1
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Targeted systematic evolution of an RNA platform neutralizing DNMT1 function and controlling DNA methylation. Nat Commun 2023; 14:99. [PMID: 36609400 PMCID: PMC9823104 DOI: 10.1038/s41467-022-35222-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/23/2022] [Indexed: 01/09/2023] Open
Abstract
DNA methylation is a fundamental epigenetic modification regulating gene expression. Aberrant DNA methylation is the most common molecular lesion in cancer cells. However, medical intervention has been limited to the use of broadly acting, small molecule-based demethylating drugs with significant side-effects and toxicities. To allow for targeted DNA demethylation, we integrated two nucleic acid-based approaches: DNMT1 interacting RNA (DiR) and RNA aptamer strategy. By combining the RNA inherent capabilities of inhibiting DNMT1 with an aptamer platform, we generated a first-in-class DNMT1-targeted approach - aptaDiR. Molecular modelling of RNA-DNMT1 complexes coupled with biochemical and cellular assays enabled the identification and characterization of aptaDiR. This RNA bio-drug is able to block DNA methylation, impair cancer cell viability and inhibit tumour growth in vivo. Collectively, we present an innovative RNA-based approach to modulate DNMT1 activity in cancer or diseases characterized by aberrant DNA methylation and suggest the first alternative strategy to overcome the limitations of currently approved non-specific hypomethylating protocols, which will greatly improve clinical intervention on DNA methylation.
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Ramirez AE, Fernández-Pérez EJ, Olivos N, Burgos CF, Boopathi S, Armijo-Weingart L, Pacheco CR, González W, Aguayo LG. The Stimulatory Effects of Intracellular α-Synuclein on Synaptic Transmission Are Attenuated by 2-Octahydroisoquinolin-2(1H)-ylethanamine. Int J Mol Sci 2021; 22:ijms222413253. [PMID: 34948050 PMCID: PMC8705949 DOI: 10.3390/ijms222413253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
α-Synuclein (αSyn) species can be detected in synaptic boutons, where they play a crucial role in the pathogenesis of Parkinson's Disease (PD). However, the effects of intracellular αSyn species on synaptic transmission have not been thoroughly studied. Here, using patch-clamp recordings in hippocampal neurons, we report that αSyn oligomers (αSynO), intracellularly delivered through the patch electrode, produced a fast and potent effect on synaptic transmission, causing a substantial increase in the frequency, amplitude and transferred charge of spontaneous synaptic currents. We also found an increase in the frequency of miniature synaptic currents, suggesting an effect located at the presynaptic site of the synapsis. Furthermore, our in silico approximation using docking analysis and molecular dynamics simulations showed an interaction between a previously described small anti-amyloid beta (Aβ) molecule, termed M30 (2-octahydroisoquinolin-2(1H)-ylethanamine), with a central hydrophobic region of αSyn. In line with this finding, our empirical data aimed to obtain oligomerization states with thioflavin T (ThT) and Western blot (WB) indicated that M30 interfered with αSyn aggregation and decreased the formation of higher-molecular-weight species. Furthermore, the effect of αSynO on synaptic physiology was also antagonized by M30, resulting in a decrease in the frequency, amplitude, and charge transferred of synaptic currents. Overall, the present results show an excitatory effect of intracellular αSyn low molecular-weight species, not previously described, that are able to affect synaptic transmission, and the potential of a small neuroactive molecule to interfere with the aggregation process and the synaptic effect of αSyn, suggesting that M30 could be a potential therapeutic strategy for synucleinopathies.
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Affiliation(s)
- Alejandra E. Ramirez
- Laboratory of Neurophysiology, Department of Physiology, Faculty of Biological Sciences, Universidad de Concepción, 160-C, Concepción 4030000, Chile; (A.E.R.); (N.O.); (C.F.B.); (L.A.-W.); (C.R.P.)
| | - Eduardo J. Fernández-Pérez
- Laboratory of Neurophysiology, Department of Physiology, Faculty of Biological Sciences, Universidad de Concepción, 160-C, Concepción 4030000, Chile; (A.E.R.); (N.O.); (C.F.B.); (L.A.-W.); (C.R.P.)
- Correspondence: (E.J.F.-P.); (L.G.A.)
| | - Nicol Olivos
- Laboratory of Neurophysiology, Department of Physiology, Faculty of Biological Sciences, Universidad de Concepción, 160-C, Concepción 4030000, Chile; (A.E.R.); (N.O.); (C.F.B.); (L.A.-W.); (C.R.P.)
| | - Carlos F. Burgos
- Laboratory of Neurophysiology, Department of Physiology, Faculty of Biological Sciences, Universidad de Concepción, 160-C, Concepción 4030000, Chile; (A.E.R.); (N.O.); (C.F.B.); (L.A.-W.); (C.R.P.)
| | - Subramanian Boopathi
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
- Center for Bioinformatics, Simulations and Modeling, The Center for Bioinformatics and Molecular Simulations (CBSM), University of Talca, Talca 3530000, Chile;
| | - Lorena Armijo-Weingart
- Laboratory of Neurophysiology, Department of Physiology, Faculty of Biological Sciences, Universidad de Concepción, 160-C, Concepción 4030000, Chile; (A.E.R.); (N.O.); (C.F.B.); (L.A.-W.); (C.R.P.)
| | - Carla R. Pacheco
- Laboratory of Neurophysiology, Department of Physiology, Faculty of Biological Sciences, Universidad de Concepción, 160-C, Concepción 4030000, Chile; (A.E.R.); (N.O.); (C.F.B.); (L.A.-W.); (C.R.P.)
| | - Wendy González
- Center for Bioinformatics, Simulations and Modeling, The Center for Bioinformatics and Molecular Simulations (CBSM), University of Talca, Talca 3530000, Chile;
- Millennium Nucleus of Ion Channels-Associated Diseases, The Center for Bioinformatics and Molecular Simulations (CBSM), University of Talca, Talca 3530000, Chile
| | - Luis G. Aguayo
- Laboratory of Neurophysiology, Department of Physiology, Faculty of Biological Sciences, Universidad de Concepción, 160-C, Concepción 4030000, Chile; (A.E.R.); (N.O.); (C.F.B.); (L.A.-W.); (C.R.P.)
- Programa de Neurociencia, Psiquiatría y Salud Mental, Anatomy Building,
Faculty of Medicine, Universidad de Concepción, Concepción 4030000, Chile
- Correspondence: (E.J.F.-P.); (L.G.A.)
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Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus. SENSORS 2020; 20:s20174977. [PMID: 32887407 PMCID: PMC7506613 DOI: 10.3390/s20174977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/29/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
The urgent need to develop a detection system for Staphylococcus aureus, one of the most common causes of infection, is prompting research towards novel approaches and devices, with a particular focus on point-of-care analysis. Biosensors are promising systems to achieve this aim. We coupled the selectivity and affinity of aptamers, short nucleic acids sequences able to recognize specific epitopes on bacterial surface, immobilized at high density on a nanostructured zirconium dioxide surface, with the rational design of specifically interacting fluorescent peptides to assemble an easy-to-use detection device. We show that the displacement of fluorescent peptides upon the competitive binding of S. aureus to immobilized aptamers can be detected and quantified through fluorescence loss. This approach could be also applied to the detection of other bacterial species once aptamers interacting with specific antigens will be identified, allowing the development of a platform for easy detection of a pathogen without requiring access to a healthcare environment.
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Zhang P, Moretti M, Allione M, Tian Y, Ordonez-Loza J, Altamura D, Giannini C, Torre B, Das G, Li E, Thoroddsen ST, Sarathy SM, Autiero I, Giugni A, Gentile F, Malara N, Marini M, Di Fabrizio E. A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growth. Commun Biol 2020; 3:457. [PMID: 32820203 PMCID: PMC7441408 DOI: 10.1038/s42003-020-01187-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/31/2020] [Indexed: 11/10/2022] Open
Abstract
Methods to produce protein amyloid fibrils, in vitro, and in situ structure characterization, are of primary importance in biology, medicine, and pharmacology. We first demonstrated the droplet on a super-hydrophobic substrate as the reactor to produce protein amyloid fibrils with real-time monitoring of the growth process by using combined light-sheet microscopy and thermal imaging. The molecular structures were characterized by Raman spectroscopy, X-ray diffraction and X-ray scattering. We demonstrated that the convective flow induced by the temperature gradient of the sample is the main driving force in the growth of well-ordered protein fibrils. Particular attention was devoted to PHF6 peptide and full-length Tau441 protein to form amyloid fibrils. By a combined experimental with the molecular dynamics simulations, the conformational polymorphism of these amyloid fibrils were characterized. The study provided a feasible procedure to optimize the amyloid fibrils formation and characterizations of other types of proteins in future studies. Zhang et al present an integrated real-time imaging and flow field control platform based on water droplet evaporation on super-hydrophobic substrate (SHS) to enable amyloid fibril aggregation. They apply this methodology to observe structural polymorphism in PHF6 peptide and full length Tau441.
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Affiliation(s)
- Peng Zhang
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Manola Moretti
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Marco Allione
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Yuansi Tian
- High-Speed Fluids Imaging Lab, Physical Science and Engineering (PSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Javier Ordonez-Loza
- Clean Combustion Research Center, Physical Science and Engineering (PSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Davide Altamura
- Istituto di Cristallografia - Consiglio Nazionale delle Ricerche (IC-CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Cinzia Giannini
- Istituto di Cristallografia - Consiglio Nazionale delle Ricerche (IC-CNR), Via Amendola 122/O, 70126, Bari, Italy
| | - Bruno Torre
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Gobind Das
- Department of Physics, Khalifa University, P.O. Box: 127788, Abu Dhabi, UAE
| | - Erqiang Li
- Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Sigurdur T Thoroddsen
- High-Speed Fluids Imaging Lab, Physical Science and Engineering (PSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - S Mani Sarathy
- Clean Combustion Research Center, Physical Science and Engineering (PSE) Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ida Autiero
- Molecular Horizon, Bettona, Italy.,National Research Council, Institute of Biostructures and Bioimaging, Naples, Italy
| | - Andrea Giugni
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Francesco Gentile
- Department of electrical Engineering and Information Technology, University Federico II, Naples, Italy
| | - Natalia Malara
- BIONEM lab, University Magna Graecia, Campus Salvatore Venuta, Viale Europa, 88100, Catanzaro, Italy
| | - Monica Marini
- Materials and Microsystems Laboratory, Department of Applied Science and Technology, Politecnico di Torino, 10129, Torino, Italy
| | - Enzo Di Fabrizio
- SMILEs Lab, Physical Science and Engineering (PSE) and Biological and Environmental Science and Engineering (BESE) Divisions, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia. .,Materials and Microsystems Laboratory, Department of Applied Science and Technology, Politecnico di Torino, 10129, Torino, Italy.
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Peters C, Bascuñán D, Burgos CF, Bobadilla C, González-Sanmiguel J, Boopathi S, Riffo N, Fernández-Pérez EJ, Tarnok ME, Aguilar LF, Gonzalez W, Aguayo LG. Characterization of a new molecule capable of inhibiting several steps of the amyloid cascade in Alzheimer's disease. Neurobiol Dis 2020; 141:104938. [PMID: 32434047 DOI: 10.1016/j.nbd.2020.104938] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/04/2020] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder in elderly people. Existent therapies are directed at alleviating some symptoms, but are not effective in altering the course of the disease. METHODS Based on our previous study that showed that an Aβ-interacting small peptide protected against the toxic effects of amyloid-beta peptide (Aβ), we carried out an array of in silico, in vitro, and in vivo assays to identify a molecule having neuroprotective properties. RESULTS In silico studies showed that the molecule, referred to as M30 (2-Octahydroisoquinolin-2(1H)-ylethanamine), was able to interact with the Aβ peptide. Additionally, in vitro assays showed that M30 blocked Aβ aggregation, association to the plasma membrane, synaptotoxicity, intracellular calcium, and cellular toxicity, while in vivo experiments demonstrated that M30 induced a neuroprotective effect by decreasing the toxicity of Aβ in the dentate gyrus of the hippocampus and improving the alteration in spatial memory in behavior assays. DISCUSSION Therefore, we propose that this new small molecule could be a useful candidate for the additional development of a treatment against AD since it appears to block multiple steps in the amyloid cascade. Overall, since there are no drugs that effectively block the progression of AD, this approach represents an innovative strategy. SIGNIFICANCE Currently, there is no effective treatment for AD and the expectations to develop an effective therapy are low. Using in silico, in vitro, and in vivo experiments, we identified a new compound that is able to inhibit Aβ-induced neurotoxicity, specifically aggregation, association to neurons, synaptic toxicity, calcium dyshomeostasis and memory impairment induced by Aβ. Because Aβ toxicity is central to AD progression, the inhibition mediated by this new molecule might be useful as a therapeutic tool.
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Affiliation(s)
- Christian Peters
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Denisse Bascuñán
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Carlos F Burgos
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Catalina Bobadilla
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | | | - Subramanian Boopathi
- The Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, Talca, Chile
| | - Nicolás Riffo
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Eduardo J Fernández-Pérez
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - María Elena Tarnok
- Laboratory of Photophysics and Molecular Spectroscopy, Chemistry, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Luis Felipe Aguilar
- Laboratory of Photophysics and Molecular Spectroscopy, Chemistry, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Wendy Gonzalez
- The Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, Talca, Chile; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca, Chile
| | - Luis G Aguayo
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile.
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Li H, Wang X, Yu H, Zhu J, Jin H, Wang A, Yang Z. Combining in vitro and in silico Approaches to Find New Candidate Drugs Targeting the Pathological Proteins Related to the Alzheimer's Disease. Curr Neuropharmacol 2018; 16:758-768. [PMID: 29086699 PMCID: PMC6080099 DOI: 10.2174/1570159x15666171030142108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 09/24/2017] [Accepted: 10/10/2017] [Indexed: 01/10/2023] Open
Abstract
Background: Alzheimer’s disease (AD) as the most common cause of dementia among older people has aroused the universal concern of the whole world. However, until now there is still none effective treatments. Consequently, the development of new drugs targeting this complicated brain disorder is urgent and needs more efforts. In this review, we detailed the current state of knowledge about new candidate drugs targeting the pathological proteins especially the drugs which are employed using the combined methods of in vitro and in silico. Methods: We looked up and reviewed online papers related to the pathogenesis and new drugs development of AD. Then, articles up to the requirements were respectively analyzed and summaried to provide the latest knowledge about the pathogenic effect and the new candidate drugs targeting Aβ and Tau proteins. Results: New candidate drugs targeting the Aβ include decreasing the production, promoting the clearence and preventing aggregation. However these drugs have mostly failed in Phase III clinical trial stage due to the unsuccessful of reversing cognition symptoms. As to tau protein, the prevention of tau aggregation and propagation is a promising strategy to synthesize/design mechanism-based drugs against tauopathies. Some candidate drugs are under research. Moreover, because of the complex pathogenesis of AD, multi-target drugs have also shed light on the treatment of AD. Conclusion: Given to the consecutive failure of Aβ-directed drugs and the feasibilities of tau-targeted therapy, more and more researchers suggested that the AD treatment should be moved from Aβ to tau or focused on considering the soluble form of Aβ and tau as a whole. Moreover, the novel in silico methods also have great potential in drug discovery, drug repositioning, virtual screening of chemical libraries. No matter how many difficulties and challenges in prevention and treatment of AD, we firmly believe that the effective and safe drugs will be found using the combined methods in the immediate future with the global effort.
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Affiliation(s)
- Hui Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaobing Wang
- Tumor Marker Research Center, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hongmei Yu
- China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Jing Zhu
- College of Pharmacy, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Hongtao Jin
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Aiping Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhaogang Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, 43210, United States
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7
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Langella E, Buonanno M, Vullo D, Dathan N, Leone M, Supuran CT, De Simone G, Monti SM. Biochemical, biophysical and molecular dynamics studies on the proteoglycan-like domain of carbonic anhydrase IX. Cell Mol Life Sci 2018; 75:3283-3296. [PMID: 29564477 PMCID: PMC11105230 DOI: 10.1007/s00018-018-2798-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/02/2018] [Accepted: 03/13/2018] [Indexed: 12/11/2022]
Abstract
Human carbonic anhydrase IX (hCA IX) is a tumour-associated enzyme present in a limited number of normal tissues, but overexpressed in several malignant human tumours. It is a transmembrane protein, where the extracellular region consists of a greatly investigated catalytic CA domain and a much less investigated proteoglycan-like (PG) domain. Considering its important role in tumour biology, here, we report for the first time the full characterization of the PG domain, providing insights into its structural and functional features. In particular, this domain has been produced at high yields in bacterial cells and characterized by means of biochemical, biophysical and molecular dynamics studies. Results show that it belongs to the family of intrinsically disordered proteins, being globally unfolded with only some local residual polyproline II secondary structure. The observed conformational flexibility may have several important roles in tumour progression, facilitating interactions of hCA IX with partner proteins assisting tumour spreading and progression.
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Affiliation(s)
- Emma Langella
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Martina Buonanno
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Daniela Vullo
- Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Florence, Italy
| | - Nina Dathan
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Claudiu T Supuran
- Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, Sesto Fiorentino, 50019, Florence, Italy
| | - Giuseppina De Simone
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone, 16, 80134, Naples, Italy.
| | - Simona Maria Monti
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone, 16, 80134, Naples, Italy.
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8
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Saini RK, Shuaib S, Goyal B. Molecular insights into Aβ42protofibril destabilization with a fluorinated compound D744: A molecular dynamics simulation study. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2656] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Suniba Shuaib
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Bhupesh Goyal
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
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9
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Fan HM, Xu Q, Wei DQ. Recent Studies on Mechanisms of New Drug Candidates for Alzheimer’s Disease Interacting with Amyloid-β Protofibrils Using Molecular Dynamics Simulations. TRANSLATIONAL BIOINFORMATICS AND ITS APPLICATION 2017. [DOI: 10.1007/978-94-024-1045-7_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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10
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Sinopoli A, Giuffrida A, Tomasello MF, Giuffrida ML, Leone M, Attanasio F, Caraci F, De Bona P, Naletova I, Saviano M, Copani A, Pappalardo G, Rizzarelli E. Ac-LPFFD-Th: A Trehalose-Conjugated Peptidomimetic as a Strong Suppressor of Amyloid-β Oligomer Formation and Cytotoxicity. Chembiochem 2016; 17:1541-9. [DOI: 10.1002/cbic.201600243] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Alessandro Sinopoli
- PhD Program in Translational Biomedicine; University of Catania; Viale A. Doria 6 95125 Catania Italy
| | - Alessandro Giuffrida
- Institute of Biostructures and Bioimaging; CNR; Via P. Gaifami 18 95126 Catania Italy
| | | | - Maria Laura Giuffrida
- Institute of Biostructures and Bioimaging; CNR; Via P. Gaifami 18 95126 Catania Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16 80134 Naples Italy
| | - Francesco Attanasio
- Institute of Biostructures and Bioimaging; CNR; Via P. Gaifami 18 95126 Catania Italy
| | - Filippo Caraci
- Department of Drug Sciences; University of Catania; Viale A. Doria 6 95125 Catania Italy
| | - Paolo De Bona
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; 660 S. Euclid Avenue Box 8231 St. Louis MO 63110 USA
| | - Irina Naletova
- Department of Biomedical Sciences; University of Catania; Viale A. Doria 6 95125 Catania Italy
| | - Michele Saviano
- Institute of Crystallography; CNR; Via G. Amendola 122/O 70126 Bari Italy
| | - Agata Copani
- Department of Drug Sciences; University of Catania; Viale A. Doria 6 95125 Catania Italy
| | - Giuseppe Pappalardo
- Institute of Biostructures and Bioimaging; CNR; Via P. Gaifami 18 95126 Catania Italy
| | - Enrico Rizzarelli
- Institute of Biostructures and Bioimaging; CNR; Via P. Gaifami 18 95126 Catania Italy
- Department of Chemical Sciences; University of Catania, Viale A. Doria 6; 95125 Catania Italy
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11
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Menon S, Sengupta N. Perturbations in inter-domain associations may trigger the onset of pathogenic transformations in PrP(C): insights from atomistic simulations. MOLECULAR BIOSYSTEMS 2016; 11:1443-53. [PMID: 25855580 DOI: 10.1039/c4mb00689e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conversion of the predominantly α-helical cellular prion protein (PrP(C)) to the misfolded β-sheet enriched Scrapie form (PrP(Sc)) is a critical event in prion pathogenesis. However, the conformational triggers that lead to the isoform conversion (PrP(C) to PrP(Sc)) remain obscure, and conjectures about the role of unusually hydrophilic, short helix H1 of the C-terminal globular domain in the transition are varied. Helix H1 is anchored to helix H3 via a few stabilizing polar interactions. We have employed fully atomistic molecular dynamics simulations to study the effects triggered by a minor perturbation in the network of these non-bonded interactions in PrP(C). The elimination of just one of the key H1-H3 hydrogen bonds led to a cascade of conformational changes that are consistent with those observed in partially unfolded intermediates of PrP(C), with pathogenic mutations and in low pH environments. Our analyses reveal that the perturbation results in the enhanced conformational flexibility of the protein. The resultant enhancement in the dynamics leads to overall increased solvent exposure of the hydrophobic core residues and concomitant disruption of the H1-H3 inter-domain salt bridge network. This study lends credence to the hypothesis that perturbing the cooperativity of the stabilizing interactions in the PrP(C) globular domain can critically affect its dynamics and may lead to structural transitions of pathological relevance.
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Affiliation(s)
- Sneha Menon
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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12
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Fan HM, Gu RX, Wang YJ, Pi YL, Zhang YH, Xu Q, Wei DQ. Destabilization of Alzheimer’s Aβ42 Protofibrils with a Novel Drug Candidate wgx-50 by Molecular Dynamics Simulations. J Phys Chem B 2015; 119:11196-202. [DOI: 10.1021/acs.jpcb.5b03116] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Huai-Meng Fan
- State
Key Laboratory of Microbial Metabolism and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ruo-Xu Gu
- State
Key Laboratory of Microbial Metabolism and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yan-Jing Wang
- State
Key Laboratory of Microbial Metabolism and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yun-Long Pi
- State
Key Laboratory of Microbial Metabolism and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yong-Hong Zhang
- Medicine
Engineering Research Center, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Qin Xu
- State
Key Laboratory of Microbial Metabolism and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Dong-Qing Wei
- State
Key Laboratory of Microbial Metabolism and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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13
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 474] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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14
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Lv M, Ma S, Tian Y, Zhang X, Lv W, Zhai H. Computational studies on the binding mechanism between triazolone inhibitors and Chk1 by molecular docking and molecular dynamics. MOLECULAR BIOSYSTEMS 2014; 11:275-86. [PMID: 25372494 DOI: 10.1039/c4mb00449c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chk1, a serine/threonine protein kinase that participates in transducing DNA damage signals, is an attractive target due to its involvement in tumor initiation and progression. As a novel Chk1 inhibitor, the triazolone's bioactivity mechanism is not clear. In this study, we carried out an integrated computational study that combines molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations to identify the key factors necessary for the bioactivities. With the aim of discerning the structural features that affect the inhibitory activity of triazolones, MK-8776, a Chk1 inhibitor that reached the clinical stage, was also used as a reference for simulations. A comparative analysis of the triazolone inhibitors at the molecular level offers valuable insight into the structural and energetic properties. A general feature is that all the studied inhibitors bind in the pocket characterized by residues Leu14, Val22, Ala35, Glu84, Tyr85, Cys86, and Leu136 of Chk1. Moreover, introducing hydrophobic groups into triazolone inhibitors is favorable for binding to Chk1, which is corroborated by residue Leu136 with a relatively large difference in the contribution between MK-8776 and five triazolones to the total binding free energies. A hydrogen bond between the polar hydrogen atoms at R1 and Cys86 can facilitate proper placement of the inhibitor in the binding pocket of Chk1 that favors binding. However, the introduction of hydrophilic groups into the R2 position diminishes binding affinity. The information provided by this research is of benefit for further rational design of novel promising inhibitors of Chk1.
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Affiliation(s)
- Min Lv
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, Gansu Province, People's Republic of China.
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15
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Eleuteri S, Di Giovanni S, Rockenstein E, Mante M, Adame A, Trejo M, Wrasidlo W, Wu F, Fraering PC, Masliah E, Lashuel HA. Novel therapeutic strategy for neurodegeneration by blocking Aβ seeding mediated aggregation in models of Alzheimer's disease. Neurobiol Dis 2014; 74:144-57. [PMID: 25173807 DOI: 10.1016/j.nbd.2014.08.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 07/14/2014] [Accepted: 08/10/2014] [Indexed: 11/24/2022] Open
Abstract
Aβ accumulation plays a central role in the pathogenesis of Alzheimer's disease (AD). Recent studies suggest that the process of Aβ nucleated polymerization is essential for Aβ fibril formation, pathology spreading and toxicity. Therefore, targeting this process represents an effective therapeutic strategy to slow or block disease progression. To discover compounds that might interfere with the Aβ seeding capacity, toxicity and pathology spreading, we screened a focused library of FDA-approved drugs in vitro using a seeding polymerization assay and identified small molecule inhibitors that specifically interfered with Aβ seeding-mediated fibril growth and toxicity. Mitoxantrone, bithionol and hexachlorophene were found to be the strongest inhibitors of fibril growth and protected primary cortical neuronal cultures against Aβ-induced toxicity. Next, we assessed the effects of these three inhibitors in vivo in the mThy1-APPtg mouse model of AD (8-month-old mice). We found that mitoxantrone and bithionol, but not hexachlorophene, stabilized diffuse amyloid plaques, reduced the levels of Aβ42 oligomers and ameliorated synapse loss, neuronal damage and astrogliosis. Together, our findings suggest that targeting fibril growth and Aβ seeding capacity constitutes a viable and effective strategy for protecting against neurodegeneration and disease progression in AD.
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Affiliation(s)
- Simona Eleuteri
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Station 19, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne, Switzerland; Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Saviana Di Giovanni
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Station 19, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne, Switzerland
| | - Edward Rockenstein
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Mike Mante
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Antony Adame
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Margarita Trejo
- Department of Pathology, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Wolf Wrasidlo
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Fang Wu
- Laboratory of Molecular and Cellular Biology of Alzheimer's Disease, Brain Mind Institute, Station 19, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Patrick C Fraering
- Laboratory of Molecular and Cellular Biology of Alzheimer's Disease, Brain Mind Institute, Station 19, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Eliezer Masliah
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Laboratory of Molecular and Cellular Biology of Alzheimer's Disease, Brain Mind Institute, Station 19, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Station 19, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne, Switzerland.
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16
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Bernhardt NA, Berhanu WM, Hansmann UHE. Mutations and seeding of amylin fibril-like oligomers. J Phys Chem B 2013; 117:16076-85. [PMID: 24294935 DOI: 10.1021/jp409777p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Seeding a protein solution with preformed fibrils can dramatically enhance the growth rate of amyloids. As the seeds do not need to be of the same protein, seeding may account for the observed correlations between amyloid diseases. In an effort to understand better the molecular mechanisms behind cross seeding we have studied in silico the effect of mutations on the seeding of amylin fibrils. Our investigations of the structural stability of decamers of wild type amylin peptides, of Y37L mutants, and of heteroassemblies of wild-type and mutant amylin molecules show that the experimentally observed efficient cross seeding can be explained based on similarity in fibril structure of components. We find that amyloids with similar side chains packing at the β-sheet interface are structurally compatible, acting as a good template for the congruent incorporation of homologues peptides. In the Y37L mutants, lack of tyrosine-specific interactions causes significant higher flexibility of the C terminal than observed in the wild-type fibril. This effects elongation of the mutant fibril leading to the longer lag times during aggregation that are observed in experiments. Our study gives guidelines for the design of ligands that could stabilize amylin fibrils.
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Affiliation(s)
- Nathan A Bernhardt
- Department of Biology, Southwestern Oklahoma State University , Weatherford, Oklahoma 73096, United States
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17
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Autiero I, Langella E, Saviano M. Insights into the mechanism of interaction between trehalose-conjugated beta-sheet breaker peptides and Aβ(1–42) fibrils by molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2013; 9:2835-41. [DOI: 10.1039/c3mb70235a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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