1
|
von Lersner A, Fernandes F, Ozawa PM, Jackson M, Masureel M, Ho H, Lima SM, Vagner T, Sung BH, Wehbe M, Franze K, Pua H, Wilson JT, Irish JM, Weaver AM, Di Vizio D, Zijlstra A. Multiparametric Single-Vesicle Flow Cytometry Resolves Extracellular Vesicle Heterogeneity and Reveals Selective Regulation of Biogenesis and Cargo Distribution. ACS NANO 2024; 18:10464-10484. [PMID: 38578701 PMCID: PMC11025123 DOI: 10.1021/acsnano.3c11561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
Mammalian cells release a heterogeneous array of extracellular vesicles (EVs) that contribute to intercellular communication by means of the cargo that they carry. To resolve EV heterogeneity and determine if cargo is partitioned into select EV populations, we developed a method named "EV Fingerprinting" that discerns distinct vesicle populations using dimensional reduction of multiparametric data collected by quantitative single-EV flow cytometry. EV populations were found to be discernible by a combination of membrane order and EV size, both of which were obtained through multiparametric analysis of fluorescent features from the lipophilic dye Di-8-ANEPPS incorporated into the lipid bilayer. Molecular perturbation of EV secretion and biogenesis through respective ablation of the small GTPase Rab27a and overexpression of the EV-associated tetraspanin CD63 revealed distinct and selective alterations in EV populations, as well as cargo distribution. While Rab27a disproportionately affects all small EV populations with high membrane order, the overexpression of CD63 selectively increased the production of one small EV population of intermediate membrane order. Multiplexing experiments subsequently revealed that EV cargos have a distinct, nonrandom distribution with CD63 and CD81 selectively partitioning into smaller vs larger EVs, respectively. These studies not only present a method to probe EV biogenesis but also reveal how the selective partitioning of cargo contributes to EV heterogeneity.
Collapse
Affiliation(s)
- Ariana
K. von Lersner
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
| | - Fabiane Fernandes
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Institute
of Applied Biosciences and Chemistry, Hogeschool
Arnhem en Nijmegen University of Applied Sciences, Nijmegen 6525 EM, Gelderland, Netherlands
| | - Patricia Midori
Murobushi Ozawa
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Marques Jackson
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
| | - Matthieu Masureel
- Department
of Structural Biology, Genentech, San Francisco, California 94080, United States
| | - Hoangdung Ho
- Department
of Structural Biology, Genentech, San Francisco, California 94080, United States
| | - Sierra M. Lima
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Tatyana Vagner
- Department
of Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Bong Hwan Sung
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Mohamed Wehbe
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kai Franze
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
- KNIME
GmbH, Konstanz 78467, Germany
| | - Heather Pua
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - John T. Wilson
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jonathan M. Irish
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Alissa M. Weaver
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Dolores Di Vizio
- Department
of Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Andries Zijlstra
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
| |
Collapse
|
2
|
Bouquiaux C, Champagne B, Beaujean P. Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes. J Chem Inf Model 2024; 64:518-531. [PMID: 38157204 DOI: 10.1021/acs.jcim.3c01568] [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: 01/03/2024]
Abstract
A multistep computational approach has been employed to study a multimillion all-atom dyed plasma membrane, with no less than 42 different lipid species spanning the major head groups and a variety of fatty acids, as well as cholesterol, with the objective of investigating its structure and dynamics, as well as its impact on the embedded di-8-ANEPPS dyes. The latter are commonly used as bioimaging probes and serve as local microscopes. So, they provide information on membrane morphology via their second harmonic nonlinear optical (NLO) responses, which have the advantage of being specific to interface regions and sensitive to the chromophore environment. In previous studies, this chromophore has only been studied in simpler membrane models, far from the complexity of real lipid bilayers, while, owing to the ever-increasing computational resources, multimillion lipid bilayers have been studied, giving access to the effects of its heterogeneity. First, using molecular dynamics (MD) simulations, it is found that the combination of lipids produces a more ordered and denser membrane compared to its homogeneous model counterparts, while the local environment of the embedded dyes becomes enriched in phosphatidylcholine. Subsequently, the second harmonic first hyperpolarizability of the probes was calculated at the TDDFT level on selected frames of MD, highlighting the influence of the lipid environment. Due to the complexity of the system, machine learning (ML) tools have been employed to establish relationships between the membrane structural parameters, the orientation of the probes, and their NLO responses. These ML approaches have revealed influential features, including the presence of diacylglycerol lipids close to the dye. On the whole, this work provides a first step toward understanding the cooperation, synergy, and interactions that occur in such complex guest-host environments, which have emerged as new targets for drug design and membrane lipid therapy.
Collapse
Affiliation(s)
- Charlotte Bouquiaux
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Benoît Champagne
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Pierre Beaujean
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000 Namur, Belgium
| |
Collapse
|
3
|
Youngworth R, Roux B. Simulating the Fluorescence of Di-8-ANEPPS in Solvents of Different Polarity. J Phys Chem B 2024; 128:184-192. [PMID: 38113410 DOI: 10.1021/acs.jpcb.3c02974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Voltage-sensitive fluorescent probes, such as di-8-amino-naphthyl-ethylene-pyridinium-propyl-sulfonate (di-8-ANEPPS), are extremely useful for monitoring the membrane potential in biological and biophysical studies. However, because di-8-ANEPPS is very sensitive to its environment, it can be difficult to distinguish the degree to which a given external factor affects the observed fluorescence. Molecular dynamics simulations based on detailed atomic models make it possible to examine the particular characteristics of the system and predict the effects of the surroundings. Here, the sensitivity of the spectra of di-8-ANEPPS to solvent polarity is investigated by modeling the electronic transition between the ground and excited states using classical molecular mechanical force fields. The absorption and emission of di-8-ANEPPS were simulated in 12 solvents of increasing polarity using nonpolarizable and polarizable force fields. While the computational results and experimental data do not match perfectly, classical Lippert plots of both models show the expected increase of the Stokes shift of di-8-ANEPPS with the orientation polarizability of the surrounding solvent.
Collapse
Affiliation(s)
- Rachael Youngworth
- Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 57th Street, Chicago, Illinois 60637, United States
| |
Collapse
|
4
|
Bouquiaux C, Beaujean P, Ramos TN, Castet F, Rodriguez V, Champagne B. First hyperpolarizability of the di-8-ANEPPS and DR1 nonlinear optical chromophores in solution. An experimental and multi-scale theoretical chemistry study. J Chem Phys 2023; 159:174307. [PMID: 37933782 DOI: 10.1063/5.0174979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023] Open
Abstract
The solvent effects on the linear and second-order nonlinear optical properties of an aminonaphtylethenylpyridinium (ANEP) dye are investigated by combining experimental and theoretical chemistry methods. On the one hand, deep near infrared (NIR) hyper-Rayleigh scattering (HRS) measurements (1840-1950 nm) are performed on solutions of di-8-ANEPPS in deuterated chloroform, dimethylformamide, and dimethylsulfoxide to determine their first hyperpolarizablity (βHRS). For the first time, these HRS experiments are carried out in the picosecond regime in the deep NIR with very moderate (≤3 mW) average input power, providing a good signal-to-noise ratio and avoiding solvent thermal effects. Moreover, the frequency dispersion of βHRS is investigated for Disperse Red 1 (DR1), a dye commonly used as HRS external reference. On the other hand, these are compared with computational chemistry results obtained by using a sequential molecular dynamics (MD) then quantum mechanics (QM) approach. The MD method allows accounting for the dynamical nature of the molecular structures. Then, the QM part is based on TDDFT/M06-2X/6-311+G* calculations using solvation models ranging from continuum to discrete ones. Measurements report a decrease of the βHRS of di-8-ANEPPS in more polar solvents and these effects are reproduced by the different solvation models. For di-8-ANEPPS and DR1, comparisons show that the use of a hybrid solvation model, combining the description of the solvent molecules around the probe by point charges with a continuum model, already achieves quasi quantitative agreement with experiment. These results are further improved by using a polarizable embedding that includes the atomic polarizabilities in the solvent description.
Collapse
Affiliation(s)
- Charlotte Bouquiaux
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Pierre Beaujean
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Tárcius N Ramos
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Frédéric Castet
- University of Bordeaux, Institut des Sciences Moléculaires, UMR 5255 CNRS, cours de la Libération 351, F-33405 Talence Cedex, France
| | - Vincent Rodriguez
- University of Bordeaux, Institut des Sciences Moléculaires, UMR 5255 CNRS, cours de la Libération 351, F-33405 Talence Cedex, France
| | - Benoît Champagne
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000 Namur, Belgium
| |
Collapse
|
5
|
Youngworth R, Roux B. Simulating the Voltage-Dependent Fluorescence of Di-8-ANEPPS in a Lipid Membrane. J Phys Chem Lett 2023; 14:8268-8276. [PMID: 37676243 PMCID: PMC10510438 DOI: 10.1021/acs.jpclett.3c01257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Voltage-sensitive fluorescent dyes such as di-8-ANEPPS (di-8-aminonaphthylethylenepyridinium propylsulfonate) are powerful tools to study biological membranes. Its fluorescence is affected by changes in the membrane potential and other factors, requiring extensive calibration to extract meaningful quantitative results. The amphiphilic di-8-ANEPPS molecule is expected to bind at the membrane-solution interface. However, atomic-level information is sparse about its position and orientation in the membrane, especially in regards to how the latter dynamically fluctuates to affect the observed fluorescence. In the present work, molecular dynamics simulations of the ground and excited states of di-8-ANEPPS embedded in a DPPC membrane as represented by classical force fields were used to investigate how the fluorescence is affected by externally applied potential. The calculations reproduce the shifts in the wavelength of emission as a function of voltage that are observed experimentally, indicating that the approach can help better understand the various factors that can affect the fluorescence of membrane-bound dyes.
Collapse
Affiliation(s)
- Rachael Youngworth
- Department
of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
| |
Collapse
|
6
|
Naim C, Vangheluwe R, Ledoux-Rak I, Champagne B, Tonnelé C, Blanchard-Desce M, Matito E, Castet F. Electric-field induced second harmonic generation responses of push-pull polyenic dyes: experimental and theoretical characterizations. Phys Chem Chem Phys 2023; 25:13978-13988. [PMID: 37191226 DOI: 10.1039/d3cp00750b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The second-order nonlinear optical properties of four series of amphiphilic cationic chromophores involving different push-pull extremities and increasingly large polyenic bridges have been investigated both experimentally, by means of electric field induced second harmonic (EFISH) generation, and theoretically, using a computational approach combining classical molecular dynamics (MD) and quantum chemical (QM) calculations. This theoretical methodology allows to describe the effects of structural fluctuations on the EFISH properties of the complexes formed by the dye and its iodine counterion, and provides a rationale to EFISH measurements. The good agreement between experimental and theoretical results proves that this MD + QM scheme constitutes a useful tool for a rational, computer-aided, design of SHG dyes.
Collapse
Affiliation(s)
- Carmelo Naim
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400 Talence, France.
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 Donostia, Euskadi, Spain.
| | - Raphaël Vangheluwe
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400 Talence, France.
| | - Isabelle Ledoux-Rak
- Laboratoire Lumière, Matière et Interfaces, Institut d'Alembert-ENS Paris Saclay-CNRS-CentraleSupelec, 4 Avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - Benoît Champagne
- Unité de Chimie Physique Théorique et Structurale, Chemistry Department, Namur Institute of Structured Matter, University of Namur, Belgium
| | - Claire Tonnelé
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 Donostia, Euskadi, Spain.
| | | | - Eduard Matito
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 Donostia, Euskadi, Spain.
- Ikerbasque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Euskadi, Spain
| | - Frédéric Castet
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400 Talence, France.
| |
Collapse
|
7
|
Bouquiaux C, Castet F, Champagne B. Influence of the Nature of the Lipid Building Blocks on the Second-Order Nonlinear Optical Responses of an Embedded Di-8-ANEPPS Probe. J Phys Chem B 2023; 127:528-541. [PMID: 36606294 DOI: 10.1021/acs.jpcb.2c08093] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The extensive collection of lipids found in cell membranes is justified by the fact that each lipid contributes to their overall structure, dynamics, and properties and so to the biological processes taking place within them. It also showcases that, in order to deepen our understanding of membranes, we need to have a tool to differentiate lipid bilayers of varying composition. In this work, we investigate a suite of single-component saturated glycerophospholipids varying only in their headgroup structure by analyzing the second harmonic generation (SHG) nonlinear optical (NLO) response of a probe, di-8-ANEPPS, embedded into the membranes. The seven hydrophilic heads chosen (phosphatidylcholine (PC), phosphatidylethanolamine (PE), diaglycerol (GL), phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), and phosphatidyc acid (PA)) represent all the major headgroups that are part of mammalian plasma membranes and provide an assortment of neutral, zwiterrionic, and charged species. First, molecular dynamics simulations revealed that the lipidic arrangement is strongly sensitive to the nature of the hydrophilic head and less to the variety in the hydrophobic region. Membranes exhibiting drastically opposite structural properties can be pointed out: 1,2-dihexadecanoyl-rac-glycerol (DPGL) is the thickest and most ordered and aligned system, whereas 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) (DPPG) is thinnest and least ordered and aligned system. The structural analyses are then confronted with the molecular NLO responses, β, computed at the time-dependent density functional theory (TDDFT) level. As the orientation of the chromophore is impacted by the various degrees of order within the lipid bilayers, the diagonal component of the β tensor parallel to the bilayer normal, βZZZ, is as well. In the end, this computational approach provides insights into the link between lipid building blocks and the NLO responses of the embedded dye.
Collapse
Affiliation(s)
- Charlotte Bouquiaux
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000Namur, Belgium
| | - Frédéric Castet
- University of Bordeaux, Institut des Sciences Moléculaires, UMR 5255 CNRS, cours de la Libération 351, F-33405 CedexTalence, France
| | - Benoît Champagne
- University of Namur, Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, rue de Bruxelles, 61, B-5000Namur, Belgium
| |
Collapse
|
8
|
Castet F, Tonnelé C, Muccioli L, Champagne B. Predicting the Second-Order Nonlinear Optical Responses of Organic Materials: The Role of Dynamics. Acc Chem Res 2022; 55:3716-3726. [PMID: 36469424 DOI: 10.1021/acs.accounts.2c00616] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The last 30 years have witnessed an ever-growing application of computational chemistry for rationalizing the nonlinear optical (NLO) responses of organic chromophores. More specifically, quantum chemical calculations proved highly helpful in gaining fundamental insights into the factors governing the magnitude and character of molecular first hyperpolarizabilities (β), be they either intrinsic to the chromophore molecular structure and arising from symmetry, chemical substitution, or π-electron delocalization, or induced by external contributions such as the laser probe or solvation and polarization effects. Most theoretical reports assumed a rigid picture of the investigated systems, the NLO responses being computed solely at the most stable geometry of the chromophores. Yet, recent developments combining classical molecular dynamics (MD) simulations and DFT calculations have evidenced the significant role of structural fluctuations, which may induce broad distributions of NLO responses, and even generate them in some instances.This Account presents recent case studies in which theoretical simulations have highlighted these effects. The discussion specifically focuses on the simulation of the second-order NLO properties that can be measured experimentally either from Hyper-Rayleigh Scattering (HRS) or Electric-Field Induced Second Harmonic Generation (EFISHG). More general but technical topics concerning several aspects of the calculations of hyperpolarizabilities are instead discussed in the Supporting Information.Selected examples include organic chromophores, photochromic systems, and ionic complexes in the liquid phase, for which the effects of explicit solvation, concentration, and chromophore aggregation are emphasized, as well as large flexible systems such as peptide chains and pyrimidine-based helical polymers, in which the relative variations of the responses were shown to be several times larger than their average values. The impact of geometrical fluctuations is also illustrated for supramolecular architectures with the examples of nanoparticles formed by organic dipolar dyes in water solution, whose soft nature allows for large shape variations translating into huge fluctuations in time of their NLO response, and of self-assembled monolayers (SAMs) based on indolino-oxazolidine or azobenzene switches, in which the geometrical distortions of the photochromic molecules, as well as their orientational and positional disorder within the SAMs, highly impact their NLO response and contrast upon switching. Finally, the effects of the rigidity and fluidity of the surrounding are evidenced for NLO dyes inserted in phospholipid bilayers.
Collapse
Affiliation(s)
- Frédéric Castet
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, F-33400Talence, France
| | - Claire Tonnelé
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018Donostia, Euskadi, Spain
| | - Luca Muccioli
- Department of Industrial Chemistry "'Toso Montanari"', University of Bologna, Viale Risorgimento 4, 40136Bologna, Italy
| | - Benoît Champagne
- Unité de Chimie Physique Théorique et Structurale, Chemistry Department, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, 5000Namur, Belgium
| |
Collapse
|
9
|
Mendanha K, Bruno Assis Oliveira L, Colherinhas G. Modeling, energetic and structural analysis of peptide membranes formed by arginine and phenylalanine (R2F4R2) using fully atomistic molecular dynamics. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
10
|
Synergistic Membrane Disturbance Improves the Antibacterial Performance of Polymyxin B. Polymers (Basel) 2022; 14:polym14204316. [PMID: 36297894 PMCID: PMC9611124 DOI: 10.3390/polym14204316] [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: 09/12/2022] [Revised: 09/29/2022] [Accepted: 10/09/2022] [Indexed: 01/24/2023] Open
Abstract
Drug-resistant Gram-negative bacteria pose a serious threat to public health, and polymyxin B (PMB) is clinically used as a last-line therapy for the treatment of infections caused by these pathogens. However, the appearance of PMB resistance calls for an effort to develop new approaches to improve its antibacterial performance. In this work, a new type of nanocomposite, composed of PMB molecules being chemically decorated on the surface of graphene oxide (GO) nanosheets, was designed, which showed potent antibacterial ability through synergistically and physically disturbing the bacterial membrane. The as-fabricated PMB@GO nanocomposites demonstrated an enhanced bacterial-killing efficiency, with a minimum inhibitory concentration (MIC) value half of that of free PMB (with an MIC value as low as 0.5 μg mL-1 over Escherichia coli), and a bacterial viability less than one fourth of that of PMB (with a bacterial reduction of 60% after 3 h treatment, and 90% after 6 h incubation). Furthermore, the nanocomposite displayed moderate cytotoxicity or hemolysis effect, with cellular viabilities over 85% at concentrations up to 16 times the MIC value. Studies on antibacterial mechanism revealed that the synergy between PMB molecules and GO nanosheets greatly facilitated the vertical insertion of the nanocomposite into the lipid membrane, leading to membrane disturbance and permeabilization. Our results demonstrate a physical mechanism for improving the antibacterial performance of PMB and developing advanced antibacterial agents for better clinic uses.
Collapse
|
11
|
Krajewski B, Rajput SS, Chołuj M, Wojaczyńska E, Miniewicz A, Alam MM, Zaleśny R. First-order hyperpolarizabilities of propellanes: elucidating structure-property relationships. Phys Chem Chem Phys 2022; 24:13534-13541. [PMID: 35612526 DOI: 10.1039/d2cp00381c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Following recent experimental work demonstrating strong nonlinear optical properties, namely second harmonic generation of light, in crystals composed of 16,20-dinitro-(3,4,8,9)-dibenzo-2,7-dioxa-5,10-diaza[4.4.4]propellane molecules [A. Miniewicz, S. Bartkiewicz, E. Wojaczyńska, T. Galica, R. Zaleśny and R. Jakubas, J. Mater. Chem. C, 2019, 7, 1255-1262] in this paper we aim to investigate "structure-property" relationships for a series of 16 propellanes presenting a wide palette of substituents with varying electron-accepting/donating capabilities. To that end, we use electronic- and vibrational-structure theories and a recently developed generalized few-state model combined with a range-separated CAM-B3LYP functional to analyze electronic and vibrational contributions to the first hyperpolarizability for the whole series of molecules. The variations in computed properties are large among the studied set of substituents and can reach an order of magnitude. It has been demonstrated that the maximum values of frequency-independent first hyperpolarizability are expected for strong electron-accepting NO2 substituents, but only at the preferred position with respect to the electronegative oxygen atom in the 1,4-oxazine moiety. This holds for electronic as well as vibrational counterparts.
Collapse
Affiliation(s)
- Bartosz Krajewski
- Department of Theoretical Physics, Faculty of Fundamental Problems of Technology, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370, Wrocław, Poland
| | - Swati Singh Rajput
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
| | - Marta Chołuj
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370, Wrocław, Poland.
| | - Elżbieta Wojaczyńska
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370, Wrocław, Poland.
| | - Andrzej Miniewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370, Wrocław, Poland.
| | - Md Mehboob Alam
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
| | - Robert Zaleśny
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370, Wrocław, Poland.
| |
Collapse
|
12
|
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.
Collapse
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;
| |
Collapse
|