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Blumenfeld Z, Bera K, Castrén E, Lester HA. Antidepressants enter cells, organelles, and membranes. Neuropsychopharmacology 2024; 49:246-261. [PMID: 37783840 PMCID: PMC10700606 DOI: 10.1038/s41386-023-01725-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 10/04/2023]
Abstract
We begin by summarizing several examples of antidepressants whose therapeutic actions begin when they encounter their targets in the cytoplasm or in the lumen of an organelle. These actions contrast with the prevailing view that most neuropharmacological actions begin when drugs engage their therapeutic targets at extracellular binding sites of plasma membrane targets-ion channels, receptors, and transporters. We review the chemical, pharmacokinetic, and pharmacodynamic principles underlying the movements of drugs into subcellular compartments. We note the relationship between protonation-deprotonation events and membrane permeation of antidepressant drugs. The key properties relate to charge and hydrophobicity/lipid solubility, summarized by the parameters LogP, pKa, and LogDpH7.4. The classical metric, volume of distribution (Vd), is unusually large for some antidepressants and has both supracellular and subcellular components. A table gathers structures, LogP, PKa, LogDpH7.4, and Vd data and/or calculations for most antidepressants and antidepressant candidates. The subcellular components, which can now be measured in some cases, are dominated by membrane binding and by trapping in the lumen of acidic organelles. For common antidepressants, such as selective serotonin reuptake inhibitors (SSRIs) and serotonin/norepinephrine reuptake inhibitors (SNRIs), the target is assumed to be the eponymous reuptake transporter(s), although in fact the compartment of target engagement is unknown. We review special aspects of the pharmacokinetics of ketamine, ketamine metabolites, and other rapidly acting antidepressants (RAADs) including methoxetamine and scopolamine, psychedelics, and neurosteroids. Therefore, the reader can assess properties that markedly affect a drug's ability to enter or cross membranes-and therefore, to interact with target sites that face the cytoplasm, the lumen of organelles, or a membrane. In the current literature, mechanisms involving intracellular targets are termed "location-biased actions" or "inside-out pharmacology". Hopefully, these general terms will eventually acquire additional mechanistic details.
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Affiliation(s)
- Zack Blumenfeld
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Kallol Bera
- Department of Neurosciences and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, USA
| | - Eero Castrén
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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2
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Ghorbani M, Dehghan G, Allahverdi A. Insight into the effect of ibuprofen on the permeability of the membrane: a molecular dynamic simulation study. J Biomol Struct Dyn 2023:1-11. [PMID: 37982256 DOI: 10.1080/07391102.2023.2283151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023]
Abstract
Studying interactions between drugs and cell membranes is of great interest to designing novel drugs, optimizing drug delivery, and discerning drug mechanism action. In this study, we investigated the physical properties of the bilayer membrane model of POPC upon interaction with ibuprofen (IBU) using molecular dynamics simulations. The area per lipid (APL) was calculated to describe the effect of ibuprofen on the packing properties of the lipid bilayer. The APL was 0.58 nm2 and 0.63 nm2 for the membrane in low and high IBU respectively, and 0.57 nm2 for the membrane without IBU. Our finding showed that the mean square deviation (MSD) increased with increased ibuprofen content. In addition, the order parameter for the hydrocarbon chain of lipids increased with increased ibuprofen content. There was an increment in the transfer free energy after the head group region while it was maximum in the hydrophobic core for hydrogen peroxide (H2O2) (∼6.2 kcal.mol-1) and H2O (∼3.4 kcal.mol-1) which then decreased to respective values of (∼4.6 kcal.mol-1), and (∼2.3 kcal.mol-1) at the center of the bilayer in the presence of IBU. It seems that in the presence of ibuprofen, the free energy profile of the permeability of water and H2O2 significantly decreased. These findings show that ibuprofen significantly influences the physical properties of the bilayer by decreasing the packing and intermolecular interaction in the hydrocarbon chain region and increasing the water permeability of the bilayer. These results may provide insights into the local cytotoxic side effects of ibuprofen and its underlying molecular mechanisms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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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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Almeida ER, Goliatt PVZC, Dos Santos HF, Picaud F. Translocation Processes of Pt(II)-Based Drugs through Human Breast Cancer Cell Membrane: In Silico Experiments. J Chem Inf Model 2023; 63:6141-6155. [PMID: 37751589 DOI: 10.1021/acs.jcim.3c00943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Breast cancer is one of the most frequent modalities of cancer worldwide, with notable mortality. The medication based on platinum drugs (cisplatin (cddp), carboplatin (cpx), and oxaliplatin (oxa)) is a conventional chemotherapy despite severe side effects and the development of drug resistance. In order to provide a deeper molecular description of the influx and efflux processes of platinum drugs through breast cancer tissues, this study focuses on molecular dynamics (MD) simulations of the passive translocation process through a realistic plasma membrane prototype of human breast cancer cell (c_memb). The results showed that the permeation events were mainly mediated by neutral lipids (DOPC, DOPE, and cholesterol), producing a low and temporary membrane deformation. The drug insertion in the region of polar heads was the most favorable stage of the translocation mechanism, especially for cddp and oxa with potential wells of -8.6 and -9.8 kcal mol-1, respectively. However, the potentials of mean force (PMF) revealed unfavorable kinetics for the permeation of these drugs through lipid tails, with energy barriers of 28.3 (cddp), 32.2 (cpx), and 30.4 kcal mol-1 (oxa). The low permeability coefficients (P) of cpx and oxa, which were 3 and 1 orders of magnitude inferior than for cddp, resulted from the high energy barriers for their traslocation processes through the membrane. The obtained results provide a more accurate picture of the permeation of Pt(II)-based drugs through breast cancer cells, which may be relevant for the design and evaluation of new platinum complexes.
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Affiliation(s)
- Eduardo R Almeida
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil
- Laboratoire de Nanomédecine, Imagerie et Thérapeutiques, EA 4662, Université de Franche-Comté, Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon cedex, France
| | - Priscila V Z Capriles Goliatt
- Programa de Pós-graduação em Modelagem Computacional (PGMC), Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil
| | - Hélio F Dos Santos
- Núcleo de Estudos em Química Computacional (NEQC), Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutiques, EA 4662, Université de Franche-Comté, Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon cedex, France
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5
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Kumar J, Chng CP, Huang C. Hydrophobic Matching Dictates over the Linear Rule of Mixtures in Binary Lipid Membranes. J Phys Chem B 2023; 127:7946-7954. [PMID: 37674349 DOI: 10.1021/acs.jpcb.3c04502] [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: 09/08/2023]
Abstract
Biological membranes feature heterogeneous mixtures of lipids with different head and tail characteristics. Their biophysical properties are dictated by the intimate interaction among different constituent lipids. Previous studies suggest that the membrane area-per-lipid (APL) deviates from the linear rule of mixtures (LRM) for binary lipid membranes, but the underlying mechanism remains elusive. Our molecular dynamics (MD) simulations of binary lipid membranes consisting of lipids with different tail characteristics reveal a competitive mechanism whereby lipids tend to deform each other to minimize the hydrophobic mismatch between their tails. Depending on the relative tail lengths and saturation levels, this may result in an either positive or negative deviation of APL from the LRM. As lipid packing plays an essential role in membrane fusion and peptide-membrane binding, our findings may help guide the selection of lipids for the effective rational design of nanoliposomes and membrane-targeting peptides.
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Affiliation(s)
- Jatin Kumar
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Changjin Huang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
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Meleleo D, Avato P, Conforti F, Argentieri MP, Messina G, Cibelli G, Mallamaci R. Interaction of Quercetin, Cyanidin, and Their O-Glucosides with Planar Lipid Models: Implications for Their Biological Effects. MEMBRANES 2023; 13:600. [PMID: 37367804 DOI: 10.3390/membranes13060600] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023]
Abstract
Flavonoids are specialized metabolites produced by plants, as free aglycones or as glycosylated derivatives, which are particularly endowed with a variety of beneficial health properties. The antioxidant, anti-inflammatory, antimicrobial, anticancer, antifungal, antiviral, anti-Alzheimer's, anti-obesity, antidiabetic, and antihypertensive effects of flavonoids are now known. These bioactive phytochemicals have been shown to act on different molecular targets in cells including the plasma membrane. Due to their polyhydroxylated structure, lipophilicity, and planar conformation, they can either bind at the bilayer interface or interact with the hydrophobic fatty acid tails of the membrane. The interaction of quercetin, cyanidin, and their O-glucosides with planar lipid membranes (PLMs) similar in composition to those of the intestine was monitored using an electrophysiological approach. The obtained results show that the tested flavonoids interact with PLM and form conductive units. The modality of interaction with the lipids of the bilayer and the alteration of the biophysical parameters of PLMs induced by the tested substances provided information on their location in the membrane, helping to elucidate the mechanism of action which underlies some pharmacological properties of flavonoids. To our knowledge, the interaction of quercetin, cyanidin, and their O-glucosides with PLM surrogates of the intestinal membrane has never been previously monitored.
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Affiliation(s)
- Daniela Meleleo
- Department of Science of Agriculture, Food, Natural Resources and Engineering, University of Foggia, 71122 Foggia, Italy
| | - Pinarosa Avato
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", 70125 Bari, Italy
| | - Filomena Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Maria Pia Argentieri
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", 70125 Bari, Italy
| | - Giovanni Messina
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Giuseppe Cibelli
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Rosanna Mallamaci
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", 70125 Bari, Italy
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7
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Lirussi F, Pyrshev K, Yesylevskyy S, Rivel T, Lopez T, Coppens E, Mura S, Couvreur P, Ramseyer C. Plasma membrane lipid bilayer is druggable: Selective delivery of gemcitabine-squalene nano-medicine to cancer cells. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166614. [PMID: 36494037 DOI: 10.1016/j.bbadis.2022.166614] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Up to now the lipid bilayers were rarely considered as targets in cancer therapy despite pronounced differences in lipid composition between plasma membranes of benign and malignant cells. In this study we demonstrate that the lipid bilayer of the plasma membrane is druggable and suitable for facilitating selective delivery of amphiphilic gemcitabine-squalene nanomedicines to cancer cells. Data from radioactive assays, fluorescent membrane probes and molecular dynamics simulations provide evidence of selective accumulation of gemcitabine-squalene in the plasma membranes with disrupted lipid asymmetry and its subsequent preferential uptake by malignant cells. This causes pronounced cytotoxicity on cancer cells in comparison to their benign counterparts originating from the same tissue.
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Affiliation(s)
- Frédéric Lirussi
- UMR 1231, Lipides Nutrition Cancer, INSERM, F-21000 Dijon, France; UFR des Sciences de Santé, Université Bourgogne Franche-Comté, F-25000 Besançon, France; Plateforme PACE, Laboratoire de Pharmacologie-Toxicologie, Centre Hospitalo-Universitaire Besançon, F-25000 Besançon, France.
| | - Kyrylo Pyrshev
- UFR des Sciences de Santé, Université Bourgogne Franche-Comté, F-25000 Besançon, France; Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, 46 Nauky ave, 03028 Kyiv, Ukraine; Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA; Department of Neurochemistry, Palladin Institute of Biochemistry of the NAS of Ukraine, 9 Leontovycha str., 01601 Kyiv, Ukraine
| | - Semen Yesylevskyy
- Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, 46 Nauky ave, 03028 Kyiv, Ukraine; Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, CZ-166 10, Prague 6, Czech Republic; Receptor.AI Inc, 20-22 Wenlock Road, London N1 7GU, United Kingdom
| | - Timothée Rivel
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France; CEITEC - Central European Institute of Technology, Masaryk University, Kamenice, CZ-62500, Brno, Czech Republic
| | - Tatiana Lopez
- UMR 1231, Lipides Nutrition Cancer, INSERM, F-21000 Dijon, France; UFR des Sciences de Santé, Université Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Eleonore Coppens
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France
| | - Simona Mura
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France
| | - Patrick Couvreur
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296, Châtenay-Malabry, France
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France
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8
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Martinho N, Marquês JMT, Todoriko I, Prieto M, de Almeida RF, Silva LC. Effect of Cisplatin and Its Cationic Analogues in the Phase Behavior and Permeability of Model Lipid Bilayers. Mol Pharm 2023; 20:918-928. [PMID: 36700695 PMCID: PMC9906771 DOI: 10.1021/acs.molpharmaceut.2c00321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Increasing evidence suggests a critical role of lipids in both the mechanisms of toxicity and resistance of cells to platinum(II) complexes. In particular, cisplatin and other analogues were reported to interact with lipids and transiently promote lipid phase changes both in the bulk membranes and in specific membrane domains. However, these processes are complex and not fully understood. In this work, cisplatin and its cationic species formed at pH 7.4 in low chloride concentrations were tested for their ability to induce phase changes in model membranes with different lipid compositions. Fluorescent probes that partition to different lipid phases were used to report on the fluidity of the membrane, and a leakage assay was performed to evaluate the effect of cisplatin in the permeability of these vesicles. The results showed that platinum(II) complex effects on membrane fluidity depend on membrane lipid composition and properties, promoting a stronger decrease in the fluidity of membranes containing gel phase. Moreover, at high concentration, these complexes were prone to alter the permeability of lipid membranes without inducing their collapse or aggregation.
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Affiliation(s)
- Nuno Martinho
- Research
Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003Lisboa, Portugal,iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering,
Instituto Superior Técnico, Universidade
de Lisboa, Av. Rovisco Pais, 1649-003Lisboa, Portugal,Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1649-003Lisboa, Portugal
| | - Joaquim M. T. Marquês
- Centro
de Química Estrutural, Institute of Molecular Sciences, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1649-003Lisboa, Portugal
| | - Iryna Todoriko
- Centro
de Química Estrutural, Institute of Molecular Sciences, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1649-003Lisboa, Portugal
| | - Manuel Prieto
- iBB—Institute
for Bioengineering and Biosciences and Department of Bioengineering,
Instituto Superior Técnico, Universidade
de Lisboa, Av. Rovisco Pais, 1649-003Lisboa, Portugal,Associate
Laboratory i4HB—Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1649-003Lisboa, Portugal
| | - Rodrigo F.M. de Almeida
- Centro
de Química Estrutural, Institute of Molecular Sciences, Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1649-003Lisboa, Portugal
| | - Liana C. Silva
- Research
Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003Lisboa, Portugal,
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9
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Surface functionalization of graphene nanosheet with poly (L-histidine) and its application in drug delivery: covalent vs non-covalent approaches. Sci Rep 2022; 12:19046. [PMID: 36351935 PMCID: PMC9646737 DOI: 10.1038/s41598-022-21619-0] [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: 08/25/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Nowadays, nanomaterials are increasingly being used as drug carriers in the treatment of different types of cancers. As a result, these applications make them attractive to researchers dealing with diagnosis and biomarkers discovery of the disease. In this study, the adsorption behavior of gemcitabine (GMC) on graphene nanosheet (GNS), in the presence and absence of Poly (L-histidine) (PLH) polymer is discussed using molecular dynamics (MD) simulation. The MD results revealed an increase in the efficiency and targeting of the drug when the polymer is covalently attached to the graphene substrate. In addition, the metadynamics simulation to investigate the effects of PLH on the adsorption capacity of the GNS, and explore the adsorption/desorption process of GMC on pristine and PLH- grafted GNS is performed. The metadynamics calculations showed that the amount of free energy of the drug in acidic conditions is higher (- 281.26 kJ/mol) than the free energy in neutral conditions (- 346.24 kJ/mol). Consequently, the PLH polymer may not only help drug adsorption but can also help in drug desorption in lower pH environments. Based on these findings, it can be said that covalent polymer bonding not only can help in the formation of a targeted drug delivery system but also can increase the adsorption capacity of the substrate.
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10
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Krisanova N, Pozdnyakova N, Pastukhov A, Dudarenko M, Shatursky O, Gnatyuk O, Afonina U, Pyrshev K, Dovbeshko G, Yesylevskyy S, Borisova T. Amphiphilic anti-SARS-CoV-2 drug remdesivir incorporates into the lipid bilayer and nerve terminal membranes influencing excitatory and inhibitory neurotransmission. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - BIOMEMBRANES 2022; 1864:183945. [PMID: 35461828 PMCID: PMC9023372 DOI: 10.1016/j.bbamem.2022.183945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/03/2022] [Accepted: 04/17/2022] [Indexed: 12/05/2022]
Abstract
Remdesivir is a novel antiviral drug, which is active against the SARS-CoV-2 virus. Remdesivir is known to accumulate in the brain but it is not clear whether it influences the neurotransmission. Here we report diverse and pronounced effects of remdesivir on transportation and release of excitatory and inhibitory neurotransmitters in rat cortex nerve terminals (synaptosomes) in vitro. Direct incorporation of remdesivir molecules into the cellular membranes was shown by FTIR spectroscopy, planar phospholipid bilayer membranes and computational techniques. Remdesivir decreases depolarization-induced exocytotic release of L-[14C] glutamate and [3H] GABA, and also [3H] GABA uptake and extracellular level in synaptosomes in a dose-dependent manner. Fluorimetric studies confirmed remdesivir-induced impairment of exocytosis in nerve terminals and revealed a decrease in synaptic vesicle acidification. Our data suggest that remdesivir dosing during antiviral therapy should be precisely controlled to prevent possible neuromodulatory action at the presynaptic level. Further studies of neurotropic and membranotropic effects of remdesivir are necessary.
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11
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Pinto SN, Mil-Homens D, Pires RF, Alves MM, Serafim G, Martinho N, Melo M, Fialho AM, Bonifácio VDB. Core-shell polycationic polyurea pharmadendrimers: new-generation of sustainable broad-spectrum antibiotics and antifungals. Biomater Sci 2022; 10:5197-5207. [PMID: 35880970 DOI: 10.1039/d2bm00679k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The efficacy of conventional antimicrobials is falling to critical levels and raising alarming concerns around the globe. In this scenery, engineered nanoparticles emerged as a solid strategy to fight growing deadly infections. Here, we show the in vitro and in vivo performance of pharmadendrimers, a novel class of engineered polyurea dendrimers that are synthetic mimics of antibacterial peptides, against a collection of both Gram-positive and Gram-negative bacteria and fungi. These nanobiomaterials are stable solids prepared by low-cost and green processes, display a dense positively charged core-shell, and are biocompatible and hemocompatible drugs. Mechanistic data, corroborated by coarse-grained molecular dynamics simulations, points towards a fast-killing mechanism via membrane disruption, triggered by electrostatic interactions. Altogether this study provides strong evidence and support for the future use of polyurea pharmadendrimers in antibacterial and antifungal nanotherapeutics.
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Affiliation(s)
- Sandra N Pinto
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Dalila Mil-Homens
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Rita F Pires
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Marta M Alves
- Centro de Química Estrutural (CQE), Institute of Molecular Sciences, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Gabriel Serafim
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Nuno Martinho
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Manuel Melo
- Instituto de Tecnologia Química Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Arsénio M Fialho
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal. .,Bioengineering Department, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Vasco D B Bonifácio
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal. .,Bioengineering Department, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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12
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Larsen AH. Molecular Dynamics Simulations of Curved Lipid Membranes. Int J Mol Sci 2022; 23:ijms23158098. [PMID: 35897670 PMCID: PMC9331392 DOI: 10.3390/ijms23158098] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and thereby be trafficked to specific locations. The description of curvature sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow researcher to closely match the conditions of experimental studies of membrane curvatures.
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13
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Experimental Investigations on the Conductance of Lipid Membranes under Differential Hydrostatic Pressure. MEMBRANES 2022; 12:membranes12050479. [PMID: 35629805 PMCID: PMC9144669 DOI: 10.3390/membranes12050479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 02/05/2023]
Abstract
The unassisted transport of inorganic ions through lipid membranes has become increasingly relevant to an expansive range of biological phenomena. Recent simulations indicate a strong influence of a lipid membrane's curvature on its permeability, which may be part of the overall cell sensitivity to mechanical stimulation. However, most ionic permeability experiments employ a flat, uncurved lipid membrane, which disregards the physiological relevance of curvature on such investigations. To fill this gap in our knowledge, we adapted a traditional experimental system consisting of a planar lipid membrane, which we exposed to a controlled, differential hydrostatic pressure. Our electrophysiology experiments indicate a strong correlation between the changes in membrane geometry elicited by the application of pressure, as inferred from capacitance measurements, and the resulting conductance. Our experiments also confirmed the well-established influence of cholesterol addition to lipid membranes in adjusting their mechanical properties and overall permeability. Therefore, the proposed experimental system may prove useful for a better understanding of the intricate connections between membrane mechanics and adjustments of cellular functionalities upon mechanical stimulation, as well as for confirmation of predictions made by simulations and theoretical modeling.
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14
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Interaction of Pelargonium sidoides Compounds with Lactoferrin and SARS-CoV-2: Insights from Molecular Simulations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095254. [PMID: 35564648 PMCID: PMC9101775 DOI: 10.3390/ijerph19095254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/17/2022] [Accepted: 04/24/2022] [Indexed: 02/07/2023]
Abstract
(1) Background: Pelargonium sidoides extracts and lactoferrin are two important natural, anti-inflammatory, and antiviral agents, which can interfere with the early stages of SARS-CoV-2 infection. Molecular docking and molecular dynamics simulation approaches have been applied to check for the occurrence of interactions of the Pelargonium sidoides compounds with lactoferrin and with SARS-CoV-2 components. (2) Methods: Computational methods have been applied to confirm the hypothesis of a direct interaction between PEL compounds and the lactoferrin protein and between Pelargonium sidoides compounds and SARS-CoV-2 Spike, 3CLPro, RdRp proteins, and membrane. Selected high-score complexes were structurally investigated through classical molecular dynamics simulation, while the interaction energies were evaluated using the molecular mechanics energies combined with generalized Born and surface area continuum solvation method. (3) Results: Computational analyses suggested that Pelargonium sidoides extracts can interact with lactoferrin without altering its structural and dynamical properties. Furthermore, Pelargonium sidoides compounds should have the ability to interfere with the Spike glycoprotein, the 3CLPro, and the lipid membrane, probably affecting the functional properties of the proteins inserted in the double layer. (4) Conclusion: Our findings suggest that Pelargonium sidoides may interfere with the mechanism of infection of SARS-CoV-2, especially in the early stages.
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15
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Wang C, Li J, Zhao L, Qian P. Shape transformations of red blood cells in the capillary and their possible connections to oxygen transportation. J Biol Phys 2022; 48:79-92. [PMID: 34799817 PMCID: PMC8866595 DOI: 10.1007/s10867-021-09594-5] [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: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
In this work, a series of numerical simulations have been performed to obtain the steady shapes of red blood cells under a shear force field in the capillary. Two possible classes of steady shapes, the axisymmetric parachute and the non-axisymmetric parachute, are found. If we assume that oxygen diffusion across the red cell membrane is mediated by membrane curvature, it is found that the non-axisymmetric parachute will be more favorable due to its special shape which enables it to have a larger portion of membrane patch capable of releasing oxygen to tissues.
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Affiliation(s)
- Caiqun Wang
- Department of Physics, School of Mathematics and Physics, University of Science and Technology Beijing, Beijing, 100083 China ,Beijing Computing Center, Beijing, 100094 China
| | - Jianfeng Li
- Department of Macromolecular Science, the State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China.
| | - Liutao Zhao
- College of Mechanical Engineering, Tianjin University, Tianjin, 300350 China ,Beijing Computing Center, Beijing, 100094 China
| | - Ping Qian
- Department of Physics, School of Mathematics and Physics, University of Science and Technology Beijing, Beijing, 100083, China.
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16
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Fujimoto K, Nagai T, Yamaguchi T. Momentum removal to obtain the position-dependent diffusion constant in constrained molecular dynamics simulation. J Comput Chem 2021; 42:2136-2144. [PMID: 34406659 DOI: 10.1002/jcc.26742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022]
Abstract
The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink-Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, τ v 0 , which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate τ v 0 value in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf-Roux method.
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Affiliation(s)
- Kazushi Fujimoto
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Tetsuro Nagai
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Tsuyoshi Yamaguchi
- Department of Materials Process Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
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17
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Cárdenas G, Pérez-Barcia Á, Mandado M, Nogueira JJ. Characterization of cisplatin/membrane interactions by QM/MM energy decomposition analysis. Phys Chem Chem Phys 2021; 23:20533-20540. [PMID: 34505588 DOI: 10.1039/d1cp03382d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We extend for the first time a quantum mechanical energy decomposition analysis scheme based on deformation electron densities to a hybrid electrostatic embedding quantum mechanics/molecular mechanics framework. The implemented approach is applied to characterize the interactions between cisplatin and a dioleyl-phosphatidylcholine membrane, which play a key role in the permeation mechanism of the drug inside the cells. The interaction energy decomposition into electrostatic, induction, dispersion and Pauli repulsion contributions is performed for ensembles of geometries to account for conformational sampling. It is evidenced that the electrostatic and repulsive components are predominant in both polar and non-polar regions of the bilayer.
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Affiliation(s)
- Gustavo Cárdenas
- Department of Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain.
| | - Álvaro Pérez-Barcia
- Department of Physical Chemistry, University of Vigo, Lagoas-Marcosende s/n, ES-36310-Vigo, Galicia, Spain.
| | - Marcos Mandado
- Department of Physical Chemistry, University of Vigo, Lagoas-Marcosende s/n, ES-36310-Vigo, Galicia, Spain.
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain. .,IADCHEM, Institute for Advanced Research in Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain
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18
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Stephenson EB, Elvira KS. Biomimetic artificial cells to model the effect of membrane asymmetry on chemoresistance. Chem Commun (Camb) 2021; 57:6534-6537. [PMID: 34106114 DOI: 10.1039/d1cc02043a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a microfluidic platform that enables the formation of bespoke asymmetric droplet interface bilayers (DIBs) as artificial cell models from naturally-derived lipids. We use them to perform pharmacokinetic assays to quantify how lipid asymmetry affects the permeability of the chemotherapy drug doxorubicin. Previous attempts to model bilayer asymmetry with DIBs have relied on the use of synthetic lipids to achieve asymmetry. Use of natural lipids serves to increase the biomimetic nature of these artificial cells, showcasing the next step towards forming a true artificial cell membrane in vitro. Here we use our microfluidic platform to form biomimetic, asymmetric and symmetric DIBs, with their asymmetry quantified through their life-mimicking degree of curvature. We subsequently examine permeability of these membranes to doxorubicin, and reveal measurable differences in its pharmacokinetics induced by membrane asymmetry, highlighting another factor that potentially contributes to chemoresistance in some forms of cancer.
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Affiliation(s)
- Elanna B Stephenson
- University of Victoria, Department of Chemistry, Victoria BC, V8W 2Y2, Canada.
| | - Katherine S Elvira
- University of Victoria, Department of Chemistry, Victoria BC, V8W 2Y2, Canada.
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19
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Aydin F, Durumeric AEP, da Hora GCA, Nguyen JDM, Oh MI, Swanson JMJ. Improving the accuracy and convergence of drug permeation simulations via machine-learned collective variables. J Chem Phys 2021; 155:045101. [PMID: 34340389 DOI: 10.1063/5.0055489] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Understanding the permeation of biomolecules through cellular membranes is critical for many biotechnological applications, including targeted drug delivery, pathogen detection, and the development of new antibiotics. To this end, computer simulations are routinely used to probe the underlying mechanisms of membrane permeation. Despite great progress and continued development, permeation simulations of realistic systems (e.g., more complex drug molecules or biologics through heterogeneous membranes) remain extremely challenging if not intractable. In this work, we combine molecular dynamics simulations with transition-tempered metadynamics and techniques from the variational approach to conformational dynamics to study the permeation mechanism of a drug molecule, trimethoprim, through a multicomponent membrane. We show that collective variables (CVs) obtained from an unsupervised machine learning algorithm called time-structure based Independent Component Analysis (tICA) improve performance and substantially accelerate convergence of permeation potential of mean force (PMF) calculations. The addition of cholesterol to the lipid bilayer is shown to increase both the width and height of the free energy barrier due to a condensing effect (lower area per lipid) and increase bilayer thickness. Additionally, the tICA CVs reveal a subtle effect of cholesterol increasing the resistance to permeation in the lipid head group region, which is not observed when canonical CVs are used. We conclude that the use of tICA CVs can enable more efficient PMF calculations with additional insight into the permeation mechanism.
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Affiliation(s)
- Fikret Aydin
- Quantum Simulation Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | | | - Gabriel C A da Hora
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - John D M Nguyen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Myong In Oh
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Jessica M J Swanson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
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20
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Phyo P, Zhao X, Templeton AC, Xu W, Cheung JK, Su Y. Understanding molecular mechanisms of biologics drug delivery and stability from NMR spectroscopy. Adv Drug Deliv Rev 2021; 174:1-29. [PMID: 33609600 DOI: 10.1016/j.addr.2021.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/20/2021] [Accepted: 02/07/2021] [Indexed: 02/06/2023]
Abstract
Protein therapeutics carry inherent limitations of membrane impermeability and structural instability, despite their predominant role in the modern pharmaceutical market. Effective formulations are needed to overcome physiological and physicochemical barriers, respectively, for improving bioavailability and stability. Knowledge of membrane affinity, cellular internalization, encapsulation, and release of drug-loaded carrier vehicles uncover the structural basis for designing and optimizing biopharmaceuticals with enhanced delivery efficiency and therapeutic efficacy. Understanding stabilizing and destabilizing interactions between protein drugs and formulation excipients provide fundamental mechanisms for ensuring the stability and quality of biological products. This article reviews the molecular studies of biologics using solution and solid-state NMR spectroscopy on structural attributes pivotal to drug delivery and stability. In-depth investigation of the structure-function relationship of drug delivery systems based on cell-penetrating peptides, lipid nanoparticles and polymeric colloidal, and biophysical and biochemical stability of peptide, protein, monoclonal antibody, and vaccine, as the integrative efforts on drug product design, will be elaborated.
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Affiliation(s)
- Pyae Phyo
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Xi Zhao
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Allen C Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Jason K Cheung
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, NJ 07033, United States.
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21
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Abstract
Background/Aim: A number of biologically active substances were proved as an alternative to conventional anticancer medicines. The aim of the study is in vitro investigation of the anticancer activity of mono- and di-Rhamnolipids (RL-1 and RL-2) against human breast cancer. Additionally, the combination with Cisplatin was analyzed. Materials and Methods: Breast cell lines (MCF-10A, MCF-7 and MDA-MB-231) were treated with RLs and in combination with Cisplatin. The viability was analyzed using MTT assay, and investigation of autophagy was performed via acridine orange staining. Results: In contrast to the healthy cells, both tested cancer lines exhibited sensitivity to RLs treatment. This effect was accompanied by an influence on the autophagy-related acidic formation process. Only for the triple-negative breast cancer cell line (MDA-MB-231) the synergistic effect of the combined treatment (10 µM Cisplatin and 1 µg/mL RL-2) was observed. Conclusion: Based on studies on the reorganization of membrane models in the presence of RL and the data about a higher amount of lipid rafts in cancer cell membranes than in non-tumorigenic, we suggest a possible mechanism of membrane remodelling by formation of endosomes. Shortly, in order to have a synergistic effect, it is necessary to have Cisplatin andRL-2 as RL2 is a molecule inducingpositive membrane curvature.
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22
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Ruano L, Cárdenas G, Nogueira JJ. The Permeation Mechanism of Cisplatin Through a Dioleoylphosphocholine Bilayer*. Chemphyschem 2021; 22:1251-1261. [PMID: 33829637 DOI: 10.1002/cphc.202100059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/07/2021] [Indexed: 01/01/2023]
Abstract
The investigation of the intermolecular interactions between platinum-based anticancer drugs and lipid bilayers is of special relevance to unveil the mechanisms involved in different steps of the anticancer mode of action of these drugs. We have simulated the permeation of cisplatin through a model membrane composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids by means of umbrella sampling classical molecular dynamics simulations. The initial physisorption of cisplatin into the polar region of the lipid membrane is controlled by long-range electrostatic interactions with the choline groups in a first step and, in a second step, by long-range electrostatic and hydrogen bond interactions with the phosphate groups. The second half of the permeation pathway, in which cisplatin diffuses through the nonpolar region of the bilayer, is characterized by the drop of the interactions with the polar heads and the rise of attractive interactions with the non-polar tails, which are dominated by van der Waals contributions. The permeation free-energy profile is explained by a complex balance between the drug/lipid interactions and the energy and entropy contributions associated with the dehydration of the drug along the permeation pathway and with the decrease and increase of the membrane ordering along the first and second half of the mechanism, respectively.
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Affiliation(s)
- Lorena Ruano
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain
| | - Gustavo Cárdenas
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain
| | - Juan J Nogueira
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain.,IADCHEM, Institute for Advanced Research in Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain
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23
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Oliveira MC, Yusupov M, Bogaerts A, Cordeiro RM. Lipid Oxidation: Role of Membrane Phase-Separated Domains. J Chem Inf Model 2021; 61:2857-2868. [PMID: 34080860 DOI: 10.1021/acs.jcim.1c00104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipid oxidation is associated with several inflammatory and neurodegenerative diseases, but many questions to unravel its effects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a significant effect on membrane function. It is reported that domain interfaces are "hot spots" for pore formation, but the underlying mechanisms and the effect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Specifically, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any effect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy.
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Affiliation(s)
- Maria C Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André, SP, Brazil.,Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Rodrigo M Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André, SP, Brazil
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24
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El Hajj F, Fuchs PFJ, Urbach W, Nassereddine M, Hamieh S, Taulier N. Molecular Study of Ultrasound-Triggered Release of Fluorescein from Liposomes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3868-3881. [PMID: 33769822 DOI: 10.1021/acs.langmuir.0c03444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Several investigations have suggested that ultrasound triggers the release of drugs encapsulated into liposomes at acoustic pressures low enough to avoid cavitation or high hyperthermia. However, the mechanism leading to this triggered release as well as the adequate composition of the liposome membrane remains unknown. Here, we investigate the ultrasound-triggered release of fluorescein disodium salt encapsulated into liposomes made of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) or 1,2-distearoylphosphatidyl-ethanolamine (DSPC) lipids with various concentrations of cholesterol (from 0 to 44 mol %). The passive release of encapsulated fluorescein was first characterized. It was observed to be higher when the membrane is in a fluid phase and increased with temperature but decreased upon addition of cholesterol. Next, the release of fluorescein was measured at different acoustic frequencies (0.8, 1.1, and 3.3 MHz) and peak-to-peak pressures (0, 2, 2.5, 5, and 8 MPa). Measurements were performed at temperatures where DOPC and DSPC liposomes were, respectively, in the fluid or gel phase. We found that the release rate did not depend on the ultrasound frequency. For DOPC liposomes, the ultrasound-triggered release of fluorescein decreased with increasing concentration of cholesterol in liposomes, while the behavior was more complex for DSPC liposomes. Overall, the triggered release from DSPC liposomes was up to ten times less than DOPC liposomes. Molecular dynamics simulations performed on a pure DOPC membrane showed that a membrane experiences, under a directional pressure of ±2.4 MPa, various changes in properties such as the area per lipid (APL). An increase in the APL was notably observed when the simulation box was laterally stretched or perpendicularly compressed, which was accompanied by an increase in the number of water molecules crossing the membrane. This suggests that ultrasound most probably enhances the diffusion of encapsulated molecules at small acoustic pressures by increasing the distance between lipids.
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Affiliation(s)
- Fatima El Hajj
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, LIB, F-75006 Paris, France
- Faculté des Sciences, Université Libanaise, Hadath 1003, Liban
| | - Patrick F J Fuchs
- Université de Paris, UFR Sciences du Vivant, F-75013 Paris, France
- Sorbonne Université, Ecole Normale Supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules (LBM), F-75005 Paris, France
| | - Wladimir Urbach
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | | | - Salah Hamieh
- Faculté des Sciences, Université Libanaise, Hadath 1003, Liban
| | - Nicolas Taulier
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, LIB, F-75006 Paris, France
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25
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Pezeshkian W, Marrink SJ. Simulating realistic membrane shapes. Curr Opin Cell Biol 2021; 71:103-111. [PMID: 33721706 DOI: 10.1016/j.ceb.2021.02.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
Abstract
Biological membranes exhibit diversity in their shapes and complexity in chemical compositions that are linked to many cellular functions. These two central features of biomembranes have been the subject of numerous simulation studies, using a diverse range of computational techniques. Currently, the field is able to capture this complexity at increasing levels of realism and connect the microscopic view on protein-lipid interactions to cellular morphologies at the level of entire organelles. Here we highlight recent advances in this topic, identify current bottlenecks, and sketch possible ways ahead.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
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26
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Goldberg E, Soba A, Gandía D, Fernández ML, Suárez C. Coupled mathematical modeling of cisplatin electroporation. Bioelectrochemistry 2021; 140:107788. [PMID: 33838515 DOI: 10.1016/j.bioelechem.2021.107788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022]
Abstract
The use of electrochemotherapy (ECT) is a well-established technique to increase the cellular uptake of cytotoxic agents within certain cancer treatment strategies. The study of the mechanisms that take part in this complex process is of high interest to gain a deeper knowledge of it, enabling the improvement of these strategies. In this work, we present a coupled multi-physics electroporation model based on a related previous one, to describe the effect of a set of electric pulses on cisplatin transport across the plasma membrane. The model applies a system of partial differential equations that includes Poisson's equation for the electric field, Nernst-Planck's equation for species transport, Maxwell's tensor and mechanical equilibrium equation for membrane deformation and Smoluchowski's equation for pore creation dynamics. Our numerical results were compared with previous numerical and experimental published data with good qualitative and quantitative agreement. These results indicate that pore aperture is favored at the cell poles by the electric field and mechanical stress forces, giving support to the dominant hypothesis of hydrophilic pore creation as the main mechanism of drug entry during an ECT treatment.
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Affiliation(s)
- Ezequiel Goldberg
- Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Alejandro Soba
- Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
| | - Daniel Gandía
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Instituto de Fısica del Plasma (INFIP), Buenos Aires, Argentina
| | - María Laura Fernández
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Instituto de Fısica del Plasma (INFIP), Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina
| | - Cecilia Suárez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Instituto de Fısica del Plasma (INFIP), Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina.
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Study of Resveratrol's Interaction with Planar Lipid Models: Insights into Its Location in Lipid Bilayers. MEMBRANES 2021; 11:membranes11020132. [PMID: 33672841 PMCID: PMC7918209 DOI: 10.3390/membranes11020132] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/16/2023]
Abstract
Resveratrol, a polyphenolic molecule found in edible fruits and vegetables, shows a wide range of beneficial effects on human health, including anti-microbial, anti-inflammatory, anti-cancer, and anti-aging properties. Due to its poor water solubility and high liposome-water partition coefficient, the biomembrane seems to be the main target of resveratrol, although the mode of interaction with membrane lipids and its location within the cell membrane are still unclear. In this study, using electrophysiological measurements, we study the interaction of resveratrol with planar lipid membranes (PLMs) of different composition. We found that resveratrol incorporates into palmitoyl-oleoyl-phosphatidylcholine (POPC) and POPC:Ch PLMs and forms conductive units unlike those found in dioleoyl-phosphatidylserine (DOPS):dioleoyl-phosphatidylethanolamine (DOPE) PLMs. The variation of the biophysical parameters of PLMs in the presence of resveratrol provides information on its location within a lipid double layer, thus contributing to an understanding of its mechanism of action.
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Yesylevskyy S, Khandelia H. EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations. J Chem Theory Comput 2021; 17:1181-1193. [DOI: 10.1021/acs.jctc.0c00800] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Semen Yesylevskyy
- Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, 03028 Kyiv, Ukraine
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France
| | - Himanshu Khandelia
- PHYLIFE: Physical Life Science, Department of Physics Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230 M, Denmark
- MEMPHYS: Center for Biomembrane Physics,
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