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Gökoğlu E, Budun SŞ, Doyuran B, Taskin-Tok T. Fluorescence Studies on the Binding Affinity and Determination of Vitamin B12 in the Presence of Fibrinogen. J Fluoresc 2024:10.1007/s10895-024-03835-1. [PMID: 39007932 DOI: 10.1007/s10895-024-03835-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024]
Abstract
The binding properties between vitamin B12 (vitB12, cyanocobalamin) and fibrinogen (Fib) were investigated by UV-vis absorption and steady-state/three-dimentional (3D) fluorescence spectra techniques as well as molecular docking. The experimental results showed that the intrinsic fluorescence of Fib quenched by vitB12 with static mechanism to form a non-fluorescent complex. The positive signs of thermodynamic parameters, ΔH (92.18 kJ/mol) and ΔS (433.5 J/molK), indicated that the hydrophobic forces were dominant in the binding mode. The molecular docking data were found to be in agreement with these experimental results and were confirmed by three hydrophobic interactions between the Trp430, Try390 residues of Fib and the vitamin. 3D spectra showed that fibrinogen undergoes a conformation change when it interacts with vitB12. Based on non-radiative energy transfer theory, binding distance was calculated to be 3.94 nm between donor (tryptophan residues of Fib) and acceptor (vitB12). The limit of detection (LOD) of vitB12 was calculated as 2.08 µM in the presence of fibrinogen. The relative standard deviation (RSD) of method was 4.28% for determinations (n = 7) of a vitB12 solution with the concentration of 7.80 µM.
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Affiliation(s)
- Elmas Gökoğlu
- Faculty of Science, Department of Chemistry, Hacettepe University, Ankara, 06800, Turkey.
| | - Seniye Şura Budun
- Faculty of Science, Department of Chemistry, Hacettepe University, Ankara, 06800, Turkey
| | - Bensu Doyuran
- Faculty of Science, Department of Chemistry, Hacettepe University, Ankara, 06800, Turkey
| | - Tugba Taskin-Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, 27310, Turkey
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, 27310, Turkey
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Bellier JP, Roman A, Christiano C, Anzai JA, Moreno S, Campbell EC, Godwin L, Li A, Chen A, Alan SM, Saba A, Yoo HB, Yang HS, Chhatwal JP, Selkoe DJ, Liu L. Identification of Fibrinogen as a Plasma Protein Binding Partner for Lecanemab Biosimilar IgG: Implications for Alzheimer's Disease Therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.591892. [PMID: 38746192 PMCID: PMC11092601 DOI: 10.1101/2024.05.01.591892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
OBJECTIVE Recombinant monoclonal therapeutic antibodies like lecanemab, which target amyloid beta in Alzheimer's disease, offer a promising approach for modifying the disease progression. Due to its relatively short half-life, Lecanemab, administered as a bi-monthly infusion (typically 10mg/kg) has a relatively brief half-life. Interaction with abundant plasma proteins binder in the bloodstream can affect pharmacokinetics of drugs, including their half-life. In this study we investigated potential plasma protein binding interaction to lecanemab using lecanemab biosimilar. METHODS Lecanemab biosimilar used in this study was based on publicly available sequences. ELISA and Western blotting were used to assess lecanemab biosimilar immunoreactivity in the fractions human plasma sample obtained through size exclusion chromatography. The binding of lecanemab biosimilar to candidate binders was confirmed by Western blotting, ELISA, and surface plasmon resonance analysis. RESULTS Using a combination of equilibrium dialysis, ELISA, and Western blotting in human plasma, we first describe the presence of likely plasma protein binding partner to lecanemab biosimilar, and then identify fibrinogen as one of them. Utilizing surface plasmon resonance, we confirmed that lecanemab biosimilar does bind to fibrinogen, although with lower affinity than to monomeric amyloid beta. CONCLUSION In the context of lecanemab therapy, these results imply that fibrinogen levels could impact the levels of free antibodies in the bloodstream and that fibrinogen might serve as a reservoir for lecanemab. More broadly, these results indicate that plasma protein binding may be an important consideration when clinically utilizing therapeutic antibodies in neurodegenerative disease.
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Kell DB, Pretorius E. Are fibrinaloid microclots a cause of autoimmunity in Long Covid and other post-infection diseases? Biochem J 2023; 480:1217-1240. [PMID: 37584410 DOI: 10.1042/bcj20230241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/17/2023]
Abstract
It is now well established that the blood-clotting protein fibrinogen can polymerise into an anomalous form of fibrin that is amyloid in character; the resultant clots and microclots entrap many other molecules, stain with fluorogenic amyloid stains, are rather resistant to fibrinolysis, can block up microcapillaries, are implicated in a variety of diseases including Long COVID, and have been referred to as fibrinaloids. A necessary corollary of this anomalous polymerisation is the generation of novel epitopes in proteins that would normally be seen as 'self', and otherwise immunologically silent. The precise conformation of the resulting fibrinaloid clots (that, as with prions and classical amyloid proteins, can adopt multiple, stable conformations) must depend on the existing small molecules and metal ions that the fibrinogen may (and is some cases is known to) have bound before polymerisation. Any such novel epitopes, however, are likely to lead to the generation of autoantibodies. A convergent phenomenology, including distinct conformations and seeding of the anomalous form for initiation and propagation, is emerging to link knowledge in prions, prionoids, amyloids and now fibrinaloids. We here summarise the evidence for the above reasoning, which has substantial implications for our understanding of the genesis of autoimmunity (and the possible prevention thereof) based on the primary process of fibrinaloid formation.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kemitorvet 200, 2800 Kgs Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
| | - Etheresia Pretorius
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
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4
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Vottero P, Tavernini S, Santin AD, Scheim DE, Tuszynski JA, Aminpour M. Computational Prediction of the Interaction of Ivermectin with Fibrinogen. Int J Mol Sci 2023; 24:11449. [PMID: 37511206 PMCID: PMC10380762 DOI: 10.3390/ijms241411449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/08/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Hypercoagulability and formation of extensive and difficult-to-lyse microclots are a hallmark of both acute COVID-19 and long COVID. Fibrinogen, when converted to fibrin, is responsible for clot formation, but abnormal structural and mechanical clot properties can lead to pathologic thrombosis. Recent experimental evidence suggests that the spike protein (SP) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may directly bind to the blood coagulation factor fibrinogen and induce structurally abnormal blood clots with heightened proinflammatory activity. Accordingly, in this study, we used molecular docking and molecular dynamics simulations to explore the potential activity of the antiparasitic drug ivermectin (IVM) to prevent the binding of the SARS-CoV-2 SP to fibrinogen and reduce the occurrence of microclots. Our computational results indicate that IVM may bind with high affinity to multiple sites on the fibrinogen peptide, with binding more likely in the central, E region, and in the coiled-coil region, as opposed to the globular D region. Taken together, our in silico results suggest that IVM may interfere with SP-fibrinogen binding and, potentially, decrease the formation of fibrin clots resistant to degradation. Additional in vitro studies are warranted to validate whether IVM binding to fibrinogen is sufficiently stable to prevent interaction with the SP, and potentially reduce its thrombo-inflammatory effect in vivo.
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Affiliation(s)
- Paola Vottero
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 1Z2, Canada; (P.V.); (M.A.)
| | - Scott Tavernini
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada;
| | - Alessandro D. Santin
- Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, P.O. Box 208063, New Haven, CT 06520-8063, USA;
| | - David E. Scheim
- US Public Health Service, Commissioned Corps, Inactive Reserve, Blacksburg, VA 24060-6367, USA;
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, AB T6G 1Z2, Canada
- DIMEAS, Politecnico di Torino, 10129 Turin, Italy
- Department of Data Science and Engineering, The Silesian University of Technology, 44-100 Gliwice, Poland
| | - Maral Aminpour
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 1Z2, Canada; (P.V.); (M.A.)
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [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: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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González-Durruthy M, Rial R, Liu Z, Ruso JM. Lysozyme allosteric interactions with β-blocker drugs. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Li X, Duan H, Song Z, Xu R. Comparative study on the interaction between fibrinogen and flavonoids. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Fadda AA, Ghanem RA, Gaffer HE, Waly MM, Tawfik EH. Synthesis, Antimicrobial Evaluation, and Molecular Docking of New Azole, Azine, Thiazole, and Chromene Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2069135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ahmed A. Fadda
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Reham A. Ghanem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University, Gamsaa, Egypt
| | | | - Mohamed M. Waly
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Eman H. Tawfik
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, Egypt
- Department of Chemistry, Faculty of Science and Arts, Taibah University, Ulla, Saudi Arabia
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Orellana N, Palma S, Torres E, Cordero ML, Vio V, Ruso JM, Juárez J, Topete A, Araya E, Vasquez-Contreras R, Kogan MJ, Hassan N. Study of the interaction of folic acid-modified gold nanorods and fibrinogen through microfluidics: implications for protein adsorption, incorporation and viability of cancer cells. NANOSCALE 2021; 13:17807-17821. [PMID: 34668502 DOI: 10.1039/d1nr03179a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Gold nanoparticles (GNPs) are an attractive nanomaterial for potential applications in therapy and diagnostics due to their capability to direct toward specific sites in the organism. However, when exposed to plasma, GNPs can interact with different biomolecules that form a dynamic nano-bio interface called a "protein corona" (PC). Remarkably, the PC could affect multiple biological processes, such as cell targeting and uptake, cytotoxicity, and nanoparticle (NP) clearance. The interaction of nanomaterials with plasmatic proteins has been widely studied under bulk conditions, however, under dynamic conditions, it has just recently been explored. Thus, to mimic a dynamic natural environment found in arteries and veins, microfluidic devices were used. In this work, gold nanorods (GNRs) were synthesized and conjugated with polyethylene glycol (PEG) to reduce their interaction with plasma proteins and increase their biocompatibility. Then, GNRs were functionalized with folic acid, a targeting ligand typically used to recognize tumor cells. The resulting nanosystem was exposed to fibrinogen (FB) to study the development and biological impact of PC formation through two strategies: bulk and laminar flow conditions. The obtained nanosystems were characterized by absorption spectrophotometry, DLS, laser Doppler microelectrophoresis, neutron activation analysis, circular dichroism spectroscopy and TEM. Finally, cell viability and cellular uptake assays were performed to study the influence of the PC on the cell viability and delivery of nanosystems.
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Affiliation(s)
- Nacaroha Orellana
- Programa Institucional de Fomento a la I+D+I, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Chile.
| | - Sujey Palma
- Programa Institucional de Fomento a la I+D+I, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Chile.
- Departamento de Química Farmacológica y Toxicológica, Facultad de Ciencias Químicas y Farmacéuticas, Laboratorio de Nanobiotecnología, Universidad de Chile, Santos Dumont 964, Independencia, Chile.
- Advanced Center for Chronic Diseases (ACCDis), Santos Dumont 964, Independencia, Santiago, Chile
| | - Estefania Torres
- Programa Institucional de Fomento a la I+D+I, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Chile.
| | - María Luisa Cordero
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Beauchef 850, Santiago, Chile
| | - Valentina Vio
- Departamento de Química Farmacológica y Toxicológica, Facultad de Ciencias Químicas y Farmacéuticas, Laboratorio de Nanobiotecnología, Universidad de Chile, Santos Dumont 964, Independencia, Chile.
- Advanced Center for Chronic Diseases (ACCDis), Santos Dumont 964, Independencia, Santiago, Chile
| | - Juan M Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Josué Juárez
- Departamento de Física, Universidad de Sonora, Unidad Centro, Hermosillo, Sonora 83000, Mexico
| | - Antonio Topete
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Eyleen Araya
- Departamento de Ciencias Quimicas, Universidad Andres Bello, Republica 275, 8370146 Santiago, Chile
| | - Rodrigo Vasquez-Contreras
- Departamento de Química Farmacológica y Toxicológica, Facultad de Ciencias Químicas y Farmacéuticas, Laboratorio de Nanobiotecnología, Universidad de Chile, Santos Dumont 964, Independencia, Chile.
- Advanced Center for Chronic Diseases (ACCDis), Santos Dumont 964, Independencia, Santiago, Chile
- Departamento de Ciencias Quimicas, Universidad Andres Bello, Republica 275, 8370146 Santiago, Chile
| | - Marcelo J Kogan
- Departamento de Química Farmacológica y Toxicológica, Facultad de Ciencias Químicas y Farmacéuticas, Laboratorio de Nanobiotecnología, Universidad de Chile, Santos Dumont 964, Independencia, Chile.
- Advanced Center for Chronic Diseases (ACCDis), Santos Dumont 964, Independencia, Santiago, Chile
| | - Natalia Hassan
- Programa Institucional de Fomento a la I+D+I, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Chile.
- Advanced Center for Chronic Diseases (ACCDis), Santos Dumont 964, Independencia, Santiago, Chile
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Rial R, González-Durruthy M, Somoza M, Liu Z, Ruso JM. Unraveling the Compositional and Molecular Features Involved in Lysozyme-Benzothiazole Derivative Interactions. Molecules 2021; 26:5855. [PMID: 34641399 PMCID: PMC8510236 DOI: 10.3390/molecules26195855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/02/2022] Open
Abstract
In this work we present a computational analysis together with experimental studies, focusing on the interaction between a benzothiazole (BTS) and lysozyme. Results obtained from isothermal titration calorimetry, UV-vis, and fluorescence were contrasted and complemented with molecular docking and machine learning techniques. The free energy values obtained both experimentally and theoretically showed excellent similarity. Calorimetry, UV-vis, and 3D/2D-lig-plot analysis revealed that the most relevant interactions between BTS and lysozyme are based on a predominance of aromatic, hydrophobic Van der Waals interactions, mainly aromatic edge-to-face (T-shaped) π-π stacking interactions between the benzene ring belonging to the 2-(methylthio)-benzothiazole moiety of BTS and the aromatic amino acid residue TRP108 of the lysozyme receptor. Next, conventional hydrogen bonding interactions contribute to the stability of the BTS-lysozyme coupling complex. In addition, mechanistic approaches performed using elastic network models revealed that the BTS ligand theoretically induces propagation of allosteric signals, suggesting non-physiological conformational flexing in large blocks of lysozyme affecting α-helices. Likewise, the BTS ligand interacts directly with allosteric residues, inducing perturbations in the conformational dynamics expressed as a moderate conformational softening in the α-helices H1, H2, and their corresponding β-loop in the lysozyme receptor, in contrast to the unbound state of lysozyme.
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Affiliation(s)
- Ramón Rial
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (R.R.); (M.G.-D.); (M.S.)
| | - Michael González-Durruthy
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (R.R.); (M.G.-D.); (M.S.)
- Department of Chemistry and Biochemistry, LAQV@REQUIMTE, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Manuel Somoza
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (R.R.); (M.G.-D.); (M.S.)
| | - Zhen Liu
- Department of Physics and Engineering, Frostburg State University, Frostburg, MD 21532, USA;
| | - Juan M. Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (R.R.); (M.G.-D.); (M.S.)
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Rial R, González-Durruthy M, Liu Z, Ruso JM. Advanced Materials Based on Nanosized Hydroxyapatite. Molecules 2021; 26:3190. [PMID: 34073479 PMCID: PMC8198166 DOI: 10.3390/molecules26113190] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 02/02/2023] Open
Abstract
The development of new materials based on hydroxyapatite has undergone a great evolution in recent decades due to technological advances and development of computational techniques. The focus of this review is the various attempts to improve new hydroxyapatite-based materials. First, we comment on the most used processing routes, highlighting their advantages and disadvantages. We will now focus on other routes, less common due to their specificity and/or recent development. We also include a block dedicated to the impact of computational techniques in the development of these new systems, including: QSAR, DFT, Finite Elements of Machine Learning. In the following part we focus on the most innovative applications of these materials, ranging from medicine to new disciplines such as catalysis, environment, filtration, or energy. The review concludes with an outlook for possible new research directions.
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Affiliation(s)
- Ramón Rial
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (R.R.); (M.G.-D.)
| | - Michael González-Durruthy
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (R.R.); (M.G.-D.)
| | - Zhen Liu
- Department of Physics and Engineering, Frostburg State University, Frostburg, MD 21532, USA;
| | - Juan M. Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; (R.R.); (M.G.-D.)
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New Mechanistic Insights on Carbon Nanotubes' Nanotoxicity Using Isolated Submitochondrial Particles, Molecular Docking, and Nano-QSTR Approaches. BIOLOGY 2021; 10:biology10030171. [PMID: 33668702 PMCID: PMC7996163 DOI: 10.3390/biology10030171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 01/08/2023]
Abstract
Single-walled carbon nanotubes can induce mitochondrial F0F1-ATPase nanotoxicity through inhibition. To completely characterize the mechanistic effect triggering the toxicity, we have developed a new approach based on the combination of experimental and computational study, since the use of only one or few techniques may not fully describe the phenomena. To this end, the in vitro inhibition responses in submitochondrial particles (SMP) was combined with docking, elastic network models, fractal surface analysis, and Nano-QSTR models. In vitro studies suggest that inhibition responses in SMP of F0F1-ATPase enzyme were strongly dependent on the concentration assay (from 3 to 5 µg/mL) for both pristine and COOH single-walled carbon nanotubes types (SWCNT). Besides, both SWCNTs show an interaction inhibition pattern mimicking the oligomycin A (the specific mitochondria F0F1-ATPase inhibitor blocking the c-ring F0 subunit). Performed docking studies denote the best crystallography binding pose obtained for the docking complexes based on the free energy of binding (FEB) fit well with the in vitro evidence from the thermodynamics point of view, following an affinity order such as: FEB (oligomycin A/F0-ATPase complex) = -9.8 kcal/mol > FEB (SWCNT-COOH/F0-ATPase complex) = -6.8 kcal/mol ~ FEB (SWCNT-pristine complex) = -5.9 kcal/mol, with predominance of van der Waals hydrophobic nano-interactions with key F0-ATPase binding site residues (Phe 55 and Phe 64). Elastic network models and fractal surface analysis were performed to study conformational perturbations induced by SWCNT. Our results suggest that interaction may be triggering abnormal allosteric responses and signals propagation in the inter-residue network, which could affect the substrate recognition ligand geometrical specificity of the F0F1-ATPase enzyme in order (SWCNT-pristine > SWCNT-COOH). In addition, Nano-QSTR models have been developed to predict toxicity induced by both SWCNTs, using results of in vitro and docking studies. Results show that this method may be used for the fast prediction of the nanotoxicity induced by SWCNT, avoiding time- and money-consuming techniques. Overall, the obtained results may open new avenues toward to the better understanding and prediction of new nanotoxicity mechanisms, rational drug design-based nanotechnology, and potential biomedical application in precision nanomedicine.
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