1
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Pritzkow S, Schauer I, Tupaki-Sreepurna A, Morales R, Soto C. Screening of Anti-Prion Compounds Using the Protein Misfolding Cyclic Amplification Technology. Biomolecules 2024; 14:1113. [PMID: 39334879 PMCID: PMC11430292 DOI: 10.3390/biom14091113] [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: 05/03/2024] [Revised: 08/10/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
Prion diseases are 100% fatal infectious neurodegenerative diseases affecting the brains of humans and other mammals. The disease is caused by the formation and replication of prions, composed exclusively of the misfolded prion protein (PrPSc). We invented and developed the protein misfolding cyclic amplification (PMCA) technology for in vitro prion replication, which allow us to replicate the infectious agent and it is commonly used for ultra-sensitive prion detection in biological fluids, tissues and environmental samples. In this article, we studied whether PMCA can be used to screen for chemical compounds that block prion replication. A small set of compounds previously shown to have anti-prion activity in various systems, mostly using cells infected with murine prions, was evaluated for their ability to prevent the replication of prions. Studies were conducted simultaneously with prions derived from 4 species, including human, cattle, cervid and mouse. Our results show that only one of these compounds (methylene blue) was able to completely inhibit prion replication in all species. Estimation of the IC50 for methylene blue inhibition of human prions causing variant Creutzfeldt-Jakob disease (vCJD) was 7.7 μM. Finally, we showed that PMCA can be used for structure-activity relationship studies of anti-prion compounds. Interestingly, some of the less efficient prion inhibitors altered the replication of prions in some species and not others, suggesting that PMCA is useful for studying the differential selectivity of potential drugs.
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Affiliation(s)
- Sandra Pritzkow
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA (R.M.)
| | - Isaac Schauer
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA (R.M.)
| | - Ananya Tupaki-Sreepurna
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA (R.M.)
| | - Rodrigo Morales
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA (R.M.)
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago 8370993, Chile
| | - Claudio Soto
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX 77030, USA (R.M.)
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2
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Shim KH, Sharma N, An SSA. Prion therapeutics: Lessons from the past. Prion 2022; 16:265-294. [PMID: 36515657 PMCID: PMC9754114 DOI: 10.1080/19336896.2022.2153551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 12/15/2022] Open
Abstract
Prion diseases are a group of incurable zoonotic neurodegenerative diseases (NDDs) in humans and other animals caused by the prion proteins. The abnormal folding and aggregation of the soluble cellular prion proteins (PrPC) into scrapie isoform (PrPSc) in the Central nervous system (CNS) resulted in brain damage and other neurological symptoms. Different therapeutic approaches, including stalling PrPC to PrPSc conversion, increasing PrPSc removal, and PrPC stabilization, for which a spectrum of compounds, ranging from organic compounds to antibodies, have been explored. Additionally, a non-PrP targeted drug strategy using serpin inhibitors has been discussed. Despite numerous scaffolds being screened for anti-prion activity in vitro, only a few were effective in vivo and unfortunately, almost none of them proved effective in the clinical studies, most likely due to toxicity and lack of permeability. Recently, encouraging results from a prion-protein monoclonal antibody, PRN100, were presented in the first human trial on CJD patients, which gives a hope for better future for the discovery of other new molecules to treat prion diseases. In this comprehensive review, we have re-visited the history and discussed various classes of anti-prion agents, their structure, mode of action, and toxicity. Understanding pathogenesis would be vital for developing future treatments for prion diseases. Based on the outcomes of existing therapies, new anti-prion agents could be identified/synthesized/designed with reduced toxicity and increased bioavailability, which could probably be effective in treating prion diseases.
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Affiliation(s)
- Kyu Hwan Shim
- Department of Bionano Technology, Gachon University, Seongnam, South Korea
| | - Niti Sharma
- Department of Bionano Technology, Gachon University, Seongnam, South Korea
| | - Seong Soo A An
- Department of Bionano Technology, Gachon University, Seongnam, South Korea
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3
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Linsenmeier L, Mohammadi B, Shafiq M, Frontzek K, Bär J, Shrivastava AN, Damme M, Song F, Schwarz A, Da Vela S, Massignan T, Jung S, Correia A, Schmitz M, Puig B, Hornemann S, Zerr I, Tatzelt J, Biasini E, Saftig P, Schweizer M, Svergun D, Amin L, Mazzola F, Varani L, Thapa S, Gilch S, Schätzl H, Harris DA, Triller A, Mikhaylova M, Aguzzi A, Altmeppen HC, Glatzel M. Ligands binding to the prion protein induce its proteolytic release with therapeutic potential in neurodegenerative proteinopathies. SCIENCE ADVANCES 2021; 7:eabj1826. [PMID: 34818048 PMCID: PMC8612689 DOI: 10.1126/sciadv.abj1826] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/20/2021] [Indexed: 05/07/2023]
Abstract
The prion protein (PrPC) is a central player in neurodegenerative diseases, such as prion diseases or Alzheimer’s disease. In contrast to disease-promoting cell surface PrPC, extracellular fragments act neuroprotective by blocking neurotoxic disease-associated protein conformers. Fittingly, PrPC release by the metalloprotease ADAM10 represents a protective mechanism. We used biochemical, cell biological, morphological, and structural methods to investigate mechanisms stimulating this proteolytic shedding. Shed PrP negatively correlates with prion conversion and is markedly redistributed in murine brain in the presence of prion deposits or amyloid plaques, indicating a sequestrating activity. PrP-directed ligands cause structural changes in PrPC and increased shedding in cells and organotypic brain slice cultures. As an exception, some PrP-directed antibodies targeting repetitive epitopes do not cause shedding but surface clustering, endocytosis, and degradation of PrPC. Both mechanisms may contribute to beneficial actions described for PrP-directed ligands and pave the way for new therapeutic strategies against currently incurable neurodegenerative diseases.
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Affiliation(s)
- Luise Linsenmeier
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Behnam Mohammadi
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Mohsin Shafiq
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Karl Frontzek
- Institute of Neuropathology, University of Zurich, Zürich, Switzerland
| | - Julia Bär
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Molecular Neurobiology Hamburg (ZMNH), UKE, Hamburg, Germany
| | - Amulya N. Shrivastava
- École Normale Supérieure, Institut de Biologie de l’ENS (IBENS), INSERM, CNRS, PSL Research University, Paris, France
| | - Markus Damme
- Institute of Biochemistry, Christian Albrechts University, Kiel, Germany
| | - Feizhi Song
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Alexander Schwarz
- Institute of Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany
| | - Stefano Da Vela
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Tania Massignan
- Dulbecco Telethon Laboratory of Prions and Amyloids, CIBIO, University of Trento, Trento, Italy
| | - Sebastian Jung
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Angela Correia
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Matthias Schmitz
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Berta Puig
- Department of Neurology, Experimental Research in Stroke and Inflammation, UKE, Hamburg, Germany
| | - Simone Hornemann
- Institute of Neuropathology, University of Zurich, Zürich, Switzerland
| | - Inga Zerr
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Cluster of Excellence RESOLV, Bochum, Germany
| | - Emiliano Biasini
- Dulbecco Telethon Laboratory of Prions and Amyloids, CIBIO, University of Trento, Trento, Italy
| | - Paul Saftig
- Institute of Biochemistry, Christian Albrechts University, Kiel, Germany
| | | | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Ladan Amin
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Federica Mazzola
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Simrika Thapa
- Calgary Prion Research Unit, University of Calgary, Calgary, Alberta, Canada
| | - Sabine Gilch
- Calgary Prion Research Unit, University of Calgary, Calgary, Alberta, Canada
| | - Hermann Schätzl
- Calgary Prion Research Unit, University of Calgary, Calgary, Alberta, Canada
| | - David A. Harris
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Antoine Triller
- École Normale Supérieure, Institut de Biologie de l’ENS (IBENS), INSERM, CNRS, PSL Research University, Paris, France
| | - Marina Mikhaylova
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Molecular Neurobiology Hamburg (ZMNH), UKE, Hamburg, Germany
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zürich, Switzerland
| | - Hermann C. Altmeppen
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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4
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Overduin M, Wille H, Westaway D. Multisite interactions of prions with membranes and native nanodiscs. Chem Phys Lipids 2021; 236:105063. [PMID: 33600804 DOI: 10.1016/j.chemphyslip.2021.105063] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/29/2021] [Accepted: 02/12/2021] [Indexed: 02/05/2023]
Abstract
Although prions are known as protein-only infectious particles, they exhibit lipid specificities, cofactor dependencies and membrane-dependent activities. Such membrane interactions play key roles in how prions are processed, presented and regulated, and hence have significant functional consequences. The expansive literature related to prion protein interactions with lipids and native nanodiscs is discussed, and provides a unique opportunity to re-evaluate the molecular composition and mechanisms of its infectious and cellular states. A family of crystal and solution structures of prions are analyzed here for the first time using the membrane optimal docking area (MODA) program, revealling the presence of structured binding elements that could mediate specific lipid recognition. A set of motifs centerred around W99, L125, Y169 and Y226 are consistently predicted as being membrane interactive and form an exposed surface which includes α helical, β strand and loop elements involving the prion protein (PrP) structural domain, while the scrapie form is radically different and doubles the size of the membrane interactive site into an extensible surface. These motifs are highly conserved throughout mammalian evolution, suggesting that prions have long been intrinsically attached to membranes at central and N- and C-terminal points, providing several opportunities for stable and specific bilayer interactions as well as multiple complexed orientations. Resistance or susceptibility to prion disease correlates with increased or decreased membrane binding propensity by mutant forms, respectively, indicating a protective role by lipids. The various prion states found in vivo are increasingly resolvable using native nanodiscs formed by styrene maleic acid (SMA) and stilbene maleic acid (STMA) copolymers rather than classical detergents, allowing the endogenous states to be tackled. These copolymers spontaneously fragment intact membranes into water-soluble discs holding a section of native bilayer, and can accommodate prion multimers and mini-fibrils. Such nanodiscs have also proven useful for understanding how β amyloid and α synuclein proteins contribute to Alzheimer's and Parkinson's diseases, providing further biomedical applications. Structural and functional insights of such proteins in styrene maleic acid lipid particles (SMALPs) can be resolved at high resolution by methods including cryo-electron microscopy (cEM), motivating continued progress in polymer design to resolve biological and pathological mechanisms.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada; Center for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - David Westaway
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada; Center for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
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5
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Spagnolli G, Massignan T, Astolfi A, Biggi S, Rigoli M, Brunelli P, Libergoli M, Ianeselli A, Orioli S, Boldrini A, Terruzzi L, Bonaldo V, Maietta G, Lorenzo NL, Fernandez LC, Codeseira YB, Tosatto L, Linsenmeier L, Vignoli B, Petris G, Gasparotto D, Pennuto M, Guella G, Canossa M, Altmeppen HC, Lolli G, Biressi S, Pastor MM, Requena JR, Mancini I, Barreca ML, Faccioli P, Biasini E. Pharmacological inactivation of the prion protein by targeting a folding intermediate. Commun Biol 2021; 4:62. [PMID: 33437023 PMCID: PMC7804251 DOI: 10.1038/s42003-020-01585-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/09/2020] [Indexed: 01/05/2023] Open
Abstract
Recent computational advancements in the simulation of biochemical processes allow investigating the mechanisms involved in protein regulation with realistic physics-based models, at an atomistic level of resolution. These techniques allowed us to design a drug discovery approach, named Pharmacological Protein Inactivation by Folding Intermediate Targeting (PPI-FIT), based on the rationale of negatively regulating protein levels by targeting folding intermediates. Here, PPI-FIT was tested for the first time on the cellular prion protein (PrP), a cell surface glycoprotein playing a key role in fatal and transmissible neurodegenerative pathologies known as prion diseases. We predicted the all-atom structure of an intermediate appearing along the folding pathway of PrP and identified four different small molecule ligands for this conformer, all capable of selectively lowering the load of the protein by promoting its degradation. Our data support the notion that the level of target proteins could be modulated by acting on their folding pathways, implying a previously unappreciated role for folding intermediates in the biological regulation of protein expression. Spagnolli, Massignan, Astolfi et al. design a new drug discovery approach, termed Pharmacological Protein Inactivation by Folding Intermediate Targeting, in which folding intermediates of disease-causing proteins are targeted. They test it on the cellular prion protein, identifying ligands stabilizing a folding intermediate and consequently promoting its degradation by the cellular quality control machinery.
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Affiliation(s)
- Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Tania Massignan
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy.,Sibylla Biotech SRL, 37121, Verona, VR, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, 06123, Perugia, PG, Italy
| | - Silvia Biggi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Marta Rigoli
- Department of Physics, University of Trento, Povo, Trento, TN, Italy
| | - Paolo Brunelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Michela Libergoli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Alan Ianeselli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Simone Orioli
- Department of Physics, University of Trento, Povo, Trento, TN, Italy.,INFN-TIFPA, University of Trento, Povo, Trento, TN, Italy
| | - Alberto Boldrini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Sibylla Biotech SRL, 37121, Verona, VR, Italy
| | - Luca Terruzzi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Sibylla Biotech SRL, 37121, Verona, VR, Italy
| | - Valerio Bonaldo
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Giulia Maietta
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Nuria L Lorenzo
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Leticia C Fernandez
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Yaiza B Codeseira
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Laura Tosatto
- Institute of Biophysics, National Council of Research, 38123 Povo, Trento, TN, Italy
| | - Luise Linsenmeier
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Beatrice Vignoli
- Department of Physics, University of Trento, Povo, Trento, TN, Italy
| | - Gianluca Petris
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy
| | - Dino Gasparotto
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Maria Pennuto
- Department of Biomedical Sciences (DBS), University of Padova, 35131, Padova, Italy.,Veneto Institute of Molecular Medicine (VIMM), 35129, Padova, Italy
| | - Graziano Guella
- Department of Physics, University of Trento, Povo, Trento, TN, Italy
| | - Marco Canossa
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy
| | - Hermann C Altmeppen
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Graziano Lolli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy
| | - Stefano Biressi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy.,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy
| | - Manuel M Pastor
- RIAIDT, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain
| | - Ines Mancini
- Department of Physics, University of Trento, Povo, Trento, TN, Italy
| | - Maria L Barreca
- Department of Pharmaceutical Sciences, University of Perugia, 06123, Perugia, PG, Italy.
| | - Pietro Faccioli
- Department of Physics, University of Trento, Povo, Trento, TN, Italy. .,INFN-TIFPA, University of Trento, Povo, Trento, TN, Italy.
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123, Povo, TN, Italy. .,Dulbecco Telethon Institute, University of Trento, 38123, Povo, TN, Italy.
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6
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Astolfi A, Spagnolli G, Biasini E, Barreca ML. The Compelling Demand for an Effective PrP C-Directed Therapy against Prion Diseases. ACS Med Chem Lett 2020; 11:2063-2067. [PMID: 33209189 PMCID: PMC7667650 DOI: 10.1021/acsmedchemlett.0c00528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Decades of research efforts have conclusively provided overwhelming evidence that the cellular prion protein (PrPC) plays a central role in prion diseases, a set of fatal and incurable neurodegenerative disorders for which no therapy is yet available. In this Viewpoint, we provide an overview of the drug discovery strategies in the field, highlighting the current therapeutic hypotheses targeting, whether directly or indirectly, PrPC as well as the antiprion agents closest to clinical application.
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Affiliation(s)
- Andrea Astolfi
- Department of Pharmaceutical Sciences, “Department of Excellence 2018-2022”, University of Perugia, 06123 Perugia PG, Italy
| | - Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO) and Dulbecco Telethon Institute, University of Trento, 38122 Trento TN, Italy
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO) and Dulbecco Telethon Institute, University of Trento, 38122 Trento TN, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, “Department of Excellence 2018-2022”, University of Perugia, 06123 Perugia PG, Italy
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7
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Reidenbach AG, Mesleh MF, Casalena D, Vallabh SM, Dahlin JL, Leed AJ, Chan AI, Usanov DL, Yehl JB, Lemke CT, Campbell AJ, Shah RN, Shrestha OK, Sacher JR, Rangel VL, Moroco JA, Sathappa M, Nonato MC, Nguyen KT, Wright SK, Liu DR, Wagner FF, Kaushik VK, Auld DS, Schreiber SL, Minikel EV. Multimodal small-molecule screening for human prion protein binders. J Biol Chem 2020; 295:13516-13531. [PMID: 32723867 PMCID: PMC7521658 DOI: 10.1074/jbc.ra120.014905] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including 19F-observed and saturation transfer difference (STD) NMR spectroscopy, differential scanning fluorimetry (DSF), DNA-encoded library selection, and in silico screening. A single benzimidazole compound was confirmed in concentration-response, but affinity was very weak (Kd > 1 mm), and it could not be advanced further. The exceptionally low hit rate observed here suggests that PrP is a difficult target for small-molecule binders. Whereas orthogonal binder discovery methods could yield high-affinity compounds, non-small-molecule modalities may offer independent paths forward against prion disease.
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Affiliation(s)
- Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael F Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dominick Casalena
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Sonia M Vallabh
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Prion Alliance, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Jayme L Dahlin
- Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Alison J Leed
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alix I Chan
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dmitry L Usanov
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jenna B Yehl
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christopher T Lemke
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Arthur J Campbell
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rishi N Shah
- Undergraduate Research Opportunities Program (UROP), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Om K Shrestha
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Joshua R Sacher
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Victor L Rangel
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jamie A Moroco
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Murugappan Sathappa
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Maria Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Kong T Nguyen
- Artificial Intelligence Molecular Screen (AIMS) Awards Program, Atomwise, San Francisco, California, USA
| | - S Kirk Wright
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - David R Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Florence F Wagner
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Virendar K Kaushik
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Douglas S Auld
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Eric Vallabh Minikel
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Prion Alliance, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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8
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Colini Baldeschi A, Vanni S, Zattoni M, Legname G. Novel regulators of PrP C expression as potential therapeutic targets in prion diseases. Expert Opin Ther Targets 2020; 24:759-776. [PMID: 32631090 DOI: 10.1080/14728222.2020.1782384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Prion diseases are rare and fatal neurodegenerative disorders. The key molecular event in these disorders is the misfolding of the physiological form of the cellular prion protein, PrPC, leading to the accumulation of a pathological isoform, PrPSc, with unique features. Both isoforms share the same primary sequence, lacking detectable differences in posttranslational modification, a major hurdle for their biochemical or biophysical independent characterization. The mechanism underlying the conversion of PrPC to PrPSc is not completely understood, so finding an effective therapy to cure prion disorders is extremely challenging. AREAS COVERED This review discusses the strategies for decreasing prion replication and throws a spotlight on the relevance of PrPC in the prion accumulation process. EXPERT OPINION PrPC is the key substrate for prion pathology; hence, the most promising therapeutic approach appears to be the targeting of PrPC to block the production of the infectious isoform. The use of RNA interference and antisense oligonucleotide technologies may offer opportunities for treatment because of their success in clinical trials for other neurodegenerative diseases.
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Affiliation(s)
- Arianna Colini Baldeschi
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA) , Trieste, Italy
| | - Silvia Vanni
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per Lo Studio E La Cura Dei Tumori (IRST) IRCCS , Meldola, Italy
| | - Marco Zattoni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA) , Trieste, Italy
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA) , Trieste, Italy
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9
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De Cecco E, Celauro L, Vanni S, Grandolfo M, Bistaffa E, Moda F, Aguzzi A, Legname G. The uptake of tau amyloid fibrils is facilitated by the cellular prion protein and hampers prion propagation in cultured cells. J Neurochem 2020; 155:577-591. [DOI: 10.1111/jnc.15040] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/08/2020] [Accepted: 04/28/2020] [Indexed: 01/24/2023]
Affiliation(s)
- Elena De Cecco
- Laboratory of Prion BiologyDepartment of NeuroscienceScuola Internazionale Superiore di Studi Avanzati (SISSA) Trieste Italy
| | - Luigi Celauro
- Laboratory of Prion BiologyDepartment of NeuroscienceScuola Internazionale Superiore di Studi Avanzati (SISSA) Trieste Italy
| | - Silvia Vanni
- Laboratory of Prion BiologyDepartment of NeuroscienceScuola Internazionale Superiore di Studi Avanzati (SISSA) Trieste Italy
| | - Micaela Grandolfo
- Laboratory of Prion BiologyDepartment of NeuroscienceScuola Internazionale Superiore di Studi Avanzati (SISSA) Trieste Italy
| | - Edoardo Bistaffa
- Unit of Neurology 5 and Neuropathology Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
| | - Fabio Moda
- Unit of Neurology 5 and Neuropathology Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
| | - Adriano Aguzzi
- Institute of Neuropathology University Hospital of Zürich Zürich Switzerland
| | - Giuseppe Legname
- Laboratory of Prion BiologyDepartment of NeuroscienceScuola Internazionale Superiore di Studi Avanzati (SISSA) Trieste Italy
- ELETTRA Sincrotrone Trieste S.C.p.A Basovizza, Trieste Italy
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10
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Zaccagnini L, Rossetti G, Tran TH, Salzano G, Gandini A, Colini Baldeschi A, Bolognesi ML, Carloni P, Legname G. In silico/in vitro screening and hit evaluation identified new phenothiazine anti-prion derivatives. Eur J Med Chem 2020; 196:112295. [DOI: 10.1016/j.ejmech.2020.112295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 12/15/2022]
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Holec SA, Block AJ, Bartz JC. The role of prion strain diversity in the development of successful therapeutic treatments. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 175:77-119. [PMID: 32958242 PMCID: PMC8939712 DOI: 10.1016/bs.pmbts.2020.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Prions are a self-propagating misfolded conformation of a cellular protein. Prions are found in several eukaryotic organisms with mammalian prion diseases encompassing a wide range of disorders. The first recognized prion disease, the transmissible spongiform encephalopathies (TSEs), affect several species including humans. Alzheimer's disease, synucleinopathies, and tauopathies share a similar mechanism of self-propagation of the prion form of the disease-specific protein reminiscent of the infection process of TSEs. Strain diversity in prion disease is characterized by differences in the phenotype of disease that is hypothesized to be encoded by strain-specific conformations of the prion form of the disease-specific protein. Prion therapeutics that target the prion form of the disease-specific protein can lead to the emergence of drug-resistant strains of prions, consistent with the hypothesis that prion strains exist as a dynamic mixture of a dominant strain in combination with minor substrains. To overcome this obstacle, therapies that reduce or eliminate the template of conversion are efficacious, may reverse neuropathology, and do not result in the emergence of drug resistance. Recent advancements in preclinical diagnosis of prion infection may allow for a combinational approach that treats the prion form and the precursor protein to effectively treat prion diseases.
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Affiliation(s)
- Sara A.M. Holec
- Institute for Applied Life Sciences and Department of Biology, University of Massachusetts Amherst, Amherst, MA, United States,Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE, United States
| | - Alyssa J. Block
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE, United States
| | - Jason C. Bartz
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE, United States,Corresponding author:
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Biggi S, Pancher M, Stincardini C, Luotti S, Massignan T, Dalle Vedove A, Astolfi A, Gatto P, Lolli G, Barreca ML, Bonetto V, Adami V, Biasini E. Identification of compounds inhibiting prion replication and toxicity by removing PrP C from the cell surface. J Neurochem 2019; 152:136-150. [PMID: 31264722 DOI: 10.1111/jnc.14805] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/19/2019] [Accepted: 06/23/2019] [Indexed: 12/11/2022]
Abstract
The vast majority of therapeutic approaches tested so far for prion diseases, transmissible neurodegenerative disorders of human and animals, tackled PrPSc , the aggregated and infectious isoform of the cellular prion protein (PrPC ), with largely unsuccessful results. Conversely, targeting PrPC expression, stability or cell surface localization are poorly explored strategies. We recently characterized the mode of action of chlorpromazine, an anti-psychotic drug known to inhibit prion replication and toxicity by inducing the re-localization of PrPC from the plasma membrane. Unfortunately, chlorpromazine possesses pharmacokinetic properties unsuitable for chronic use in vivo, namely low specificity and high toxicity. Here, we employed HEK293 cells stably expressing EGFP-PrP to carry out a semi-automated high content screening (HCS) of a chemical library directed at identifying non-cytotoxic molecules capable of specifically relocalizing PrPC from the plasma membrane as well as inhibiting prion replication in N2a cell cultures. We identified four candidate hits inducing a significant reduction in cell surface PrPC , one of which also inhibited prion propagation and toxicity in cell cultures in a strain-independent fashion. This study defines a new screening method and novel anti-prion compounds supporting the notion that removing PrPC from the cell surface could represent a viable therapeutic strategy for prion diseases.
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Affiliation(s)
- Silvia Biggi
- Dulbecco Telethon Laboratory of Prions and Amyloids, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michael Pancher
- HTS Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Claudia Stincardini
- Dulbecco Telethon Laboratory of Prions and Amyloids, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Silvia Luotti
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Tania Massignan
- HTS Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Andrea Dalle Vedove
- Laboratory of Protein Crystallography and Structure-Based Drug Design, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Pamela Gatto
- HTS Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Graziano Lolli
- Laboratory of Protein Crystallography and Structure-Based Drug Design, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Valentina Bonetto
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Valentina Adami
- HTS Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Emiliano Biasini
- Dulbecco Telethon Laboratory of Prions and Amyloids, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
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Vorberg I, Chiesa R. Experimental models to study prion disease pathogenesis and identify potential therapeutic compounds. Curr Opin Pharmacol 2019; 44:28-38. [PMID: 30878006 DOI: 10.1016/j.coph.2019.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/13/2019] [Accepted: 02/13/2019] [Indexed: 01/02/2023]
Abstract
Prion diseases are devastating neurodegenerative disorders for which no drugs are available. The successful development of therapeutics depends on drug screening platforms and preclinical models that recapitulate key molecular and pathological features of the disease. Innovative experimental tools have been developed over the last few years that might facilitate drug discovery, including cell-free prion replication assays and prion-infected flies. However, there is still room for improvement. Animal models of genetic prion disease are few, and only partially recapitulate the complexity of the human disorder. Moreover, we still lack a human cell culture model suitable for high-content anti-prion drug screening. This review provides an overview of the models currently used in prion research, and discusses their promise and limitations for drug discovery.
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Affiliation(s)
- Ina Vorberg
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany; Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany.
| | - Roberto Chiesa
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy.
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Abstract
Prion diseases are associated with the conversion of the cellular prion protein (PrPC), a glycoprotein expressed at the surface of a wide variety of cell types, into a misfolded conformer (the scrapie form of PrP, or PrPSc) that accumulates in brain tissues of affected individuals. PrPSc is a self-catalytic protein assembly capable of recruiting native conformers of PrPC, and causing their rearrangement into new PrPSc molecules. Several previous attempts to identify therapeutic agents against prion diseases have targeted PrPSc, and a number of compounds have shown potent anti-prion effects in experimental models. Unfortunately, so far, none of these molecules has successfully been translated into effective therapies for prion diseases. Moreover, mounting evidence suggests that PrPSc might be a difficult pharmacological target because of its poorly defined structure, heterogeneous composition, and ability to generate different structural conformers (known as prion strains) that can elude pharmacological intervention. In the last decade, a less intuitive strategy to overcome all these problems has emerged: targeting PrPC, the common substrate of any prion strain replication. This alternative approach possesses several technical and theoretical advantages, including the possibility of providing therapeutic effects also for other neurodegenerative disorders, based on recent observations indicating a role for PrPC in delivering neurotoxic signals of different misfolded proteins. Here, we provide an overview of compounds claimed to exert anti-prion effects by directly binding to PrPC, discussing pharmacological properties and therapeutic potentials of each chemical class.
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Affiliation(s)
| | - Nunzio Iraci
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy.
| | - Silvia Biggi
- Dulbecco Telethon Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy.
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy.
| | - Emiliano Biasini
- Dulbecco Telethon Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy.
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy.
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