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Bonada M, Pittarello M, De Fazio E, Gans A, Alimonti P, Slika H, Legnani F, Di Meco F, Tyler B. Pediatric Hemispheric High-Grade Gliomas and H3.3-G34 Mutation: A Review of the Literature on Biological Features and New Therapeutic Strategies. Genes (Basel) 2024; 15:1038. [PMID: 39202398 PMCID: PMC11353413 DOI: 10.3390/genes15081038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/25/2024] [Accepted: 08/02/2024] [Indexed: 09/03/2024] Open
Abstract
Pediatric high-grade glioma (pHGG) encompasses a wide range of gliomas with different genomic, epigenomic, and transcriptomic features. Almost 50% of pHGGs present a mutation in genes coding for histone 3, including the subtype harboring the H3.3-G34 mutation. In this context, histone mutations are frequently associated with mutations in TP53 and ATRX, along with PDGFRA and NOTCH2NL amplifications. Moreover, the H3.3-G34 histone mutation induces epigenetic changes in immune-related genes and exerts modulatory functions on the microenvironment. Also, the functionality of the blood-brain barrier (BBB) has an impact on treatment response. The prognosis remains poor with conventional treatments, thus eliciting the investigation of additional and alternative therapies. Promising molecular targets include PDGFRA amplification, BRAF mutation, EGFR amplification, NF1 loss, and IDH mutation. Considering that pHGGs harboring the H3.3-G34R mutation appear to be more susceptible to immunotherapies (ITs), different options have been recently explored, including immune checkpoint inhibitors, antibody mediated IT, and Car-T cells. This review aims to summarize the knowledge concerning cancer biology and cancer-immune cell interaction in this set of pediatric gliomas, with a focus on possible therapeutic options.
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Affiliation(s)
- Marta Bonada
- Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133 Milan, Italy; (M.B.); (F.L.); (F.D.M.)
- Department of Oncology and Hemato-Oncology, University of Milan School of Medicine, Via Rudini 8, 20122 Milan, Italy;
| | - Matilde Pittarello
- Department of Biomedical Sciences, Humanitas University, 20072 Milan, Italy;
| | - Emerson De Fazio
- Department of Medicine, Vita-Salute San Raffaele University School of Medicine, 20132 Milan, Italy;
| | - Alessandro Gans
- Department of Oncology and Hemato-Oncology, University of Milan School of Medicine, Via Rudini 8, 20122 Milan, Italy;
- ASST Ovest Milanese, Neurology and Stroke Unit, Neuroscience Department, 20025 Legnano, Italy
| | - Paolo Alimonti
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02120, USA;
| | - Hasan Slika
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA;
| | - Federico Legnani
- Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133 Milan, Italy; (M.B.); (F.L.); (F.D.M.)
- Department of Oncology and Hemato-Oncology, University of Milan School of Medicine, Via Rudini 8, 20122 Milan, Italy;
| | - Francesco Di Meco
- Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133 Milan, Italy; (M.B.); (F.L.); (F.D.M.)
- Department of Oncology and Hemato-Oncology, University of Milan School of Medicine, Via Rudini 8, 20122 Milan, Italy;
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA;
| | - Betty Tyler
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA;
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Lee S, Poojari CS, Maznichenko A, Roesel D, Swiderska I, Pohl P, Hub JS, Roke S. Dynamic Second Harmonic Imaging of Proton Translocation Through Water Needles in Lipid Membranes. J Am Chem Soc 2024; 146:19818-19827. [PMID: 38991220 PMCID: PMC11273352 DOI: 10.1021/jacs.4c02810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 07/13/2024]
Abstract
Proton translocation through lipid membranes is a fundamental process in the field of biology. Several theoretical models have been developed and presented over the years to explain the phenomenon, yet the exact mechanism is still not well understood. Here, we show that proton translocation is directly related to membrane potential fluctuations. Using high-throughput wide-field second harmonic (SH) microscopy, we report apparently universal transmembrane potential fluctuations in lipid membrane systems. Molecular simulations and free energy calculations suggest that H+ permeation proceeds predominantly across a thin, membrane-spanning water needle and that the transient transmembrane potential drives H+ ions across the water needle. This mechanism differs from the transport of other cations that require completely open pores for transport and follows naturally from the well-known Grotthuss mechanism for proton transport in bulk water. Furthermore, SH imaging and conductivity measurements reveal that the rate of proton transport depends on the structure of the hydrophobic core of bilayer membranes.
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Affiliation(s)
- Seonwoo Lee
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI),
and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Chetan S. Poojari
- Theoretical
Physics and Center for Biophysics, Saarland
University, Saarbrücken 66123, Germany
| | - Anna Maznichenko
- Institute
of Biophysics, Johannes Kepler University
Linz, Gruberstraße 40, Linz 4020, Austria
| | - David Roesel
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI),
and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Iwona Swiderska
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI),
and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Peter Pohl
- Institute
of Biophysics, Johannes Kepler University
Linz, Gruberstraße 40, Linz 4020, Austria
| | - Jochen S. Hub
- Theoretical
Physics and Center for Biophysics, Saarland
University, Saarbrücken 66123, Germany
| | - Sylvie Roke
- Laboratory
for fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI),
and Institute of Materials Science (IMX), School of Engineering (STI),
and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
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3
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Semenov AY, Tikhonov AN. Electrometric and Electron Paramagnetic Resonance Measurements of a Difference in the Transmembrane Electrochemical Potential: Photosynthetic Subcellular Structures and Isolated Pigment-Protein Complexes. MEMBRANES 2023; 13:866. [PMID: 37999352 PMCID: PMC10673362 DOI: 10.3390/membranes13110866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
A transmembrane difference in the electrochemical potentials of protons (ΔμH+) serves as a free energy intermediate in energy-transducing organelles of the living cell. The contributions of two components of the ΔμH+ (electrical, Δψ, and concentrational, ΔpH) to the overall ΔμH+ value depend on the nature and lipid composition of the energy-coupling membrane. In this review, we briefly consider several of the most common instrumental (electrometric and EPR) methods for numerical estimations of Δψ and ΔpH. In particular, the kinetics of the flash-induced electrometrical measurements of Δψ in bacterial chromatophores, isolated bacterial reaction centers, and Photosystems I and II of the oxygenic photosynthesis, as well as the use of pH-sensitive molecular indicators and kinetic data regarding pH-dependent electron transport in chloroplasts, have been reviewed. Further perspectives on the application of these methods to solve some fundamental and practical problems of membrane bioenergetics are discussed.
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Affiliation(s)
- Alexey Yu. Semenov
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia;
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4
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Sargolzaei M, Nikoofard H. Design of prodrug for stereoisomers of omapatrilat to cross the blood-brain barrier using docking, homology modeling, MD, and QM/MM methods. J Biomol Struct Dyn 2023:1-13. [PMID: 37728537 DOI: 10.1080/07391102.2023.2259488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
In this study, we designed a suitable ester prodrug for omapatrilat to penetrate the blood-brain barrier and treat CNS diseases. Based on the ADMET properties, the methyl carboxylate ester of omapatrilat was chosen from among several prodrug structures. Sixteen methyl carboxylate esters were constructed for omapatrilat. The structure of brain carboxylesterase was derived via homology modeling, and molecular docking was used to determine the most potent stereoisomers against brain carboxylesterase. The top three stereoisomer complexes, and the apo form of the protein, were then considered using molecular dynamics simulation and MM/GBSA analysis. Following the simulation, structural analysis was performed using RMSD, RMSF, Rg, and hydrogen bond analysis tools. Our data demonstrated that the prodrug of RSSR is a suitable structure for crossing the blood-brain barrier and binding to brain carboxylesterase. In addition, we found via QM/MM calculation that the catalytic reaction of the prodrug of RSSR against brain carboxylesterase occurs via two steps, including acylation and diacylation steps. Based on our findings, we propose a clinical trial of a methyl carboxylate ester prodrug of omapatrilat's RSSR for the treatment of brain diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohsen Sargolzaei
- Faculty of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Hossein Nikoofard
- Faculty of Chemistry, Shahrood University of Technology, Shahrood, Iran
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5
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Experimental Models of In Vitro Blood-Brain Barrier for CNS Drug Delivery: An Evolutionary Perspective. Int J Mol Sci 2023; 24:ijms24032710. [PMID: 36769032 PMCID: PMC9916529 DOI: 10.3390/ijms24032710] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Central nervous system (CNS) disorders represent one of the leading causes of global health burden. Nonetheless, new therapies approved against these disorders are among the lowest compared to their counterparts. The absence of reliable and efficient in vitro blood-brain barrier (BBB) models resembling in vivo barrier properties stands out as a significant roadblock in developing successful therapy for CNS disorders. Therefore, advancement in the creation of robust and sensitive in vitro BBB models for drug screening might allow us to expedite neurological drug development. This review discusses the major in vitro BBB models developed as of now for exploring the barrier properties of the cerebral vasculature. Our main focus is describing existing in vitro models, including the 2D transwell models covering both single-layer and co-culture models, 3D organoid models, and microfluidic models with their construction, permeability measurement, applications, and limitations. Although microfluidic models are better at recapitulating the in vivo properties of BBB than other models, significant gaps still exist for their use in predicting the performance of neurotherapeutics. However, this comprehensive account of in vitro BBB models can be useful for researchers to create improved models in the future.
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6
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Williams-Noonan BJ, Speer MN, Le TC, Sadek MM, Thompson PE, Norton RS, Yuriev E, Barlow N, Chalmers DK, Yarovsky I. Membrane Permeating Macrocycles: Design Guidelines from Machine Learning. J Chem Inf Model 2022; 62:4605-4619. [PMID: 36178379 DOI: 10.1021/acs.jcim.2c00809] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellular targets or be developed as orally bioavailable drugs. Here, we describe a random forest (RF) machine learning model for the prediction of passive membrane permeation rates developed using a set of over 1000 bRo5 macrocyclic compounds. The model is based on easily calculated chemical features/descriptors as independent variables. Our random forest (RF) model substantially outperforms a multiple linear regression model based on the same features and achieves better performance metrics than previously reported models using the same underlying data. These features include: (1) polar surface area in water, (2) the octanol-water partitioning coefficient, (3) the number of hydrogen-bond donors, (4) the sum of the topological distances between nitrogen atoms, (5) the sum of the topological distances between nitrogen and oxygen atoms, and (6) the multiple molecular path count of order 2. The last three features represent molecular flexibility, the ability of the molecule to adopt different conformations in the aqueous and membrane interior phases, and the molecular "chameleonicity." Guided by the model, we propose design guidelines for membrane-permeating macrocycles. It is anticipated that this model will be useful in guiding the design of large, bioactive molecules for medicinal chemistry and chemical biology applications.
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Affiliation(s)
- Billy J Williams-Noonan
- School of Engineering, RMIT University, Melbourne3001, Australia.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Melissa N Speer
- University of Melbourne, Faculty of Engineering and Information Technology, Carlton3053, Australia
| | - Tu C Le
- School of Engineering, RMIT University, Melbourne3001, Australia
| | - Maiada M Sadek
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia.,ARC Centre for Fragment-Based Design, Monash University, Parkville, 3052, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne3001, Australia
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7
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Seneviratne R, Catania R, Rappolt M, Jeuken LJC, Beales PA. Membrane mixing and dynamics in hybrid POPC/poly(1,2-butadiene- block-ethylene oxide) (PBd- b-PEO) lipid/block co-polymer giant vesicles. SOFT MATTER 2022; 18:1294-1301. [PMID: 35048939 DOI: 10.1039/d1sm01591e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lipids and block copolymers can individually self-assemble into vesicles, each with their own particular benefits and limitations. Combining polymers with lipids allows for further optimisation of the vesicle membranes for bionanotechnology applications. Here, POPC lipid is mixed with poly(1,2-butadiene-block-ethylene oxide) of two different molecular weights (PBd22-PEO14, Mr = 1800 g mol-1 and PBd12-PEO11, Mr = 1150 g mol-1) in order to investigate how increasing the polymer fraction affects membrane mixing, hydration and fluidity. Intensity contributions of fluorescently labelled lipid and polymer within mixed GUV membranes confirm membrane homogeneity within the hybrids. General polarisation measurements of Laurdan in GUVs showed little change in membrane hydration as polymer fraction is increased, which suggests good structural compatibility between lipids and polymers that gives rise to well-mixed vesicles. Membrane fluidity in hybrid GUVs was found to decrease non-linearly with increasing polymer fraction. However, the diffusion coefficients for the fluorescent polymer in hybrid membranes did not change significantly with increasing polymer content. While increasing the polymer fraction does reduce the movement of lipids through a polymer-rich matrix, insignificant difference in diffusion coefficients of the polymer suggests that its diffusion is minimally affected by increasing lipid composition in the range studied. These results lay further foundations for the wider development of hybrid vesicles with controlled properties for advanced biotechnologies.
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Affiliation(s)
- Rashmi Seneviratne
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Rosa Catania
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael Rappolt
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK
| | - Lars J C Jeuken
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul A Beales
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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8
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Guntner AS, Bögl T, Mlynek F, Buchberger W. Large-Scale Evaluation of Collision Cross Sections to Investigate Blood-Brain Barrier Permeation of Drugs. Pharmaceutics 2021; 13:pharmaceutics13122141. [PMID: 34959422 PMCID: PMC8703848 DOI: 10.3390/pharmaceutics13122141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Successful drug administration to the central nervous system requires accurate adjustment of the drugs’ molecular properties. Therefore, structure-derived descriptors of potential brain therapeutic agents are essential for an early evaluation of pharmacokinetics during drug development. The collision cross section (CCS) of molecules was recently introduced as a novel measurable parameter to describe blood-brain barrier (BBB) permeation. This descriptor combines molecular information about mass, structure, volume, branching and flexibility. As these chemical properties are known to influence cerebral pharmacokinetics, CCS determination of new drug candidates may provide important additional spatial information to support existing models of BBB penetration of drugs. Besides measuring CCS, calculation is also possible; but however, the reliability of computed CCS values for an evaluation of BBB permeation has not yet been fully investigated. In this work, prediction tools based on machine learning were used to compute CCS values of a large number of compounds listed in drug libraries as negative or positive with respect to brain penetration (BBB+ and BBB− compounds). Statistical evaluation of computed CCS and several other descriptors could prove the high value of CCS. Further, CCS-deduced maximum molecular size of BBB+ drugs matched the dimensions of BBB pores. A threshold for transcellular penetration and possible permeation through pore-like openings of cellular tight-junctions is suggested. In sum, CCS evaluation with modern in silico tools shows high potential for its use in the drug development process.
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Affiliation(s)
- Armin Sebastian Guntner
- Institute of Analytical and General Chemistry, Johannes Kepler University, 4040 Linz, Austria
| | - Thomas Bögl
- Institute of Analytical and General Chemistry, Johannes Kepler University, 4040 Linz, Austria
| | - Franz Mlynek
- Institute of Analytical and General Chemistry, Johannes Kepler University, 4040 Linz, Austria
| | - Wolfgang Buchberger
- Institute of Analytical and General Chemistry, Johannes Kepler University, 4040 Linz, Austria
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9
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The Effect of the Osmotically Active Compound Concentration Difference on the Passive Water and Proton Fluxes across a Lipid Bilayer. Int J Mol Sci 2021; 22:ijms222011099. [PMID: 34681757 PMCID: PMC8540289 DOI: 10.3390/ijms222011099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
The molecular details of the passive water flux across the hydrophobic membrane interior are still a matter of debate. One of the postulated mechanisms is the spontaneous, water-filled pore opening, which facilitates the hydrophilic connection between aqueous phases separated by the membrane. In the paper, we provide experimental evidence showing that the spontaneous lipid pore formation correlates with the membrane mechanics; hence, it depends on the composition of the lipid bilayer and the concentration of the osmotically active compound. Using liposomes as an experimental membrane model, osmotically induced water efflux was measured with the stopped-flow technique. Shapes of kinetic curves obtained at low osmotic pressure differences are interpreted in terms of two events: the lipid pore opening and water flow across the aqueous channel. The biological significance of the dependence of the lipid pore formation on the concentration difference of an osmotically active compound was illustrated by the demonstration that osmotically driven water flow can be accompanied by the dissipation of the pH gradient. The application of the Helfrich model to describe the probability of lipid pore opening was validated by demonstrating that the probability of pore opening correlates with the membrane bending rigidity. The correlation was determined by experimentally derived bending rigidity coefficients and probabilities of lipid pores opening.
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10
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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11
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Zhang Y, Haider K, Kaur D, Ngo VA, Cai X, Mao J, Khaniya U, Zhu X, Noskov S, Lazaridis T, Gunner MR. Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.
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Affiliation(s)
- Yingying Zhang
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Kamran Haider
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Van A. Ngo
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Xiuhong Cai
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Junjun Mao
- Levich Institute, School of Engineering, City College of New York, City University of New York, New York, NY 10031, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Xuyu Zhu
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Sergei Noskov
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, Calgary, AB, Canada
| | - Themis Lazaridis
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
- Department of Chemistry, City College of New York, City University of New York, New York, NY 10031, USA
| | - M. R. Gunner
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
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12
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Choudhari M, Hejmady S, Narayan Saha R, Damle S, Singhvi G, Alexander A, Kesharwani P, Kumar Dubey S. Evolving new-age strategies to transport therapeutics across the blood-brain-barrier. Int J Pharm 2021; 599:120351. [PMID: 33545286 DOI: 10.1016/j.ijpharm.2021.120351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/24/2021] [Accepted: 01/30/2021] [Indexed: 12/25/2022]
Abstract
A basic understanding of the blood-brain barrier (BBB) is essential for the novel advancements in targeting drugs specific to the brain. Neoplasm compromising the internal structure of BBB that results in impaired vasculature is called as blood tumor barrier (BTB). Besides, the BBB serves as a chief hindrance to the passage of a drug into the brain parenchyma. The small and hydrophilic drugs majorly display an absence of desired molecular characteristics required to cross the BBB. Furthermore, all classes of biologics have failed in the clinical trials of brain diseases over the past years since these biologics are large molecules that do not cross the BBB. Also, new strategies have been discovered that use the Trojan horse technology with the re-engineered biologics for BBB transport. Thus, this review delivers information about the different grades of tumors (I-IV) i.e. examples of BBB/BTB heterogenicity along with the different mechanisms for transporting the therapeutics into the brain tumors by crossing BBB. This review also provides insights into the emerging approaches of peptide delivery and the non-invasive and brain-specific molecular Trojan horse targeting technologies. Also, the several challenges in the clinical development of BBB penetrating IgG fusion protein have been discussed.
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Affiliation(s)
- Manisha Choudhari
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Pilani Campus, Rajasthan 333031, India
| | - Siddhanth Hejmady
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Pilani Campus, Rajasthan 333031, India
| | - Ranendra Narayan Saha
- Birla Institute of Technology and Science, Pilani, Dubai Campus, United Arab Emirates
| | - Shantanu Damle
- Colorcon Asia Pvt. Ltd., Verna Industrial Estate, Verna 403722, Goa, India
| | - Gautam Singhvi
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Pilani Campus, Rajasthan 333031, India
| | - Amit Alexander
- National Institute of Pharmaceutical Education and Research (NIPER GUWAHATI), Department of Pharmaceutical Technology (Formulations), Department of Pharmaceuticals, Ministry of Chemical and Fertilizers, Government of India, Sila Village, Nizsundarighopa, Changsari, Kamrup (R), Guwahati, Assam 781101, India
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Sunil Kumar Dubey
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, Pilani Campus, Rajasthan 333031, India; R&D Healthcare Division Emami Ltd., 13, BT Road, Belgharia, Kolkata 700056, India.
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13
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Kadry H, Noorani B, Cucullo L. A blood-brain barrier overview on structure, function, impairment, and biomarkers of integrity. Fluids Barriers CNS 2020; 17:69. [PMID: 33208141 PMCID: PMC7672931 DOI: 10.1186/s12987-020-00230-3] [Citation(s) in RCA: 664] [Impact Index Per Article: 166.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/07/2020] [Indexed: 02/07/2023] Open
Abstract
The blood–brain barrier is playing a critical role in controlling the influx and efflux of biological substances essential for the brain’s metabolic activity as well as neuronal function. Thus, the functional and structural integrity of the BBB is pivotal to maintain the homeostasis of the brain microenvironment. The different cells and structures contributing to developing this barrier are summarized along with the different functions that BBB plays at the brain–blood interface. We also explained the role of shear stress in maintaining BBB integrity. Furthermore, we elaborated on the clinical aspects that correlate between BBB disruption and different neurological and pathological conditions. Finally, we discussed several biomarkers that can help to assess the BBB permeability and integrity in-vitro or in-vivo and briefly explain their advantages and disadvantages.
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Affiliation(s)
- Hossam Kadry
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, 1300 S. Coulter Street, Amarillo, TX, 79106, USA
| | - Behnam Noorani
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, 1300 S. Coulter Street, Amarillo, TX, 79106, USA
| | - Luca Cucullo
- Dept. of Foundational Medical Studies, Oakland University William Beaumont School of Medicine, Office 415, Rochester, MI, 48309, USA.
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14
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Guan X, Wei DQ, Hu D. Free Energy Calculations on the Water-Chain-Assisted and the Dehydration Mechanisms of Transmembrane Ion Permeation. J Chem Theory Comput 2019; 16:700-710. [DOI: 10.1021/acs.jctc.9b00671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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Marzuoli I, Margreitter C, Fraternali F. Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description. J Chem Theory Comput 2019; 15:5175-5193. [PMID: 31433640 PMCID: PMC7377650 DOI: 10.1021/acs.jctc.9b00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Membranes
are a crucial component of both bacterial and mammalian
cells, being involved in signaling, transport, and compartmentalization.
This versatility requires a variety of lipid species to tailor the
membrane’s behavior as needed, increasing the complexity of
the system. Molecular dynamics simulations have been successfully
applied to study model membranes and their interactions with proteins,
elucidating some crucial mechanisms at the atomistic detail and thus
complementing experimental techniques. An accurate description of
the functional interplay of the diverse membrane components crucially
depends on the selected parameters that define the adopted force field.
A coherent parameterization for lipids and proteins is therefore needed.
In this work, we propose and validate new lipid head group parameters
for the GROMOS 54A8 force field, making use of recently published
parametrizations for key chemical moieties present in lipids. We make
use additionally of a new canonical set of partial charges for lipids,
chosen to be consistent with the parameterization of soluble molecules
such as proteins. We test the derived parameters on five phosphocholine
model bilayers, composed of lipid patches four times larger than the
ones used in previous studies, and run 500 ns long simulations of
each system. Reproduction of experimental data like area per lipid
and deuterium order parameters is good and comparable with previous
parameterizations, as well as the description of liquid crystal to
gel-phase transition. On the other hand, the orientational behavior
of the head groups is more realistic for this new parameter set, and
this can be crucial in the description of interactions with other
polar molecules. For that reason, we tested the interaction of the
antimicrobial peptide lactoferricin with two model membranes showing
that the new parameters lead to a weaker peptide–membrane binding
and give a more realistic outcome in comparing binding to antimicrobial
versus mammal membranes.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Christian Margreitter
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
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16
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Zhang Z, Lu C, Wang P, Li A, Zhang H, Xu S. Structural Basis and Mechanism for Vindoline Dimers Interacting with α,β-Tubulin. ACS OMEGA 2019; 4:11938-11948. [PMID: 31460305 PMCID: PMC6682054 DOI: 10.1021/acsomega.9b00947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Vinblastine and its derivatives used in clinics as antitumor drugs often cause drug resistance and some serious side effects; thus, it is necessary to study new vinblastine analogues with strong anticancer cytotoxicity and low toxicity. We designed a dimer molecule using two vindoline-bonded dimer vindoline (DVB) and studied its interaction with α,β-tubulin through the double-sided adhesive mechanism to explore its anticancer cytotoxicity. In our work, DVB was docked into the interface between α-tubulin and β-tubulin to construct a complex protein structure, and then it was simulated for 100 ns using the molecular dynamics technology to become a stable and refined complex protein structure. Based on such a refined structure, the quantum chemistry at the level of the MP2/6-31G(d,p) method was used to calculate the binding energies for DVB interacting with respective residues. By the obtained binding energies, the active site residues for interaction with DVB were found. Up to 20 active sites of residues within α,β-tubulin interacting with DVB are labeled in β-Asp179, β-Glu207, β-Tyr210, β-Asp211, β-Phe214, β-Pro222, β-Tyr224, and β-Leu227 and α-Asn249, α-Arg308, α-Lys326, α-Asn329, α-Ala333, α-Thr334, α-Lys336, α-Lys338, α-Arg339, α-Ser340, α-Thr349, and α-Phe351. The total binding energy between DVB and α,β-tubulin is about -251.0 kJ·mol-1. The sampling average force potential (PMF) method was further used to study the dissociation free energy (ΔG) along the separation trajectory of α,β-tubulin under the presence of DVB based on the refined structure of DVB with α,β-tubulin. Because of the presence of DVB within the interface between α- and β-tubulin, ΔG is 252.3 kJ·mol-1. In contrast to the absence of DVB, the separation of pure β-tubulin needs a free energy of 196.9 kJ·mol-1. The data show that the presence of DVB adds more 55.4 kJ·mol-1 of ΔG to hinder the normal separation of α,β-tubulin. Compared to vinblastine existing, the free energy required for the separation of α,β-tubulin is 220.5 kJ·mol-1. Vinblastine and DVB can both be considered through the same double-sided adhesive mechanism to give anticancer cytotoxicity. Because of the presence of DVB, a larger free energy is needed for the separation of α,β-tubulin, which suggests that DVB should have stronger anticancer cytotoxicity than vinblastine and shows that DVB has a broad application prospect.
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Affiliation(s)
- Zhengqiong Zhang
- College
of Chemical Science and Technology and Pharmacy, Key Laboratory of
Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University, Kunming 650091, China
| | - Chengqi Lu
- College
of Chemical Science and Technology and Pharmacy, Key Laboratory of
Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University, Kunming 650091, China
| | - Pei Wang
- College
of Chemical Science and Technology and Pharmacy, Key Laboratory of
Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University, Kunming 650091, China
| | - Aijing Li
- College
of Chemical Science and Technology and Pharmacy, Key Laboratory of
Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University, Kunming 650091, China
| | - Hongbo Zhang
- College
of Mathematics, Yunnan Normal University, Kunming 650500, China
| | - Sichuan Xu
- College
of Chemical Science and Technology and Pharmacy, Key Laboratory of
Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University, Kunming 650091, China
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17
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Abstract
This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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18
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Abstract
Spontaneous solute and solvent permeation through membranes is of vital importance to human life, be it gas exchange in red blood cells, metabolite excretion, drug/toxin uptake, or water homeostasis. Knowledge of the underlying molecular mechanisms is the sine qua non of every functional assignment to membrane transporters. The basis of our current solubility diffusion model was laid by Meyer and Overton. It correlates the solubility of a substance in an organic phase with its membrane permeability. Since then, a wide range of studies challenging this rule have appeared. Commonly, the discrepancies have their origin in ill-used measurement approaches, as we demonstrate on the example of membrane CO2 transport. On the basis of the insight that scanning electrochemical microscopy offered into solute concentration distributions in immediate membrane vicinity of planar membranes, we analyzed the interplay between chemical reactions and diffusion for solvent transport, weak acid permeation, and enzymatic reactions adjacent to membranes. We conclude that buffer reactions must also be considered in spectroscopic investigations of weak acid transport in vesicular suspensions. The evaluation of energetic contributions to membrane translocation of charged species demonstrates the compatibility of the resulting membrane current with the solubility diffusion model. A local partition coefficient that depends on membrane penetration depth governs spontaneous membrane translocation of both charged and uncharged molecules. It is determined not only by the solubility in an organic phase but also by other factors like cholesterol concentration and intrinsic electric membrane potentials.
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Affiliation(s)
- Christof Hannesschlaeger
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
| | - Andreas Horner
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
| | - Peter Pohl
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
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19
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Proton leakage across lipid bilayers: Oxygen atoms of phospholipid ester linkers align water molecules into transmembrane water wires. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:439-451. [PMID: 30904457 DOI: 10.1016/j.bbabio.2019.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/20/2019] [Accepted: 03/10/2019] [Indexed: 12/31/2022]
Abstract
Up to half of the cellular energy gets lost owing to membrane proton leakage. The permeability of lipid bilayers to protons is by several orders of magnitude higher than to other cations, which implies efficient proton-specific passages. The nature of these passages remains obscure. By combining experimental measurements of proton flow across phosphatidylcholine vesicles, steered molecular dynamics (MD) simulations of phosphatidylcholine bilayers and kinetic modelling, we have analyzed whether protons could pass between opposite phospholipid molecules when they sporadically converge. The MD simulations showed that each time, when the phosphorus atoms of the two phosphatidylcholine molecules got closer than 1.6 nm, the eight oxygen atoms of their ester linkages could form a transmembrane 'oxygen passage' along which several water molecules aligned into a water wire. Proton permeability along such water wires would be limited by rearrangement of oxygen atoms, which could explain the experimentally shown independence of the proton permeability of pH, H2O/D2O substitution, and membrane dipole potential. We suggest that protons can cross lipid bilayers by moving along short, self-sustaining water wires supported by oxygen atoms of lipid ester linkages.
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20
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Zhou X, Xu Z, Li A, Zhang Z, Xu S. Double-sides sticking mechanism of vinblastine interacting with α,β-tubulin to get activity against cancer cells. J Biomol Struct Dyn 2018; 37:4080-4091. [PMID: 30451089 DOI: 10.1080/07391102.2018.1539412] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Vinblastine (VLB) and its derivatives have been used for clinical first-line drugs to treat various cancers. Due to the resistance and serious side effects from using VLB and its derivatives, there is a need to discover and develop novel VLB derivatives with high activity against cancer cells. In order to better discover and develop new VLB derivatives, we need to study the structural basis of VLB's anti-cancer cytotoxicity and the mechanism of its interaction with α,β-tubulins. Based on the crystal structure of α,β-microtubule complex protein, the molecular dynamics method including the sampling PMF method was used to study the variation of dissociation free energy (ΔG) of α,β-tubulins under different system conditions, and then from which to study the mechanism of the interaction between VLB and α,β-tubulins. The obtained results show that the dissociation of pure α,β-tubulins requires 197.8 kJ·mol-1 for ΔG. When the VLB molecule exists between the interface of α,β-tubulins, the dissociation ΔG of α,β-tubulins reaches 220.5 kJ·mol-1, which is greater than that of pure α,β-tubulin. The VLB molecule is formed by connecting a vindoline moiety (VM) molecule with a catharanthine moiety (CM) molecule through a carbon-carbon bond, which is a larger molecule. When the CM molecule exists in the middle of α,β-tubulin interface, the dissociation ΔG of α,β-tubulins is 46.2 kJ·mol-1, during which the CM moves with β-tubulin. When the VM molecule exists between the middle of α,β-tubulin interface, the dissociation ΔG of α,β-tubulins is 86.7 kJ·mol-1, during which it moves with α-tubulin. Therefore, the VLB molecule is like a double-sides tape to stick α-tubulin and β-tubulin together. The VLB molecule intervenes the dynamic equilibrium between dissociation and aggregation of α-tubulin and β-tubulin by a double-sides sticking mechanism to exert high activity with toxicity against cancer cell. Besides, our results demonstrate that VLB has its structural basis for anticancer cytotoxicity due to its two compositions composed of a CM molecule and a VM molecule although they have little toxicity against cancer cell alone.
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Affiliation(s)
- Xiaowen Zhou
- a 1 College of Chemical Science and Technology and Pharmacy, Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University , Kunming , P. R. China
| | - Zeren Xu
- a 1 College of Chemical Science and Technology and Pharmacy, Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University , Kunming , P. R. China
| | - Aijing Li
- a 1 College of Chemical Science and Technology and Pharmacy, Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University , Kunming , P. R. China
| | - Zhengqiong Zhang
- a 1 College of Chemical Science and Technology and Pharmacy, Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University , Kunming , P. R. China
| | - Sichuan Xu
- a 1 College of Chemical Science and Technology and Pharmacy, Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University , Kunming , P. R. China
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21
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Moss FR, Shuken SR, Mercer JAM, Cohen CM, Weiss TM, Boxer SG, Burns NZ. Ladderane phospholipids form a densely packed membrane with normal hydrazine and anomalously low proton/hydroxide permeability. Proc Natl Acad Sci U S A 2018; 115:9098-9103. [PMID: 30150407 PMCID: PMC6140541 DOI: 10.1073/pnas.1810706115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ladderane lipids are unique to anaerobic ammonium-oxidizing (anammox) bacteria and are enriched in the membrane of the anammoxosome, an organelle thought to compartmentalize the anammox process, which involves the toxic intermediate hydrazine (N2H4). Due to the slow growth rate of anammox bacteria and difficulty of isolating pure ladderane lipids, experimental evidence of the biological function of ladderanes is lacking. We have synthesized two natural and one unnatural ladderane phosphatidylcholine lipids and compared their thermotropic properties in self-assembled bilayers to distinguish between [3]- and [5]-ladderane function. We developed a hydrazine transmembrane diffusion assay using a water-soluble derivative of a hydrazine sensor and determined that ladderane membranes are as permeable to hydrazine as straight-chain lipid bilayers. However, pH equilibration across ladderane membranes occurs 5-10 times more slowly than across straight-chain lipid membranes. Langmuir monolayer analysis and the rates of fluorescence recovery after photobleaching suggest that dense ladderane packing may preclude formation of proton/hydroxide-conducting water wires. These data support the hypothesis that ladderanes prevent the breakdown of the proton motive force rather than blocking hydrazine transmembrane diffusion in anammox bacteria.
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Affiliation(s)
- Frank R Moss
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Steven R Shuken
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jaron A M Mercer
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Carolyn M Cohen
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, Stanford University, Menlo Park, CA 94025
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305;
| | - Noah Z Burns
- Department of Chemistry, Stanford University, Stanford, CA 94305;
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22
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A reconstitution method for integral membrane proteins in hybrid lipid-polymer vesicles for enhanced functional durability. Methods 2018; 147:142-149. [PMID: 29410153 DOI: 10.1016/j.ymeth.2018.01.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 11/22/2022] Open
Abstract
Hybrid vesicles composed of lipids and block copolymers hold promise for increasing liposome stability and providing a stable environment for membrane proteins. Recently we reported the successful functional reconstitution of the integral membrane protein cytochrome bo3 (ubiquinol oxidase) into hybrid vesicles composed of a blend of phospholipids and a block copolymer (PBd-PEO). We demonstrated that these novel membrane environments stabilise the enzymes' activity, prolonging their functional lifetime [Chem. Commun. 52 (2016) 11020-11023]. This approach holds great promise for applications of membrane proteins where enhanced durability, stability and shelf-life will be essential to creating a viable technology. Here we present a detailed account of our methods for membrane protein reconstitution into hybrid vesicles and discuss tips and challenges when using block copolymers compared to pure phospholipid systems that are more common materials for this purpose. We also extend the characterisation of these hybrid vesicles beyond what we have previously reported and show: (i) hybrid membranes are less permeable to protons than phospholipid bilayers; (ii) extended enzyme activity data is presented over a period of 500 days, which fully reveals the truly remarkable enhancement in functional lifetime that hybrid vesicles facilitate.
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23
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Deplazes E, Poger D, Cornell B, Cranfield CG. The effect of hydronium ions on the structure of phospholipid membranes. Phys Chem Chem Phys 2018; 20:357-366. [DOI: 10.1039/c7cp06776c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This work studies the mechanisms by which hydronium ions modulate the structure of phospholipid bilayers.
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Affiliation(s)
- Evelyne Deplazes
- School of Biomedical Sciences
- Curtin Health Innovation Research Institute and Curtin Institute for Computation
- Curtin University
- Perth
- Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
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24
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Li AJ, Xie W, Wang M, Xu SC. Molecular Mechanism and Dynamics of S-Deoxyephedrine Moving through Molecular Channels within D 3R. ACS OMEGA 2017; 2:8896-8910. [PMID: 31457418 PMCID: PMC6645573 DOI: 10.1021/acsomega.7b01161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/17/2017] [Indexed: 06/10/2023]
Abstract
In this article, the trajectories of S-deoxyephedrine (SBD) along molecular channels within the complex protein structure of third dopamine receptor (D3R) are analyzed via molecular dynamic techniques, including potential mean force calculations of umbrella samplings from the 4.5 version of the GROMACS program. Changes in free energy due to the movement of SBD within D3R are determined, and the molecular dynamic mechanisms of SBD transmitting along molecular channels are probed. Molecular simulated results show that the change in free energy is calculated as 171.7 kJ·mol-1 for the transmission of SBD toward the outside of the cell along the y+ axis functional molecular channel and is 275.0 kJ·mol-1 for movement toward the intracellular structure along the y- axis. Within the internal structure of D3R, the changes in free energy are determined to be 103.6, 242.1, 459.7, and 127.8 kJ·mol-1 for transmission of SBD along the x+, x-, z+, and z- axes, respectively, toward the cell bilayer membrane, which indicates that SBD leaves much more easily along the x+ axis through the gap between the TM5 (the fifth transmembrane helix) and TM6 (the sixth transmembrane helix) from the internal structure of D3R. The values of free-energy changes indicate that SBD molecules can clear the protective channel within D3R, which helps dopamine molecules to leave the D3R internal structure along the x+ axis and to prevent them for exerting excessive neurotransmitter function. Therefore, our results suggest that SBD is effective for development as a drug for treating schizophrenia and its pharmacology is closely related to its dynamics and mechanisms within the molecular pathway of dopamine receptors.
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Affiliation(s)
- Ai Jing Li
- College
of Chemical Science and Technology and Pharmacy and Key Laboratory
of Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University, Kunming 650091, P. R.
China
| | - Wei Xie
- College
of Chemical Science and Technology and Pharmacy and Key Laboratory
of Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University, Kunming 650091, P. R.
China
| | - Ming Wang
- College
of Chemical Science and Technology and Pharmacy and Key Laboratory
of Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University, Kunming 650091, P. R.
China
| | - Si Chuan Xu
- College
of Chemical Science and Technology and Pharmacy and Key Laboratory
of Education Ministry for Medicinal Chemistry of Natural Resource, Yunnan University, Kunming 650091, P. R.
China
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25
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Zeng Z, Shen ZL, Zhai S, Xu JL, Liang H, Shen Q, Li QY. Transport of curcumin derivatives in Caco-2 cell monolayers. Eur J Pharm Biopharm 2017; 117:123-131. [DOI: 10.1016/j.ejpb.2017.04.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 03/11/2017] [Accepted: 04/06/2017] [Indexed: 01/18/2023]
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26
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Gonzalez MA, Barriga HMG, Richens JL, Law RV, O'Shea P, Bresme F. How does ytterbium chloride interact with DMPC bilayers? A computational and experimental study. Phys Chem Chem Phys 2017; 19:9199-9209. [DOI: 10.1039/c7cp01400g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lanthanide salts have been studied for many years, primarily in Nuclear Magnetic Resonance (NMR) experiments of mixed lipid–protein systems and more recently to study lipid flip-flop in model membrane systems.
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Affiliation(s)
| | | | | | - Robert V. Law
- Department of Chemistry
- Imperial College London
- London
- UK
| | - Paul O'Shea
- Department of Chemistry
- Imperial College London
- London
- UK
- School of Life Sciences
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27
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Strbak O, Kanuchova Z, Krafcik A. Proton Gradients as a Key Physical Factor in the Evolution of the Forced Transport Mechanism Across the Lipid Membrane. ORIGINS LIFE EVOL B 2016; 46:523-531. [PMID: 27038470 DOI: 10.1007/s11084-016-9496-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/15/2015] [Indexed: 12/29/2022]
Abstract
A critical phase in the transition from prebiotic chemistry to biological evolution was apparently an asymmetric ion flow across the lipid membrane. Due to imbalance in the ion flow, the early lipid vesicles could selectively take the necessary molecules from the environment, and release the side-products from the vesicle. Natural proton gradients played a definitively crucial role in this process, since they remain the basis of energy transfer in the present-day cells. On the basis of this supposition, and the premise of the early vesicle membrane's impermeability to protons, we have shown that the emergence of the proton gradient in the lipid vesicle could be a key physical factor in the evolution of the forced transport mechanism (pore formation and active transport) across the lipid bilayer. This driven flow of protons across the membrane is the result of the electrochemical proton gradient and osmotic pressures on the integrity of the lipid vesicle. At a critical number of new lipid molecules incorporated into the vesicle, the energies associated with the creation of the proton gradient exceed the bending stiffness of the lipid membrane, and overlap the free energy of the lipid bilayer pore formation.
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Affiliation(s)
- Oliver Strbak
- Department of Imaging Methods, Institute of Measurement Science, Slovak Academy of Sciences, Dubravska cesta 9, 841 04, Bratislava, Slovakia.
| | - Zuzana Kanuchova
- Astronomical Institute, Slovak Academy of Sciences, 059 60, Tatranska Lomnica, Slovakia
| | - Andrej Krafcik
- Department of Imaging Methods, Institute of Measurement Science, Slovak Academy of Sciences, Dubravska cesta 9, 841 04, Bratislava, Slovakia
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Xie W, Wang M, Li A, Xu SC. Molecular dynamics simulation of d-Benzedrine transmitting through molecular channels within D 3R. J Biomol Struct Dyn 2016; 35:1672-1684. [PMID: 27191827 DOI: 10.1080/07391102.2016.1190947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dex-Benzedrine (known as d-Benzedrine or SAT) acts in dopamine receptors of central nerve cell system. In clinic, SAT is used to treat a variety of diseases; meanwhile, it has dependence and addiction. In order to investigate the pharmacology and addiction mechanisms of SAT as a medicine, in this paper, we have studied the structure of D3R complex protein with SAT, and based on which, using potential mean force with umbrella samplings and the simulated phospholipid bilayer membrane (or POPC bilayer membrane), the molecular dynamics simulation was performed to obtain free energy changes upon the trajectories for SAT moving along the molecular channels within D3R. The free energy change for SAT transmitting toward the outside of cell along the functional molecular channel within D3R is 83.5 kJ mol-1. The change of free energy for SAT to permeate into the POPC bilayer membrane along the protective molecular channel within D3R is 87.7 kJ mol-1. Our previous work gave that the free energy for Levo-Benzedrine (RAT) transmitting toward the outside of cell along the functional molecular channel within D3R is 91.4 kJ mol-1, while it is 117.7 kJ mol-1 for RAT to permeate into the POPC bilayer membrane along the protective molecular channel within D3R. The values of free energy suggest that SAT relatively prefers likely to pass through the functional molecular channel within D3R for increasing the release of dopamine molecules resulting in a variety of functional effects for SAT. The obtained results show that the pharmacology and addiction mechanisms of SAT as a drug are closely related to the molecular dynamics and mechanism for SAT transmitting along molecular channels within D3R.
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Affiliation(s)
- Wei Xie
- a Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology and Pharmacy Academy , Yunnan University , Kunming 650091 , China
| | - Ming Wang
- a Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology and Pharmacy Academy , Yunnan University , Kunming 650091 , China
| | - Aijing Li
- a Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology and Pharmacy Academy , Yunnan University , Kunming 650091 , China
| | - Si-Chuan Xu
- a Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology and Pharmacy Academy , Yunnan University , Kunming 650091 , China
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Awasthi N, Hub JS. Simulations of Pore Formation in Lipid Membranes: Reaction Coordinates, Convergence, Hysteresis, and Finite-Size Effects. J Chem Theory Comput 2016; 12:3261-9. [DOI: 10.1021/acs.jctc.6b00369] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Neha Awasthi
- Institute for Microbiology
and Genetics, Georg-August-Universität, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Jochen S. Hub
- Institute for Microbiology
and Genetics, Georg-August-Universität, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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Permeability across lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2254-2265. [PMID: 27085977 DOI: 10.1016/j.bbamem.2016.03.032] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 11/22/2022]
Abstract
Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Casciola M, Tarek M. A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2278-2289. [PMID: 27018309 DOI: 10.1016/j.bbamem.2016.03.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/26/2022]
Abstract
The transport of chemical compounds across the plasma membrane into the cell is relevant for several biological and medical applications. One of the most efficient techniques to enhance this uptake is reversible electroporation. Nevertheless, the detailed molecular mechanism of transport of chemical species (dyes, drugs, genetic materials, …) following the application of electric pulses is not yet fully elucidated. In the past decade, molecular dynamics (MD) simulations have been conducted to model the effect of pulsed electric fields on membranes, describing several aspects of this phenomenon. Here, we first present a comprehensive review of the results obtained so far modeling the electroporation of lipid membranes, then we extend these findings to study the electrotransfer across lipid bilayers subject to microsecond pulsed electric fields of Tat11, a small hydrophilic charged peptide, and of siRNA. We use in particular a MD simulation protocol that allows to characterize the transport of charged species through stable pores. Unexpectedly, our results show that for an electroporated bilayer subject to transmembrane voltages in the order of 500mV, i.e. consistent with experimental conditions, both Tat11 and siRNA can translocate through nanoelectropores within tens of ns. We discuss these results in comparison to experiments in order to rationalize the mechanism of drug uptake by cells. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Maura Casciola
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; Department of Information Engineering, Electronics and Telecommunications (D.I.E.T), Sapienza University of Rome, 00184 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy
| | - Mounir Tarek
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; CNRS, UMR 7565, F-54506 Vandoeuvre les Nancy, France.
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Kirsch SA, Böckmann RA. Membrane pore formation in atomistic and coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:2266-2277. [PMID: 26748016 DOI: 10.1016/j.bbamem.2015.12.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022]
Abstract
Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sonja A Kirsch
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
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Alskär LC, Bergström CAS. Models for Predicting Drug Absorption From Oral Lipid-Based Formulations. CURRENT MOLECULAR BIOLOGY REPORTS 2015; 1:141-147. [PMID: 26594613 PMCID: PMC4643850 DOI: 10.1007/s40610-015-0023-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this review, we describe the in vitro tools currently used to identify when a lipid-based formulation has the potential to deliver a poorly water-soluble drug via the oral route. We describe the extent to which these tools reflect the in vivo performance of the formulation and, more importantly, we present strategies that we foresee will improve the in vitro-in vivo correlations. We also present emerging computational methods that are likely to allow large parts of the formulation development to be carried out in the computer rather than in the test tube. We suggest that these computational tools will also improve the mechanistic understanding of in vivo formulation performance in the complex and dynamic environment of the gut.
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Affiliation(s)
- Linda C. Alskär
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Center, P.O Box 580, SE-751 23 Uppsala, Sweden
| | - Christel A. S. Bergström
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Center, P.O Box 580, SE-751 23 Uppsala, Sweden
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Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products. Future Med Chem 2015; 7:2121-30. [PMID: 26067057 DOI: 10.4155/fmc.15.78] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Many cyclic peptide natural products are larger and structurally more complex than conventional small molecule drugs. Although some molecules in this class are known to possess favorable pharmacokinetic properties, there have been few reports on the membrane permeabilities of cyclic peptide natural products. Here, we present the passive membrane permeabilities of 39 cyclic peptide natural products, and interpret the results using a computational permeability prediction algorithm based on their known or calculated 3D conformations. We found that the permeabilities of these compounds, measured in a parallel artificial membrane permeability assay, spanned a wide range and demonstrated the important influence of conformation on membrane permeability. These results will aid in the development of these compounds as a viable drug paradigm.
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35
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Trainito C, Français O, Le Pioufle B. Analysis of pulsed electric field effects on cellular tissue with Cole–Cole model: Monitoring permeabilization under inhomogeneous electrical field with bioimpedance parameter variations. INNOV FOOD SCI EMERG 2015. [DOI: 10.1016/j.ifset.2015.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Takáts-Nyeste A, Derényi I. Development of hat-shaped liposomes on solid supports. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:15261-15265. [PMID: 25491649 DOI: 10.1021/la503774t] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We introduce a simple dynamical model which can explain the development of hat-shaped surface attached liposomes by taking membrane self-adhesion into account. The model reveals that hat formation is a general phenomenon, although it is difficult to observe experimentally. We show under what conditions hat-shaped vesicles can become observable. One such scenario, in consistency with AFM measurements, is that the dynamics is slowed down by the low rate of the outflow of the internal fluid of the vesicle through the narrow space between the two bilayers of the brim.
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Affiliation(s)
- Annamária Takáts-Nyeste
- ELTE-MTA "Lendulet" Biophysics Research Group, Department of Biological Physics, Eötvös University , Pázmány P. stny. 1A, H-1117 Budapest, Hungary
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37
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Wilson MA, Nguyen TH, Pohorille A. Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance. J Chem Phys 2014; 141:22D519. [DOI: 10.1063/1.4900879] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Michael A. Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, California 94035, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94132, USA
| | - Thuy Hien Nguyen
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, USA
| | - Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, California 94035, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94132, USA
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38
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Takáts-Nyeste A, Derényi I. Rupture of lipid vesicles near solid surfaces. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:052710. [PMID: 25493819 DOI: 10.1103/physreve.90.052710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Indexed: 06/04/2023]
Abstract
The behavior of lipid vesicles near solid surfaces, despite its scientific and technological significance, is poorly understood. By simultaneously taking into account (i) the dynamics of spontaneous pore opening and closing in surface bound vesicles; (ii) their volume loss via leakage through the pores; (iii) and the propagation of their contact line, we have developed a simple model that can fully describe the detailed mechanism of and provide the necessary conditions for the rupture of vesicles and the subsequent formation of supported lipid bilayers. The predictions of the model are in qualitative agreement with many of the experimental observations.
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Affiliation(s)
- Annamária Takáts-Nyeste
- ELTE-MTA "Lendulet" Biophysics Research Group, Department of Biological Physics, Eötvös University, Pázmány P. stny. 1A, H-1117 Budapest, Hungary
| | - Imre Derényi
- ELTE-MTA "Lendulet" Biophysics Research Group, Department of Biological Physics, Eötvös University, Pázmány P. stny. 1A, H-1117 Budapest, Hungary
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39
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Török Z, Crul T, Maresca B, Schütz GJ, Viana F, Dindia L, Piotto S, Brameshuber M, Balogh G, Péter M, Porta A, Trapani A, Gombos I, Glatz A, Gungor B, Peksel B, Vigh L, Csoboz B, Horváth I, Vijayan MM, Hooper PL, Harwood JL, Vigh L. Plasma membranes as heat stress sensors: from lipid-controlled molecular switches to therapeutic applications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1594-618. [PMID: 24374314 DOI: 10.1016/j.bbamem.2013.12.015] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/09/2013] [Accepted: 12/18/2013] [Indexed: 12/31/2022]
Abstract
The classic heat shock (stress) response (HSR) was originally attributed to protein denaturation. However, heat shock protein (Hsp) induction occurs in many circumstances where no protein denaturation is observed. Recently considerable evidence has been accumulated to the favor of the "Membrane Sensor Hypothesis" which predicts that the level of Hsps can be changed as a result of alterations to the plasma membrane. This is especially pertinent to mild heat shock, such as occurs in fever. In this condition the sensitivity of many transient receptor potential (TRP) channels is particularly notable. Small temperature stresses can modulate TRP gating significantly and this is influenced by lipids. In addition, stress hormones often modify plasma membrane structure and function and thus initiate a cascade of events, which may affect HSR. The major transactivator heat shock factor-1 integrates the signals originating from the plasma membrane and orchestrates the expression of individual heat shock genes. We describe how these observations can be tested at the molecular level, for example, with the use of membrane perturbers and through computational calculations. An important fact which now starts to be addressed is that membranes are not homogeneous nor do all cells react identically. Lipidomics and cell profiling are beginning to address the above two points. Finally, we observe that a deregulated HSR is found in a large number of important diseases where more detailed knowledge of the molecular mechanisms involved may offer timely opportunities for clinical interventions and new, innovative drug treatments. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy.
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Affiliation(s)
- Zsolt Török
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary.
| | - Tim Crul
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Bruno Maresca
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Gerhard J Schütz
- Institute of Applied Physics, Vienna University of Technology, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - Felix Viana
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, 03550 San Juan de Alicante, Spain
| | - Laura Dindia
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Stefano Piotto
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Mario Brameshuber
- Institute of Applied Physics, Vienna University of Technology, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - Gábor Balogh
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Mária Péter
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Amalia Porta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Alfonso Trapani
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Imre Gombos
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Attila Glatz
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Burcin Gungor
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Begüm Peksel
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - László Vigh
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Bálint Csoboz
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Ibolya Horváth
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary
| | - Mathilakath M Vijayan
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada; Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Phillip L Hooper
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Medical School, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK
| | - László Vigh
- Institute of Biochemistry, Biological Research Centre of the Hung. Acad. Sci., Szeged H-6726, Hungary.
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The alteration of lipid bilayer dynamics by phloretin and 6-ketocholestanol. Chem Phys Lipids 2013; 178:38-44. [PMID: 24316311 DOI: 10.1016/j.chemphyslip.2013.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/13/2013] [Accepted: 11/14/2013] [Indexed: 02/06/2023]
Abstract
Lipid bilayer properties are quantified with a variety of arbitrary selected parameters such as molecular packing and dynamics, electrostatic potentials or permeability. In the paper we determined the effect of phloretin and 6-ketocholestanol (dipole potential modifying agents) on the membrane hydration and efficiency of the trans-membrane water flow. The dynamics of water molecules within the lipid bilayer interface was evaluated using solvent relaxation method, whereas the osmotically induced trans-membrane water flux was estimated with the stopped-flow method using the liposome shrinkage kinetics. The presence of phloretin or 6-ketocholestanol resulted in a change of both, the interfacial hydration level and osmotically driven water fluxes. Specifically, the presence of 6-ketocholestanol reduced the amount and mobility of water in the membrane interface. It also slows the osmotically induced water flow. The interfacial hydration change caused by phloretin was much smaller and the effect on osmotically induced water flow was opposite to that of 6-ketocholestanol.
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41
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Krylov NA, Pentkovsky VM, Efremov RG. Nontrivial behavior of water in the vicinity and inside lipid bilayers as probed by molecular dynamics simulations. ACS NANO 2013; 7:9428-9442. [PMID: 24070369 DOI: 10.1021/nn4042392] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The atomic-scale diffusion of water in the presence of several lipid bilayers mimicking biomembranes is characterized via unconstrained molecular dynamics (MD) simulations. Although the overall water dynamics corresponds well to literature data, namely, the efficient braking near polar head groups of lipids, a number of interesting and biologically relevant details observed in this work have not been sufficiently discussed so far; for instance, the fact that waters "sense" the membrane unexpectedly early, before water density begins to decrease. In this "transitional zone" the velocity distributions of water and their H-bonding patterns deviate from those in the bulk solution. The boundaries of this zone are well preserved even despite the local (<1 nm size) perturbation of the lipid bilayer, thus indicating a decoupling of the surface and bulk dynamics of water. This is in excellent agreement with recent experimental data. Near the membrane surface, water movement becomes anisotropic, that is, solvent molecules preferentially move outward the bilayer. Deep in the membrane interior, the velocities can even exceed those in the bulk solvent and undergo large-scale fluctuations. The analysis of MD trajectories of individual waters in the middle part of the acyl chain region of lipids reveals a number of interesting rare phenomena, such as the fast (ca. 50 ps) breakthrough across the membrane or long-time (up to 750 ps) "roaming" between lipid leaflets. The analysis of these events was accomplished to delineate the mechanisms of spontaneous water permeation inside the hydrophobic membrane core. It was shown that such nontrivial dynamics of water in an "alien" environment is driven by the dynamic heterogeneities of the local bilayer structure and the formation of transient atomic-scale "defects" in it. The picture observed in lipid bilayers is drastically different from that in a primitive membrane mimic, a hydrated cyclohexane slab. The possible biological impact of such phenomena in equilibrated lipid bilayers is discussed.
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Affiliation(s)
- Nikolay A Krylov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia
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Nagpal K, Singh SK, Mishra DN. Drug targeting to brain: a systematic approach to study the factors, parameters and approaches for prediction of permeability of drugs across BBB. Expert Opin Drug Deliv 2013; 10:927-55. [DOI: 10.1517/17425247.2013.762354] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
The blood-brain barrier (BBB) prevents the brain uptake of most pharmaceuticals. This property arises from the epithelial-like tight junctions within the brain capillary endothelium. The BBB is anatomically and functionally distinct from the blood-cerebrospinal fluid barrier at the choroid plexus. Certain small molecule drugs may cross the BBB via lipid-mediated free diffusion, providing the drug has a molecular weight <400 Da and forms <8 hydrogen bonds. These chemical properties are lacking in the majority of small molecule drugs, and all large molecule drugs. Nevertheless, drugs can be reengineered for BBB transport, based on the knowledge of the endogenous transport systems within the BBB. Small molecule drugs can be synthesized that access carrier-mediated transport (CMT) systems within the BBB. Large molecule drugs can be reengineered with molecular Trojan horse delivery systems to access receptor-mediated transport (RMT) systems within the BBB. Peptide and antisense radiopharmaceuticals are made brain-penetrating with the combined use of RMT-based delivery systems and avidin-biotin technology. Knowledge on the endogenous CMT and RMT systems expressed at the BBB enable new solutions to the problem of BBB drug transport.
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45
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Schaefer JJ, Ma C, Harris JM. Confocal Raman microscopy probing of temperature-controlled release from individual, optically-trapped phospholipid vesicles. Anal Chem 2012; 84:9505-12. [PMID: 23043532 DOI: 10.1021/ac302346n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Control of permeability of phospholipid vesicle (liposome) membranes is critical to their applications in analytical sensing, in fundamental studies of chemistry in small volumes, and in encapsulation and release of payloads for site-directed drug delivery. Applications of liposome formulations in drug delivery often take advantage of the enhanced permeability of phospholipid membranes at their gel-to-fluid phase transition, where the release of encapsulated molecules can be initiated by an increase in temperature. Despite numerous successful liposome formulations for encapsulation and release methods to study the kinetics, this process has been limited to investigations of bulk vesicle dispersions, which provide little or no information about the vesicle membrane structure and its relationship to the kinetics of trans-membrane transport. In this work, confocal Raman microscopy is adapted to study temperature-dependent release of a model compound, 3-nitrobenzene sulfonate (3-NBS), from individual optically trapped phospholipid vesicles, while simultaneously monitoring structural changes in the vesicle membrane reported by vibrational modes of phospholipid acyl chains and the local environment of the encapsulated compound. The confocal geometry allows efficient excitation and collection of Raman scattering from a single vesicle, while optical trapping allows more than hour-long observations of the same vesicle. With window factor analysis to resolve component spectra, temperature-controlled release of 3-NBS through vesicle membranes composed of pure 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) was measured and compared to transport through a lysolipid-containing membrane specifically formulated for efficient drug delivery.
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Affiliation(s)
- Jonathan J Schaefer
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Molecular Dynamics Simulations of Lipid Membrane Electroporation. J Membr Biol 2012; 245:531-43. [DOI: 10.1007/s00232-012-9434-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
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Ganesan N, Bauer BA, Lucas TR, Patel S, Taufer M. Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs). J Comput Chem 2011; 32:2958-73. [PMID: 21793003 DOI: 10.1002/jcc.21871] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/25/2011] [Accepted: 05/21/2011] [Indexed: 01/19/2023]
Abstract
We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.
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Affiliation(s)
- Narayan Ganesan
- Department of Computer and Information Science, University of Delaware, Newark, Delaware 19716, USA
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48
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A view of hydrogen/hydroxide flux across lipid membranes. J Membr Biol 2010; 237:21-30. [PMID: 20871986 DOI: 10.1007/s00232-010-9303-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 08/27/2010] [Indexed: 10/19/2022]
Abstract
A topic emerging roughly 30 years ago and engendering an incompletely resolved controversy is reviewed in this article: the relatively high permeability and pH independence associated with H(+)/OH(-) passive movements across lipid membranes. We summarize the expected characteristics of simple H(+)/OH(-) diffusion and those of a reaction between H(+) and OH(-) being attracted from opposite surfaces and condensing in an interfacial zone of the membrane. An interfacial H(+)/OH(-) reaction mechanism gives the experimentally observed behavior of an H(+)/OH(-) flux that is independent of the pH measurement range. This mechanism assumes that H(+) and OH(-) within the interfacial zone become electrostatically aligned on opposite sides of the hydrophobic membrane core. Electrostatic attraction and charge delocalization among a small cluster of water molecules surrounding the ions reduce the Born energy for H(+)/OH(-) insertion into lipid. This transmembrane condensation model predicts the magnitude of the experimentally determined H(+)/OH(-) flux, which is significantly greater than that of other monovalent ions. The consequences of an elevated H(+)/OH(-) permeability compared to other ions and the relative pH independence of this flux have consequences for understanding the chemical evolution of life.
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Zappacosta R, Semeraro M, Baroncini M, Silvi S, Aschi M, Credi A, Fontana A. Liposome destabilization by a 2,7-diazapyrenium derivative through formation of transient pores in the lipid bilayer. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:952-959. [PMID: 20333693 DOI: 10.1002/smll.200902306] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The effect of the luminescent heteroaromatic electron acceptor N,N'-dimethyl-2,7-diazapyrenium dichloride (DM-DAP(2+)) on the stability of 1-palmitoyl-2-oleoylphosphatydilcholine (POPC) liposomes is determined on the basis of the rate of release of different fluorescent probes entrapped within the liposome. The experiments show that DM-DAP(2+) exerts a substantial destabilizing action on the liposomal bilayer, particularly at low concentrations. Molecular dynamics simulations suggest that the activity of DM-DAP(2+) is related to its tendency to surround itself with water molecules, conceivably favoring the formation of transient pores across the bilayer.
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Affiliation(s)
- Romina Zappacosta
- Dipartimento di Scienze del Farmaco Università G. d'Annunzio Via dei Vestini, 66013 Chieti, Italy
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50
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Missner A, Pohl P. 110 years of the Meyer-Overton rule: predicting membrane permeability of gases and other small compounds. Chemphyschem 2009; 10:1405-14. [PMID: 19514034 PMCID: PMC3045804 DOI: 10.1002/cphc.200900270] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Indexed: 01/04/2023]
Abstract
The transport of gaseous compounds across biological membranes is essential in all forms of life. Although it was generally accepted that gases freely penetrate the lipid matrix of biological membranes, a number of studies challenged this doctrine as they found biological membranes to have extremely low gas-permeability values. These observations led to the identification of several membrane-embedded "gas" channels, which facilitate the transport of biological active gases, such as carbon dioxide, nitric oxide, and ammonia. However, some of these findings are in contrast to the well-established solubility-diffusion model (also known as the Meyer-Overton rule), which predicts membrane permeabilities from the molecule's oil-water partition coefficient. Herein, we discuss recently reported violations of the Meyer-Overton rule for small molecules, including carboxylic acids and gases, and show that Meyer and Overton continue to rule.
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Affiliation(s)
- Andreas Missner
- Institut für Biophysik, Johannes Kepler Universität, Altenberger Str. 69, 4040 Linz (Austria), Fax: (+43) 732-2468-9270
| | - Peter Pohl
- Institut für Biophysik, Johannes Kepler Universität, Altenberger Str. 69, 4040 Linz (Austria), Fax: (+43) 732-2468-9270
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