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Lugtu-Pe JA, Zhang X, Mirzaie S, Chang HHR, AL-Mousawi N, Chen K, Li Y, Kane A, Bar-Shalom D, Wu XY. An emerging terpolymeric nanoparticle pore former as an internal recrystallization inhibitor of celecoxib in controlled release amorphous solid dispersion beads: Experimental studies and molecular dynamics analysis. Acta Pharm Sin B 2024; 14:2669-2684. [PMID: 38828156 PMCID: PMC11143779 DOI: 10.1016/j.apsb.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 06/05/2024] Open
Abstract
Solid oral controlled release formulations feature numerous clinical advantages for drug candidates with adequate solubility and dissolution rate. However, most new chemical entities exhibit poor water solubility, and hence are exempt from such benefits. Although combining drug amorphization with controlled release formulation is promising to elevate drug solubility, like other supersaturating systems, the problem of drug recrystallization has yet to be resolved, particularly within the dosage form. Here, we explored the potential of an emerging, non-leachable terpolymer nanoparticle (TPN) pore former as an internal recrystallization inhibitor within controlled release amorphous solid dispersion (CRASD) beads comprising a poorly soluble drug (celecoxib) reservoir and insoluble polymer (ethylcellulose) membrane. Compared to conventional pore former, polyvinylpyrrolidone (PVP), TPN-containing membranes exhibited superior structural integrity, less crystal formation at the CRASD bead surface, and greater extent of celecoxib release. All-atom molecular dynamics analyses revealed that in the presence of TPN, intra-molecular bonding, crystal formation tendency, diffusion coefficient, and molecular flexibility of celecoxib were reduced, while intermolecular H-bonding was increased as compared to PVP. This work suggests that selection of a pore former that promotes prolonged molecular separation within a nanoporous controlled release membrane structure may serve as an effective strategy to enhance amorphicity preservation inside CRASD.
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Affiliation(s)
- Jamie Anne Lugtu-Pe
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Xuning Zhang
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Candoo Pharmatech Company Inc., Mississauga L5N 5M1, Canada
| | - Sako Mirzaie
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Hao Han R. Chang
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Nour AL-Mousawi
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Department of Pharmacy, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Kuan Chen
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Yongqiang Li
- Candoo Pharmatech Company Inc., Mississauga L5N 5M1, Canada
| | - Anil Kane
- Patheon by Thermo Fisher Scientific, Toronto Region Operations (TRO), Mississauga L5N 3X4, Canada
| | - Daniel Bar-Shalom
- Department of Pharmacy, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Xiao Yu Wu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
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2
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Krmic M, Perez E, Scollan P, Ivanchenko K, Gamez Hernandez A, Giancaspro J, Rosario J, Ceja-Vega J, Gudyka J, Porteus R, Lee S. Aspirin Interacts with Cholesterol-Containing Membranes in a pH-Dependent Manner. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:16444-16456. [PMID: 37939382 PMCID: PMC10666536 DOI: 10.1021/acs.langmuir.3c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
Aspirin has been used for broad therapeutic treatment, including secondary prevention of cardiovascular disease associated with increased cholesterol levels. Aspirin and other nonsteroidal anti-inflammatory drugs have been shown to interact with lipid membranes and change their biophysical properties. In this study, mixed lipid model bilayers made from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) or 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) comprising varying concentrations of cholesterol (10:1, 4:1, and 1:1 mole ratio of lipid:chol), prepared by the droplet interface bilayer method, were used to examine the effects of aspirin at various pH on transbilayer water permeability. The presence of aspirin increases the water permeability of POPC bilayers in a concentration-dependent manner, with a greater magnitude of increase at pH 3 compared to pH 7. In the presence of cholesterol, aspirin is similarly shown to increase water permeability; however, the extent of the increase depends on both the concentration of cholesterol and the pH, with the least pronounced enhancement in water permeability at high cholesterol levels at pH 7. A fusion of data from differential scanning calorimetry, confocal Raman microspectrophotometry, and interfacial tensiometric measurements demonstrates that aspirin can promote significant thermal, structural, and interfacial property perturbations in the mixed-lipid POPC or DOPC membranes containing cholesterol, indicating a disordering effect on the lipid membranes. Our findings suggest that aspirin fluidizes phosphocholine membranes in both cholesterol-free and cholesterol-enriched states and that the overall effect is greater when aspirin is in a neutral state. These results confer a deeper comprehension of the divergent effects of aspirin on biological membranes having heterogeneous compositions, under varying physiological pH and different cholesterol compositions, with implications for a better understanding of the gastrointestinal toxicity induced by the long term use of this important nonsteroidal anti-inflammatory molecule.
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Affiliation(s)
- Michael Krmic
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Escarlin Perez
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Patrick Scollan
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Katherine Ivanchenko
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Alondra Gamez Hernandez
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Joseph Giancaspro
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Juan Rosario
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Jasmin Ceja-Vega
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Jamie Gudyka
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Riley Porteus
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Sunghee Lee
- Department of Chemistry and Biochemistry, Iona University, 715 North Avenue, New Rochelle, New York 10801, United States
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3
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Ghorbani M, Dehghan G, Allahverdi A. Concentration-dependent mechanism of the binding behavior of ibuprofen to the cell membrane: A molecular dynamic simulation study. J Mol Graph Model 2023; 124:108581. [PMID: 37536233 DOI: 10.1016/j.jmgm.2023.108581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023]
Abstract
Ibuprofen is a commonly used drug for treating headaches, pain, and fever. The lipid bilayer is the primary and most important interface for drugs to interact with biological systems. However, the molecular interactions between ibuprofen and the cell membrane are not well understood. Our findings suggest that the interactions between ibuprofen and the bilayer involve multiple steps and depend on the concentration of the drug. At low concentrations of ibuprofen, it can bind to the surface of the lipid bilayer. The electrostatic and vdW energies of IBU-lipid at 0 ns of the simulation were -22.5 ± 3.2 and -5.9 ± 1.2 kj.mol-1 Fig. 2. In the following, the vdW energy of the IBU-lipid was increased by around -134.6 ± 3.7 kj.mol-1 whereas the electrostatic energy of the IBU-lipid was significantly decreased. This binding is facilitated by electrostatic and vdW interactions between ibuprofen and the head group of lipids. In the second step, ibuprofen is inserted into the lipid bilayer and positioned at the interface between the bilayer and the aqueous phase. In high concentrations of ibuprofen, it moved to the central region of the lipid bilayer. At this concentration, the physical and structural properties of the cell membrane change significantly. Results from the radial distribution function analysis indicate that at low concentrations, ibuprofen molecules are situated close to the head groups of phosphate groups. However, at high concentrations of ibuprofen, these molecules move to the inner side of the lipid bilayer. In addition, our findings indicate that at low concentrations of ibuprofen, these molecules did not significantly alter the physical properties of the cell membrane. In contrast, at high concentrations of ibuprofen, the physical parameters of the hydrocarbon tails, such as thickness, fluidity, and order, changed dramatically. APL parameter for POPC membrane increased slightly to 0.60 and 0.63 nm2 in the presence of low and high concentrations of ibuprofen molecules. The three-step interaction between ibuprofen and the lipid bilayer involves several events, such as the movement of ibuprofen molecules towards the central region of the lipid bilayer and the deformation and alteration of the structural and stability properties of the cell membrane. These effects are observed only at high concentrations of ibuprofen. It appears that the side effects of ibuprofen overdose are related to changes in the properties of the cell membrane and, subsequently, the function of membrane-anchored target proteins.
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Affiliation(s)
| | | | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences Tarbiat Modares University, Jalal Ale Ahmad Highway, P.O. Box: 14115-111, Tehran, Iran.
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4
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Gastaldi MS, Felsztyna I, Miguel V, Sánchez-Borzone ME, García DA. Theoretical and Experimental Study of Molecular Interactions of Fluralaner with Lipid Membranes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2134-2142. [PMID: 36688903 DOI: 10.1021/acs.jafc.2c06811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Fluralaner is a relatively new insecticide belonging to the isoxazoline group, whose action mechanism involves the blocking of GABAA-receptors in the insect nervous system. Because of its high hydrophobicity, fluralaner could bioaccumulate and reach toxic local concentrations. Since there are no data available about the penetration and persistence of isoxazolines in biological membranes, we intend to evaluate fluralaner permanence as a pollutant by using model membranes. We used experimental and in silico models to characterize the incorporation of fluralaner into the lipid phase at different packing states. We determined its impact in the membrane structure and organization. Our results confirm that fluralaner is capable of penetrating, holding, and accumulating in the lipid membrane and provide details on its precise location and orientation. These properties would allow fluralaner to reach high local concentrations in different membranes and organs, which could be dangerous for vertebrate organisms if its handling is not properly controlled.
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Affiliation(s)
- María Salomé Gastaldi
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
| | - Iván Felsztyna
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
| | - Virginia Miguel
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
| | - Mariela E Sánchez-Borzone
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
| | - Daniel A García
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
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5
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Watkins SL. Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry. MEMBRANES 2023; 13:148. [PMID: 36837651 PMCID: PMC9961006 DOI: 10.3390/membranes13020148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
There has been an almost exponential increase in the use of molecular dynamics simulations in basic research and industry over the last 5 years, with almost a doubling in the number of publications each year. Many of these are focused on neurological membranes, and biological membranes in general, applied to the medical industry. A smaller portion have utilized membrane simulations to answer more basic questions related to the function of specific proteins, chemicals or biological processes. This review covers some newer studies, alongside studies from the last two decades, to determine changes in the field. Some of these are basic, while others are more profound, such as multi-component embedded membrane machinery. It is clear that many facets of the discipline remain the same, while the focus on and uses of the technology are broadening in scope and utilization as a general research tool. Analysis of recent literature provides an overview of the current methodologies, covers some of the recent trends or advances and tries to make predictions of the overall path membrane molecular dynamics will follow in the coming years. In general, the overview presented is geared towards the general scientific community, who may wish to introduce the use of these methodologies in light of these changes, making molecular dynamic simulations more feasible for general scientific or medical research.
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Affiliation(s)
- Stephan L Watkins
- Plant Pathology and CRGB, Oregon State University, 2701 SW Campus Way, Corvallis, OR 97331, USA
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6
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Kadyrov J, Ruiz-Perez L, Benson HAE, Mancera RL. Characterisation of the Molecular Mechanism of Permeation of the Prodrug Me-5ALA across the Human Stratum Corneum Using Molecular Dynamics Simulations. Int J Mol Sci 2022; 23:ijms232416001. [PMID: 36555643 PMCID: PMC9786775 DOI: 10.3390/ijms232416001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/24/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The barrier imposed by the outer layer of the skin, the stratum corneum, creates an almost impermeable environment for exogenous substances. Few lipophilic drugs with low molecular mass can passively diffuse through this layer, highlighting the need to develop methods to enable the delivery of more drugs via the transdermal route. The prodrug approach involves modifying the structure of a drug molecule to enhance its permeability across the skin, but it is often difficult to predict how exactly changes in chemical structure affect permeation. This study uses molecular dynamics simulations to predict permeability values and adequately characterise the molecular mechanism of permeation of the prodrugs Me-5ALA and its parent compound 5ALA across a molecular model of the lipid bilayers of the human stratum corneum. The influence of increased hydrophobicity in Me-5ALA on its permeation revealed a reduction in hydrogen bonding capability that enables it to interact more favourably with the hydrophobic region of the bilayer and diffuse at a faster rate with less resistance, thus making it a better permeant compared to its more hydrophilic parent compound. This molecular simulation approach offers a promising route for the rational design of drug molecules that can permeate effectively across the stratum corneum.
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Affiliation(s)
- Janonna Kadyrov
- Curtin Medical School, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 5845, Australia
| | - Lanie Ruiz-Perez
- Curtin Medical School, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 5845, Australia
| | - Heather A. E. Benson
- Curtin Medical School, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 5845, Australia
- Basil Hetzel Institute for Translational Health Research, 37a Woodville Road, Woodville South, SA 5011, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA 5001, Australia
| | - Ricardo L. Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 5845, Australia
- Correspondence:
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Ranaudo A, Greco C, Moro G, Zucchi A, Mattiello S, Beverina L, Cosentino U. Partition of the Reactive Species of the Suzuki-Miyaura Reaction between Aqueous and Micellar Environments. J Phys Chem B 2022; 126:9408-9416. [PMID: 36330777 PMCID: PMC9677424 DOI: 10.1021/acs.jpcb.2c04591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Suzuki-Miyaura reaction between the aryl halide (1) and the phenyl boronic acid (2), in the presence of the palladium(0) complex (3) as catalyst, gives the cross-coupling product (4) in quantitative yield when performed in basic aqueous solution of the nonionic surfactant Kolliphor-EL (K-EL). The partition between the aqueous and micellar environments of the species of this reaction has been investigated by means of Molecular Dynamics (MD) simulations. Starting from the K-EL molecules dispersed in water, a micelle model has been generated by MD simulations, adopting the 2016H66 force field. Reagent and product species have been described with the same force field, once the reliability of this force field has been tested comparing the n-octanol/water partition free energies calculated from the MD and Free Energy Perturbation (FEP) method with those obtained from the quantum-mechanical SMD method. The potential of mean force for the transfer process between water and the micellar phase of the different species has been calculated by the MD simulations and the Umbrella Sampling (US) method. The overall picture that emerges from these results confirms that the molecular species involved in this reaction prefers the micellar environment and concentrates in different but close zones of the micelle. This supports the experimental evidence that the use of suitable surfactant agents promotes reactivity, allowing micelles to behave as nanoreactors in which reactive species are solubilized and enhance their local concentration.
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Affiliation(s)
- Anna Ranaudo
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza della Scienza 1, Milan 20126, Italy,
| | - Claudio Greco
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza della Scienza 1, Milan 20126, Italy
| | - Giorgio Moro
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, Milan 20126, Italy
| | - Anita Zucchi
- Department
of Materials Science, University of Milano-Bicocca, Via Roberto Cozzi 55, Milan 20125, Italy
| | - Sara Mattiello
- Department
of Materials Science, University of Milano-Bicocca, Via Roberto Cozzi 55, Milan 20125, Italy
| | - Luca Beverina
- Department
of Materials Science, University of Milano-Bicocca, Via Roberto Cozzi 55, Milan 20125, Italy
| | - Ugo Cosentino
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza della Scienza 1, Milan 20126, Italy
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Drug–Membrane Interaction as Revealed by Spectroscopic Methods: The Role of Drug Structure in the Example of Rifampicin, Levofloxacin and Rapamycin. BIOPHYSICA 2022. [DOI: 10.3390/biophysica2040032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We have investigated the nature of the interaction of small organic drug molecules with lipid membranes of various compositions. Using infrared spectroscopy and differential scanning calorimetry methods, we studied the role of the structure of the active molecule in interaction with the membrane using the example of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylcholine:cardiolipin (DPPC:CL) liposomes. We discovered the key role of the heterocycle in interaction with the polar part of the bilayer and the network of unsaturated bonds in interaction with the hydrophobic part. For rifampicin and levofloxacin, the main binding sites were phosphate and carbonyl groups of lipids, and in the case of anionic liposomes we found a slight penetration of rifampicin into the hydrophobic part of the bilayer. For rapamycin, experimental confirmation of the localization of the molecule in the region of fatty acid chains was obtained, and perturbation in the region of phosphate groups was demonstrated for the first time. The process of phase transition of liposomal forms of rifampicin and levofloxacin was studied. DPPC liposomes accelerate the phase transition when loaded with a drug. DPPC:CL liposomes are less susceptible to changes in the phase transition rate.
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9
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Bringas M, Luck M, Müller P, Scheidt HA, Di Lella S. Effects of the RNA-Polymerase Inhibitors Remdesivir and Favipiravir on the Structure of Lipid Bilayers-An MD Study. MEMBRANES 2022; 12:941. [PMID: 36295700 PMCID: PMC9608901 DOI: 10.3390/membranes12100941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
The structure and dynamics of membranes are crucial to ensure the proper functioning of cells. There are some compounds used in therapeutics that show nonspecific interactions with membranes in addition to their specific molecular target. Among them, two compounds recently used in therapeutics against COVID-19, remdesivir and favipiravir, were subjected to molecular dynamics simulation assays. In these, we demonstrated that the compounds can spontaneously bind to model lipid membranes in the presence or absence of cholesterol. These findings correlate with the corresponding experimental results recently reported by our group. In conclusion, insertion of the compounds into the membrane is observed, with a mean position close to the phospholipid head groups.
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Affiliation(s)
- Mauro Bringas
- Instituto de Química Biológica—Ciencias Exactas y Naturales (IQUIBICEN)—CONICET and Departamento de Química Biológica FCEN, Universidad de Buenos Aires, Int. Güiraldes 2160, Buenos Aires C1428EGA, Argentina
| | - Meike Luck
- Department of Biology, Humboldt Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Peter Müller
- Department of Biology, Humboldt Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Holger A. Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16–18, D-04107 Leipzig, Germany
| | - Santiago Di Lella
- Instituto de Química Biológica—Ciencias Exactas y Naturales (IQUIBICEN)—CONICET and Departamento de Química Biológica FCEN, Universidad de Buenos Aires, Int. Güiraldes 2160, Buenos Aires C1428EGA, Argentina
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10
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Dałek P, Drabik D, Wołczańska H, Foryś A, Jagas M, Jędruchniewicz N, Przybyło M, Witkiewicz W, Langner M. Bioavailability by design — Vitamin D3 liposomal delivery vehicles. NANOMEDICINE: NANOTECHNOLOGY, BIOLOGY AND MEDICINE 2022; 43:102552. [PMID: 35346834 PMCID: PMC8957331 DOI: 10.1016/j.nano.2022.102552] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022]
Abstract
Vitamin D3 deficiency has serious health consequences, as demonstrated by its effect on severity and recovery after COVID-19 infection. Because of high hydrophobicity, its absorption and subsequent redistribution throughout the body are inherently dependent on the accompanying lipids and/or proteins. The effective oral vitamin D3 formulation should ensure penetration of the mucus layer followed by internalization by competent cells. Isothermal titration calorimetry and computer simulations show that vitamin D3 molecules cannot leave the hydrophobic environment, indicating that their absorption is predominantly driven by the digestion of the delivery vehicle. In the clinical experiment, liposomal vitamin D3 was compared to the oily formulation. The results obtained show that liposomal vitamin D3 causes a rapid increase in the plasma concentration of calcidiol. No such effect was observed when the oily formulation was used. The effect was especially pronounced for people with severe vitamin D3 deficiency.
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Affiliation(s)
- Paulina Dałek
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wrocław University of Science and Technology, Wrocław, Poland; Lipid Systems sp. z o.o., Wrocław, Poland.
| | - Dominik Drabik
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wrocław University of Science and Technology, Wrocław, Poland
| | | | - Aleksander Foryś
- Centre of Polymer and Carbon Materials, Polish Academy of Sciences, Zabrze, Poland
| | | | | | - Magdalena Przybyło
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wrocław University of Science and Technology, Wrocław, Poland; Lipid Systems sp. z o.o., Wrocław, Poland
| | - Wojciech Witkiewicz
- Research and Development Centre, Specialized Hospital in Wrocław, Wrocław, Poland
| | - Marek Langner
- Laboratory for Biophysics of Macromolecular Aggregates, Department of Biomedical Engineering, Wrocław University of Science and Technology, Wrocław, Poland; Lipid Systems sp. z o.o., Wrocław, Poland
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11
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Tzeliou CE, Mermigki MA, Tzeli D. Review on the QM/MM Methodologies and Their Application to Metalloproteins. Molecules 2022; 27:molecules27092660. [PMID: 35566011 PMCID: PMC9105939 DOI: 10.3390/molecules27092660] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/12/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor.
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Affiliation(s)
- Christina Eleftheria Tzeliou
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece; (C.E.T.); (M.A.M.)
| | - Markella Aliki Mermigki
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece; (C.E.T.); (M.A.M.)
| | - Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece; (C.E.T.); (M.A.M.)
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 116 35 Athens, Greece
- Correspondence: ; Tel.: +30-210-727-4307
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12
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Menon AP, Dong W, Lee TH, Aguilar MI, Duan M, Kapoor S. Mutually Exclusive Interactions of Rifabutin with Spatially Distinct Mycobacterial Cell Envelope Membrane Layers Offer Insights into Membrane-Centric Therapy of Infectious Diseases. ACS BIO & MED CHEM AU 2022; 2:395-408. [PMID: 35996474 PMCID: PMC9389580 DOI: 10.1021/acsbiomedchemau.2c00010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anjana P. Menon
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- IITB-Monash Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Wanqian Dong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Tzong-Hsien Lee
- IITB-Monash Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Marie-Isabel Aguilar
- IITB-Monash Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Mojie Duan
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- IITB-Monash Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan
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13
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MacDermott-Opeskin HI, Gupta V, O’Mara ML. Lipid-mediated antimicrobial resistance: a phantom menace or a new hope? Biophys Rev 2022; 14:145-162. [PMID: 35251360 PMCID: PMC8880301 DOI: 10.1007/s12551-021-00912-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/14/2021] [Indexed: 02/06/2023] Open
Abstract
Abstract The proposition of a post-antimicrobial era is all the more realistic with the continued rise of antimicrobial resistance. The development of new antimicrobials is failing to counter the ever-increasing rates of bacterial antimicrobial resistance. This necessitates novel antimicrobials and drug targets. The bacterial cell membrane is an essential and highly conserved cellular component in bacteria and acts as the primary barrier for entry of antimicrobials into the cell. Although previously under-exploited as an antimicrobial target, the bacterial cell membrane is attractive for the development of novel antimicrobials due to its importance in pathogen viability. Bacterial cell membranes are diverse assemblies of macromolecules built around a central lipid bilayer core. This lipid bilayer governs the overall membrane biophysical properties and function of its membrane-embedded proteins. This mini-review will outline the mechanisms by which the bacterial membrane causes and controls resistance, with a focus on alterations in the membrane lipid composition, chemical modification of constituent lipids, and the efflux of antimicrobials by membrane-embedded efflux systems. Thorough insight into the interplay between membrane-active antimicrobials and lipid-mediated resistance is needed to enable the rational development of new antimicrobials. In particular, the union of computational approaches and experimental techniques for the development of innovative and efficacious membrane-active antimicrobials is explored.
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Affiliation(s)
- Hugo I. MacDermott-Opeskin
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
| | - Vrinda Gupta
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
| | - Megan L. O’Mara
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601 Australia
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14
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Wang X, Wang L, Li F, Teng Y, Ji C, Wu H. Toxicity pathways of lipid metabolic disorders induced by typical replacement flame retardants via data-driven analysis, in silico and in vitro approaches. CHEMOSPHERE 2022; 287:132419. [PMID: 34600017 DOI: 10.1016/j.chemosphere.2021.132419] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/13/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Endocrine-disrupting chemicals can interfere with hormone action via various pathways, thereby increasing the risk of adverse health outcomes. Organophosphorus ester (OPEs) retardants, a group of new emerging endocrine disruption chemicals, have been referred to as metabolism disruptors and reported to induce chronic health problems. However, the toxicity pathways were mainly focused on nuclear receptor signaling pathways. Significantly, the membrane receptor pathway (such as G protein-coupled estrogen receptor 1 (GPER) signaling pathway) had been gradually realized as the important role in respond more effective to lipid metabolism disorder than traditional nuclear receptors, whereas the detailed mechanism was unclear yet. Therefore, this study innovatively integrated the bibliometric analysis, in silico and in vitro approach to develop toxicity pathways for the mechanism interpretation. Bibliometric analysis found that the typical OPEs - triphenyl phosphate was a major concern of lipid metabolism abnormality. Results verified that TPP could damage the structures of cell membranes and exert an agonistic effect of GPER as the molecular initiating event. Then, the activated GPER could trigger the PI3K-Akt/NCOR1 and mTOR/S6K2/PPARα transduction pathways as key event 1 (KE1) and affect the process of lipid metabolism and synthesis (CPT1A, CPT2, SREBF2 and SCD) as KE2. As a result, these alterations led to lipid accumulation as adverse effect at cellular-levels. Furthermore, the potential outcomes (such as immunity damage, weight change and steatohepatitis) at high biological levels were expanded. These findings improved knowledge to deeply understand toxicity pathways of phosphorus flame retardants and then provided a theoretical basis for risk assessments.
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Affiliation(s)
- Xiaoqing Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Li Wang
- Yantai Yuhuangding Hosp, Dept Western Med, Yuhuangdingdong Rd 20, Yantai, 264000, Shandong, PR China
| | - Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Yuefa Teng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Chenglong Ji
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China
| | - Huifeng Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China.
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15
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Radhakrishnan N, Kaul SC, Wadhwa R, Sundar D. Phosphatidylserine Exposed Lipid Bilayer Models for Understanding Cancer Cell Selectivity of Natural Compounds: A Molecular Dynamics Simulation Study. MEMBRANES 2022; 12:64. [PMID: 35054590 PMCID: PMC8780679 DOI: 10.3390/membranes12010064] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/20/2021] [Accepted: 12/27/2021] [Indexed: 12/17/2022]
Abstract
Development of drugs that are selectively toxic to cancer cells and safe to normal cells is crucial in cancer treatment. Evaluation of membrane permeability is a key metric for successful drug development. In this study, we have used in silico molecular models of lipid bilayers to explore the effect of phosphatidylserine (PS) exposure in cancer cells on membrane permeation of natural compounds Withaferin A (Wi-A), Withanone (Wi-N), Caffeic Acid Phenethyl Ester (CAPE) and Artepillin C (ARC). Molecular dynamics simulations were performed to compute permeability coefficients. The results indicated that the exposure of PS in cancer cell membranes facilitated the permeation of Wi-A, Wi-N and CAPE through a cancer cell membrane when compared to a normal cell membrane. In the case of ARC, PS exposure did not have a notable influence on its permeability coefficient. The presented data demonstrated the potential of PS exposure-based models for studying cancer cell selectivity of drugs.
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Affiliation(s)
- Navaneethan Radhakrishnan
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India;
| | - Sunil C. Kaul
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan;
| | - Renu Wadhwa
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan;
| | - Durai Sundar
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India;
- School of Artificial Intelligence, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India
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16
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Lagoutte-Renosi J, Allemand F, Ramseyer C, Yesylevskyy S, Davani S. Molecular modeling in cardiovascular pharmacology: Current state of the art and perspectives. Drug Discov Today 2021; 27:985-1007. [PMID: 34863931 DOI: 10.1016/j.drudis.2021.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/02/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023]
Abstract
Molecular modeling in pharmacology is a promising emerging tool for exploring drug interactions with cellular components. Recent advances in molecular simulations, big data analysis, and artificial intelligence (AI) have opened new opportunities for rationalizing drug interactions with their pharmacological targets. Despite the obvious utility and increasing impact of computational approaches, their development is not progressing at the same speed in different fields of pharmacology. Here, we review current in silico techniques used in cardiovascular diseases (CVDs), cardiological drug discovery, and assessment of cardiotoxicity. In silico techniques are paving the way to a new era in cardiovascular medicine, but their use somewhat lags behind that in other fields.
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Affiliation(s)
- Jennifer Lagoutte-Renosi
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire de Pharmacologie Clinique et Toxicologie-CHU de Besançon, 25000 Besançon, France
| | - Florentin Allemand
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Semen Yesylevskyy
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France; Department of Physics of Biological Systems, Institute of Physics of The National Academy of Sciences of Ukraine, Nauky Sve. 46, Kyiv, Ukraine; Receptor.ai inc, 16192 Coastal Highway, Lewes, DE, USA
| | - Siamak Davani
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire de Pharmacologie Clinique et Toxicologie-CHU de Besançon, 25000 Besançon, France.
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17
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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18
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Ferraz L, Sauer M, Sousa MJ, Branduardi P. The Plasma Membrane at the Cornerstone Between Flexibility and Adaptability: Implications for Saccharomyces cerevisiae as a Cell Factory. Front Microbiol 2021; 12:715891. [PMID: 34434179 PMCID: PMC8381377 DOI: 10.3389/fmicb.2021.715891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
In the last decade, microbial-based biotechnological processes are paving the way toward sustainability as they implemented the use of renewable feedstocks. Nonetheless, the viability and competitiveness of these processes are often limited due to harsh conditions such as: the presence of feedstock-derived inhibitors including weak acids, non-uniform nature of the substrates, osmotic pressure, high temperature, extreme pH. These factors are detrimental for microbial cell factories as a whole, but more specifically the impact on the cell’s membrane is often overlooked. The plasma membrane is a complex system involved in major biological processes, including establishing and maintaining transmembrane gradients, controlling uptake and secretion, intercellular and intracellular communication, cell to cell recognition and cell’s physical protection. Therefore, when designing strategies for the development of versatile, robust and efficient cell factories ready to tackle the harshness of industrial processes while delivering high values of yield, titer and productivity, the plasma membrane has to be considered. Plasma membrane composition comprises diverse macromolecules and it is not constant, as cells adapt it according to the surrounding environment. Remarkably, membrane-specific traits are emerging properties of the system and therefore it is not trivial to predict which membrane composition is advantageous under certain conditions. This review includes an overview of membrane engineering strategies applied to Saccharomyces cerevisiae to enhance its fitness under industrially relevant conditions as well as strategies to increase microbial production of the metabolites of interest.
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Affiliation(s)
- Luís Ferraz
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria João Sousa
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
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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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Rybenkov VV, Zgurskaya HI, Ganguly C, Leus IV, Zhang Z, Moniruzzaman M. The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux. Chem Rev 2021; 121:5597-5631. [PMID: 33596653 PMCID: PMC8369882 DOI: 10.1021/acs.chemrev.0c01137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.
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Affiliation(s)
- Valentin V Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhen Zhang
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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21
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Sharifian Gh M. Recent Experimental Developments in Studying Passive Membrane Transport of Drug Molecules. Mol Pharm 2021; 18:2122-2141. [PMID: 33914545 DOI: 10.1021/acs.molpharmaceut.1c00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to measure the passive membrane permeation of drug-like molecules is of fundamental biological and pharmaceutical importance. Of significance, passive diffusion across the cellular membranes plays an effective role in the delivery of many pharmaceutical agents to intracellular targets. Hence, approaches for quantitative measurement of membrane permeability have been the topics of research for decades, resulting in sophisticated biomimetic systems coupled with advanced techniques. In this review, recent developments in experimental approaches along with theoretical models for quantitative and real-time analysis of membrane transport of drug-like molecules through mimetic and living cell membranes are discussed. The focus is on time-resolved fluorescence-based, surface plasmon resonance, and second-harmonic light scattering approaches. The current understanding of how properties of the membrane and permeant affect the permeation process is discussed.
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Affiliation(s)
- Mohammad Sharifian Gh
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908, United States
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22
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Wood M, Morales M, Miller E, Braziel S, Giancaspro J, Scollan P, Rosario J, Gayapa A, Krmic M, Lee S. Ibuprofen and the Phosphatidylcholine Bilayer: Membrane Water Permeability in the Presence and Absence of Cholesterol. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:4468-4480. [PMID: 33826350 DOI: 10.1021/acs.langmuir.0c03638] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The interactions between drugs and cell membranes can modulate the structural and physical properties of membranes. The resultant perturbations of the membrane integrity may affect the conformation of the proteins inserted within the membrane, disturbing the membrane-hosted biological functions. In this study, the droplet interface bilayer (DIB), a model cell membrane, is used to examine the effects of ibuprofen, a nonsteroidal anti-inflammatory drug (NSAID), on transbilayer water permeability, which is a fundamental membrane biophysical property. Our results indicate that the presence of neutral ibuprofen (pH 3) increases the water permeability of the lipid membranes composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). When cholesterol is present with the DOPC, however, the water permeability is not influenced by addition of ibuprofen, regardless of the cholesterol content in DOPC. Given the fact that cholesterol is generally considered to impact packing in the hydrocarbon chain regions, our findings suggest that a potential competition between opposing effects of ibuprofen molecules and cholesterol on the hydrocarbon core environment of the phospholipid assembly may influence the overall water transport phenomena. Results from confocal Raman microspectroscopy and interfacial tensiometry show that ibuprofen molecules induce substantial structural and dynamic changes in the DOPC lipid bilayer. These results, demonstrating that the presence of ibuprofen increases the water permeability of pure DOPC but not that of DOPC-cholesterol mixtures, provide insight into the differential effect of a representative NSAID on heterogeneous biological membranes, depending upon the local composition and structure, results which will signal increased understanding of the gastrointestinal damage and toxicity induced by these molecules.
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Affiliation(s)
- Megan Wood
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Michael Morales
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Elizabeth Miller
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Samuel Braziel
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Joseph Giancaspro
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Patrick Scollan
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Juan Rosario
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Alyssa Gayapa
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Michael Krmic
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
| | - Sunghee Lee
- Department of Chemistry, Iona College, 715 North Avenue, New Rochelle, New York 10801, United States
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23
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Lopes-de-Campos D, Pereira-Leite C, Fontaine P, Coutinho A, Prieto M, Sarmento B, Jakobtorweihen S, Nunes C, Reis S. Interface-Mediated Mechanism of Action-The Root of the Cytoprotective Effect of Immediate-Release Omeprazole. J Med Chem 2021; 64:5171-5184. [PMID: 33847502 DOI: 10.1021/acs.jmedchem.1c00251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Omeprazole is usually administered under an enteric coating. However, there is a Food and Drug Administration-approved strategy that enables its release in the stomach. When locally absorbed, omeprazole shows a higher efficacy and a cytoprotective effect, whose mechanism was still unknown. Therefore, we aimed to assess the effect of the absorption route on the gastric mucosa. 2D and 3D models of dipalmitoylphosphatidylcholine (DPPC) at different pH values (5.0 and 7.4) were used to mimic different absorption conditions. Several experimental techniques, namely, fluorescence studies, X-ray scattering methodologies, and Langmuir monolayers coupled with microscopy, X-ray diffraction, and infrared spectroscopy techniques, were combined with molecular dynamics simulations. The results showed that electrostatic and hydrophobic interactions between omeprazole and DPPC rearranged the conformational state of DPPC. Omeprazole intercalates among DPPC molecules, promoting domain formation with untilted phospholipids. Hence, the local release of omeprazole enables its action as a phospholipid-like drug, which can reinforce and protect the gastric mucosa.
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Affiliation(s)
- Daniela Lopes-de-Campos
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Catarina Pereira-Leite
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Philippe Fontaine
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, BP48, 91192 Gif-sur-Yvette, France
| | - Ana Coutinho
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal.,Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Manuel Prieto
- IBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Bruno Sarmento
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IINFACTS, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Instituto Universitário de Ciências da Saúde, 4585-116 Gandra, Portugal
| | - Sven Jakobtorweihen
- Institute of Thermal Separation Processes, Hamburg University of Technology, 21073 Hamburg, Germany
| | - Cláudia Nunes
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Salette Reis
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
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24
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Yuan Y, Liu X, Liu T, Liu W, Zhu Y, Zhang H, Zhao C. Molecular dynamics exploring of atmosphere components interacting with lung surfactant phospholipid bilayers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140547. [PMID: 32659550 DOI: 10.1016/j.scitotenv.2020.140547] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/18/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
Sulfur dioxide (SO2), nitrogen oxide (NO2) and ozone (O3) in the atmosphere are significantly correlated with various respiratory and cardiovascular diseases. High doses of each of these gases or a mixture can change the physical and chemical properties of the lung membrane, thus leading to an increased pulmonary vascular permeability and structural failure of the alveolar cell membrane. In the present study, detailed molecular dynamic (MD) modeling was applied to investigate the effects of SO2, NO2, O3 and mixtures of these gases on the dipalmitoyl phosphatidylcholine (DPPC) phospholipid bilayer. The results showed that several key physical properties, including the mass density, lipid ordering parameter, lipid diffusion, and electrostatic potential of the cell membrane, have been changed by the binding of different compounds. This resulted in significant variations and more disorder in the DPPC bilayer. The multiple analyses of membrane properties proved the toxicity of NO2, O3, and SO2 to the DPPC bilayer, providing a theoretical basis for the experimental phenomenon that SO2, NO2 and O3 can cause lung cell apoptosis. For the single systems, the damage to DPPC bilayer caused by O3 was more serious than NO2 and SO2. More importantly, the MD simulations using the mixtures of SO2, NO2, and O3 showed a much greater decline of membrane fluidity and the aggravation of membrane damage than the single systems, indicating a synergistic effect when NO2, SO2, and O3 coexisted in the atmosphere, which could lead to much more severe damage and greater toxicities to the lung.
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Affiliation(s)
- Yongna Yuan
- School of Information Science & Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xinhe Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Tingting Liu
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou 730000, China
| | - Wencheng Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yu Zhu
- Department of Ecology and Environment of Gansu Province, Lanzhou 730000, China
| | - Haixia Zhang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Chunyan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China.
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25
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Kabedev A, Hossain S, Hubert M, Larsson P, Bergström CAS. Molecular Dynamics Simulations Reveal Membrane Interactions for Poorly Water-Soluble Drugs: Impact of Bile Solubilization and Drug Aggregation. J Pharm Sci 2020; 110:176-185. [PMID: 33152373 DOI: 10.1016/j.xphs.2020.10.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 01/19/2023]
Abstract
Molecular transport mechanisms of poorly soluble hydrophobic drug compounds to lipid membranes were investigated using molecular dynamics (MD) simulations. The model compound danazol was used to investigate the mechanism(s) by which bile micelles delivered it to the membrane. The interactions between lipid membrane and pure drug aggregates-in the form of amorphous aggregates and nanocrystals-were also studied. Our simulations indicate that bile micelles formed in the intestinal fluid may facilitate danazol incorporation into cellular membranes through two different mechanisms. The micelle may be acting as: i) a shuttle that presents the danazol directly to the membrane or ii) an elevator that moves the solubilized danazol with it as the colloidal structure itself becomes incorporated and solubilized within the membrane. The elevator hypothesis was supported by complementary lipid monolayer adsorption experiments. In these experiments, colloidal structures formed with simulated intestinal fluid were observed to rapidly incorporate into the monolayer. Simulations of membrane interaction with drug aggregates showed that both the amorphous aggregates and crystalline nanostructures incorporated into the membrane. However, the amorphous aggregates solubilized more quickly than the nanocrystals into the membrane, thereby improving the danazol absorption.
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Affiliation(s)
- Aleksei Kabedev
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Shakhawath Hossain
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Madlen Hubert
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Per Larsson
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden; The Swedish Drug Delivery Center (SweDeliver), Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden; The Swedish Drug Delivery Center (SweDeliver), Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.
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26
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Felsztyna I, Sánchez-Borzone ME, Miguel V, García DA. The insecticide fipronil affects the physical properties of model membranes: A combined experimental and molecular dynamics simulations study in Langmuir monolayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183378. [DOI: 10.1016/j.bbamem.2020.183378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/31/2022]
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27
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Li J, Jin X, Zhang L, Yang Y, Liu R, Li Z. Comparison of Different Chitosan Lipid Nanoparticles for Improved Ophthalmic Tetrandrine Delivery: Formulation, Characterization, Pharmacokinetic and Molecular Dynamics Simulation. J Pharm Sci 2020; 109:3625-3635. [PMID: 32946897 DOI: 10.1016/j.xphs.2020.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/25/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
In this study, three different chitosan, namely carboxymethyl chitosan (CMC), hydroxypropyl chitosan (HPC) and trimethyl chitosan (TMC) were used as cationic materials to prepare tetrandrine lipid nanoparticles (TET-LNPs) for the treatment of glaucoma. In vitro drug release and pre-corneal retention were used to select the optimal chitosan. In vitro drug release curves of three kinds of LNPs showed a sustained release and TMC-TET-LNPs were the slowest. Moreover, compared with CMC-TET-LNPs and HPC-TET-LNPs, TMC-TET-LNPs had longer corneal retention time. Afterwards, the characteristics of TMC-TET-LNPs were investigated. The ocular irritation study revealed no sign of irritation in rabbit eyes. The pharmacokinetic studies showed that the area under the curve of TMC-TET-LNPs was increased by 2.03 times than TET solution (p < 0.01). Furthermore, the drug biofilm interactions were evaluated by molecular dynamics (MD) simulation. In MD simulation, the strong hydrophobic group of TET interacted with the tail of POPC, making it hard to enter the hydrophobic region of the membrane, thereby restricting TET ocular bioavailability. The experiments and MD simulation indicated that TMC-TET-LNPs had great potential for ocular administration and MD simulation could predict transmembrane transport of drugs.
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Affiliation(s)
- Jinjing Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| | - Xin Jin
- Military Medicine Section, Logistics University of Chinese People's Armed Police Force, 1 Huizhihuan Road, Dongli District, Tianjin 300309, China
| | - Lingling Zhang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| | - Yang Yang
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
| | - Rui Liu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China.
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyang Lake Road, West Zone of Tuanbo New City, Jinghai District, Tianjin 301617, China
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28
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Zhang Y, Zhang HX, Zheng QC. In Silico Study of Membrane Lipid Composition Regulating Conformation and Hydration of Influenza Virus B M2 Channel. J Chem Inf Model 2020; 60:3603-3615. [PMID: 32589410 DOI: 10.1021/acs.jcim.0c00329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The proton conduction of transmembrane influenza virus B M2 (BM2) proton channel is possibly mediated by the membrane environment, but the detailed molecular mechanism is challenging to determine. In this work, how membrane lipid composition regulates the conformation and hydration of BM2 channel is elucidated in silico. The appearance of several important hydrogen-bond networks has been discovered, as the addition of negatively charged lipid palmitoyloleoyl phosphatidylglycerol (POPG) and cholesterol reduces membrane fluidity and augments membrane rigidity. A more rigid membrane environment is beneficial to expand the channel, allow more water to enter the channel, promote channel hydration, and then even affect the proton conduction facilitated by the hydrated channel. Thus, membrane environment could be identified as an important influence factor of conformation and hydration of BM2. These findings can provide a unique perspective for understanding the mechanism of membrane lipid composition regulating conformation and hydration of BM2 and have important significance to the further study of anti-influenza virus B drugs.
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Affiliation(s)
- Yue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Hong-Xing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023, People's Republic of China
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29
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Lolicato F, Juhola H, Zak A, Postila PA, Saukko A, Rissanen S, Enkavi G, Vattulainen I, Kepczynski M, Róg T. Membrane-Dependent Binding and Entry Mechanism of Dopamine into Its Receptor. ACS Chem Neurosci 2020; 11:1914-1924. [PMID: 32538079 PMCID: PMC7735663 DOI: 10.1021/acschemneuro.9b00656] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Synaptic neurotransmission has recently been proposed to function via either a membrane-independent or a membrane-dependent mechanism, depending on the neurotransmitter type. In the membrane-dependent mechanism, amphipathic neurotransmitters first partition to the lipid headgroup region and then diffuse along the membrane plane to their membrane-buried receptors. However, to date, this mechanism has not been demonstrated for any neurotransmitter-receptor complex. Here, we combined isothermal calorimetry measurements with a diverse set of molecular dynamics simulation methods to investigate the partitioning of an amphipathic neurotransmitter (dopamine) and the mechanism of its entry into the ligand-binding site. Our results show that the binding of dopamine to its receptor is consistent with the membrane-dependent binding and entry mechanism. Both experimental and simulation results showed that dopamine favors binding to lipid membranes especially in the headgroup region. Moreover, our simulations revealed a ligand-entry pathway from the membrane to the binding site. This pathway passes through a lateral gate between transmembrane alpha-helices 5 and 6 on the membrane-facing side of the protein. All in all, our results demonstrate that dopamine binds to its receptor by a membrane-dependent mechanism, and this is complemented by the more traditional binding mechanism directly through the aqueous phase. The results suggest that the membrane-dependent mechanism is common in other synaptic receptors, too.
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Affiliation(s)
- Fabio Lolicato
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Biochemistry Center, Heidelberg University, D-69120 Heidelberg, Germany
| | - Hanna Juhola
- Computational Physics Laboratory, Tampere University, FI-33100 Tampere, Finland
| | - Agata Zak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Pekka A. Postila
- Institute of Biomedicine, Faculty of Medicine, University of Turku, FI-20014 Turku, Finland
| | - Annina Saukko
- Department of Applied Physics, University of Eastern Finland, P.O.B. 1627, FI-70211 Kuopio, Finland
- Department of Medical Physics, Turku University Hospital, FI-20520 Turku, Finland
| | - Sami Rissanen
- Computational Physics Laboratory, Tampere University, FI-33100 Tampere, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational Physics Laboratory, Tampere University, FI-33100 Tampere, Finland
- MEMPHYS − Center for Biomembrane Physics
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
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30
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Martinotti C, Ruiz-Perez L, Deplazes E, Mancera RL. Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes. Chemphyschem 2020; 21:1486-1514. [PMID: 32452115 DOI: 10.1002/cphc.202000219] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/22/2020] [Indexed: 12/12/2022]
Abstract
Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.
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Affiliation(s)
- Carlo Martinotti
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Lanie Ruiz-Perez
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and, Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
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31
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Schwöbel JAH, Ebert A, Bittermann K, Huniar U, Goss KU, Klamt A. COSMOperm: Mechanistic Prediction of Passive Membrane Permeability for Neutral Compounds and Ions and Its pH Dependence. J Phys Chem B 2020; 124:3343-3354. [DOI: 10.1021/acs.jpcb.9b11728] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Andrea Ebert
- UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
- Institute of Biophysics, Johannes Kepler University, Gruberstraße 40, 4020 Linz, Austria
| | - Kai Bittermann
- UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Uwe Huniar
- BIOVIA, Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Kai-Uwe Goss
- UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany
- Institute of Chemistry, University of Halle-Wittenberg, Kurt Mothes Str. 2, D-06120 Halle, Germany
| | - Andreas Klamt
- BIOVIA, Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, D-51379 Leverkusen, Germany
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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32
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The Interaction of Flavonols with Membrane Components: Potential Effect on Antioxidant Activity. J Membr Biol 2020; 253:57-71. [DOI: 10.1007/s00232-019-00105-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 12/14/2019] [Indexed: 11/25/2022]
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33
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Yang H, Li H, Zhou M, Wei T, Tang C, Liu L, Zhou Y, Long X. A relationship between membrane permeation and partitioning of nitroaromatic explosives and their functional groups. A computational study. Phys Chem Chem Phys 2020; 22:8791-8799. [DOI: 10.1039/d0cp00549e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nitroaromatic explosives, such as 2,4,6-trinitrotoluene, are representative aromatic compounds, which are generally highly toxic.
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Affiliation(s)
- Hong Yang
- School of Materials Science and Engineering
- Tsinghua University
- Beijing 100084
- China
- Institute of Chemical Materials
| | - Huarong Li
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Mi Zhou
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Tong Wei
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Can Tang
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Liu Liu
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Yang Zhou
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
| | - Xinping Long
- Institute of Chemical Materials
- China Academy of Engineering and Physics
- Mianyang 621900
- China
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34
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Wood I, Fabian L, Moglioni A, Cabeça LF, de Paula E, Pickholz M. Combining nuclear magnetic resonance with molecular dynamics simulations to address sumatriptan interaction with model membranes. Chem Phys Lipids 2019; 225:104792. [DOI: 10.1016/j.chemphyslip.2019.104792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/21/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
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35
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Marzuoli I, Margreitter C, Fraternali F. Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description. J Chem Theory Comput 2019; 15:5175-5193. [PMID: 31433640 PMCID: PMC7377650 DOI: 10.1021/acs.jctc.9b00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Membranes
are a crucial component of both bacterial and mammalian
cells, being involved in signaling, transport, and compartmentalization.
This versatility requires a variety of lipid species to tailor the
membrane’s behavior as needed, increasing the complexity of
the system. Molecular dynamics simulations have been successfully
applied to study model membranes and their interactions with proteins,
elucidating some crucial mechanisms at the atomistic detail and thus
complementing experimental techniques. An accurate description of
the functional interplay of the diverse membrane components crucially
depends on the selected parameters that define the adopted force field.
A coherent parameterization for lipids and proteins is therefore needed.
In this work, we propose and validate new lipid head group parameters
for the GROMOS 54A8 force field, making use of recently published
parametrizations for key chemical moieties present in lipids. We make
use additionally of a new canonical set of partial charges for lipids,
chosen to be consistent with the parameterization of soluble molecules
such as proteins. We test the derived parameters on five phosphocholine
model bilayers, composed of lipid patches four times larger than the
ones used in previous studies, and run 500 ns long simulations of
each system. Reproduction of experimental data like area per lipid
and deuterium order parameters is good and comparable with previous
parameterizations, as well as the description of liquid crystal to
gel-phase transition. On the other hand, the orientational behavior
of the head groups is more realistic for this new parameter set, and
this can be crucial in the description of interactions with other
polar molecules. For that reason, we tested the interaction of the
antimicrobial peptide lactoferricin with two model membranes showing
that the new parameters lead to a weaker peptide–membrane binding
and give a more realistic outcome in comparing binding to antimicrobial
versus mammal membranes.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Christian Margreitter
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology , King's College London , London SE1 1UL , U.K
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36
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Yue Z, Li C, Voth GA, Swanson JMJ. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J Am Chem Soc 2019; 141:13421-13433. [PMID: 31382734 DOI: 10.1021/jacs.9b04387] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Permeability (Pm) across biological membranes is of fundamental importance and a key factor in drug absorption, distribution, and development. Although the majority of drugs will be charged at some point during oral delivery, our understanding of membrane permeation by charged species is limited. The canonical model assumes that only neutral molecules partition into and passively permeate across membranes, but there is mounting evidence that these processes are also facile for certain charged species. However, it is unknown whether such ionizable permeants dynamically neutralize at the membrane surface or permeate in their charged form. To probe protonation-coupled permeation in atomic detail, we herein apply continuous constant-pH molecular dynamics along with free energy sampling to study the permeation of a weak base propranolol (PPL), and evaluate the impact of including dynamic protonation on Pm. The simulations reveal that PPL dynamically neutralizes at the lipid-tail interface, which dramatically influences the permeation free energy landscape and explains why the conventional model overestimates the assigned intrinsic permeability. We demonstrate how fixed-charge-state simulations can account for this effect, and propose a revised model that better describes pH-coupled partitioning and permeation. Our results demonstrate how dynamic changes in protonation state may play a critical role in the permeation of ionizable molecules, including pharmaceuticals and drug-like molecules, thus requiring a revision of the standard picture.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Chenghan Li
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Gregory A Voth
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Jessica M J Swanson
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
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37
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 432] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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38
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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39
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Liu Y, Pang X, Song J, Liu X, Song J, Yuan Y, Zhao C. Exploring the membrane toxicity of decabromodiphenyl ethane (DBDPE): Based on cell membranes and lipid membranes model. CHEMOSPHERE 2019; 216:524-532. [PMID: 30388688 DOI: 10.1016/j.chemosphere.2018.10.140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 10/08/2018] [Accepted: 10/19/2018] [Indexed: 06/08/2023]
Abstract
Decabromodiphenyl ethane (DBDPE) is widely used in industry as an alternative to the decabromodiphenyl ether (BDEs). The large-scale use of DBDPE could lead to rapid growth of the human accumulation level of DBDPE. However, the biophysics of accumulation of DBDPE in cell membranes, as one of determinants of DBDPE metabolism is not clear. In the present study, detailed observations of cell lactate dehydrogenase (LDH) and reactive oxygen species (ROS) levels measurements proved that the DBDPE exposure to cell could result in significant cell membrane damage by concentration-dependent manners. The fluorescence anisotropy analysis supported the evidence that high concentration DBDPE bound decreased membrane fluidity significantly. Besides it, a detailed molecular dynamic (MD) simulation was approached to investigate the effects of DBDPE on the DPPC (dipalmitoyl phosphatidylcholine) phospholipid bilayer, which was constructed as the model of cell membrane. The molecular dynamic simulation revealed that DBDPE molecules can easily enter the membrane from the aqueous phase. Under the concentration of a threshold, the DBDPE molecules tended to aggregate inside the DPPC bilayer and caused pore formation. The bound of high concentration of DBDPE could result in significant variations in DPPC bilayer with a less dense, more disorder and rougher layer. The knowledge about DBDPEs interactions with lipid membranes is fundamentally essential to understand the in vivo process of DBDPE and the physical basis for the toxicity of DBDPE in cell membranes.
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Affiliation(s)
- Yaquan Liu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Xinyue Pang
- Henan University of Science and Technology, Luoyang, 471023, China
| | - Jiarui Song
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Xinhe Liu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Juanjuan Song
- Pulmonary Hospital of Lanzhou, Lanzhou, 730000, China
| | - Yongna Yuan
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Chunyan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China.
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40
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Licofelone-DPPC Interactions: Putting Membrane Lipids on the Radar of Drug Development. Molecules 2019; 24:molecules24030516. [PMID: 30709010 PMCID: PMC6384739 DOI: 10.3390/molecules24030516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/20/2019] [Accepted: 01/30/2019] [Indexed: 02/08/2023] Open
Abstract
(1) Background: Membrane lipids have been disregarded in drug development throughout the years. Recently, they gained attention in drug design as targets, but they are still disregarded in the latter stages. Thus, this study aims to highlight the relevance of considering membrane lipids in the preclinical phase of drug development. (2) Methods: The interactions of a drug candidate for clinical use (licofelone) with a membrane model system made of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) were evaluated by combining Langmuir isotherms, Brewster angle microscopy (BAM), polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS), and grazing-incidence X-ray diffraction (GIXD) measurements. (3) Results: Licofelone caused the expansion of the DPPC isotherm without changing the lipid phase transition profile. Moreover, licofelone induced the reduction of DPPC packing density, while increasing the local order of the DPPC acyl chains. (4) Conclusions: The licofelone-induced alterations in the structural organization of phosphatidylcholine monolayers may be related to its pharmacological actions. Thus, the combination of studying drug-membrane interactions with the pharmacological characterization that occurs in the preclinical stage may gather additional information about the mechanisms of action and toxicity of drug candidates. Ultimately, the addition of this innovative step shall improve the success rate of drug development.
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41
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Klamt A, Schwöbel J, Huniar U, Koch L, Terzi S, Gaudin T. COSMOplex: self-consistent simulation of self-organizing inhomogeneous systems based on COSMO-RS. Phys Chem Chem Phys 2019; 21:9225-9238. [PMID: 30994133 DOI: 10.1039/c9cp01169b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
During the past 20 years, the efficient combination of quantum chemical calculations with statistical thermodynamics by the COSMO-RS method has become an important alternative to force-field based simulations for the accurate prediction of free energies of molecules in liquid systems. While it was originally restricted to homogeneous liquids, it later has been extended to the prediction of the free energy of molecules in inhomogeneous systems such as micelles, biomembranes, or liquid interfaces, but these calculations were based on external input about the structure of the inhomogeneous system. Here we report the rigorous extension of COSMO-RS to a self-consistent prediction of the structure and the free energies of molecules in self-organizing inhomogeneous systems. This extends the application range to many new areas, such as the prediction of micellar structures and critical micelle concentrations, finite loading effects in micelles and biomembranes, the free energies and structure of liquid interfaces, microemulsions, and many more related topics, which often are of great practical importance.
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Affiliation(s)
- Andreas Klamt
- COSMOlogic GmbH & Co KG, Imbacher Weg 46, D-51379 Leverkusen, Germany.
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42
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Lopes-de-Araújo J, Reis S, Nunes C. Topotecan effect on the structure of normal and cancer plasma membrane lipid models: A multi-model approach. Eur J Pharm Sci 2018; 123:515-523. [DOI: 10.1016/j.ejps.2018.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/25/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022]
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43
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Association of ibuprofen at the polar/apolar interface of lipid membranes. Arch Biochem Biophys 2018; 654:77-84. [DOI: 10.1016/j.abb.2018.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 12/11/2022]
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44
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Menichetti R, Kanekal KH, Kremer K, Bereau T. In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force. J Chem Phys 2018; 147:125101. [PMID: 28964031 DOI: 10.1063/1.4987012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The partitioning of small molecules in cell membranes-a key parameter for pharmaceutical applications-typically relies on experimentally available bulk partitioning coefficients. Computer simulations provide a structural resolution of the insertion thermodynamics via the potential of mean force but require significant sampling at the atomistic level. Here, we introduce high-throughput coarse-grained molecular dynamics simulations to screen thermodynamic properties. This application of physics-based models in a large-scale study of small molecules establishes linear relationships between partitioning coefficients and key features of the potential of mean force. This allows us to predict the structure of the insertion from bulk experimental measurements for more than 400 000 compounds. The potential of mean force hereby becomes an easily accessible quantity-already recognized for its high predictability of certain properties, e.g., passive permeation. Further, we demonstrate how coarse graining helps reduce the size of chemical space, enabling a hierarchical approach to screening small molecules.
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Affiliation(s)
- Roberto Menichetti
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kiran H Kanekal
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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45
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Metronidazole within phosphatidylcholine lipid membranes: New insights to improve the design of imidazole derivatives. Eur J Pharm Biopharm 2018; 129:204-214. [PMID: 29859282 DOI: 10.1016/j.ejpb.2018.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Metronidazole is a imidazole derivative with antibacterial and antiprotozoal activity. Despite its therapeutic efficacy, several studies have been developing new imidazole derivatives with lower toxicity. Considering that drug-membrane interactions are key factors for drugs pharmacokinetic and pharmacodynamic properties, the aim of this work is to provide new insights into the structure-toxicity relationship of metronidazole within phosphatidylcholine membranes. For that purpose, lipid membrane models (liposomes and monolayers) composed of dipalmitoylphosphatidylcholine were used. Experimental techniques (determination of partition coefficients and Langmuir isotherm measurements) were combined with molecular dynamics simulations. Different pHs and lipid phases were evaluated to enable a better extrapolation for in vivo conditions. The partition of metronidazole depends on the pH and on the biphasic system (octanol/water or DPPC/water system). At pH 1.2, metronidazole is hydrophilic. At pH 7.4, metronidazole disturbs the order and the packing of phospholipids. For this toxic effect, the hydroxyl group of the side chain of metronidazole is crucial by interacting with the water embedded in the membrane and with the phosphate group and the apolar chains of phospholipids.
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46
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Lyu Y, Xiang N, Mondal J, Zhu X, Narsimhan G. Characterization of Interactions between Curcumin and Different Types of Lipid Bilayers by Molecular Dynamics Simulation. J Phys Chem B 2018; 122:2341-2354. [PMID: 29394060 DOI: 10.1021/acs.jpcb.7b10566] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yuan Lyu
- Department of Agricultural
and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ning Xiang
- Department of Agricultural
and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jagannath Mondal
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 36/P, Gopanapally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500107, India
| | - Xiao Zhu
- Research
Computing, Rosen Center for Advanced Computing, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ganesan Narsimhan
- Department of Agricultural
and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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47
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Loureiro DRP, Soares JX, Lopes D, Macedo T, Yordanova D, Jakobtorweihen S, Nunes C, Reis S, Pinto MMM, Afonso CMM. Accessing lipophilicity of drugs with biomimetic models: A comparative study using liposomes and micelles. Eur J Pharm Sci 2018; 115:369-380. [PMID: 29366962 DOI: 10.1016/j.ejps.2018.01.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/12/2018] [Accepted: 01/13/2018] [Indexed: 12/24/2022]
Abstract
Lipophilicity is a physicochemical property of crucial importance in drug discovery and drug design. Biomimetic models, such as liposomes and micelles, constitute a valuable tool for the assessment of lipophilicity through the determination of partition coefficients (log Kp). However, the lack of standardization hampers the judgment about which model or method has the best and broadest passive drug permeation predictive capacity. This work provides a comparative analysis between the methodologies based on biomimetic models to determine the partition coefficient (log Kp). For that purpose, a set of reference substances preconized by the Organization for Economic Cooperation and Development (OECD) guidelines was used. The biomimetic models employed were liposomes and micelles composed by 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) and hexadecylphosphocholine (HePC), respectively. Both lipids were used as representative phospholipids of natural membranes. The partition coefficients between biomimetic models and aqueous phases were determined by derivative spectroscopy at physiological conditions (37 °C and pH 7.4). The partition coefficients obtained using biomimetic models are quite different and more reliable than the ones obtained using an octanol/water system. Comparing the performance of the two biomimetic models, micelles revealed to be suitable only for substances with high molar absorption coefficient and log Kp > 3, but in general liposomes are the best model for accessing lipophilicity of drugs. Furthermore, a comparison between experimental data and the partition coefficients determined by the computational method COSMOmic is also provided and discussed. As a final summarizing result, a decision tree is provided in order to guide the selection of a tool for assessing the lipophilicity of drugs.
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Affiliation(s)
- Daniela R P Loureiro
- Department of Chemical Sciences, Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - José X Soares
- LAQV-REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Daniela Lopes
- LAQV-REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Tiago Macedo
- Department of Chemical Sciences, Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Denitsa Yordanova
- Institute of Thermal Separation Processes, Hamburg University of Technology, Germany
| | - Sven Jakobtorweihen
- Institute of Thermal Separation Processes, Hamburg University of Technology, Germany
| | - Cláudia Nunes
- LAQV-REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Salette Reis
- LAQV-REQUIMTE, Department of Chemical Sciences, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Madalena M M Pinto
- Department of Chemical Sciences, Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Porto, Portugal
| | - Carlos M M Afonso
- Department of Chemical Sciences, Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Porto, Portugal.
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48
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Rosilio V. How Can Artificial Lipid Models Mimic the Complexity of Molecule–Membrane Interactions? ACTA ACUST UNITED AC 2018. [DOI: 10.1016/bs.abl.2017.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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49
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Yordanova D, Ritter E, Smirnova I, Jakobtorweihen S. Micellization and Partition Equilibria in Mixed Nonionic/Ionic Micellar Systems: Predictions with Molecular Models. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:12306-12316. [PMID: 28967760 DOI: 10.1021/acs.langmuir.7b02813] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In practical applications, surfactant solutions are mostly used in mixtures of nonionic and ionic surfactants because they have improved characteristics compared to those of single surfactant solutions. By adjusting the composition of the micelles and the pH value, the solubilization of solutes can be enhanced. Nevertheless, the partitioning of solutes between nonionic/ionic mixed micelles and the aqueous phase is studied to a much lesser extent than for single surfactant solutions. Theoretical methods to predict partition equilibria in mixed micelles are of interest for screening studies. For those, the composition of the mixed micelle has to be known. Here we investigate mixtures of TX-114 (Triton X-114), Brij35 (C12E23), SDS (sodium dodecyl sulfate), and CTAB (cetyltrimethylammonium bromide). First, to investigate the surfactant compositions in the micelles, molecular dynamics (MD) self-assembly simulations were applied. Thereafter, the predictive COSMO-RS model, which applies the pseudophase approach, and its extension to anisotropic systems termed COSMOmic were compared for the prediction of partition equilibria in mixed micelles, where various molar ratios of the surfactants were considered. It could be demonstrated that both methods are applicable and lead to reasonable predictions for neutral molecules. However, taking into account the three-dimensional structure of the micelle is beneficial because the calculations with COSMOmic are in better agreement with experimental results. Because the partitioning behavior of ionizable molecules in mixed micelles is of particular interest, the partitioning of ionized isovanillin in mixed Brij35/CTAB micelles at different micelle compositions was calculated with COSMOmic. Using a thermodynamic cycle, the position-dependent pKa of isovanillin within the micelle is calculated on the basis of COSMOmic free energy profiles. As a result, the protolytic equilibrium of isovanillin within the micelles can be taken into account, which is crucial for the reliable prediction of partition coefficients.
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Affiliation(s)
- D Yordanova
- Hamburg University of Technology , Institute of Thermal Separation Processes, Eissendorfer Str. 38, 21073 Hamburg, Germany
| | - E Ritter
- Hamburg University of Technology , Institute of Thermal Separation Processes, Eissendorfer Str. 38, 21073 Hamburg, Germany
| | - I Smirnova
- Hamburg University of Technology , Institute of Thermal Separation Processes, Eissendorfer Str. 38, 21073 Hamburg, Germany
| | - S Jakobtorweihen
- Hamburg University of Technology , Institute of Thermal Separation Processes, Eissendorfer Str. 38, 21073 Hamburg, Germany
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50
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Markthaler D, Gebhardt J, Jakobtorweihen S, Hansen N. Molecular Simulations of Thermodynamic Properties for the System α
-Cyclodextrin/Alcohol in Aqueous Solution. CHEM-ING-TECH 2017. [DOI: 10.1002/cite.201700057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Daniel Markthaler
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Julia Gebhardt
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
| | - Sven Jakobtorweihen
- Hamburg University of Technology; Institute of Thermal Separation Processes; Eißendorfer Straße 38 21073 Hamburg Germany
| | - Niels Hansen
- University of Stuttgart; Institute of Thermodynamics and Thermal Process Engineering; Pfaffenwaldring 9 70569 Stuttgart Germany
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