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Seol Y, Markiewicz M, Beil S, Schubert S, Jungmann D, Wasserscheid P, Stolte S. Aquatic toxicity, bioaccumulation potential, and human estrogen/androgen activity of three oxo-Liquid Organic Hydrogen Carrier (oxo-LOHC) systems. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135102. [PMID: 39003805 DOI: 10.1016/j.jhazmat.2024.135102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/24/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024]
Abstract
The Liquid Organic Hydrogen Carrier (LOHC) technology offers a technically attractive way for hydrogen storage. If LOHC systems were to fully replace liquid fossil fuels, they would need to be handled at the multi-million tonne scale. To date, LOHC systems on the market based on toluene or benzyltoluene still offer potential for improvements. Thus, it is of great interest to investigate potential LOHCs that promise better performance and environmental/human hazard profiles. In this context, we investigated the acute aquatic toxicity of oxygen-containing LOHC (oxo-LOHC) systems. Toxic Ratio (TR) values of oxo-LOHC compounds classify them baseline toxicants (0.1 < TR < 10). Additionally, the mixture toxicity test conducted with D. magna suggests that the overall toxicity of a benzophenone-based system can be accurately predicted using a concentration addition model. The estimation of bioconcentration factors (BCF) through the use of the membrane-water partition coefficient indicates that oxo-LOHCs are unlikely to be bioaccumulative (BCF < 2000). None of the oxo-LOHC compounds exhibited hormonal disrupting activities at the tested concentration of 2 mg/L in yeast-based reporter gene assays. Therefore, the oxo-LOHC systems seem to pose a low level of hazard and deserve more attention in ongoing studies searching for the best hydrogen storage technologies.
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Affiliation(s)
- Yohan Seol
- Institute of Water Chemistry, Dresden University of Technology, 01069 Dresden, Germany
| | - Marta Markiewicz
- Institute of Water Chemistry, Dresden University of Technology, 01069 Dresden, Germany
| | - Stephan Beil
- Institute of Water Chemistry, Dresden University of Technology, 01069 Dresden, Germany
| | - Sara Schubert
- Institute of Hydrobiology, Dresden University of Technology, 01069 Dresden, Germany
| | - Dirk Jungmann
- Institute of Hydrobiology, Dresden University of Technology, 01069 Dresden, Germany
| | - Peter Wasserscheid
- Institute of Chemical Reaction Engineering, Friedrich Alexander University of Erlangen Nürnberg, Egerlandstraße 3, 91058 Erlangen, Germany; Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nuremberg for Renewable Energy, 91058 Erlangen, Germany; Forschungszentrum Jülich GmbH, Institute for a Sustainable Hydrogen Economy, 52428 Jülich, Germany
| | - Stefan Stolte
- Institute of Water Chemistry, Dresden University of Technology, 01069 Dresden, Germany.
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2
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Antle JP, LaRock MA, Falls Z, Ng C, Atilla-Gokcumen GE, Aga DS, Simpson SM. Building Chemical Intuition about Physicochemical Properties of C8-Per-/Polyfluoroalkyl Carboxylic Acids through Computational Means. ACS ES&T ENGINEERING 2023; 4:196-208. [PMID: 38860110 PMCID: PMC11164130 DOI: 10.1021/acsestengg.3c00267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
We have predicted acid dissociation constants (pK a), octanol-water partition coefficients (K OW), and DMPC lipid membrane-water partition coefficients (K lipid-w) of 150 different eight-carbon-containing poly-/perfluoroalkyl carboxylic acids (C8-PFCAs) utilizing the COnductor-like Screening MOdel for Realistic Solvents (COSMO-RS) theory. Different trends associated with functionalization, degree of fluorination, degree of saturation, degree of chlorination, and branching are discussed on the basis of the predicted values for the partition coefficients. In general, functionalization closest to the carboxylic headgroup had the greatest impact on the value of the predicted physicochemical properties.
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Affiliation(s)
- Jonathan P Antle
- Department of Chemistry, University at Buffalo, the State University of New York (SUNY), Buffalo, New York 14260, United States
| | - Michael A LaRock
- Department of Chemistry, St. Bonaventure University, St. Bonaventure, New York 14778, United States
| | - Zackary Falls
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, United States
| | - Carla Ng
- Department of Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - G Ekin Atilla-Gokcumen
- Department of Chemistry, University at Buffalo, the State University of New York (SUNY), Buffalo, New York 14260, United States
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, the State University of New York (SUNY), Buffalo, New York 14260, United States
| | - Scott M Simpson
- Department of Chemistry, St. Bonaventure University, St. Bonaventure, New York 14778, United States
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3
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Potter TD, Haywood N, Teixeira A, Hodges G, Barrett EL, Miller MA. Partitioning into phosphatidylcholine-cholesterol membranes: liposome measurements, coarse-grained simulations, and implications for bioaccumulation. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023. [PMID: 37158124 DOI: 10.1039/d3em00081h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Membrane-water partitioning is an important physical property for the assessment of bioaccumulation and environmental impact. Here, we advance simulation methodology for predicting the partitioning of small molecules into lipid membranes and compare the computational predictions to experimental measurements in liposomes. As a step towards high-throughput screening, we present an automated mapping and parametrization procedure to produce coarse-grained models compatible with the Martini 3 force field. The methodology is general and can also be used for other applications where coarse-grained simulations are appropriate. This article addresses the effect on membrane-water partitioning of adding cholesterol to POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membranes. Nine contrasting neutral, zwitterionic and charged solutes are tested. Agreement between experiment and simulation is generally good, with the most challenging cases being permanently charged solutes. For all solutes, partitioning is found to be insensitive to membrane cholesterol concentration up to 25% mole fraction. Hence, for assessment of bioaccumulation into a range of membranes (such as those found in fish), partitioning data measured in pure lipid membranes are still informative.
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Affiliation(s)
- Thomas D Potter
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom.
| | - Nicola Haywood
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom
| | - Alexandre Teixeira
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom
| | - Geoff Hodges
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom
| | - Elin L Barrett
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom
| | - Mark A Miller
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom.
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4
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Piasentin N, Lian G, Cai Q. In Silico Prediction of Stratum Corneum Partition Coefficients via COSMOmic and Molecular Dynamics Simulations. J Phys Chem B 2023; 127:2719-2728. [PMID: 36930176 PMCID: PMC10068742 DOI: 10.1021/acs.jpcb.2c08566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Stratum corneum (SC) is the main barrier of human skin where the inter-corneocytes lipids provide the main pathway for transdermal permeation of functional actives of skin care and health. Molecular dynamics (MD) has been increasingly used to simulate the SC lipid bilayer structure so that the barrier property and its affecting factors can be elucidated. Among reported MD simulation studies, solute partition in the SC lipids, an important parameter affecting SC permeability, has received limited attention. In this work, we combine MD simulation with COSMOmic to predict the partition coefficients of dermatologically relevant solutes in SC lipid bilayer. Firstly, we run MD simulations to obtain equilibrated SC lipid bilayers with different lipid types, compositions, and structures. Then, the simulated SC lipid bilayer structures are fed to COSMOmic to calculate the partition coefficients of the solutes. The results show that lipid types and bilayer geometries play a minor role in the predicted partition coefficients. For the more lipophilic solutes, the predicted results of solute partition in SC lipid bilayers agree well with reported experimental values of solute partition in extracted SC lipids. For the more hydrophilic molecules, there is a systematical underprediction. Nevertheless, the MD/COSMOmic approach correctly reproduces the phenomenological correlation between the SC lipid/water partition coefficients and the octanol/water partition coefficients. Overall, the results show that the MD/COSMOmic approach is a fast and valid method for predicting solute partitioning into SC lipids and hence supporting the assessment of percutaneous absorption of skin care ingredients, dermatological drugs as well as environmental pollutants.
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Affiliation(s)
- Nicola Piasentin
- Department of Chemical and Process Engineering, University of Surrey, Guildford GU27XH, U.K.,Unilever R&D Colworth, Unilever, Sharnbrook MK441LQ, U.K
| | - Guoping Lian
- Department of Chemical and Process Engineering, University of Surrey, Guildford GU27XH, U.K.,Unilever R&D Colworth, Unilever, Sharnbrook MK441LQ, U.K
| | - Qiong Cai
- Department of Chemical and Process Engineering, University of Surrey, Guildford GU27XH, U.K
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5
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Han F, Liu J, Wang Y, Li J, Lyu B, Zhao Y, Wu Y. Penetration of Perfluorooctanesulfonate Isomers and Their Alternatives from Maternal Blood to Milk and Its Associations with Chemical Properties and Milk Primary Components. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2457-2463. [PMID: 36734054 DOI: 10.1021/acs.est.2c07401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Perfluorooctanesulfonate (PFOS) and its alternatives, including chlorinated polyfluorinated ether sulfonates (Cl-PFESAs), are mainly detected per- and polyfluoroalkyl substances (PFAS) in human samples such as milk. However, the mechanism of their blood to milk transfer was not well studied. Here, 145 paired maternal serum and human milk samples were analyzed for six PFOS isomers and Cl-PFESAs to evaluate the transfer efficiency from maternal serum to human milk (TEHM/MS). Besides physicochemical properties, this study for the first time evaluated the influencing effects of the primary components in human milk (carbohydrate, lipid, and protein) on TEHM/MS of PFAS. No significant association was observed between TEHM/MS and the albumin binding affinity of the compounds (p = 0.601), but TEHM/MS was significantly negatively correlated with the logarithmic octanol-water partition coefficients (r2 = 0.853, p = 0.001), the logarithmic membrane-water partition coefficients (r2 = 0.679, p = 0.012), and the carbohydrate contents in human milk. The effect of carbohydrate was further confirmed using in vitro tests. The negative associations between TEHM/MS and hydrophobicity, membrane passive permeability, and the carbohydrate content in human milk consistently indicated that passive diffusion through the paracellular route might be the main transfer pathway for PFOS and Cl-PFESAs from blood to milk in humans.
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Affiliation(s)
- Feng Han
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (No. 2019RU014), China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Jiaying Liu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yuxin Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (No. 2019RU014), China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Jingguang Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (No. 2019RU014), China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Bing Lyu
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (No. 2019RU014), China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Yunfeng Zhao
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (No. 2019RU014), China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Yongning Wu
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (No. 2019RU014), China National Center for Food Safety Risk Assessment, Beijing 100021, China
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6
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Ranaudo A, Greco C, Moro G, Zucchi A, Mattiello S, Beverina L, Cosentino U. Partition of the Reactive Species of the Suzuki-Miyaura Reaction between Aqueous and Micellar Environments. J Phys Chem B 2022; 126:9408-9416. [PMID: 36330777 PMCID: PMC9677424 DOI: 10.1021/acs.jpcb.2c04591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Suzuki-Miyaura reaction between the aryl halide (1) and the phenyl boronic acid (2), in the presence of the palladium(0) complex (3) as catalyst, gives the cross-coupling product (4) in quantitative yield when performed in basic aqueous solution of the nonionic surfactant Kolliphor-EL (K-EL). The partition between the aqueous and micellar environments of the species of this reaction has been investigated by means of Molecular Dynamics (MD) simulations. Starting from the K-EL molecules dispersed in water, a micelle model has been generated by MD simulations, adopting the 2016H66 force field. Reagent and product species have been described with the same force field, once the reliability of this force field has been tested comparing the n-octanol/water partition free energies calculated from the MD and Free Energy Perturbation (FEP) method with those obtained from the quantum-mechanical SMD method. The potential of mean force for the transfer process between water and the micellar phase of the different species has been calculated by the MD simulations and the Umbrella Sampling (US) method. The overall picture that emerges from these results confirms that the molecular species involved in this reaction prefers the micellar environment and concentrates in different but close zones of the micelle. This supports the experimental evidence that the use of suitable surfactant agents promotes reactivity, allowing micelles to behave as nanoreactors in which reactive species are solubilized and enhance their local concentration.
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Affiliation(s)
- Anna Ranaudo
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza della Scienza 1, Milan 20126, Italy,
| | - Claudio Greco
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza della Scienza 1, Milan 20126, Italy
| | - Giorgio Moro
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, Milan 20126, Italy
| | - Anita Zucchi
- Department
of Materials Science, University of Milano-Bicocca, Via Roberto Cozzi 55, Milan 20125, Italy
| | - Sara Mattiello
- Department
of Materials Science, University of Milano-Bicocca, Via Roberto Cozzi 55, Milan 20125, Italy
| | - Luca Beverina
- Department
of Materials Science, University of Milano-Bicocca, Via Roberto Cozzi 55, Milan 20125, Italy
| | - Ugo Cosentino
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza della Scienza 1, Milan 20126, Italy
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7
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Stahn M, Grimme S, Salthammer T, Hohm U, Palm WU. Quantum chemical calculation of the vapor pressure of volatile and semi volatile organic compounds. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:2153-2166. [PMID: 36222641 DOI: 10.1039/d2em00271j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The vapor pressure is a specific and temperature-dependent parameter that describes the volatility of a substance and thus its driving force for evaporation or sublimation into the gas phase. Depending on the magnitude of the vapor pressure, there are different methods for experimental determination. However, these are usually associated with a corresponding amount of effort and become less accurate as the vapor pressure decreases. For purposes of vapor pressure prediction, algorithms were developed that are usually based on quantitative structure-activity relationships (QSAR). The quantum mechanical (QM) approach followed here applies an alternative, much less empirical strategy, where the change in Gibbs free energy for the transition from the condensed to the gas phase is obtained from conformer ensembles computed for each phase separately. The results of this automatic, so-called CRENSO workflow are compared with experimentally determined vapor pressures for a large set of environmentally relevant compounds. In addition, comparisons are made with the single structure-based COSMO-RS QM approach, linear-free-energy relationships (LFER) as well as results from the SPARC program. We show that our CRENSO workflow is superior to conventional prediction models and provides reliable vapor pressures for liquids and sub-cooled liquids over a wide pressure range.
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Affiliation(s)
- Marcel Stahn
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, 53115 Bonn, Germany
| | - Tunga Salthammer
- Department of Material Analysis and Indoor Chemistry, Fraunhofer WKI, 38108 Braunschweig, Germany.
| | - Uwe Hohm
- Institute of Physical and Theoretical Chemistry, University of Braunschweig - Institute of Technology, 38106 Braunschweig, Germany
| | - Wolf-Ulrich Palm
- Institute of Sustainable and Environmental Chemistry, Leuphana University Lüneburg, 21335 Lüneburg, Germany
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8
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Phase equilibrium modeling of mixtures containing conformationally flexible molecules with the COSMO-SAC model. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Piasentin N, Lian G, Cai Q. Evaluation of Constrained and Restrained Molecular Dynamics Simulation Methods for Predicting Skin Lipid Permeability. ACS OMEGA 2021; 6:35363-35374. [PMID: 34984268 PMCID: PMC8717400 DOI: 10.1021/acsomega.1c04684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/04/2021] [Indexed: 05/05/2023]
Abstract
Recently, molecular dynamics (MD) simulations have been utilized to investigate the barrier properties of human skin stratum corneum (SC) lipid bilayers. Different MD methods and force fields have been utilized, with predicted permeabilities varying by few orders of magnitude. In this work, we compare constrained MD simulations with restrained MD simulations to obtain the potential of the mean force and the diffusion coefficient profile for the case of a water molecule permeating across an SC lipid bilayer. Corresponding permeabilities of the simulated lipid bilayer are calculated via the inhomogeneous solubility diffusion model. Results show that both methods perform similarly, but restrained MD simulations have proven to be the more robust approach for predicting the potential of the mean force profile. Critical to both methods are the sampling of the whole trans-bilayer axis and the following symmetrization process. Re-analysis of the previously reported free energy profiles showed that some of the discrepancies in the reported permeability values is due to misquotation of units, while some are due to the inaccurately obtained potential of the mean force. By using the existing microscopic geometrical models via the intercellular lipid pathway, the permeation through the whole SC is predicted from the MD simulation results, and the predicted barrier properties have been compared to experimental data from the literature with good agreement.
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Affiliation(s)
- Nicola Piasentin
- Department
of Chemical and Process Engineering, University
of Surrey, Guildford GU27XH, U.K..
- Unilever
R&D Colworth, Unilever, Sharnbrook MK441LQ, U.K..
| | - Guoping Lian
- Department
of Chemical and Process Engineering, University
of Surrey, Guildford GU27XH, U.K..
- Unilever
R&D Colworth, Unilever, Sharnbrook MK441LQ, U.K..
- . Phone: +44 1234 222741
| | - Qiong Cai
- Department
of Chemical and Process Engineering, University
of Surrey, Guildford GU27XH, U.K..
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10
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Timmons PB, Hewage CM. Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca. Sci Rep 2021; 11:22468. [PMID: 34789753 PMCID: PMC8599514 DOI: 10.1038/s41598-021-01769-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/03/2021] [Indexed: 01/13/2023] Open
Abstract
Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defence peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-\documentclass[12pt]{minimal}
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\begin{document}$$\alpha$$\end{document}α-helix that spans between Ile\documentclass[12pt]{minimal}
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\begin{document}$$^{26}$$\end{document}26, and a cyclic disulfide-bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide’s interactions with sodium dodecyl sulfate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its \documentclass[12pt]{minimal}
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\begin{document}$$\alpha$$\end{document}α-helical conformation between residues Ile\documentclass[12pt]{minimal}
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\begin{document}$$^{26}$$\end{document}26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.
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Affiliation(s)
- Patrick B Timmons
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
| | - Chandralal M Hewage
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
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11
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Timmons PB, Hewage CM. Biophysical study of the structure and dynamics of the antimicrobial peptide maximin 1. J Pept Sci 2021; 28:e3370. [PMID: 34569121 DOI: 10.1002/psc.3370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/18/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022]
Abstract
Maximin 1 is a cationic, amphipathic antimicrobial peptide found in the skin secretions and brains of the Chinese red belly toad Bombina maxima. The 27 amino acid residue-long peptide is biologically interesting as it possesses a variety of biological activities, including antibacterial, antifungal, antiviral, antitumour and spermicidal activities. Its three-dimensional structural model was obtained in a 50/50% water/2,2,2-trifluoroethanol-d3 mixture using two-dimensional NMR spectroscopy. Maximin 1 was found to adopt an α-helical structure from residue Ile2 to Ala26 . The peptide is amphipathic, showing a clear separation between polar and non-polar residues. The interactions with sodium dodecyl sulfate micelles, a widely-used bacterial membrane-mimicking environment, were modelled using molecular dynamics simulations. The peptide maintains an α-helical conformation, occasionally displaying a flexibility around the Gly9 and Gly16 residues, which is likely responsible for the peptide's low haemolytic activity. It is found to preferentially adopt a position parallel to the micellar surface, establishing a number of hydrophobic and electrostatic interactions with the micelle.
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Affiliation(s)
- Patrick B Timmons
- UCD School of Biomolecular and Biomedical Science,UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Chandralal M Hewage
- UCD School of Biomolecular and Biomedical Science,UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
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12
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Banerjee T, Samanta A. Chemical computational approaches for optimization of effective surfactants in enhanced oil recovery. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2020-0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Abstract
The surfactant flooding becomes an attractive method among several Enhanced Oil Recovery (EOR) processes to improve the recovery of residual oil left behind in the reservoir after secondary oil recovery process. The designing of a new effective surfactant is a comparatively complex and often time consuming process as well as cost-effective due to its dependency on the crude oil and reservoir properties. An alternative chemical computational approach is focused in this article to optimize the performance of effective surfactant system for EOR. The molecular dynamics (MD), dissipative particle dynamics (DPD) and density functional theory (DFT) simulations are mostly used chemical computational approaches to study the behaviour in multiple phase systems like surfactant/oil/brine. This article highlighted a review on the impact of surfactant head group structure on oil/water interfacial property like interfacial tensions, interface formation energy, interfacial thickness by MD simulation. The effect of entropy in micelle formation has also discussed through MD simulation. The polarity, dipole moment, charge distribution and molecular structure optimization have been illustrated by DFT. A relatively new coarse-grained method, DPD is also emphasized the phase behaviour of surfactant/oil/brine as well as polymer-surfactant complex system.
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Affiliation(s)
- Tandrima Banerjee
- Department of Chemical Sciences , Indian Institute of Science Education and Research (IISER) Kolkata , West Bengal 741246 , India
| | - Abhijit Samanta
- School of Engineering and Applied Sciences , The Neotia University , Sarisha , West Bengal 743368 , India
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13
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Molecular simulations of lipid membrane partitioning and translocation by bacterial quorum sensing modulators. PLoS One 2021; 16:e0246187. [PMID: 33561158 PMCID: PMC7872223 DOI: 10.1371/journal.pone.0246187] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
Quorum sensing (QS) is a bacterial communication process mediated by both native and non-native small-molecule quorum sensing modulators (QSMs), many of which have been synthesized to disrupt QS pathways. While structure-activity relationships have been developed to relate QSM structure to the activation or inhibition of QS receptors, less is known about the transport mechanisms that enable QSMs to cross the lipid membrane and access intracellular receptors. In this study, we used atomistic MD simulations and an implicit solvent model, called COSMOmic, to analyze the partitioning and translocation of QSMs across lipid bilayers. We performed umbrella sampling at atomistic resolution to calculate partitioning and translocation free energies for a set of naturally occurring QSMs, then used COSMOmic to screen the water-membrane partition and translocation free energies for 50 native and non-native QSMs that target LasR, one of the LuxR family of quorum-sensing receptors. This screening procedure revealed the influence of systematic changes to head and tail group structures on membrane partitioning and translocation free energies at a significantly reduced computational cost compared to atomistic MD simulations. Comparisons with previously determined QSM activities suggest that QSMs that are least likely to partition into the bilayer are also less active. This work thus demonstrates the ability of the computational protocol to interrogate QSM-bilayer interactions which may help guide the design of new QSMs with engineered membrane interactions.
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Synergistic Computational Modeling Approaches as Team Players in the Game of Solubility Predictions. J Pharm Sci 2020; 110:22-34. [PMID: 33217423 DOI: 10.1016/j.xphs.2020.10.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 11/23/2022]
Abstract
Several approaches to predict and model drug solubility have been used in the drug discovery and development processes during the last decades. Each of these approaches have their own benefits and place, and are typically used as standalone approaches rather than in concert. The synergistic effects of these are often overlooked, partly due to the need of computational experts to perform the modeling and simulations as well as analyzing the data obtained. Here we provide our views on how these different approaches can be used to retrieve more information on drug solubility, ranging from multivariate data analysis over thermodynamic cycle modeling to molecular dynamics simulations. We are discussing aqueous solubility as well as solubility in more complex mixed solvents and media with colloidal structures present. We conclude that the field of computational pharmaceutics is in its early days but with a bright future ahead. However, education of computational formulators with broad knowledge of modeling and simulation approaches is imperative if computational pharmaceutics is to reach its full potential.
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Schwöbel JAH, Ebert A, Bittermann K, Huniar U, Goss KU, Klamt A. COSMOperm: Mechanistic Prediction of Passive Membrane Permeability for Neutral Compounds and Ions and Its pH Dependence. J Phys Chem B 2020; 124:3343-3354. [DOI: 10.1021/acs.jpcb.9b11728] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Andrea Ebert
- UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
- Institute of Biophysics, Johannes Kepler University, Gruberstraße 40, 4020 Linz, Austria
| | - Kai Bittermann
- UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Uwe Huniar
- BIOVIA, Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Kai-Uwe Goss
- UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
- Institute of Chemistry, University of Halle-Wittenberg, Kurt Mothes Str. 2, D-06120 Halle, Germany
| | - Andreas Klamt
- BIOVIA, Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, D-51379 Leverkusen, Germany
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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16
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Structural and positional studies of the antimicrobial peptide brevinin‐1BYa in membrane‐mimetic environments. J Pept Sci 2019; 25:e3208. [DOI: 10.1002/psc.3208] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/04/2019] [Accepted: 07/12/2019] [Indexed: 11/07/2022]
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Insights into conformation and membrane interactions of the acyclic and dicarba-bridged brevinin-1BYa antimicrobial peptides. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:701-710. [DOI: 10.1007/s00249-019-01395-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/10/2019] [Accepted: 08/13/2019] [Indexed: 02/03/2023]
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18
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William N, Nelson A, Gutsell S, Hodges G, Rabone J, Teixeira A. Hg-supported phospholipid monolayer as rapid screening device for low molecular weight narcotic compounds in water. Anal Chim Acta 2019; 1069:98-107. [PMID: 31084746 DOI: 10.1016/j.aca.2019.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 11/27/2022]
Abstract
This study positions the fabricated Pt/Hg-supported phospholipid sensor element in the context of more conventional biomembrane-based screening platforms. The technology has been used together with immobilised artificial membrane (IAM) chromatography and COSMOmic simulation methods to screen the interaction of a series of low molecular weight narcotic organic compounds in water with phosphatidylcholine (PC) membranes. For these chemicals it is shown that toxicity to aquatic species is related to compound hydrophobicity which is associated with compound accumulation in the phospholipid membrane as modelled by IAM chromatography measurements and COSMOmic simulations. In contrast, the Hg-supported dioleoyl phosphatidylcholine (DOPC) sensor element records membrane damage/modification which is indirectly related to general toxicity and directly related to compound structure. Electrochemical limit of detection (LoD) values depend on molecular structure and range from 20 μmolL-1 for substituted phenols to 23 mmolL-1 for aliphatics. Rapid cyclic voltammetry (RCV) "fingerprints" showed that the major structural classes of compounds: alkyl/chlorobenzenes, substituted phenols, quaternary ammonium compounds and neutral amines interacted distinctively with the DOPC on Hg and that these observations correlated with and supported those predicted by the COSMOmic simulations of the compound/DMPC association. In addition, the compatibility of the electrochemical and COSMOmic methods validates the electrochemical device as a meaningful high throughput technology to screen compounds in water and report on the mechanistic details of their interaction with phospholipid layers.
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Affiliation(s)
- N William
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - A Nelson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - S Gutsell
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, UK
| | - G Hodges
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, UK
| | - J Rabone
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, UK
| | - A Teixeira
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, UK
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Turchi M, Cai Q, Lian G. In Silico Prediction of the Thermodynamic Equilibrium of Solute Partition in Multiphase Complex Fluids: A Case Study of Oil-Water Microemulsion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:10855-10865. [PMID: 31335154 DOI: 10.1021/acs.langmuir.9b01513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Multiphase complex fluids such as micelles, microemulsions, and dispersions are ubiquitous in product formulations of foods, pharmaceuticals, cosmetics, and fine chemicals. Quantifying how active solutes partition in the microstructure of such multiphase fluids is necessary for designing formulations that can optimally deliver the benefits of functional actives. In this paper, we at first predict the structure of a heptane/butanol/sodium dodecyl sulfate droplet in water that self-assembled to form a microemulsion through the molecular dynamics (MD) simulation and subsequently investigate the thermodynamic equilibrium of solute partitioning using COSMOmic. To our knowledge, this is the first time that the MD/COSMOmic approach is used for predicting solute partitioning in a microemulsion. The predicted partition coefficients are compared to experimental values derived from retention measurements of the same microemulsion. We show that the experimental data of droplet-water partition coefficients (Kdroplet/w) can be reliably predicted by the method that combines MD simulations with COSMOmic.
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Affiliation(s)
- Mattia Turchi
- Unilever Research Colworth , Colworth Park , Sharnbrook, Bedfordshire MK44 1LQ , U.K
- Department of Chemical and Process Engineering , University of Surrey , Guildford GU2 7XH , U.K
| | - Qiong Cai
- Department of Chemical and Process Engineering , University of Surrey , Guildford GU2 7XH , U.K
| | - Guoping Lian
- Unilever Research Colworth , Colworth Park , Sharnbrook, Bedfordshire MK44 1LQ , U.K
- Department of Chemical and Process Engineering , University of Surrey , Guildford GU2 7XH , U.K
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20
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Mechanistic skin penetration model by the COSMOperm method: Routes of permeation, vehicle effects and skin variations in the healthy and compromised skin. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.comtox.2019.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Turchi M, Cai Q, Lian G. An evaluation of in-silico methods for predicting solute partition in multiphase complex fluids – A case study of octanol/water partition coefficient. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2018.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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22
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Hossain S, Kabedev A, Parrow A, Bergström CAS, Larsson P. Molecular simulation as a computational pharmaceutics tool to predict drug solubility, solubilization processes and partitioning. Eur J Pharm Biopharm 2019; 137:46-55. [PMID: 30771454 PMCID: PMC6434319 DOI: 10.1016/j.ejpb.2019.02.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/05/2019] [Accepted: 02/13/2019] [Indexed: 01/12/2023]
Abstract
In this review we will discuss how computational methods, and in particular classical molecular dynamics simulations, can be used to calculate solubility of pharmaceutically relevant molecules and systems. To the extent possible, we focus on the non-technical details of these calculations, and try to show also the added value of a more thorough and detailed understanding of the solubilization process obtained by using computational simulations. Although the main focus is on classical molecular dynamics simulations, we also provide the reader with some insights into other computational techniques, such as the COSMO-method, and also discuss Flory-Huggins theory and solubility parameters. We hope that this review will serve as a valuable starting point for any pharmaceutical researcher, who has not yet fully explored the possibilities offered by computational approaches to solubility calculations.
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Affiliation(s)
- Shakhawath Hossain
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; Swedish Drug Delivery Forum (SDDF), Uppsala University, Sweden
| | - Aleksei Kabedev
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden
| | - Albin Parrow
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; Swedish Drug Delivery Forum (SDDF), Uppsala University, Sweden
| | - Per Larsson
- Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; Swedish Drug Delivery Forum (SDDF), Uppsala University, Sweden.
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23
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NMR model structure of the antimicrobial peptide maximin 3. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:203-212. [DOI: 10.1007/s00249-019-01346-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/17/2022]
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24
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Droge STJ. Membrane-Water Partition Coefficients to Aid Risk Assessment of Perfluoroalkyl Anions and Alkyl Sulfates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:760-770. [PMID: 30572703 DOI: 10.1021/acs.est.8b05052] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This study determined the sorption affinity to artificial phospholipid membranes ( KMW) for series of perfluorinated carboxylates (PFCAs), perfluorinated sulfonates (PFSAs), alkyl sulfates (C xSO4), and 1-alkanesulfonates (C xSO3). A sorbent dilution assay with solid supported lipid membranes (SSLM) showed consistent CF2 unit increments of 0.59, and CH2 unit increments of 0.53, for the log KMW of perfluorinated and hydrogenated anions, respectively. PFSAs sorbed 0.90 log units stronger than analogue PFCAs; C xSO4 sorbed 0.75 log units stronger than analogue C xSO3 anions. The log KMW values for the octyl analogues increase in the order H(CH2)8SO3- (1.74) < H(CH2)8SO4- (2.58) < F(CF2)8CO2- (PFNA, 4.04) < F(CF2)8SO3- (PFOS, 4.88). Intrinsic partition ratios determined on a phospholipid coated HPLC column (IAM-HPLC) closely aligned with SSLM KMW values. COSMO-RS based molecular calculations of KMW aligned with SSLM KMW values for hydrogenated anions with C8-C14 alkyl chains but strongly underestimated CF2 and CH2 unit increments for C4-C8 based anions. Dividing the critical narcotic membrane burden of 100 mmol/kg by the experimental KMW predicts lethal baseline toxicity concentrations (LC50,narc). The LC50,narc coincides with the lowest reported acute LC50 values for several anionic surfactants but were on average about an order of magnitude lower.
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Affiliation(s)
- Steven T J Droge
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED) , Universiteit van Amsterdam (UvA) , Science Park 904 , 1098XH Amsterdam , Netherlands
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25
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Klamt A, Schwöbel J, Huniar U, Koch L, Terzi S, Gaudin T. COSMOplex: self-consistent simulation of self-organizing inhomogeneous systems based on COSMO-RS. Phys Chem Chem Phys 2019; 21:9225-9238. [PMID: 30994133 DOI: 10.1039/c9cp01169b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
During the past 20 years, the efficient combination of quantum chemical calculations with statistical thermodynamics by the COSMO-RS method has become an important alternative to force-field based simulations for the accurate prediction of free energies of molecules in liquid systems. While it was originally restricted to homogeneous liquids, it later has been extended to the prediction of the free energy of molecules in inhomogeneous systems such as micelles, biomembranes, or liquid interfaces, but these calculations were based on external input about the structure of the inhomogeneous system. Here we report the rigorous extension of COSMO-RS to a self-consistent prediction of the structure and the free energies of molecules in self-organizing inhomogeneous systems. This extends the application range to many new areas, such as the prediction of micellar structures and critical micelle concentrations, finite loading effects in micelles and biomembranes, the free energies and structure of liquid interfaces, microemulsions, and many more related topics, which often are of great practical importance.
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Affiliation(s)
- Andreas Klamt
- COSMOlogic GmbH & Co KG, Imbacher Weg 46, D-51379 Leverkusen, Germany.
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26
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Koneva AS, Ritter E, Anufrikov YA, Lezov AA, Klestova AO, Smirnova NA, Safonova EA, Smirnova I. Mixed aqueous solutions of nonionic surfactants Brij 35/Triton X-100: Micellar properties, solutes' partitioning from micellar liquid chromatography and modelling with COSMOmic. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2017.10.044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Loureiro DRP, Soares JX, Lopes D, Macedo T, Yordanova D, Jakobtorweihen S, Nunes C, Reis S, Pinto MMM, Afonso CMM. Accessing lipophilicity of drugs with biomimetic models: A comparative study using liposomes and micelles. Eur J Pharm Sci 2018; 115:369-380. [PMID: 29366962 DOI: 10.1016/j.ejps.2018.01.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/12/2018] [Accepted: 01/13/2018] [Indexed: 12/24/2022]
Abstract
Lipophilicity is a physicochemical property of crucial importance in drug discovery and drug design. Biomimetic models, such as liposomes and micelles, constitute a valuable tool for the assessment of lipophilicity through the determination of partition coefficients (log Kp). However, the lack of standardization hampers the judgment about which model or method has the best and broadest passive drug permeation predictive capacity. This work provides a comparative analysis between the methodologies based on biomimetic models to determine the partition coefficient (log Kp). For that purpose, a set of reference substances preconized by the Organization for Economic Cooperation and Development (OECD) guidelines was used. The biomimetic models employed were liposomes and micelles composed by 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) and hexadecylphosphocholine (HePC), respectively. Both lipids were used as representative phospholipids of natural membranes. The partition coefficients between biomimetic models and aqueous phases were determined by derivative spectroscopy at physiological conditions (37 °C and pH 7.4). The partition coefficients obtained using biomimetic models are quite different and more reliable than the ones obtained using an octanol/water system. Comparing the performance of the two biomimetic models, micelles revealed to be suitable only for substances with high molar absorption coefficient and log Kp > 3, but in general liposomes are the best model for accessing lipophilicity of drugs. Furthermore, a comparison between experimental data and the partition coefficients determined by the computational method COSMOmic is also provided and discussed. As a final summarizing result, a decision tree is provided in order to guide the selection of a tool for assessing the lipophilicity of drugs.
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Affiliation(s)
- Daniela R P Loureiro
- Department of Chemical Sciences, Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - José X Soares
- LAQV-REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Daniela Lopes
- LAQV-REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Tiago Macedo
- Department of Chemical Sciences, Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Denitsa Yordanova
- Institute of Thermal Separation Processes, Hamburg University of Technology, Germany
| | - Sven Jakobtorweihen
- Institute of Thermal Separation Processes, Hamburg University of Technology, Germany
| | - Cláudia Nunes
- LAQV-REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Salette Reis
- LAQV-REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Madalena M M Pinto
- Department of Chemical Sciences, Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Porto, Portugal
| | - Carlos M M Afonso
- Department of Chemical Sciences, Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Porto, Portugal.
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28
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Golius A, Gorb L, Isayev O, Leszczynski J. Diffusion of energetic compounds through biological membrane: Application of classical MD and COSMOmic approximations. J Biomol Struct Dyn 2018; 37:247-255. [PMID: 29301457 DOI: 10.1080/07391102.2018.1424037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Computational studies of the potential biological impact of several energetic compounds were performed. The most commonly used explosives were considered in the present studies: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,4-dinitroanisole (DNAN), and 5-Nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO). The effect of such factors as ionic strength and presence of DMSO in the water solution on the structure of the membrane were considered using the POPC lipid bilayer as an example. Molecular dynamics (MD) simulations revealed that, even on a short-time scale, the influence of those additives is noticeable, and therefore those factors should always be taken into account. The MD and the COSMOmic approaches were used to elucidate the ability of the energetic compounds to penetrate the living cell. Calculated free energy profiles and partitioning coefficients revealed distributions of the compounds in the lipid bilayer as well as an overall ability to enter the cell. MD in this case provides a better representation of the free energy profile, while the COSMOmic approach works better to predict log(Klipw) values. The effect of the functional group was observed for the profiles that were obtained using the MD method.
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Affiliation(s)
- Anastasiia Golius
- a Department of Chemistry, Physics and Atmospheric Science , Jackson State University , Jackson , Mississippi , USA
| | - Leonid Gorb
- b Institute of Molecular Biology and Genetics , Kyiv , Ukraine
| | - Olexander Isayev
- c Division of Chemical Biology and Medicinal Chemistry , Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , North Carolina , USA
| | - Jerzy Leszczynski
- a Department of Chemistry, Physics and Atmospheric Science , Jackson State University , Jackson , Mississippi , USA
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29
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Yordanova D, Ritter E, Smirnova I, Jakobtorweihen S. Micellization and Partition Equilibria in Mixed Nonionic/Ionic Micellar Systems: Predictions with Molecular Models. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:12306-12316. [PMID: 28967760 DOI: 10.1021/acs.langmuir.7b02813] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In practical applications, surfactant solutions are mostly used in mixtures of nonionic and ionic surfactants because they have improved characteristics compared to those of single surfactant solutions. By adjusting the composition of the micelles and the pH value, the solubilization of solutes can be enhanced. Nevertheless, the partitioning of solutes between nonionic/ionic mixed micelles and the aqueous phase is studied to a much lesser extent than for single surfactant solutions. Theoretical methods to predict partition equilibria in mixed micelles are of interest for screening studies. For those, the composition of the mixed micelle has to be known. Here we investigate mixtures of TX-114 (Triton X-114), Brij35 (C12E23), SDS (sodium dodecyl sulfate), and CTAB (cetyltrimethylammonium bromide). First, to investigate the surfactant compositions in the micelles, molecular dynamics (MD) self-assembly simulations were applied. Thereafter, the predictive COSMO-RS model, which applies the pseudophase approach, and its extension to anisotropic systems termed COSMOmic were compared for the prediction of partition equilibria in mixed micelles, where various molar ratios of the surfactants were considered. It could be demonstrated that both methods are applicable and lead to reasonable predictions for neutral molecules. However, taking into account the three-dimensional structure of the micelle is beneficial because the calculations with COSMOmic are in better agreement with experimental results. Because the partitioning behavior of ionizable molecules in mixed micelles is of particular interest, the partitioning of ionized isovanillin in mixed Brij35/CTAB micelles at different micelle compositions was calculated with COSMOmic. Using a thermodynamic cycle, the position-dependent pKa of isovanillin within the micelle is calculated on the basis of COSMOmic free energy profiles. As a result, the protolytic equilibrium of isovanillin within the micelles can be taken into account, which is crucial for the reliable prediction of partition coefficients.
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Affiliation(s)
- D Yordanova
- Hamburg University of Technology , Institute of Thermal Separation Processes, Eissendorfer Str. 38, 21073 Hamburg, Germany
| | - E Ritter
- Hamburg University of Technology , Institute of Thermal Separation Processes, Eissendorfer Str. 38, 21073 Hamburg, Germany
| | - I Smirnova
- Hamburg University of Technology , Institute of Thermal Separation Processes, Eissendorfer Str. 38, 21073 Hamburg, Germany
| | - S Jakobtorweihen
- Hamburg University of Technology , Institute of Thermal Separation Processes, Eissendorfer Str. 38, 21073 Hamburg, Germany
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30
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Predicting Critical Micelle Concentrations with Molecular Dynamics Simulations and COSMOmic. CHEM-ING-TECH 2017. [DOI: 10.1002/cite.201700061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Yordanova D, Ritter E, Gerlach T, Jensen JH, Smirnova I, Jakobtorweihen S. Solute Partitioning in Micelles: Combining Molecular Dynamics Simulations, COSMOmic, and Experiments. J Phys Chem B 2017; 121:5794-5809. [DOI: 10.1021/acs.jpcb.7b03147] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- D. Yordanova
- Institute of Thermal Separation
Processes, Hamburg University of Technology, Eissendorfer Strasse 38, 21073 Hamburg, Germany
| | - E. Ritter
- Institute of Thermal Separation
Processes, Hamburg University of Technology, Eissendorfer Strasse 38, 21073 Hamburg, Germany
| | - T. Gerlach
- Institute of Thermal Separation
Processes, Hamburg University of Technology, Eissendorfer Strasse 38, 21073 Hamburg, Germany
| | - J. H. Jensen
- Institute of Thermal Separation
Processes, Hamburg University of Technology, Eissendorfer Strasse 38, 21073 Hamburg, Germany
| | - I. Smirnova
- Institute of Thermal Separation
Processes, Hamburg University of Technology, Eissendorfer Strasse 38, 21073 Hamburg, Germany
| | - S. Jakobtorweihen
- Institute of Thermal Separation
Processes, Hamburg University of Technology, Eissendorfer Strasse 38, 21073 Hamburg, Germany
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32
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Ritter E, Racheva R, Jakobtorweihen S, Smirnova I. Influence of d -glucose as additive on thermodynamics and physical properties of aqueous surfactant two-phase systems for the continuous micellar extraction. Chem Eng Res Des 2017. [DOI: 10.1016/j.cherd.2017.02.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Droge STJ, Hermens JLM, Gutsell S, Rabone J, Hodges G. Predicting the phospholipophilicity of monoprotic positively charged amines. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:307-323. [PMID: 28218330 DOI: 10.1039/c6em00615a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The sorption affinity of eighty-six charged amine structures to phospholipid monolayers (log KIAM) was determined using immobilized artificial membrane high-performance liquid chromatography (IAM-HPLC). The amine compounds covered the most prevalent types of polar groups, widely ranged in structural complexity, and included forty-seven pharmaceuticals, as well as several narcotics and pesticides. Amine type specific corrective increments were used to align log KIAM data with bilayer membrane sorption coefficients (KMW(IAM)). Using predicted sorption affinities of neutral amines, we evaluated the difference (scaling factor ΔMW) with the measured log KMW(IAM) for cationic amines. The ΔMW values were highly variable, ranging from -2.37 to +2.3 log units. For each amine type, polar amines showed lower ΔMW values than hydrocarbon based amines (CxHyN+). COSMOmic software was used to directly calculate the partitioning coefficient of ionic structures into a phospholipid bilayer (KDMPC-W,cation), including quaternary ammonium compounds. The resulting root mean square error (RMSE) between log KDMPC-W,cation and log KMW(IAM) was 0.83 for all eighty-six polar amines, and 0.47 for sixty-eight CxHyN+ amines. The polar amines were then split into five groups depending on polarity and structural complexity, and corrective increments for each group were defined to improve COSMOmic predictions. Excluding only the group with sixteen complex amine structures (≥4 polar groups, Mw > 400, including several macrolide antibiotics), the resulting RMSE for corrected KDMPC-W,cation values improved to 0.45 log units for the remaining set of 138 polar and CxHyN+ amines.
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Affiliation(s)
- S T J Droge
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 104, 3508 TD Utrecht, The Netherlands
| | - J L M Hermens
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 104, 3508 TD Utrecht, The Netherlands
| | - S Gutsell
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, Bedford, UK
| | - J Rabone
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, Bedford, UK
| | - G Hodges
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, Bedford, UK
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Droge STJ, Hermens JLM, Rabone J, Gutsell S, Hodges G. Phospholipophilicity of CxHyN(+) amines: chromatographic descriptors and molecular simulations for understanding partitioning into membranes. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2016; 18:1011-23. [PMID: 27118065 DOI: 10.1039/c6em00118a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Using immobilized artificial membrane high-performance liquid chromatography (IAM-HPLC) the sorption affinity of 70 charged amine structures to phospholipids was determined. The amines contained only 1 charged moiety and no other polar groups, the rest of the molecule being aliphatic and/or aromatic hydrocarbon groups. We systematically evaluated the influence of the amine type (1°, 2°, 3° amines and quaternary ammonium), alkyl chain branching, phenyl ring positioning, charge positioning (terminal vs. central in the molecule) on the phospholipid-water partitioning coefficient (KPLIPW). These experimental results were compared with quantum-chemistry based three-dimensional (3D) molecular simulations of the partitioning of charged amines, including the most likely solute conformers, using a hydrated phospholipid bilayer in the COSMOmic module of COSMOtherm software. Both IAM-HPLC retention data and the simulations suggest that the molecular orientation of charged amines at the location in the bilayer with the lowest calculated Gibbs free energy exerts a strong influence over the partitioning within the membrane. The most favourable position of charged amines coincides with the region where the phosphate anions in the phospholipid bilayer are most abundant. Hydrocarbon units oriented in this layer are located more towards the aqueous phase and contribute less to the overall membrane affinity than hydrocarbon units extending into the more hydrophobic core of the bilayer. COSMOmic simulations explain most of the trends between the structural differences observed in IAM-HPLC based KPLIPW. For this set of cationic structures, the mean absolute difference between COSMOmic simulations and IAM-HPLC data, accounting only for amine type corrective increments, is 0.31 log units.
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Affiliation(s)
- S T J Droge
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 104, 3508 TD Utrecht, The Netherlands.
| | - J L M Hermens
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 104, 3508 TD Utrecht, The Netherlands.
| | - J Rabone
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, Bedford, UK
| | - S Gutsell
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, Bedford, UK
| | - G Hodges
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, Bedford, UK
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35
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Yamin P, Isele-Holder R, Leonhard K. Predicting Octanol/Water Partition Coefficients of Alcohol Ethoxylate Surfactants Using a Combination of Molecular Dynamics and the Conductor-like Screening Model for Realistic Solvents. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.5b04955] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peyman Yamin
- Chair of
Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
| | - Rolf Isele-Holder
- Chair of
Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
| | - Kai Leonhard
- Chair of
Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
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36
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Golius A, Gorb L, Michalkova Scott A, Hill FC, Shukla M, Goins AB, Johnson DR, Leszczynski J. Experimental and computational study of membrane affinity for selected energetic compounds. CHEMOSPHERE 2016; 148:322-327. [PMID: 26820779 DOI: 10.1016/j.chemosphere.2016.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/14/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
The affinity of various energetic compounds for a biological membrane was investigated using experimental and computational techniques. We measured octanol-water (log(Kow)) and liposome-water (log(Klipw)) partition coefficients for the following chemicals: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), 2,4-dinitroanisole (DNAN), 2methoxy-5-nitrophenol (2M5NP), 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrophenol (2,4-DNP). In order to determine log(Klipw) experimentally, we used artificial solid supported lipid liposomes produced under trade mark TRANSIL. Log(Kow) value were predicted with several program packages including the COSMOthermX software. Log(Klipw) were estimated with COSMOmic as implemented in the COSMOthermX program package. In order to verify accuracy of our experimentally obtained results, we performed basic statistical analysis of data taken from the literature. We concluded that compounds considered in this study possess a moderate ability to penetrate into membranes. Comparison of both coefficients has shown that in general, the log(Kow) values are slightly smaller than log(Klipw).
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Affiliation(s)
- Anastasiia Golius
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, USA
| | | | | | - Frances C Hill
- U.S. Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Manoj Shukla
- U.S. Army Engineer Research and Development Center, Vicksburg, MS, USA
| | | | | | - Jerzy Leszczynski
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, USA.
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37
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Bittermann K, Spycher S, Goss KU. Comparison of different models predicting the phospholipid-membrane water partition coefficients of charged compounds. CHEMOSPHERE 2016; 144:382-91. [PMID: 26383265 DOI: 10.1016/j.chemosphere.2015.08.065] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 05/19/2023]
Abstract
A large fraction of commercially used chemicals is ionizable. This results in the need for mechanistic models to describe the physicochemical properties of ions, like the membrane-water partition coefficient (K(mw)), which is related to toxicity and bioaccumulation. In this work we compare 3 different and already existing modelling approaches to describe the liposome-water partition coefficient (K(lipw)) of organic ions, including 36 cations, 56 anions, 2 divalent cations and 2 zwitterions (plus 207 neutral compounds for ensuring model consistency). 1) The empirical correlation with the octanol-water partition coefficient of the corresponding neutral species yielded better results for the prediction of anions (RMSE = 0.79) than for cations (RMSE = 1.14). Though describing most anions reasonably well, the lack of mechanistic basis and the poor performance for cations constrain the usage of this model. 2) The polyparameter linear free energy relationship (pp-LFER) model performs worse (RMSE = 1.26/1.12 for anions/cations). The different physicochemical environments, due to different sorption depths into the membrane of the different species, cannot be described with a single pp-LFER model. 3) COSMOmic is based on quantum chemistry and fluid phase thermodynamics and has the widest applicability domain. It was the only model applicable for multiply charged ions and gave the best results for anions (RMSE = 0.66) and cations (RMSE = 0.71). We expect COSMOmic to contribute to a better estimation of the environmental risk of ionizable emerging pollutants.
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Affiliation(s)
- Kai Bittermann
- UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany.
| | - Simon Spycher
- ELPR Ltd., Litzibuch, CH-8966 Oberwil-Lieli, Switzerland.
| | - Kai-Uwe Goss
- UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; University of Halle-Wittenberg, Institute of Chemistry, Kurt Mothes Str. 2, D-06120 Halle, Germany.
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38
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Genheden S, Essex JW. A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes. J Chem Theory Comput 2015; 11:4749-59. [PMID: 26574264 DOI: 10.1021/acs.jctc.5b00469] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes.
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Affiliation(s)
- Samuel Genheden
- School of Chemistry, University of Southampton, Highfield , SO17 1BJ, Southampton, United Kingdom
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield , SO17 1BJ, Southampton, United Kingdom
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39
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Yordanova D, Smirnova I, Jakobtorweihen S. Molecular Modeling of Triton X Micelles: Force Field Parameters, Self-Assembly, and Partition Equilibria. J Chem Theory Comput 2015; 11:2329-40. [DOI: 10.1021/acs.jctc.5b00026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. Yordanova
- Hamburg University of Technology, Institute
of Thermal Separation Processes, Eissendorfer Strasse 38, 21073 Hamburg, Germany
| | - I. Smirnova
- Hamburg University of Technology, Institute
of Thermal Separation Processes, Eissendorfer Strasse 38, 21073 Hamburg, Germany
| | - S. Jakobtorweihen
- Hamburg University of Technology, Institute
of Thermal Separation Processes, Eissendorfer Strasse 38, 21073 Hamburg, Germany
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40
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Bittermann K, Spycher S, Endo S, Pohler L, Huniar U, Goss KU, Klamt A. Prediction of Phospholipid–Water Partition Coefficients of Ionic Organic Chemicals Using the Mechanistic Model COSMOmic. J Phys Chem B 2014; 118:14833-42. [DOI: 10.1021/jp509348a] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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41
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Paloncýová M, DeVane RH, Murch BP, Berka K, Otyepka M. Rationalization of reduced penetration of drugs through ceramide gel phase membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13942-13948. [PMID: 25354090 DOI: 10.1021/la503289v] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Since computing resources have advanced enough to allow routine molecular simulation studies of drug molecules interacting with biologically relevant membranes, a considerable amount of work has been carried out with fluid phospholipid systems. However, there is very little work in the literature on drug interactions with gel phase lipids. This poses a significant limitation for understanding permeation through the stratum corneum where the primary pathway is expected to be through a highly ordered lipid matrix. To address this point, we analyzed the interactions of p-aminobenzoic acid (PABA) and its ethyl (benzocaine) and butyl (butamben) esters with two membrane bilayers, which differ in their fluidity at ambient conditions. We considered a dioleoylphosphatidylcholine (DOPC) bilayer in a fluid state and a ceramide 2 (CER2, ceramide NS) bilayer in a gel phase. We carried out unbiased (100 ns long) and biased z-constraint molecular dynamics simulations and calculated the free energy profiles of all molecules along the bilayer normal. The free energy profiles converged significantly slower for the gel phase. While the compounds have comparable affinities for both membranes, they exhibit penetration barriers almost 3 times higher in the gel phase CER2 bilayer. This elevated barrier and slower diffusion in the CER2 bilayer, which are caused by the high ordering of CER2 lipid chains, explain the low permeability of the gel phase membranes. We also compared the free energy profiles from MD simulations with those obtained from COSMOmic. This method provided the same trends in behavior for the guest molecules in both bilayers; however, the penetration barriers calculated by COSMOmic did not differ between membranes. In conclusion, we show how membrane fluid properties affect the interaction of drug-like molecules with membranes.
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Affiliation(s)
- Markéta Paloncýová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tř. 17. listopadu 12, 771 46, Olomouc, Czech Republic
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42
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Natesan S, Lukacova V, Peng M, Subramaniam R, Lynch S, Wang Z, Tandlich R, Balaz S. Structure-based prediction of drug distribution across the headgroup and core strata of a phospholipid bilayer using surrogate phases. Mol Pharm 2014; 11:3577-95. [PMID: 25179490 PMCID: PMC4186683 DOI: 10.1021/mp5003366] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Solvation of drugs in the core (C)
and headgroup (H) strata of
phospholipid bilayers affects their physiological transport rates
and accumulation. These characteristics, especially a complete drug
distribution profile across the bilayer strata, are tedious to obtain
experimentally, to the point that even simplified preferred locations
are only available for a few dozen compounds. Recently, we showed
that the partition coefficient (P) values in the
system of hydrated diacetyl phosphatidylcholine (DAcPC) and n-hexadecane (C16), as surrogates of the H- and C-strata
of the bilayer composed of the most abundant mammalian phospholipid,
PC, agree well with the preferred bilayer location of compounds. High P values are typical for lipophiles accumulating in the
core, and low P values are characteristic of cephalophiles
preferring the headgroups. This simple pattern does not hold for most
compounds, which usually have more even distribution and may also
accumulate at the H/C interface. To model complete distribution, the
correlates of solvation energies are needed for each drug state in
the bilayer: (1) for the H-stratum it is the DAcPC/W P value, calculated as the ratio of the C16/W and C16/DAcPC (W for
water) P values; (2) for the C-stratum, the C16/W P value; (3) for the H/C interface, the P values for all plausible molecular poses are characterized using
the fragment DAcPC/W and C16/W solvation parameters for the parts
of the molecule embedded in the H- and C-strata, respectively. The
correlates, each scaled by two Collander coefficients, were used in
a nonlinear, mass-balance based model of intrabilayer distribution,
which was applied to the easily measurable overall P values of compounds in the DMPC (M = myristoyl) bilayers and monolayers
as the dependent variables. The calibrated model for 107 neutral compounds
explains 94% of experimental variance, achieves similar cross-validation
levels, and agrees well with the nontrivial, experimentally determined
bilayer locations for 27 compounds. The resulting structure-based
prediction system for intrabilayer distribution will facilitate more
realistic modeling of passive transport and drug interactions with
those integral membrane proteins, which have the binding sites located
in the bilayer, such as some enzymes, influx and efflux transporters,
and receptors. If only overall bilayer accumulation is of interest,
the 1-octanol/W P values suffice to model the studied
set.
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Affiliation(s)
- Senthil Natesan
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences , Vermont Campus, Colchester, Vermont 05446, United States
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43
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Jakobtorweihen S, Zuniga AC, Ingram T, Gerlach T, Keil FJ, Smirnova I. Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic. J Chem Phys 2014; 141:045102. [DOI: 10.1063/1.4890877] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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44
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Paloncýová M, Fabre G, DeVane RH, Trouillas P, Berka K, Otyepka M. Benchmarking of Force Fields for Molecule–Membrane Interactions. J Chem Theory Comput 2014; 10:4143-51. [DOI: 10.1021/ct500419b] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Markéta Paloncýová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Gabin Fabre
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 Listopadu 12, 771 46 Olomouc, Czech Republic
- LCSN
EA1069, Faculté de Pharmacie, Université de Limoges, 2 Rue de
Docteur Marcland, 87025 Limoges Cedex, France
| | - Russell H. DeVane
- Corporate Modeling and
Simulation, Procter and Gamble, 8611
Beckett Road, West Chester, Ohio 45069, United States
| | - Patrick Trouillas
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 Listopadu 12, 771 46 Olomouc, Czech Republic
- INSERM
UMR-S850, Faculté de Pharmacie, Université de Limoges, 2 Rue du
Docteur Marcland, 87025 Limoges Cedex, France
- Laboratoire
de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, B-7000 Mons, Belgium
| | - Karel Berka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 Listopadu 12, 771 46 Olomouc, Czech Republic
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45
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Storm S, Jakobtorweihen S, Smirnova I. Solubilization in Mixed Micelles Studied by Molecular Dynamics Simulations and COSMOmic. J Phys Chem B 2014; 118:3593-604. [DOI: 10.1021/jp410636w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sandra Storm
- Hamburg University of Technology, Institute of Thermal Separation Processes, 21073 Hamburg, Germany
| | - Sven Jakobtorweihen
- Hamburg University of Technology, Institute of Thermal Separation Processes, 21073 Hamburg, Germany
| | - Irina Smirnova
- Hamburg University of Technology, Institute of Thermal Separation Processes, 21073 Hamburg, Germany
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46
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Paloncýová M, DeVane R, Murch B, Berka K, Otyepka M. Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region. J Phys Chem B 2014; 118:1030-9. [DOI: 10.1021/jp4112052] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Markéta Paloncýová
- Department
of Physical Chemistry, Faculty of Science, Regional Centre
of Advanced Technologies and Materials, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Russell DeVane
- Corporate Modeling & Simulation, Procter & Gamble, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Bruce Murch
- Corporate Modeling & Simulation, Procter & Gamble, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Karel Berka
- Department
of Physical Chemistry, Faculty of Science, Regional Centre
of Advanced Technologies and Materials, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Department
of Physical Chemistry, Faculty of Science, Regional Centre
of Advanced Technologies and Materials, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
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47
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Storm S, Jakobtorweihen S, Smirnova I, Panagiotopoulos AZ. Molecular dynamics simulation of SDS and CTAB micellization and prediction of partition equilibria with COSMOmic. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11582-92. [PMID: 23941607 DOI: 10.1021/la402415b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Molecular dynamics (MD) simulations of the self-assembly of different ionic surfactants have been performed in order to obtain representative micellar structures. Subsequently, these structures were used to predict the partition behavior of various solutes in these micelles with COSMOmic, an extension of COSMO-RS. This paper includes multiple self-assembled micelles of SDS (sodium dodecyl sulfate, anionic surfactant) and CTAB (cetyltrimethylammoniumbromide, cationic surfactant) at different concentrations. Micellar size, density profiles, and shape (eccentricity) have been investigated. However, the size strongly depends on the functional definition of a micelle. For this reason, we present a method based on the free monomer concentration in aqueous solution as an optimization criterion for the micelle definition. The combination of MD with COSMOmic has the benefit of combining detailed atomistic information from MD with fast calculations of COSMOmic. For the first time the influence of micelle structure on pratition equilibria, predicted with COSMOmic, were investigated. In case of SDS more than 4600 and for CTAB more than 800 single micelles have been studied. The predictions of the partition coefficients with COSMOmic are in good agreement with experimental data. Additionally, the most favorable locations of selected molecules in the micelles as well as probable energy barriers are determined even for complex solutes such as toluene, propanolol, ephedrine, acetone, phenol, lidocaine, syringic acid, coumarin, isovanillin, ferulic acid, and vanillic acid. This method can therefore be applied as a potential screening tool for solutes (e.g., drugs) to find the optimal solute-surfactant combination.
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Affiliation(s)
- Sandra Storm
- Institute of Thermal Separation Processes, ‡Institute of Chemical Reaction Engineering, Hamburg University of Technology , D-21073 Hamburg, Germany
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48
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Mehling T, Ingram T, Storm S, Bobe U, Liu F, Michel M, Smirnova I. Estimation of LPC/water partition coefficients using molecular modeling and micellar liquid chromatography. Colloids Surf A Physicochem Eng Asp 2013. [DOI: 10.1016/j.colsurfa.2013.04.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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49
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Ingram T, Storm S, Kloss L, Mehling T, Jakobtorweihen S, Smirnova I. Prediction of micelle/water and liposome/water partition coefficients based on molecular dynamics simulations, COSMO-RS, and COSMOmic. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:3527-37. [PMID: 23398189 DOI: 10.1021/la305035b] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Liposomes and micelles find various applications as potential solubilizers in extraction processes or in drug delivery systems. Thermodynamic and transport processes governing the interactions of different kinds of solutes in liposomes or micelles can be analyzed regarding the free energy profiles of the solutes in the system. However, free energy profiles in heterogeneous systems such as micelles are experimentally almost not accessible. Therefore, the development of predictive methods is desirable. Molecular dynamics (MD) simulations reliably simulate the structure and dynamics of lipid membranes and micelles, whereas COSMO-RS accurately reproduces solvation free energies in different solvents. For the first time, free energy profiles in micellar systems, as well as mixed lipid bilayers, are investigated, taking advantage of both methods: MD simulations and COSMO-RS, referred to as COSMOmic (Klamt, A.; Huniar, U.; Spycher, S.; Keldenich, J. COSMOmic: A Mechanistic Approach to the Calculation of Membrane-Water Partition Coefficients and Internal Distributions within Membranes and Micelles. J. Phys. Chem. B 2008, 112, 12148-12157). All-atom molecular dynamics simulations of the system SDS/water and CTAB/water have been applied in order to retrieve representative micelle structures for further analysis with COSMOmic. For the system CTAB/water, different surfactant concentrations were considered, which results in different micelle sizes. Free energy profiles of more than 200 solutes were predicted and validated by means of experimental partition coefficients. To our knowledge, these are the first quantitative predictions of micelle/water partition coefficients, which are based on whole free energy profiles from molecular methods. Further, the partitioning in lipid bilayer systems containing different hydrophobic tail groups (DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), SOPC (stearoyl-oleoylphosphatidylcholine), DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine), and POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine)) as well as mixed bilayers was calculated. Experimental partition coefficients (log P) were reproduced with a root-mean-square error (RMSE) of 0.62. To determine the influence of cholesterol as an important component of cellular membranes, free energy profiles in the presence of cholesterol were calculated and shown to be in good agreement with experimental data.
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Affiliation(s)
- Thomas Ingram
- Institute of Thermal Separation Processes, Hamburg University of Technology, Eissendorfer Strasse 38, D-21073 Hamburg, Germany.
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