Parsley, and SwissParam). We observe that host-guest binding enthalpies are strongly sensitive to the selection of force field and water model. In terms of water models, we find that TIP3P and its derivative Bind3P are the best performing models for this particular host-guest system. The performance is generally better for aliphatic compounds than for aromatic ones, suggesting that aromaticity remains a difficult property to include accurately in these simple force fields.
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Affiliation(s)
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
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24
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Celebi AT, Jamali SH, Bardow A, Vlugt TJH, Moultos OA. Finite-size effects of diffusion coefficients computed from molecular dynamics: a review of what we have learned so far. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1810685] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alper T. Celebi
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Seyed Hossein Jamali
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - André Bardow
- Energy & Process Systems Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Zürich, Switzerland
| | - Thijs J. H. Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
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