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Ghasemitarei M, Ghorbi T, Yusupov M, Zhang Y, Zhao T, Shali P, Bogaerts A. Effects of Nitro-Oxidative Stress on Biomolecules: Part 1-Non-Reactive Molecular Dynamics Simulations. Biomolecules 2023; 13:1371. [PMID: 37759771 PMCID: PMC10527456 DOI: 10.3390/biom13091371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes.
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Affiliation(s)
- Maryam Ghasemitarei
- Department of Physics, Sharif University of Technology, Tehran 14588-89694, Iran
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Tayebeh Ghorbi
- Department of Physics, Sharif University of Technology, Tehran 14588-89694, Iran
| | - Maksudbek Yusupov
- School of Engineering, New Uzbekistan University, Tashkent 100007, Uzbekistan
- School of Engineering, Central Asian University, Tashkent 111221, Uzbekistan
- Laboratory of Thermal Physics of Multiphase Systems, Arifov Institute of Ion-Plasma and Laser Technologies, Academy of Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Yuantao Zhang
- School of Electrical Engineering, Shandong University, Jinan 250061, China
| | - Tong Zhao
- School of Electrical Engineering, Shandong University, Jinan 250061, China
| | - Parisa Shali
- Research Unit Plasma Technology, Department of Applied Physics, Faculty of Engineering and Agriculture, Ghent University, 9000 Ghent, Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
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Ferretti G, Serafini S, Angiolillo A, Monterosso P, Di Costanzo A, Matrone C. Advances in peripheral blood biomarkers of patients with Alzheimer's disease: Moving closer to personalized therapies. Biomed Pharmacother 2023; 165:115094. [PMID: 37392653 DOI: 10.1016/j.biopha.2023.115094] [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: 04/16/2023] [Revised: 06/17/2023] [Accepted: 06/27/2023] [Indexed: 07/03/2023] Open
Abstract
Recently, measurable peripheral biomarkers in the plasma of patients with Alzheimer's disease (AD) have gained considerable clinical interest. Several studies have identified one or more blood signatures that may facilitate the development of novel diagnostic and therapeutic strategies. For instance, changes in peripheral amyloid β42 (Aβ42) levels have been largely investigated in patients with AD and correlated with the progression of the pathology, although with controversial results. In addition, tumor necrosis factor α (TNFα) has been identified as an inflammatory biomarker strongly associated with AD, and several studies have consistently suggested the pharmacological targeting of TNFα to reduce systemic inflammation and prevent neurotoxicity in AD. Moreover, alterations in plasma metabolite levels appear to predict the progression of systemic processes relevant to brain functions. In this study, we analyzed the changes in the levels of Aβ42, TNFα, and plasma metabolites in subjects with AD and compared the results with those in healthy elderly (HE) subjects. Differences in plasma metabolites of patients with AD were analyzed with respect to Aβ42, TNFα, and the Mini-Mental State Examination (MMSE) score, searching for plasma signatures that changed simultaneously. In addition, the phosphorylation levels of the Tyr682 residue of the amyloid precursor protein (APP), which we previously proposed as a biomarker of AD, were measured in five HE and five AD patients, in whom the levels of Aβ42, TNFα, and two plasma lipid metabolites increased simultaneously. Overall, this study highlights the potential of combining different plasma signatures to define specific clinical phenotypes of patient subgroups, thus paving the way for the stratification of patients with AD and development of personalized approaches.
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Affiliation(s)
- Gabriella Ferretti
- Unit of Pharmacology, Department of Neuroscience, Faculty of Medicine, University of Naples Federico II, Via Pansini, 5 80131 Naples, Italy
| | - Sara Serafini
- Unit of Pharmacology, Department of Neuroscience, Faculty of Medicine, University of Naples Federico II, Via Pansini, 5 80131 Naples, Italy
| | - Antonella Angiolillo
- Department of Medicine and Health Sciences, Center for Research and Training in Aging Medicine, University of Molise, 86100 Campobasso, Italy
| | - Paola Monterosso
- Unit of Pharmacology, Department of Neuroscience, Faculty of Medicine, University of Naples Federico II, Via Pansini, 5 80131 Naples, Italy
| | - Alfonso Di Costanzo
- Department of Medicine and Health Sciences, Center for Research and Training in Aging Medicine, University of Molise, 86100 Campobasso, Italy
| | - Carmela Matrone
- Unit of Pharmacology, Department of Neuroscience, Faculty of Medicine, University of Naples Federico II, Via Pansini, 5 80131 Naples, Italy.
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Yordanova V, Hazarosova R, Vitkova V, Momchilova A, Robev B, Nikolova B, Krastev P, Nuss P, Angelova MI, Staneva G. Impact of Truncated Oxidized Phosphatidylcholines on Phospholipase A 2 Activity in Mono- and Polyunsaturated Biomimetic Vesicles. Int J Mol Sci 2023; 24:11166. [PMID: 37446342 DOI: 10.3390/ijms241311166] [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: 05/23/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The interplay between inflammatory and redox processes is a ubiquitous and critical phenomenon in cell biology that involves numerous biological factors. Among them, secretory phospholipases A2 (sPLA2) that catalyze the hydrolysis of the sn-2 ester bond of phospholipids are key players. They can interact or be modulated by the presence of truncated oxidized phosphatidylcholines (OxPCs) produced under oxidative stress from phosphatidylcholine (PC) species. The present study examined this important, but rarely considered, sPLA2 modulation induced by the changes in biophysical properties of PC vesicles comprising various OxPC ratios in mono- or poly-unsaturated PCs. Being the most physiologically active OxPCs, 1-palmitoyl-2-(5'-oxo-valeroyl)-sn-glycero-3-phosphocholine (POVPC) and 1-palmitoyl-2-glutaryl-sn-glycero-3-phosphocholine (PGPC) have been selected for our study. Using fluorescence spectroscopy methods, we compared the effect of OxPCs on the lipid order as well as sPLA2 activity in large unilamellar vesicles (LUVs) made of the heteroacid PC, either monounsaturated [1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)], or polyunsaturated [1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PDPC)] at a physiological temperature. The effect of OxPCs on vesicle size was also assessed in both the mono- and polyunsaturated PC matrices. Results: OxPCs decrease the membrane lipid order of POPC and PDPC mixtures with PGPC inducing a much larger decrease in comparison with POVPC, indicative that the difference takes place at the glycerol level. Compared with POPC, PDPC was able to inhibit sPLA2 activity showing a protective effect of PDPC against enzyme hydrolysis. Furthermore, sPLA2 activity on its PC substrates was modulated by the OxPC membrane content. POVPC down-regulated sPLA2 activity, suggesting anti-inflammatory properties of this truncated oxidized lipid. Interestingly, PGPC had a dual and opposite effect, either inhibitory or enhancing on sPLA2 activity, depending on the protocol of lipid mixing. This difference may result from the chemical properties of the shortened sn-2-acyl chain residues (aldehyde group for POVPC, and carboxyl for PGPC), being, respectively, zwitterionic or anionic under hydration at physiological conditions.
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Affiliation(s)
- Vesela Yordanova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Rusina Hazarosova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Victoria Vitkova
- Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussee Blvd., 1784 Sofia, Bulgaria
| | - Albena Momchilova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Bozhil Robev
- Department of Medical Oncology, University Hospital "Sv. Ivan Rilski", 15 Acad. Ivan Geshov Blvd., 1431 Sofia, Bulgaria
| | - Biliana Nikolova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Plamen Krastev
- Cardiology Clinic, University Hospital "St. Ekaterina", 52 Pencho Slaveikov Blvd., 1431 Sofia, Bulgaria
| | - Philippe Nuss
- Centre de Recherche Saint-Antoine, INSERM UMRS 938, Sorbonne Université, 75012 Paris, France
- Department of Psychiatry, Saint-Antoine Hospital, DMU Neuroscience, Sorbonne University, Assistance Publique-Hôpitaux de Paris (AP-HP), 75012 Paris, France
| | - Miglena I Angelova
- Department of Physics, Faculty of Sciences and Engineering, Sorbonne University, 75005 Paris, France
- Matière et Systèmes Complexes (MSC), CNRS UMR 7057, University Paris Cite-Diderot, 75013 Paris, France
| | - Galya Staneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
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Alekseeva AS, Boldyrev IA. Alternative Targets for sPLA2 Activity: Role of Membrane-Enzyme Interactions. MEMBRANES 2023; 13:618. [PMID: 37504984 PMCID: PMC10384401 DOI: 10.3390/membranes13070618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/29/2023]
Abstract
The secreted phospholipases A2 (sPLA2s) play important roles both physiologically and pathologically, with their expression increasing significantly in diseases such as sepsis, inflammation, different cancers, glaucoma, obesity, Alzheimer's disease and even COVID-19. The fact has led to a large-scale search for inhibitors of these enzymes. In total, several dozen promising molecules have been proposed, but not a single one has successfully passed clinical trials. The failures in clinical studies motivated in-depth fundamental studies of PLA2s. Here we review alternative ways to control sPLA2 activity, outside its catalytic site. The concept can be realized by preventing sPLA2 from attaching to the membrane surface; by binding to an external protein which blocks sPLA2 hydrolytic activity; by preventing sPLA2 from orienting properly on the membrane surface; and by preventing substrate binding to the enzyme, keeping the catalytic site unaltered. Evidence in the literature is summarized in the review with the aim to serve as a starting point for new types of sPLA2 inhibitors.
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Affiliation(s)
- Anna S Alekseeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ivan A Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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sPLA2 Wobbles on the Lipid Bilayer between Three Positions, Each Involved in the Hydrolysis Process. Toxins (Basel) 2022; 14:toxins14100669. [PMID: 36287938 PMCID: PMC9610741 DOI: 10.3390/toxins14100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/14/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Secreted phospholipases A2 (sPLA2s) are peripheral membrane enzymes that hydrolyze phospholipids in the sn-2 position. The action of sPLA2 is associated with the work of two active sites. One, the interface binding site (IBS), is needed to bind the enzyme to the membrane surface. The other one, the catalytic site, is needed to hydrolyze the substrate. The interplay between sites, how the substrate protrudes to, and how the hydrolysis products release from, the catalytic site remains in the focus of investigations. Here, we report that bee venom PLA2 has two additional interface binding modes and enzyme activity through constant switching between three different orientations (modes of binding), only one of which is responsible for substrate uptake from the bilayer. The finding was obtained independently using atomic force microscopy and molecular dynamics. Switching between modes has biological significance: modes are steps of the enzyme moving along the membrane, product release in biological milieu, and enzyme desorption from the bilayer surface.
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Nasri Z, Memari S, Wenske S, Clemen R, Martens U, Delcea M, Bekeschus S, Weltmann K, von Woedtke T, Wende K. Singlet-Oxygen-Induced Phospholipase A 2 Inhibition: A Major Role for Interfacial Tryptophan Dioxidation. Chemistry 2021; 27:14702-14710. [PMID: 34375468 PMCID: PMC8596696 DOI: 10.1002/chem.202102306] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Indexed: 11/16/2022]
Abstract
Several studies have revealed that various diseases such as cancer have been associated with elevated phospholipase A2 (PLA2 ) activity. Therefore, the regulation of PLA2 catalytic activity is undoubtedly vital. In this study, effective inactivation of PLA2 due to reactive species produced from cold physical plasma as a source to model oxidative stress is reported. We found singlet oxygen to be the most relevant active agent in PLA2 inhibition. A more detailed analysis of the plasma-treated PLA2 identified tryptophan 128 as a hot spot, rich in double oxidation. The significant dioxidation of this interfacial tryptophan resulted in an N-formylkynurenine product via the oxidative opening of the tryptophan indole ring. Molecular dynamics simulation indicated that the efficient interactions between the tryptophan residue and phospholipids are eliminated following tryptophan dioxidation. As interfacial tryptophan residues are predominantly involved in the attaching of membrane enzymes to the bilayers, tryptophan dioxidation and indole ring opening leads to the loss of essential interactions for enzyme binding and, consequently, enzyme inactivation.
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Affiliation(s)
- Zahra Nasri
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Seyedali Memari
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
- Institute of Anatomy and Cell BiologyUniversity Medicine GreifswaldFriedrich-Loeffler-Straße 23cGreifswald17487Germany
| | - Sebastian Wenske
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Ramona Clemen
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Ulrike Martens
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Straße 4Greifswald17489Germany
- Center for Innovation Competence (ZIK) HIKE (Humoral Immune Reactions in Cardiovascular Diseases)University of GreifswaldGreifswaldFleischmannstraße 4217489Germany
| | - Mihaela Delcea
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Straße 4Greifswald17489Germany
- Center for Innovation Competence (ZIK) HIKE (Humoral Immune Reactions in Cardiovascular Diseases)University of GreifswaldGreifswaldFleischmannstraße 4217489Germany
| | - Sander Bekeschus
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Klaus‐Dieter Weltmann
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Thomas von Woedtke
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
- Institute for Hygiene and Environmental MedicineUniversity Medicine GreifswaldGreifswaldWalther-Rathenau-Straße 49 A17489Germany
| | - Kristian Wende
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
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Onishchenko N, Tretiakova D, Vodovozova E. Spotlight on the protein corona of liposomes. Acta Biomater 2021; 134:57-78. [PMID: 34364016 DOI: 10.1016/j.actbio.2021.07.074] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/19/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022]
Abstract
Although an established drug delivery platform, liposomes have not fulfilled their true potential. In the body, interactions of liposomes are mediated by the layer of plasma proteins adsorbed on the surface, the protein corona. The review aims to collect the data of the last decade on liposome protein corona, tracing the path from interactions of individual proteins to the effects mediated by the protein corona in vivo. It offers a classification of the approaches to exploitation of the protein corona-rather than elimination thereof-based on the bilayer composition-corona composition-molecular interactions-biological performance framework. The multitude of factors that affect each level of this relationship urge to the widest implementation of bioinformatics tools to predict the most effective liposome compositions relying on the data on protein corona. Supplementing the picture with new pieces of accurately reported experimental data will contribute to the accuracy and efficiency of the predictions. STATEMENT OF SIGNIFICANCE: The review focuses on liposomes as an established nanomedicine platform and analyzes the available data on how the protein corona formed on liposome surface in biological fluids affects performance of the liposomes. The review offers a rigorous account of existing literature and critical analysis of methodology currently applied to the assessment of liposome-plasma protein interactions. It introduces a classification of the approaches to exploitation of the protein corona and tailoring liposome carriers to advance the field of nanoparticulate drug delivery systems for the benefit of patients.
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Alekseeva AS, Volynsky PE, Boldyrev IA. Estimation of the Phospholipase A2 Selectivity on POPC/POPG Membranes Using the Interaction Map. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2021. [DOI: 10.1134/s1990747821050032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
The regulation of the activity and selectivity of phospholipase A2 (PLA2), which is capable of cleaving fatty acid in the second position (sn-2) of the phospholipid, is carried out through the membrane-binding and catalytic sites of the enzyme. For hydrolytic activity, PLA2 must first bind to the phospholipid membrane, and the binding efficiency depends on the composition of the membrane. The membrane-binding site of PLA2 is formed by several tens of amino acids and its composition differs from enzyme to enzyme; hydrophobic and positively charged amino acids play a key role in the interaction. In this work, we investigated the interaction of PLA2 from bee venom with phospholipid bilayers of palmitoyl oleoylphosphatidylcholine (POPC) containing different amounts of palmitoyloleoylphosphatidylglycerol (POPG). On the basis of the measurements of the protein intrinsic fluorescence and the anisotropy of the fluorescence of the lipid probe we propose the construction of lipid–protein interaction maps, which reflect both the efficiency of protein binding and changes in the structure of the membrane. These changes cause alterations in the fluorescence anisotropy of the label, which in turn is a measure of the mobility of the lipid environment of the fluorescent probe. Analysis of interaction maps showed that there is a relationship between lipid mobility and enzyme binding efficiency: the optimum interaction of PLA2 with membranes from a POPC/POPG mixture lies in the region of the highest lipid mobility, and not in the region of the highest negative charge. This dependence complements the existing understanding of the process of recognition of the membrane surface by the enzyme and the selection of lipids by the enzyme already bound to the membrane. The proposed mapping method can be extended to other membrane-active proteins.
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