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Li J, Monje-Galvan V. Effect of Glycone Diversity on the Interaction of Triterpenoid Saponins and Lipid Bilayers. ACS APPLIED BIO MATERIALS 2024; 7:553-563. [PMID: 36854194 DOI: 10.1021/acsabm.2c00928] [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] [Indexed: 03/02/2023]
Abstract
Triterpenoid saponins are organic compounds widely available in the plant kingdom. These molecules have received extensive attention due to their antibacterial activity against both Gram-negative and Gram-positive bacteria. Recent studies identified the antibacterial activity of saponins closely relates to their interaction with bacterial membrane lipids; however, molecular details of this interaction remain unclear. Increased understanding of the mechanisms to disrupt bacterial lipid bilayers can help to mitigate development of antibiotic resistance. Here, we examined the effect of chemical structure and deprotonation states of saponin on its interaction with a bacterial membrane model using molecular dynamics simulations. We run multiple simulations with a ternary lipid mixture of POPE/POPG/DPPG (80/15/5 mol %) and different saponin molecules. While all saponin structures can permanently bind the membrane, their location and orientation inside the bilayer depend on the sugar chains attached to their backbone. Similarly, cluster formation and stability also depend on the chemical structure of the saponin molecule. Deprotonation site affects interactions with the bilayer by modulating hydrophilicity of the molecules. At the low concentrations simulated in this work, there is no statistically significant change in the membrane properties upon saponin(s) binding, but the molecules do preferentially partition to POPE lipid environment.
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Affiliation(s)
- Jinhui Li
- Department of Chemical and Biomolecular Engineering, State University of New York (SUNY) at Buffalo, Buffalo, New York 14260, United States
| | - Viviana Monje-Galvan
- Department of Chemical and Biomolecular Engineering, State University of New York (SUNY) at Buffalo, Buffalo, New York 14260, United States
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Visos-Varela I, Zapata-Cachafeiro M, Pintos-Rodríguez S, Bugarín-González R, González-Barcala FJ, Herdeiro MT, Piñeiro-Lamas M, Figueiras A, Salgado-Barreira Á. Outpatient atorvastatin use and severe COVID-19 outcomes: A population-based study. J Med Virol 2023; 95:e28971. [PMID: 37486310 DOI: 10.1002/jmv.28971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/09/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023]
Abstract
Evidence of the effect of statins on patients with coronavirus disease (2019) COVID-19 is inconsistent. The aim of this study was to evaluate the association between chronic use of statins-both overall and by active ingredient-and severe outcomes of COVID-19 (risk of hospitalization and mortality), progression to severe outcomes, and susceptibility to the virus. We conducted a population-based case-control study with data from electronic records to assess the risk of (1) hospitalization: cases were patients admitted due to COVID-19 and controls were subjects without COVID-19; (2) mortality: cases were hospitalized patients who died due to COVID-19 and controls were subjects without COVID-19; (3) progression: cases were hospitalized COVID-19 subjects and controls were nonhospitalized COVID-19 patients; and (4) susceptibility: cases were patients with COVID-19 (both hospitalized and nonhospitalized) and controls were subjects without COVID-19. We collected data on 2821 hospitalized cases, 26 996 nonhospitalized cases, and 52 318 controls. Chronic use of atorvastatin was associated with a decreased risk of hospitalization (adjusted odds ratios [aOR] = 0.83; 95% confidence interval [CI]: 0.74-0.92) and mortality (aOR = 0.70; 95% CI: 0.53-0.93), attributable in part to a lower risk of susceptibility to the virus (aOR = 0.91; 95% CI: 0.86-0.96). Simvastatin was associated with a reduced risk of mortality (aOR = 0.59; 95% CI: 0.40-0.87). The wide degree of heterogeneity observed in the estimated odds ratios (ORs) of the different statins suggests that there is no class effect. The results of this real-world study suggest that chronic use of atorvastatin (and to a lesser degree, of simvastatin) is associated with a decrease in risk of severe COVID-19 outcomes.
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Affiliation(s)
- Irene Visos-Varela
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Maruxa Zapata-Cachafeiro
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Santiago de Compostela, Spain
- Institute of Health Research of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública-CIBERESP), Santiago de Compostela, Spain
| | - Samuel Pintos-Rodríguez
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Rosendo Bugarín-González
- Monforte de Lemos Health Center, Health Area of Lugo, A Mariña and Monforte de Lemos, SERGAS, Monforte de Lemos, Lugo, Spain
| | - Francisco Javier González-Barcala
- Spanish Biomedical Research Networking Centre-CIBERES, Santiago de Compostela, Spain
- Pneumoloxy Department, Santiago de Compostela University Hospital Complex, Santiago de Compostela, Spain
| | - Maria T Herdeiro
- Department of Medical Sciences, iBiMED-Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - María Piñeiro-Lamas
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública-CIBERESP), Santiago de Compostela, Spain
| | - Adolfo Figueiras
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Santiago de Compostela, Spain
- Institute of Health Research of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública-CIBERESP), Santiago de Compostela, Spain
| | - Ángel Salgado-Barreira
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Santiago de Compostela, Spain
- Institute of Health Research of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública-CIBERESP), Santiago de Compostela, Spain
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Clop EM, Fraceto LF, Miguel V, Gastaldi S, de Paula E, Perillo MA. Combined in-silico and in-vitro experiments support acid-base equilibrium as a tool to estimate the localization depth of 4-nitrophenol within a phospholipid bilayer. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184009. [PMID: 35896126 DOI: 10.1016/j.bbamem.2022.184009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/09/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
The interaction and location of 4-nitrophenol (PNP) in biomembranes are relevant in the bioaccumulation and potentiation of the intensive toxic effects of this persistent organic pollutant. In this work, in-silico analyses predicted that, in a fluid phospholipid bilayer, the minimum energy of the protonated (PNPH) and deprotonated (PNP-) species is located within the glycerol and choline region, respectively. This was experimentally confirmed by acid-base equilibrium experiments and theory, allowing the estimation of the mean location of PNP within a bilayer region with a dielectric constant D = 50.6 compatible with the phosphate/choline moiety of egg-yolk phosphatidylcholine unilamellar (EPC) vesicles. The comparison with the D = 43.2 value obtained in Triton X-100 micelles allow predicting a mean surface potential of ψ = 25.37 mV for the EPC-water interface. Changes in the chemical shifts and longitudinal relaxation times of EPC hydrogens by 1H NMR confirm the deeper location of the PNPH within the glycerol region and at the choline region (PNP-) at higher pH. Intermolecular PNP-EPC dipolar interactions within the choline region was also demonstrated at pH 10.2 using ROESY experiments. Additional information was obtained trough 31P NMR, that detected an increase in the anisotropy at the membrane interface after insertion of PNP which probably act as a bridge between choline moieties rigidizing the crystalline structure at that spot. Concluding, here we provide experimental support to the "pH-piston hypothesis" proposed some decades ago in the pharmaceutical field, and that reinforce the importance of the environmental conditions (e.g. pH) to modulate the bioavailability of this highly toxic pollutant.
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Affiliation(s)
- Eduardo M Clop
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina; CONICET-Universidad Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Leonardo F Fraceto
- Depto de Engenharia Ambiental, Universidade Estadual Paulista Julio de Mesquita Filho, Sorocaba, SP, Brazil
| | - Virginia Miguel
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina; CONICET-Universidad Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Salomé Gastaldi
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina; CONICET-Universidad Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina
| | - Eneida de Paula
- Depto de Bioquímica e Biologia Tecidual, Inst. Biologia, Universidade Estadual de Campinas, SP, Brazil
| | - María Angélica Perillo
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Av. Vélez Sársfield 1611, 5016 Córdoba, Argentina; CONICET-Universidad Nacional de Córdoba, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Córdoba, Argentina.
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Hull JA, Mietzsch M, Chipman P, Strugatsky D, McKenna R. Structural characterization of an envelope-associated adeno-associated virus type 2 capsid. Virology 2022; 565:22-28. [PMID: 34638006 PMCID: PMC9911311 DOI: 10.1016/j.virol.2021.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 01/28/2023]
Abstract
Adeno-associated virus (AAV) are classified as non-enveloped ssDNA viruses. However, AAV capsids embedded within exosomes have been observed, and it has been suggested that the AAV membrane associated accessory protein (MAAP) may play a role in envelope-associated AAV (EA-AAV) capsid formation. Here, we observed and selected sufficient homogeneous EA-AAV capsids of AAV2, produced using the Sf9 baculoviral expression system, to determine the cryo-electron microscopy (cryo-EM) structure at 3.14 Å resolution. The reconstructed map confirmed that the EA-AAV capsid, showed no significant structural variation compared to the non-envelope capsid. In addition, the Sf9 expression system used implies the notion that MAAP may enhance exosome AAV encapsulation. Furthermore, we speculate that these EA-AAV capsids may have therapeutic benefits over the currently used non-envelope AAV capsids, with advantages in immune evasion and/or improved infectivity.
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Affiliation(s)
- Joshua A Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0245, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0245, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0245, USA
| | - David Strugatsky
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610-0245, USA.
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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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Shurshalova GS, Scheidt HA, Fischer M, Huster D, Aganov AV, Klochkov VV. Interaction of the pitavastatin with model membranes. Biochem Biophys Rep 2021; 28:101143. [PMID: 34632116 PMCID: PMC8487990 DOI: 10.1016/j.bbrep.2021.101143] [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: 07/16/2021] [Revised: 09/07/2021] [Accepted: 09/21/2021] [Indexed: 11/27/2022] Open
Abstract
Pitavastatin is a statin drug that, by competitively inhibiting 3-hydroxy-3-methylglutaryl-coenzyme A reductase, can lower serum cholesterol levels of low-density lipoprotein (LDL) accompanied by side effects due to pleiotropic effects leading to statin intolerance. These effects can be explained by the lipophilicity of statins, which creates membrane affinity and causes statin localization in cellular membranes. In the current report, the interaction of pitavastatin with POPC model membranes and its influence on the membrane structure were investigated using H, H and P solid-state NMR spectroscopy. Our experiments show the average localization of pitavastatin at the lipid/water interface of the membrane, which is biased towards the hydrocarbon core in comparison to other statin molecules. The membrane binding of pitavastatin also introduced an isotropic component into the 31P NMR powder spectra, suggesting that some of the lamellar POPC molecules are converted into highly curved structures. Solid-state NMR spectroscopy shows pitavastatin effect on the bilayer •Pitavastatin lowers the POPC order parameters •Pitavastatin localize in the upper chain of the POPC bilayer •Isotropic membrane phases are observed in the presence of pitavastatin
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Affiliation(s)
- Guzel S Shurshalova
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany.,Institute of Physics, Kazan (Volga Region) Federal University, 18 Kremlevskaya St., 420008 Kazan, Russian Federation
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Markus Fischer
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Albert V Aganov
- Institute of Physics, Kazan (Volga Region) Federal University, 18 Kremlevskaya St., 420008 Kazan, Russian Federation
| | - Vladimir V Klochkov
- Institute of Physics, Kazan (Volga Region) Federal University, 18 Kremlevskaya St., 420008 Kazan, Russian Federation
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Teo RD, Tieleman DP. Modulation of Phospholipid Bilayer Properties by Simvastatin. J Phys Chem B 2021; 125:8406-8418. [PMID: 34296883 DOI: 10.1021/acs.jpcb.1c03359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Simvastatin (Zocor) is one of the most prescribed drugs for reducing high cholesterol. Although simvastatin is ingested in its inactive lactone form, it is converted to its active dihydroxyheptanoate form by carboxylesterases in the liver. The dihydroxyheptanoate form can also be converted back to its original lactone form. Unfortunately, some of the side effects associated with the intake of simvastatin and other lipophilic statins at higher doses include statin-associated myopathy (SAM) and, in more severe cases, kidney failure. While the cause of SAM is unknown, it is hypothesized that these side effects are dependent on the localization of statins in lipid bilayers and their impact on bilayer properties. In this work, we carry out all-atom molecular dynamics simulations on both the lactone and dihydroxyheptanoate forms of simvastatin (termed "SN" and "SA", respectively) with a pure 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer and a POPC/cholesterol (30 mol %) binary mixture as membrane models. Additional simulations were carried out with multiple simvastatin molecules to mimic in vitro conditions that produced pleiotropic effects. Both SN and SA spontaneously diffused into the lipid bilayer, and a longer simulation time of 4 μs was needed for the complete incorporation of multiple SAs into the bilayer. By constructing potential mean force and electron density profiles, we find that SN localizes deeper within the hydrophobic interior of the bilayer and that SA has a greater tendency to form hydrogen-bonding interactions with neighboring water molecules and lipid headgroups. For the pure POPC bilayer, both SN and SA increase membrane order, while membrane fluidity increases for the POPC/cholesterol bilayer.
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Affiliation(s)
- Ruijie D Teo
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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