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Selivanovitch E, Ostwalt A, Chao Z, Daniel S. Emerging Designs and Applications for Biomembrane Biosensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:339-366. [PMID: 39018354 DOI: 10.1146/annurev-anchem-061622-042618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
Nature has inspired the development of biomimetic membrane sensors in which the functionalities of biological molecules, such as proteins and lipids, are harnessed for sensing applications. This review provides an overview of the recent developments for biomembrane sensors compatible with either bulk or planar sensing applications, namely using lipid vesicles or supported lipid bilayers, respectively. We first describe the individual components required for these sensing platforms and the design principles that are considered when constructing them, and we segue into recent applications being implemented across multiple fields. Our goal for this review is to illustrate the versatility of nature's biomembrane toolbox and simultaneously highlight how biosensor platforms can be enhanced by harnessing it.
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Affiliation(s)
- Ekaterina Selivanovitch
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA;
| | - Alexis Ostwalt
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA;
| | - Zhongmou Chao
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA;
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA;
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2
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Hernández-Galván G, Mercado-Uribe H. Dehydration of biological membranes in a non-condensing environment. SOFT MATTER 2023; 19:9173-9178. [PMID: 37991897 DOI: 10.1039/d3sm01181j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
The study of the dehydration process in a cell membrane allows a better understanding of how water is bound to it. While in prior studies, cell dehydration was commonly analyzed under osmotic stress conditions, in the present work, we focus on the dehydration driven by evaporation in a restricted condensing environment. Using a thermogravimetry method, we studied the dehydration of Escherichia coli through isothermal evaporation in the presence of a gas flux. To figure out the loss of mass in this situation, we first evaluated the dynamics of water evaporation of a suspension of multilamellar liposomes. We found that the evaporation of liposomal suspensions composed of individual lipids is constant, although slightly restricted by the presence of liposomes, while the evaporation of liposomal suspensions composed of a mixture of different lipids follows an exponential decay. This is explained considering that the internal pressure at the air-water interface is proportional to the amount of bound water. The evaporation of water from a biomass sample follows this latter behaviour.
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Affiliation(s)
| | - H Mercado-Uribe
- CINVESTAV-Monterrey, PIIT, Apodaca, Nuevo León, 66600, Mexico.
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3
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Davoudi S, Raemdonck K, Braeckmans K, Ghysels A. Capric Acid and Myristic Acid Permeability Enhancers in Curved Liposome Membranes. J Chem Inf Model 2023; 63:6789-6806. [PMID: 37917127 DOI: 10.1021/acs.jcim.3c00936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Liposomes are considered as advanced drug delivery systems for cancer treatment. A generation of pH-sensitive liposomes is being developed that use fatty acids (FAs) as a trigger for drug release in tumor tissues. However, FAs are also known to enhance permeability, and it is unclear whether FAs in liposomes may cause drug leakage or premature drug release. The passive permeability of the drug through the membrane of the liposome is thus a crucial factor for timely drug delivery. To investigate how the curvature and lipid composition of liposomes affect their passive permeability, coarse-grained molecular dynamics were performed. The permeability was determined with a counting method. Flat bilayers and three liposomes with varying diameters were studied, which had varying lipid compositions of dipalmitoylphosphatidylcholine, cholesterol, and deprotonated or neutral saturated FAs. The investigated permeants were water and two other small permeants, which have different free energy profiles (solubility) across the membrane. First, for the curvature effect, our results showed that curvature increases the water permeability by reducing the membrane thickness. The permeability increase for water is about a factor of 1.7 for the most curved membranes. However, a high curvature decreases permeability for permeants with free energy profiles that are a mix of wells and barriers in the headgroup region of the membrane. Importantly, the type of experimental setup is expected to play a dominant role in the permeability value, i.e., whether permeants are escaping or entering the liposomes. Second, for the composition effect, FAs decrease both the area per lipid (APL) and the membrane thickness, resulting in permeability increases of up to 55%. Cholesterol has a similar effect on the APL but has the opposite impact on membrane thickness and permeability. Therefore, FAs and cholesterol have opposing effects on permeability, with cholesterol's effect being slightly stronger in our simulated bilayers. As all permeability values were well within a factor of 2, and with liposomes usually being larger and less curved in experimental applications, it can be concluded that the passive drug release from a pH-sensitive liposome does not seem to be significantly affected by the presence of FAs.
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Affiliation(s)
- Samaneh Davoudi
- IBiTech─BioMMedA Group, Ghent University, Corneel Heymanslaan 10, Block B-Entrance 36, 9000 Gent, Belgium
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory for General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Gent, Belgium
| | - Kevin Braeckmans
- Bio-Photonic Imaging Group, Laboratory for General Biochemistry and Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Gent, Belgium
| | - An Ghysels
- IBiTech─BioMMedA Group, Ghent University, Corneel Heymanslaan 10, Block B-Entrance 36, 9000 Gent, Belgium
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4
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Bernardi A, Bennett WFD, He S, Jones D, Kirshner D, Bennion BJ, Carpenter TS. Advances in Computational Approaches for Estimating Passive Permeability in Drug Discovery. MEMBRANES 2023; 13:851. [PMID: 37999336 PMCID: PMC10673305 DOI: 10.3390/membranes13110851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/25/2023]
Abstract
Passive permeation of cellular membranes is a key feature of many therapeutics. The relevance of passive permeability spans all biological systems as they all employ biomembranes for compartmentalization. A variety of computational techniques are currently utilized and under active development to facilitate the characterization of passive permeability. These methods include lipophilicity relations, molecular dynamics simulations, and machine learning, which vary in accuracy, complexity, and computational cost. This review briefly introduces the underlying theories, such as the prominent inhomogeneous solubility diffusion model, and covers a number of recent applications. Various machine-learning applications, which have demonstrated good potential for high-volume, data-driven permeability predictions, are also discussed. Due to the confluence of novel computational methods and next-generation exascale computers, we anticipate an exciting future for computationally driven permeability predictions.
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Affiliation(s)
| | | | | | | | | | | | - Timothy S. Carpenter
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (A.B.); (W.F.D.B.); (S.H.); (D.J.); (D.K.); (B.J.B.)
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Pandey P, MacKerell AD. Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. J Chem Inf Model 2023; 63:5903-5915. [PMID: 37682640 PMCID: PMC10603762 DOI: 10.1021/acs.jcim.3c00514] [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] [Indexed: 09/10/2023]
Abstract
Membrane permeability of drug molecules plays a significant role in the development of new therapeutic agents. Accordingly, methods to predict the passive permeability of drug candidates during a medicinal chemistry campaign offer the potential to accelerate the drug design process. In this work, we combine the physics-based site identification by ligand competitive saturation (SILCS) method and data-driven artificial intelligence (AI) to create a high-throughput predictive model for the passive permeability of druglike molecules. In this study, we present a comparative analysis of four regression models to predict membrane permeabilities of small druglike molecules; of the tested models, Random Forest was the most predictive yielding an R2 of 0.81 for the independent data set. The input feature vector used to train the developed prediction model includes absolute free energy profiles of ligands through a POPC-cholesterol bilayer based on ligand grid free energy (LGFE) profiles obtained from the SILCS approach. The use of the membrane free energy profiles from SILCS offers information on the physical forces contributing to ligand permeability, while the use of AI yields a more predictive model trained on experimental PAMPA permeability data for a collection of 229 molecules. This combination allows for rapid estimations of ligand permeability at a level of accuracy beyond currently available predictive models while offering insights into the contributions of the functional groups in the ligands to the permeability barrier, thereby offering quantitative information to facilitate rational ligand design.
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Affiliation(s)
- Poonam Pandey
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-633, Baltimore, Maryland 21201, United States
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Kim MC, Lee YJ. Analysis of Time-Dependent Pharmacokinetics Using In Vitro-In Vivo Extrapolation and Physiologically Based Pharmacokinetic Modeling. Pharmaceutics 2022; 14:pharmaceutics14122562. [PMID: 36559055 PMCID: PMC9780873 DOI: 10.3390/pharmaceutics14122562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 11/24/2022] Open
Abstract
SCR430, a sorafenib derivative, is an investigational drug exhibiting anti-tumor action. This study aimed to have a mechanistic understanding of SCR430's time-dependent pharmacokinetics (TDPK) through an ex vivo study combined with an in vitro-in vivo extrapolation (IVIVE) and physiologically based pharmacokinetic (PBPK) modeling. A non-compartmental pharmacokinetic analysis was performed after intravenous SCR430 administration in female Sprague-Dawley rats for a control group (no treatment), a vehicle group (vehicle only, 14 days, PO), and a repeated-dosing group (SCR430, 30 mg/kg/day, 14 days, PO). In addition, hepatic uptake and metabolism modulation were investigated using isolated hepatocytes from each group of rats. The minimal PBPK model based on IVIVE was constructed to explain SCR430's TDPK. Repeated SCR430 administration decreased the systemic exposure by 4.4-fold, which was explained by increased hepatic clearance (4.7-fold). The ex vivo study using isolated hepatocytes from each group suggested that the increased hepatic uptake (9.4-fold), not the metabolic activity, contributes to the increased hepatic clearance. The minimal PBPK modeling based on an ex vivo study could explain the decreased plasma levels after the repeated doses. The current study demonstrates the TDPK after repeated dosing by hepatic uptake induction, not hepatic metabolism, as well as the effectiveness of an ex vivo approach combined with IVIVE and PBPK modeling to investigate the TDPK.
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Affiliation(s)
- Min-Chang Kim
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemungu, Seoul 02453, Republic of Korea
- Division of Biopharmaceutics, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Young-Joo Lee
- Division of Biopharmaceutics, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Integrated Drug Development and Natural Products, Kyung Hee University, Seoul 02447, Republic of Korea
- Correspondence:
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7
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The next frontier in ADME science: Predicting transporter-based drug disposition, tissue concentrations and drug-drug interactions in humans. Pharmacol Ther 2022; 238:108271. [DOI: 10.1016/j.pharmthera.2022.108271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 12/25/2022]
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8
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Strutt R, Sheffield F, Barlow NE, Flemming AJ, Harling JD, Law RV, Brooks NJ, Barter LMC, Ces O. UV-DIB: label-free permeability determination using droplet interface bilayers. LAB ON A CHIP 2022; 22:972-985. [PMID: 35107110 DOI: 10.1039/d1lc01155c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Simple diffusion of molecular entities through a phospholipid bilayer, is a phenomenon of great importance to the pharmaceutical and agricultural industries. Current model lipid systems to probe this typically only employ fluorescence as a readout, thus limiting the range of assessable chemical matter that can be studied. We report a new technology platform, the UV-DIB, which facilitates label free measurement of small molecule translocation rates. This is based upon the coupling of droplet interface bilayer technology with implemented fiber optics to facilitate analysis via ultraviolet spectroscopy, in custom designed PMMA wells. To improve on current DIB technology, the platform was designed to be reusable, with a high sampling rate and a limit of UV detection in the low μM regime. We demonstrate the use of our system to quantify passive diffusion in a reproducible and rapid manner where the system was validated by investigating multiple permeants of varying physicochemical properties across a range of lipid interfaces, each demonstrating differing kinetics. Our system permits the interrogation of structural dependence on the permeation rate of a given compound. We present this ability from two structural perspectives, that of the membrane, and the permeant. We observed a reduction in permeability between pure DOPC and DPhPC interfaces, concurring with literature and demonstrating our ability to study the effects of lipid composition on permeability. In relation to the effects of permeant structure, our device facilitated the rank ordering of various compounds from the xanthine class of compounds, where the structure of each permeant differed by a single group alteration. We found that DIBs were stable up to 5% DMSO, a molecule often used to aid solubilisation of pharmaceutical and agrochemical compounds. The ability of our device to rank-order compounds with such minor structural differences provides a level of precision that is rarely seen in current, industrially applied technologies.
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Affiliation(s)
- Robert Strutt
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK.
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK
| | - Felix Sheffield
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK.
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK
| | - Nathan E Barlow
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK.
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK
| | - Anthony J Flemming
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - John D Harling
- Medicinal Chemistry, GlaxoSmithKline, Stevenage, SG1 2NY, UK
| | - Robert V Law
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK.
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK
| | - Nicholas J Brooks
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK.
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK
| | - Laura M C Barter
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK.
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK
| | - Oscar Ces
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK.
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Shepherd's Bush, London, W12 0BZ, UK
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9
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Shoji A, Kang C, Fujioka K, Rose JP, Sun R. Assessing the Intestinal Permeability of Small Molecule Drugs via Diffusion Motion on a Multidimensional Free Energy Surface. J Chem Theory Comput 2021; 18:503-515. [PMID: 34851637 DOI: 10.1021/acs.jctc.1c00661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A protocol that accurately assesses the intestinal permeability of small molecule compounds plays an essential role in decreasing the cost and time in inventing a new drug. This manuscript presents a novel computational method to study the passive permeation of small molecule drugs based on the inhomogeneous solubility-diffusion model. The multidimensional free energy surface of the drug transiting through a lipid bilayer is computed with transition-tempered metadynamics that accurately captures the mechanisms of passive permeation. The permeability is computed by following the diffusion motion of the drug molecules along the minimal free energy path found on the multidimensional free energy surface. This computational method is assessed by studying the permeability of five small molecule drugs (ketoprofen, naproxen, metoprolol, propranolol, and salicylic acid). The results demonstrate a remarkable agreement between the computed permeabilities and those measured with the intestinal assay. The in silico method reported in this manuscript also reproduces the permeability measured from the intestinal assay (in vivo) better than the cell-based assays (e.g., PAMPA and Caco-2) do. In addition, the multidimensional free energy surface reveals the interplay between the structure of the small molecule and its permeability, shedding light on strategies of drug optimization.
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Affiliation(s)
- Alyson Shoji
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Christopher Kang
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - Kazuumi Fujioka
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
| | - John P Rose
- DDCS, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Rui Sun
- Department of Chemistry, The University of Hawai'i at Manoa, Honolulu, Hawaii 96822, United States
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10
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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11
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Kiiski I, Ollikainen E, Artes S, Järvinen P, Jokinen V, Sikanen T. Drug glucuronidation assays on human liver microsomes immobilized on microfluidic flow-through reactors. Eur J Pharm Sci 2021; 158:105677. [DOI: 10.1016/j.ejps.2020.105677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/06/2020] [Accepted: 12/07/2020] [Indexed: 11/26/2022]
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12
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Wadhwa R, Yadav NS, Katiyar SP, Yaguchi T, Lee C, Ahn H, Yun CO, Kaul SC, Sundar D. Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane. Sci Rep 2021; 11:2352. [PMID: 33504873 PMCID: PMC7840742 DOI: 10.1038/s41598-021-81729-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/30/2020] [Indexed: 12/23/2022] Open
Abstract
Poor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs-withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.
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Affiliation(s)
- Renu Wadhwa
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan
| | - Neetu Singh Yadav
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110 016, India
| | - Shashank P Katiyar
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110 016, India
| | - Tomoko Yaguchi
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan
| | - Chohee Lee
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan.,Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsinmi-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Hyomin Ahn
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan.,Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsinmi-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.,GeneMedicine Co., Ltd, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Chae-Ok Yun
- Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsinmi-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.,GeneMedicine Co., Ltd, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.,Institute of Nano Science and Technology (INST), 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Sunil C Kaul
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan.
| | - Durai Sundar
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110 016, India.
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13
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Yee SM, Gillams RJ, McLain SE, Lorenz CD. Effects of lipid heterogeneity on model human brain lipid membranes. SOFT MATTER 2021; 17:126-135. [PMID: 33155582 DOI: 10.1039/d0sm01766c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cell membranes naturally contain a heterogeneous lipid distribution. However, homogeneous bilayers are commonly preferred and utilised in computer simulations due to their relative simplicity, and the availability of lipid force field parameters. Recently, experimental lipidomics data for the human brain cell membranes under healthy and Alzheimer's disease (AD) conditions were investigated, since disruption to the lipid composition has been implicated in neurodegenerative disorders, including AD [R. B. Chan et al., J. Biol. Chem., 2012, 287, 2678-2688]. In order to observe the effects of lipid complexity on the various bilayer properties, molecular dynamics simulations were used to study four membranes with increasing heterogeneity: a pure POPC membrane, a POPC and cholesterol membrane in a 1 : 1 ratio (POPC-CHOL), and to our knowledge, the first realistic models of a healthy brain membrane and an Alzheimer's diseased brain membrane. Numerous structural, interfacial, and dynamical properties, including the area per lipid, interdigitation, dipole potential, and lateral diffusion of the two simple models, POPC and POPC-CHOL, were analysed and compared to those of the complex brain models consisting of 27 lipid components. As the membranes gain heterogeneity, a number of alterations were found in the structural and dynamical properties, and more significant differences were observed in the lateral diffusion. Additionally, we observed snorkeling behaviour of the lipid tails that may play a role in the permeation of small molecules across biological membranes. In this work, atomistic description of realistic brain membrane models is provided, which can add insight towards the permeability and transport pathways of small molecules across these membrane barriers.
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Affiliation(s)
- Sze May Yee
- Department of Physics, King's College London, London WC2R 2LS, UK.
| | - Richard J Gillams
- School of Electronics and Computer Science, and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sylvia E McLain
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
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Alves MA, Lamichhane S, Dickens A, McGlinchey A, Ribeiro HC, Sen P, Wei F, Hyötyläinen T, Orešič M. Systems biology approaches to study lipidomes in health and disease. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1866:158857. [PMID: 33278596 DOI: 10.1016/j.bbalip.2020.158857] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/13/2020] [Accepted: 11/27/2020] [Indexed: 12/15/2022]
Abstract
Lipids have many important biological roles, such as energy storage sources, structural components of plasma membranes and as intermediates in metabolic and signaling pathways. Lipid metabolism is under tight homeostatic control, exhibiting spatial and dynamic complexity at multiple levels. Consequently, lipid-related disturbances play important roles in the pathogenesis of most of the common diseases. Lipidomics, defined as the study of lipidomes in biological systems, has emerged as a rapidly-growing field. Due to the chemical and functional diversity of lipids, the application of a systems biology approach is essential if one is to address lipid functionality at different physiological levels. In parallel with analytical advances to measure lipids in biological matrices, the field of computational lipidomics has been rapidly advancing, enabling modeling of lipidomes in their pathway, spatial and dynamic contexts. This review focuses on recent progress in systems biology approaches to study lipids in health and disease, with specific emphasis on methodological advances and biomedical applications.
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Affiliation(s)
- Marina Amaral Alves
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Santosh Lamichhane
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Alex Dickens
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Aidan McGlinchey
- School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
| | | | - Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
| | - Fang Wei
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, PR China
| | | | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
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15
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Siwy CM, Delfing BM, Smith AK, Klimov DK. Partitioning of Benzoic Acid into 1,2-Dimyristoyl- sn-glycero-3-phosphocholine and Blood-Brain Barrier Mimetic Bilayers. J Chem Inf Model 2020; 60:4030-4046. [PMID: 32672960 DOI: 10.1021/acs.jcim.0c00590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using an all-atom explicit water model and replica exchange umbrella sampling simulations, we investigated the molecular mechanisms of benzoic acid partitioning into two model lipid bilayers. The first was formed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids, whereas the second was composed of an equimolar mixture of DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine, palmitoylsphingomyelin, and cholesterol to constitute a blood-brain barrier (BBB) mimetic bilayer. Comparative analysis of benzoic acid partitioning into the two bilayers has revealed qualitative similarities. Partitioning into the DMPC and BBB bilayers is thermodynamically favorable although insertion into the former lowers the free energy of benzoic acid by approximately an additional 1 kcal mol-1. The partitioning energetics for the two bilayers is also largely similar based on the balance of benzoic acid interactions with apolar fatty acid tails, polar lipid headgroups, and water. In both bilayers, benzoic acid retains a considerable number of residual water molecules until reaching the bilayer midplane where it experiences nearly complete dehydration. Upon insertion into the bilayers, benzoic acid undergoes several rotations primarily determined by the interactions with the lipid headgroups. Nonetheless, in addition to the depth of the free energy minimum, the BBB bilayer differs from the DMPC counterpart by a much deeper location of the free energy minimum and the appearance of a high free energy barrier and positioning of benzoic acid near the midplane. Furthermore, DMPC and BBB bilayers exhibit different structural responses to benzoic acid insertion. Taken together, the BBB mimetic bilayer is preferable for an accurate description of benzoic acid partitioning.
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Affiliation(s)
- Christopher M Siwy
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Bryan M Delfing
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Amy K Smith
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
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16
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Fleury JB. Enhanced water permeability across a physiological droplet interface bilayer doped with fullerenes. RSC Adv 2020; 10:19686-19692. [PMID: 35515425 PMCID: PMC9054109 DOI: 10.1039/d0ra01413c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/23/2020] [Indexed: 11/21/2022] Open
Abstract
We measure the water permeability across a physiological lipid bilayer produced by the droplet interface bilayer (DiB) technique. This lipid bilayer can be considered as physiologically relevant because it presents a lipidic composition close to human cell membranes. The measured water permeability coefficients across this lipid bilayer are reported as a function of the cholesterol concentration. It is found that the water permeability coefficients decreased with increasing cholesterol concentration, in agreement with the existing literature. And, consistently, the extracted corresponding activation energies increase with increasing cholesterol concentration in the lipid bilayer. Hence having demonstrated the robustness of the experimental system, we extend this study by exploring the influence of fullerenes on the water permeability of a physiological lipid bilayer. Interestingly, we observe a significant increase of the measured water permeability coefficients across this lipid bilayer for large fullerenes concentration. This enhanced permeability might be related to the conductive properties of fullerenes. We measure the water permeability across a physiological lipid bilayer produced by the droplet interface bilayer technique.![]()
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Affiliation(s)
- Jean-Baptiste Fleury
- Experimental Physics and Center for Biophysics, Saarland University D-66123 Saarbruecken Germany +49 681 302 70121
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17
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Takeda K, Fujimoto K, Yoshii N, Okazaki S. Molecular dynamics study of solubilization of cyclohexane, benzene, and phenol into mixed micelles composed of sodium dodecyl sulfate and octaethylene glycol monododecyl ether. J Comput Chem 2019; 40:2722-2729. [PMID: 31429106 DOI: 10.1002/jcc.26047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 02/04/2023]
Abstract
Molecular dynamics calculations of a mixed micelle composed of sodium dodecyl sulfate (SDS) and octaethylene glycol monododecyl ether (C12 E8 ) were performed for six compositions (SDS/C12 E8 = 100/0, 80/20, 60/40, 40/60, 20/80, and 0/100) to investigate the composition dependence of the mixed micelle structure and solubilization of cyclohexane, benzene, and phenol molecules by the micelle. The radial density distribution of the hydrophilic polyoxyethylene (POE) group of C12 E8 as a function of distance from the micelle center is very sharp for micelles with high SDS content because the POE group captures a Na+ ion in solution and wraps around it to form a compact crown-ether-like complex. The hydrophobic dodecyl groups of SDS and C12 E8 were separately distributed in the mixed micelle core. ΔG(r) evaluated for each solute showed that despite the structural changes of the micelle the binding strength of the solute molecules to the micelle did not change significantly. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Kosuke Takeda
- Analytical Science Research Laboratories, Kao Corporation, 1334 Minato, Wakayama-Shi Wakayama, 640-8580, Japan.,Department of Materials Chemistry, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8603, Japan
| | - Kazushi Fujimoto
- Department of Materials Chemistry, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8603, Japan
| | - Noriyuki Yoshii
- Department of Materials Chemistry, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8603, Japan.,Center for Computational Science, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8603, Japan.,Center for Computational Science, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8603, Japan
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18
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Shahane G, Ding W, Palaiokostas M, Azevedo HS, Orsi M. Interaction of Antimicrobial Lipopeptides with Bacterial Lipid Bilayers. J Membr Biol 2019; 252:317-329. [PMID: 31098677 PMCID: PMC6790193 DOI: 10.1007/s00232-019-00068-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/03/2019] [Indexed: 02/07/2023]
Abstract
The resistance of pathogens to traditional antibiotics is currently a global issue of enormous concern. As the discovery and development of new antibiotics become increasingly challenging, synthetic antimicrobial lipopeptides (AMLPs) are now receiving renewed attention as a new class of antimicrobial agents. In contrast to traditional antibiotics, AMLPs act by physically disrupting the cell membrane (rather than targeting specific proteins), thus reducing the risk of inducing bacterial resistance. In this study, we use microsecond-timescale atomistic molecular dynamics simulations to quantify the interaction of a short AMLP (C16-KKK) with model bacterial lipid bilayers. In particular, we investigate how fundamental transmembrane properties change in relation to a range of lipopeptide concentrations. A number of structural, mechanical, and dynamical features are found to be significantly altered in a non-linear fashion. At 10 mol% concentration, lipopeptides have a condensing effect on bacterial bilayers, characterized by a decrease in the area per lipid and an increase in the bilayer order. Higher AMLP concentrations of 25 and 40 mol% destabilize the membrane by disrupting the bilayer core structure, inducing membrane thinning and water leakage. Important transmembrane properties such as the lateral pressure and dipole potential profiles are also affected. Potential implications on membrane function and associated proteins are discussed.
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Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Helena S Azevedo
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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19
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Senik SV, Psurtseva NV, Shavarda AL, Kotlova ER. Role of lipids in the thermal plasticity of basidial fungus Favolaschia manipularis. Can J Microbiol 2019; 65:870-879. [PMID: 31398296 DOI: 10.1139/cjm-2019-0284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this study, we examined the lipid composition of two strains of the tropical basidiomycete Favolaschia manipularis (Berk.) Teng, which differ in their adaptive potential to high (35 °C) and low (5 °C) temperatures. The results suggest that adaptation to extreme temperatures involves a change in the molecular composition of sterols, in addition to other well-known mechanisms of regulating membrane thickness and fluidity, such as changes in the lipid unsaturation and in the proportion of bilayer- and non-bilayer-forming lipids. It was demonstrated for the first time that adaptation to high temperature stress in fungi is accompanied by the accumulation of 9(11)-dehydroergosterol and ergosterol peroxide. Furthermore, increased thermal plasticity correlates with high storage lipid (triglycerides) content, accumulation of phosphatidic acid in the membrane, and an equal proportion of bilayer and non-bilayer lipids in the membrane.
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Affiliation(s)
- Svetlana V Senik
- Komarov Botanical Institute, Russian Academy of Sciences, 2 Professor Popov Street, St. Petersburg 197376, Russia.,Komarov Botanical Institute, Russian Academy of Sciences, 2 Professor Popov Street, St. Petersburg 197376, Russia
| | - Nadezhda V Psurtseva
- Komarov Botanical Institute, Russian Academy of Sciences, 2 Professor Popov Street, St. Petersburg 197376, Russia.,Komarov Botanical Institute, Russian Academy of Sciences, 2 Professor Popov Street, St. Petersburg 197376, Russia
| | - Alexey L Shavarda
- Komarov Botanical Institute, Russian Academy of Sciences, 2 Professor Popov Street, St. Petersburg 197376, Russia.,Komarov Botanical Institute, Russian Academy of Sciences, 2 Professor Popov Street, St. Petersburg 197376, Russia
| | - Ekaterina R Kotlova
- Komarov Botanical Institute, Russian Academy of Sciences, 2 Professor Popov Street, St. Petersburg 197376, Russia.,Komarov Botanical Institute, Russian Academy of Sciences, 2 Professor Popov Street, St. Petersburg 197376, Russia
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20
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Effects of Cholesterol on Water Permittivity of Biomimetic Ion Pair Amphiphile Bilayers: Interplay between Membrane Bending and Molecular Packing. Int J Mol Sci 2019; 20:ijms20133252. [PMID: 31269714 PMCID: PMC6651711 DOI: 10.3390/ijms20133252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 06/28/2019] [Accepted: 06/28/2019] [Indexed: 02/04/2023] Open
Abstract
Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic amphiphiles, is an inexpensive phospholipid substitute to fabricate vesicles with various pharmaceutical applications. Modulating the physicochemical and permeation properties of IPA vesicles are important for carrier designs. Here, we applied molecular dynamics simulations to examine the cholesterol effects on the structures, mechanics, and water permittivity of hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium- hexadecylsulfate (DTMA-HS) IPA bilayers. Structural and mechanical analyses indicate that both IPA systems are in gel phase at 298 K. Adding cholesterol induces alkyl chain ordering around the rigid sterol ring and increases the cavity density within the hydrophilic region of both IPA bilayers. Furthermore, the enhanced alkyl chain ordering and the membrane deformation energy induced by cholesterol increase the permeation free energy penalty. In contrast, cholesterol has minor effects on the water local diffusivities within IPA membranes. Overall, the cholesterol reduces the water permittivity of rigid IPA membranes due to the synergistic effects of increased alkyl chain ordering and enhanced membrane mechanical modulus. The results provide molecular insights into the effects of molecular packing and mechanical deformations on the water permittivity of biomimetic IPA membranes, which is critical for designing IPA vesicular carriers.
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21
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Lomize AL, Hage JM, Schnitzer K, Golobokov K, LaFaive MB, Forsyth AC, Pogozheva ID. PerMM: A Web Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. J Chem Inf Model 2019; 59:3094-3099. [PMID: 31259547 DOI: 10.1021/acs.jcim.9b00225] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The PerMM web server and database were developed for quantitative analysis and visualization of passive translocation of bioactive molecules across lipid membranes. The server is the first physics-based web tool that calculates membrane binding energies and permeability coefficients of diverse molecules through artificial and natural membranes (phospholipid bilayers, PAMPA-DS, blood-brain barrier, and Caco-2/MDCK cell membranes). It also visualizes the transmembrane translocation pathway as a sequence of translational and rotational positions of a permeant as it moves across the lipid bilayer, along with the corresponding changes in solvation energy. The server can be applied for prediction of permeability coefficients of compounds with diverse chemical scaffolds to facilitate selection and optimization of potential drug leads. The complementary PerMM database allows comparison of computationally and experimentally determined permeability coefficients for more than 500 compounds in different membrane systems. The website and database are freely accessible at https://permm.phar.umich.edu/ .
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| | - Jacob M Hage
- Department of Electrical Engineering and Computer Science, College of Engineering , University of Michigan , 1221 Beal Ave , Ann Arbor , Michigan 48109-2102 , United States
| | - Kevin Schnitzer
- Department of Electrical Engineering and Computer Science, College of Engineering , University of Michigan , 1221 Beal Ave , Ann Arbor , Michigan 48109-2102 , United States
| | - Konstantin Golobokov
- Department of Electrical Engineering and Computer Science, College of Engineering , University of Michigan , 1221 Beal Ave , Ann Arbor , Michigan 48109-2102 , United States
| | - Mitchell B LaFaive
- Department of Electrical Engineering and Computer Science, College of Engineering , University of Michigan , 1221 Beal Ave , Ann Arbor , Michigan 48109-2102 , United States
| | - Alexander C Forsyth
- Department of Computer Science, College of Literature, Science, and the Arts , University of Michigan , 2260 Hayward Street , Ann Arbor , Michigan 48109-2121 , United States
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
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22
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Lomize AL, Pogozheva ID. Physics-Based Method for Modeling Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. J Chem Inf Model 2019; 59:3198-3213. [PMID: 31259555 DOI: 10.1021/acs.jcim.9b00224] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assessment of permeability is a critical step in the drug development process for selection of drug candidates with favorable ADME properties. We have developed a novel physics-based method for fast computational modeling of passive permeation of diverse classes of molecules across lipid membranes. The method is based on heterogeneous solubility-diffusion theory and operates with all-atom 3D structures of solutes and the anisotropic solvent model of the lipid bilayer characterized by transbilayer profiles of dielectric and hydrogen bonding capacity parameters. The optimal translocation pathway of a solute is determined by moving an ensemble of representative conformations of the molecule through the dioleoyl-phosphatidylcholine (DOPC) bilayer and optimizing their rotational orientations in every point of the transmembrane trajectory. The method calculates (1) the membrane-bound state of the solute molecule; (2) free energy profile of the solute along the permeation pathway; and (3) the permeability coefficient obtained by integration over the transbilayer energy profile and assuming a constant size-dependent diffusivity along the membrane normal. The accuracy of the predictions was evaluated against experimental permeability coefficients measured in pure lipid membranes (for 78 compounds, R2 was 0.88 and rmse was 1.15 log units), PAMPA-DS (for 280 compounds, R2 was 0.75 and rmse was 1.59 log units), BBB (for 182 compounds, R2 was 0.69 and rmse was 0.87 log units), and Caco-2/MDCK assays (for 165 compounds, R2 was 0.52 and rmse was 0.89 log units).
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| | - Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
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23
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Kim AV, Shelepova EA, Selyutina OY, Meteleva ES, Dushkin AV, Medvedev NN, Polyakov NE, Lyakhov NZ. Glycyrrhizin-Assisted Transport of Praziquantel Anthelmintic Drug through the Lipid Membrane: An Experiment and MD Simulation. Mol Pharm 2019; 16:3188-3198. [PMID: 31198045 DOI: 10.1021/acs.molpharmaceut.9b00390] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Praziquantel (PZQ) is one of the most widespread anthelmintic drugs. However, the frequent insufficient application of PZQ after oral administration is associated with its low solubility, penetration rate, and bioavailability. In the present study, the permeation of PZQ through a 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC) membrane was investigated to probe glycyrrhizin-assisted transport. Glycyrrhizin (or glycyrrhizic acid, GA), a natural saponin, shows the ability to enhance the therapeutic activity of various drugs when it is used as a drug delivery system. However, the molecular mechanism of this effect is still under debate. In the present study, the transport rate was measured experimentally by a parallel artificial membrane permeation assay (PAMPA) and molecular dynamics (MD) simulation with DOPC lipid bilayers. The formation of the noncovalent supramolecular complex of PZQ with disodium salt of GA (Na2GA) in an aqueous solution was proved by the NMR relaxation technique. PAMPA experiments show a strong increase in the amount of the penetrating praziquantel molecules in comparison with a saturated aqueous solution of pure drug used as a control. MD simulation of PZQ penetration through the bilayer demonstrates an increase in permeability into the membrane in the presence of a glycyrrhizin molecule. A decrease in the free energy barrier in the middle of the lipid bilayer was obtained, associated with the hydrogen bond between PZQ and GA. Also, GA reduces the local bilayer surface resistance to penetration of PZQ by rearranging the surface lipid headgroups. This study clarifies the mechanism of increasing the drug's bioavailability in the presence of glycyrrhizin.
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Affiliation(s)
- Alexandra V Kim
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Ekaterina A Shelepova
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Olga Yu Selyutina
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia
| | - Elizaveta S Meteleva
- Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
| | - Alexander V Dushkin
- Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
| | - Nikolai N Medvedev
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Nikolay E Polyakov
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
| | - Nikolay Z Lyakhov
- Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
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24
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Teixeira MH, Arantes GM. Effects of lipid composition on membrane distribution and permeability of natural quinones. RSC Adv 2019; 9:16892-16899. [PMID: 35516391 PMCID: PMC9064471 DOI: 10.1039/c9ra01681c] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/20/2019] [Indexed: 11/21/2022] Open
Abstract
Natural quinones are amphiphilic molecules that function as mobile charge carriers in biological energy transduction. Their distribution and permeation across membranes are important for binding to enzymatic complexes and for proton translocation. Here, we employ molecular dynamics simulations and free energy calculations with a carefully calibrated classical force-field to probe quinone distribution and permeation in a multi-component bilayer trying to mimic the composition of membranes involved in bioenergetic processes. Ubiquinone, ubiquinol, plastoquinone and menaquinone molecules with short and long isoprenoid tails are simulated. We find that penetration of water molecules bound to the polar quinone head increases considerably in the less ordered and porous bilayer formed by di-linoleoyl (18:2) phospholipids, resulting in a lower free energy barrier for quinone permeation and faster transversal diffusion. In equilibrium, quinone and quinol heads localize preferentially near lipid glycerol groups, but do not perform specific contacts with lipid polar heads. Quinone distribution is not altered significantly by the quinone head, tail and lipid composition in comparison to a single-component bilayer. This study highlights the role of lipid acyl chain unsaturation for permeation and transversal diffusion of polar molecules across biological membranes.
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Affiliation(s)
- Murilo Hoias Teixeira
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo Av. Prof. Lineu Prestes 748 05508-900 São Paulo SP Brazil
| | - Guilherme Menegon Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo Av. Prof. Lineu Prestes 748 05508-900 São Paulo SP Brazil
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25
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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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26
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Structural and barrier properties of the skin ceramide lipid bilayer: a molecular dynamics simulation study. J Mol Model 2019; 25:140. [PMID: 31041534 DOI: 10.1007/s00894-019-4008-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/29/2019] [Indexed: 10/26/2022]
Abstract
Skin provides excellent protection against the harsh external environment and foreign substances. The lipid matrix of the stratum corneum, which contains various kinds of ceramides, plays a major role in the barrier function of the skin. Here we report a study of the effects of ceramide type on the structural and transport properties of ceramide bilayers using molecular dynamics (MD) simulations. Specifically, the effects of headgroup chemistry (number and positions of hydroxyl groups) and tail structure (unsaturation of the sphingoid moiety) on the structural and transport properties of various ceramide bilayers at 310 K were analyzed. Theoretical results for structural properties such as area per lipid, bilayer thickness, lateral arrangement, order parameter, and hydrogen bonding are reported here and compared with corresponding experimental data. Our study revealed that the presence of a double bond disrupts the bilayer packing, which leads to a low area compressibility modulus, a large area per lipid, and low bilayer thickness. Furthermore, the effect of structural changes on water permeation was studied using steered MD simulations. Water permeation was found to be influenced by headgroup polarity, chain packing, and the ability of the water to hydrogen bond with the ceramides. The molecular-level information obtained from the current study should aid the design of mixed bilayer systems with desired properties and provide the basis for the development of higher order coarse-grained models.
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