1
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Mercer RCC, Le NTT, Fraser DG, Houser MCQ, Beeler AB, Harris DA. Sigma Receptor Ligands Are Potent Antiprion Compounds that Act Independently of Sigma Receptor Binding. ACS Chem Neurosci 2024; 15:2265-2282. [PMID: 38743607 DOI: 10.1021/acschemneuro.4c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Prion diseases are invariably fatal neurodegenerative diseases of humans and other animals for which there are no effective treatment options. Previous work from our laboratory identified phenethylpiperidines as a novel class of anti-prion compounds. While working to identify the molecular target(s) of these molecules, we unexpectedly discovered ten novel antiprion compounds based on their known ability to bind to the sigma receptors, σ1R and σ2R, which are currently being tested as therapeutic or diagnostic targets for cancer and neuropsychiatric disorders. Surprisingly, however, knockout of the respective genes encoding σ1R and σ2R (Sigmar1 and Tmem97) in prion-infected N2a cells did not alter the antiprion activity of these compounds, demonstrating that these receptors are not the direct targets responsible for the antiprion effects of their ligands. Further investigation of the most potent molecules established that they are efficacious against multiple prion strains and protect against downstream prion-mediated synaptotoxicity. While the precise details of the mechanism of action of these molecules remain to be determined, the present work forms the basis for further investigation of these compounds in preclinical studies. Given the therapeutic utility of several of the tested compounds, including rimcazole and haloperidol for neuropsychiatric conditions, (+)-pentazocine for neuropathic pain, and the ongoing clinical trials of SA 4503 and ANAVEX2-73 for ischemic stroke and Alzheimer's disease, respectively, this work has immediate implications for the treatment of human prion disease.
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Affiliation(s)
- Robert C C Mercer
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Nhat T T Le
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Douglas G Fraser
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Mei C Q Houser
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Aaron B Beeler
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - David A Harris
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
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2
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Li Q, Zhu Y, Meng X, Tong HHY, Liu H. Experiment and molecular dynamics simulations reveal proanthocyanidin B2 and B3 can inhibit prion aggregation by different mechanisms. J Biomol Struct Dyn 2024; 42:2424-2436. [PMID: 37144732 DOI: 10.1080/07391102.2023.2209663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Prion diseases are a group of fatal neurodegenerative diseases caused by the misfolding and aggregation of prion protein (PrP), and the inhibition of PrP aggregation is one of the most effective therapeutic strategies. Proanthocyanidin B2 (PB2) and B3 (PB3), the effective natural antioxidants have been evaluated for the inhibition of amyloid-related protein aggregation. Since PrP has similar aggregation mechanism with other amyloid-related proteins, will PB2 and PB3 affect the aggregation of PrP? In this paper, experimental and molecular dynamics (MD) simulation methods were combined to investigate the influence of PB2 and PB3 on PrP aggregation. Thioflavin T assays showed PB2 and PB3 could inhibit PrP aggregation in a concentrate-dependent manner in vitro. To understand the underlying mechanism, we performed 400 ns all-atom MD simulations. The results suggested PB2 could stabilize the α2 C-terminus and the hydrophobic core of protein by stabilizing two important salt bridges R156-E196 and R156-D202, and consequently made global structure of protein more stable. Surprisingly, PB3 could not stabilize PrP, which may inhibit PrP aggregation through a different mechanism. Since dimerization is the first step of aggregation, will PB3 inhibit PrP aggregation by inhibiting the dimerization? To verify our assumption, we then explored the effect of PB3 on protein dimerization by performing 800 ns MD simulations. The results suggested PB3 could reduce the residue contacts and hydrogen bonds between two monomers, preventing dimerization process of PrP. The possible inhibition mechanism of PB2 and PB3 on PrP aggregation could provide useful information for drug development against prion diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Qin Li
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Yongchang Zhu
- College of Chemical Engineering, Shijiazhuang University, Shijiazhuang, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Henry H Y Tong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
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3
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Mercer RCC, Le NTT, Houser MCQ, Beeler AB, Harris DA. Sigma receptor ligands are potent anti-prion compounds that act independently of sigma receptor binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569035. [PMID: 38077011 PMCID: PMC10705434 DOI: 10.1101/2023.11.28.569035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2024]
Abstract
Prion diseases are invariably fatal neurodegenerative diseases of humans and other animals for which there are no treatment options. Previous work from our laboratory identified phenethyl piperidines as novel class of anti-prion compounds. While working to identify the molecular target(s) of these molecules, we unexpectedly discovered ten novel anti-prion compounds based on their known ability to bind to the sigma receptors, σ 1 R and 2 R, which are currently being tested as therapeutic or diagnostic targets for cancer and neuropsychiatric disorders. Surprisingly, however, knockout of the respective genes encoding σ 1 R and σ 2 R ( Sigmar1 and Tmem97 ), in prion infected N2a cells did not alter the anti-prion activity of these compounds, demonstrating that these receptors are not the direct targets responsible the anti-prion effects of their ligands. Further investigation of the most potent molecules established that they are efficacious against multiple prion strains and protect against downstream prion-mediated synaptotoxicity. While the precise details of the mechanism of action of these molecules remains to be determined, the present work forms the basis for further investigations of these compounds in pre-clinical studies. Given the therapeutic utility of several of the tested compounds, including rimcazole and haloperidol for neuropsychiatric conditions, (+)-pentazocine for neuropathic pain, and the ongoing clinical trials of SA 4503 and ANAVEX2-73 for ischemic stroke and Alzheimer's disease, respectively, this work has immediate implications for the treatment of human prion disease.
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4
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Yu Q, Cai Q, Liang W, Zhong K, Liu J, Li H, Chen Y, Li H, Fang S, Zhong R, Liu S, Lin S. Design of phenothiazine-based cationic amphiphilic derivatives incorporating arginine residues: Potential membrane-active broad-spectrum antimicrobials combating pathogenic bacteria in vitro and in vivo. Eur J Med Chem 2023; 260:115733. [PMID: 37643545 DOI: 10.1016/j.ejmech.2023.115733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Multidrug-resistant bacteria infections pose an increasingly serious threat to human health, and the development of antimicrobials is far from meeting the clinical demand. It is urgent to discover and develop novel antibiotics to combat bacterial resistance. Currently, the development of membrane active antimicrobial agents is an attractive strategy to cope with antimicrobial resistance issues. In this study, the synthesis and biological evaluation of cationic amphiphilic phenothiazine-based derivatives were reported. Among them, the most promising compound 30 bearing a n-heptyl group and two arginine residues displayed potent bactericidal activity against both Gram-positive (MICs = 1.56 μg/mL) and Gram-negative bacteria (MICs = 3.125-6.25 μg/mL). Compound 30 showed low hemolysis activity (HC50 = 281.4 ± 1.6 μg/mL) and low cytotoxicity (CC50 > 50 μg/mL) toward mammalian cells, as well as excellent salt resistance. Compound 30 rapidly killed bacteria by acting on the bacterial cell membrane and appeared less prone to resistance. Importantly, compound 30 showed potent in vivo efficacy in a murine model of bacterial keratitis. Hence, the results suggested compound 30 has a promising prospect as a broad-spectrum antibacterial agent for the treatment of drug-resistant bacterial infections.
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Affiliation(s)
- Qian Yu
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Qiongna Cai
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Wanxin Liang
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Kewen Zhong
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jiayong Liu
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Haizhou Li
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Yongzhi Chen
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Hongxia Li
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shanfang Fang
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Rongcui Zhong
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shouping Liu
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Shuimu Lin
- The Fifth Affiliated Hospital & Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
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Jheng CP, Lee CI. Combination of structure-based virtual screening, molecular docking and molecular dynamics approaches for the discovery of anti-prion fibril flavonoids. Front Mol Biosci 2023; 9:1088733. [PMID: 36685276 PMCID: PMC9849400 DOI: 10.3389/fmolb.2022.1088733] [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: 11/03/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Prion diseases are a group of rare neurodegenerative diseases caused by the structural conversion of cellular prion into Scrapie prion resulting aggregated fibrils. Therapy of prion diseases has been developed for several decades, especially drug designs based on the structure of prion monomers. Unfortunately, none of the designed anti-prion drugs function well clinically. To fight against prion fibrils, a drug design based on the precise structure of mammalian prion fibrils is highly required. Fortunately, based on the advantage of newly advanced cryo-electron microscopy (cryo-EM) in the deconvolution of large complexes, three prion fibril structures were resolved in the last 2 years. Based on the cryo-EM solved prion fibril structures, we are able to find some molecules fighting against prion fibrils. Quercetin, one flavonoid molecule in the polyphenol group, has been found to disaggregate the prion fibrils in vitro. In this study, we performed the molecular docking and molecular dynamics simulation on quercetin-like molecules possessing pharmacological properties to evaluate the anti-prion ability of tested molecules. As a result, four quercetin-like molecules interact with prion fibril and decrease the β-strand content by converting some β-strands into loop and helical structures to disintegrate the existing fibril structure. The results of this study are significant in the treatment of prion diseases, and the approaches used in this study are applicable to other amyloid diseases.
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Affiliation(s)
- Cheng-Ping Jheng
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan
| | - Cheng-I Lee
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan,Center for Nano Bio-Detections, National Chung Cheng University, Chia-Yi, Taiwan,Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chia-Yi, Taiwan,*Correspondence: Cheng-I Lee,
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6
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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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7
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Ilie IM, Caflisch A. Antibody binding increases the flexibility of the prion protein. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140827. [PMID: 35931365 DOI: 10.1016/j.bbapap.2022.140827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/29/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Prion diseases are associated with the conversion of the cellular prion protein (PrP) into a pathogenic conformer (PrPSc). A proposed therapeutic approach to avoid the pathogenic transformation is to develop antibodies that bind to PrP and stabilize its structure. POM1 and POM6 are two monoclonal antibodies that bind the globular domain of PrP and have different biological responses, i.e., trigger neurotoxicity mimicking prion infections (POM1) or prevent neurotoxicity (POM6). The crystal structures of PrP in complex with the two antibodies show similar epitopes which seems inconsistent with the opposite phenotypes. Here, we investigate the influence of the POM1 and POM6 antibodies on the flexibility of the mouse PrP by molecular dynamics simulations. The simulations reveal that the POM6/PrP interface is less stable than the POM1/PrP interface, ascribable to localized polar mismatches at the interface, despite the former complex having a larger epitope than the latter. In the presence of any of the two antibodies, the flexibility of the globular domain increases everywhere except for the β1-α1 loop in the POM1/PrP complex which suggests the involvement of this loop in the pathological conversion. The secondary structure of PrP is preserved whereas the polar interactions involving residues Glu146, Arg156 and Arg208 are modified upon antibody binding.
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Affiliation(s)
- Ioana M Ilie
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland.
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland.
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8
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Roterman I, Stapor K, Gądek K, Gubała T, Nowakowski P, Fabian P, Konieczny L. On the Dependence of Prion and Amyloid Structure on the Folding Environment. Int J Mol Sci 2021; 22:ijms222413494. [PMID: 34948291 PMCID: PMC8707753 DOI: 10.3390/ijms222413494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 01/22/2023] Open
Abstract
Currently available analyses of amyloid proteins reveal the necessity of the existence of radical structural changes in amyloid transformation processes. The analysis carried out in this paper based on the model called fuzzy oil drop (FOD) and its modified form (FOD-M) allows quantifying the role of the environment, particularly including the aquatic environment. The starting point and basis for the present presentation is the statement about the presence of two fundamentally different methods of organizing polypeptides into ordered conformations—globular proteins and amyloids. The present study shows the source of the differences between these two paths resulting from the specificity of the external force field coming from the environment, including the aquatic and hydrophobic one. The water environment expressed in the fuzzy oil drop model using the 3D Gauss function directs the folding process towards the construction of a micelle-like system with a hydrophobic core in the central part and the exposure of polarity on the surface. The hydrophobicity distribution of membrane proteins has the opposite characteristic: Exposure of hydrophobicity at the surface of the membrane protein with an often polar center (as in the case of ion channels) is expected. The structure of most proteins is influenced by a more or less modified force field generated by water through the appropriate presence of a non-polar (membrane-like) environment. The determination of the proportion of a factor different from polar water enables the assessment of the protein status by indicating factors favoring the structure it represents.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, 31-034 Kopernika 7, 30-688 Krakow, Poland
- Correspondence:
| | - Katarzyna Stapor
- Department of Applied Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Krzysztof Gądek
- Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland; (K.G.); (T.G.); (P.N.)
| | - Tomasz Gubała
- Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland; (K.G.); (T.G.); (P.N.)
| | - Piotr Nowakowski
- Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland; (K.G.); (T.G.); (P.N.)
| | - Piotr Fabian
- Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Leszek Konieczny
- Department of Medical Biochemistry, Jagiellonian University Medical College, 31-034 Kopernika 7, 31-034 Krakow, Poland;
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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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10
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Wang X, Gorfe AA, Putkey JA. Antipsychotic phenothiazine drugs bind to KRAS in vitro. JOURNAL OF BIOMOLECULAR NMR 2021; 75:233-244. [PMID: 34176062 DOI: 10.1007/s10858-021-00371-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
We used NMR to show that the antipsychotic phenothiazine drugs promazine and promethazine bind to GDP-KRAS. Promazine also binds to oncogenic GDP-KRAS(G12D), and to wild type GppNHp-KRAS. A panel of additional phenothiazines bind to GDP-KRAS but with lower affinity than promazine or promethazine. Binding is most dependent on substitutions at C-2 of the tricyclic phenothiazine ring. Promazine was used to generate an NMR-driven HADDOCK model of the drug/GDP-KRAS complex. The structural model shows the tricyclic phenothiazine ring of promazine associates with the hydrophobic pocket p1 that is bordered by the central β sheet and Switch II in KRAS. Binding appears to stabilize helix 2 in a conformation that is similar to that seen in KRAS bound to other small molecules. Association of phenothiazines with KRAS may affect normal KRAS signaling that could contribute to multiple biological activities of these antipsychotic drugs. Moreover, the phenothiazine ring represents a new core scaffold on which to design modulators of KRAS activity.
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Affiliation(s)
- Xu Wang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, TX, 77030, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, TX, 77030, USA
| | - John A Putkey
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, TX, 77030, USA.
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11
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Agamennone M, Storchi L, Marrone A, Paciotti R. Hampering the early aggregation of PrP-E200K protein by charge-based inhibitors: a computational study. J Comput Aided Mol Des 2021; 35:751-770. [PMID: 34110550 PMCID: PMC8213589 DOI: 10.1007/s10822-021-00393-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/04/2021] [Indexed: 11/25/2022]
Abstract
A multilayered computational workflow was designed to identify a druggable binding site on the surface of the E200K pathogenic mutant of the human prion protein, and to investigate the effect of the binding of small molecules in the inhibition of the early aggregation of this protein. At this purpose, we developed an efficient computational tool to scan the molecular interaction properties of a whole MD trajectory, thus leading to the characterization of plausible binding regions on the surface of PrP-E200K. These structural data were then employed to drive structure-based virtual screening and fragment-based approaches to the seeking of small molecular binders of the PrP-E200K. Six promising compounds were identified, and their binding stabilities were assessed by MD simulations. Therefore, analyses of the molecular electrostatic potential similarity between the bound complexes and unbound protein evidenced their potential activity as charged-based inhibitors of the PrP-E200K early aggregation.
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Affiliation(s)
| | - Loriano Storchi
- Department of Pharmacy, University "G d'Annunzio" of Chieti-Pescara, Chieti, Italy
- Molecular Discovery Limited, Middlesex, London, UK
| | - Alessandro Marrone
- Department of Pharmacy, University "G d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Roberto Paciotti
- Department of Pharmacy, University "G d'Annunzio" of Chieti-Pescara, Chieti, Italy.
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12
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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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13
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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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14
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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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15
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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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16
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Development and structural determination of an anti-PrP C aptamer that blocks pathological conformational conversion of prion protein. Sci Rep 2020; 10:4934. [PMID: 32188933 PMCID: PMC7080826 DOI: 10.1038/s41598-020-61966-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/05/2020] [Indexed: 01/07/2023] Open
Abstract
Prion diseases comprise a fatal neuropathy caused by the conversion of prion protein from a cellular (PrPC) to a pathological (PrPSc) isoform. Previously, we obtained an RNA aptamer, r(GGAGGAGGAGGA) (R12), that folds into a unique G-quadruplex. The R12 homodimer binds to a PrPC molecule, inhibiting PrPC-to-PrPSc conversion. Here, we developed a new RNA aptamer, r(GGAGGAGGAGGAGGAGGAGGAGGA) (R24), where two R12s are tandemly connected. The 50% inhibitory concentration for the formation of PrPSc (IC50) of R24 in scrapie-infected cell lines was ca. 100 nM, i.e., much lower than that of R12 by two orders. Except for some antibodies, R24 exhibited the lowest recorded IC50 and the highest anti-prion activity. We also developed a related aptamer, r(GGAGGAGGAGGA-A-GGAGGAGGAGGA) (R12-A-R12), IC50 being ca. 500 nM. The structure of a single R12-A-R12 molecule determined by NMR resembled that of the R12 homodimer. The quadruplex structure of either R24 or R12-A-R12 is unimolecular, and therefore the structure could be stably formed when they are administered to a prion-infected cell culture. This may be the reason they can exert high anti-prion activity.
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17
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Abskharon R, Wang F, Wohlkonig A, Ruan J, Soror S, Giachin G, Pardon E, Zou W, Legname G, Ma J, Steyaert J. Structural evidence for the critical role of the prion protein hydrophobic region in forming an infectious prion. PLoS Pathog 2019; 15:e1008139. [PMID: 31815959 PMCID: PMC6922452 DOI: 10.1371/journal.ppat.1008139] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 12/19/2019] [Accepted: 10/09/2019] [Indexed: 11/18/2022] Open
Abstract
Prion or PrPSc is the proteinaceous infectious agent causing prion diseases in various mammalian species. Despite decades of research, the structural basis for PrPSc formation and prion infectivity remains elusive. To understand the role of the hydrophobic region in forming infectious prion at the molecular level, we report X-ray crystal structures of mouse (Mo) prion protein (PrP) (residues 89-230) in complex with a nanobody (Nb484). Using the recombinant prion propagation system, we show that the binding of Nb484 to the hydrophobic region of MoPrP efficiently inhibits the propagation of proteinase K resistant PrPSc and prion infectivity. In addition, when added to cultured mouse brain slices in high concentrations, Nb484 exhibits no neurotoxicity, which is drastically different from other neurotoxic anti-PrP antibodies, suggesting that the Nb484 can be a potential therapeutic agent against prion disease. In summary, our data provides the first structure-function evidence supporting a crucial role of the hydrophobic region of PrP in forming an infectious prion.
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Affiliation(s)
- Romany Abskharon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, United States of America
- National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt
| | - Fei Wang
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, United States of America
- * E-mail: (FW); (JM); (JS)
| | - Alexandre Wohlkonig
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
| | - Juxin Ruan
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, United States of America
| | - Sameh Soror
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
- Center of Excellence, Helwan Structural Biology Research, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Gabriele Giachin
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
| | - Wenquan Zou
- Departments of Pathology and Neurology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Jiyan Ma
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, United States of America
- * E-mail: (FW); (JM); (JS)
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
- * E-mail: (FW); (JM); (JS)
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18
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Baral PK, Yin J, Aguzzi A, James MNG. Transition of the prion protein from a structured cellular form (PrP C ) to the infectious scrapie agent (PrP Sc ). Protein Sci 2019; 28:2055-2063. [PMID: 31583788 DOI: 10.1002/pro.3735] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 11/07/2022]
Abstract
Prion diseases in mammals are caused by a conformational transition of the cellular prion protein from its native conformation (PrPC ) to a pathological isoform called "prion protein scrapie" (PrPSc ). A molecular level of understanding of this conformational transition will be helpful in unveiling the disease etiology. Experimental structural biological techniques (NMR and X-ray crystallography) have been used to unravel the atomic level structural information for the prion and its binding partners. More than one hundred three-dimensional structures of the mammalian prions have been deposited in the protein databank. Structural studies on the prion protein and its structural transitions will deepen our understanding of the molecular basis of prion pathogenesis and will provide valuable guidance for future structure-based drug discovery endeavors.
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Affiliation(s)
- Pravas K Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jiang Yin
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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19
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20
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Ladner-Keay CL, Ross L, Perez-Pineiro R, Zhang L, Bjorndahl TC, Cashman N, Wishart DS. A simple in vitro assay for assessing the efficacy, mechanisms and kinetics of anti-prion fibril compounds. Prion 2018; 12:280-300. [PMID: 30223704 PMCID: PMC6277192 DOI: 10.1080/19336896.2018.1525254] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 09/01/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022] Open
Abstract
Prion diseases are caused by the conversion of normal cellular prion proteins (PrP) into lethal prion aggregates. These prion aggregates are composed of proteinase K (PK) resistant fibrils and comparatively PK-sensitive oligomers. Currently there are no anti-prion pharmaceuticals available to treat or prevent prion disease. Methods of discovering anti-prion molecules rely primarily on relatively complex cell-based, tissue slice or animal-model assays that measure the effects of small molecules on the formation of PK-resistant prion fibrils. These assays are difficult to perform and do not detect the compounds that directly inhibit oligomer formation or alter prion conversion kinetics. We have developed a simple cell-free method to characterize the impact of anti-prion fibril compounds on both the oligomer and fibril formation. In particular, this assay uses shaking-induced conversion (ShIC) of recombinant PrP in a 96-well format and resolution enhanced native acidic gel electrophoresis (RENAGE) to generate, assess and detect PrP fibrils in a high throughput fashion. The end-point PrP fibrils from this assay can be further characterized by PK analysis and negative stain transmission electron microscopy (TEM). This cell-free, gel-based assay generates metrics to assess anti-prion fibril efficacy and kinetics. To demonstrate its utility, we characterized the action of seven well-known anti-prion molecules: Congo red, curcumin, GN8, quinacrine, chloropromazine, tetracycline, and TUDCA (taurourspdeoxycholic acid), as well as four suspected anti-prion compounds: trans-resveratrol, rosmarinic acid, myricetin and ferulic acid. These findings suggest that this in vitro assay could be useful in identifying and comprehensively assessing novel anti-prion fibril compounds. Abbreviations: PrP, prion protein; PK, proteinase K; ShIC, shaking-induced conversion; RENAGE, resolution enhanced native acidic gel electrophoresis; TEM, transmission electron microscopy; TUDCA, taurourspdeoxycholic acid; BSE, bovine spongiform encephalopathy; CWD, chronic wasting disease; CJD, Creutzfeldt Jakob disease; GSS, Gerstmann-Sträussler-Scheinker syndrome; FFI, fatal familial insomnia; PrPc, cellular prion protein; recPrPC, recombinant monomeric prion protein; PrPSc, infectious particle of misfolded prion protein; RT-QuIC, real-time quaking-induced conversion; PMCA, Protein Misfolding Cyclic Amplification; LPS, lipopolysaccharide; EGCG, epigallocatechin gallate; GN8, 2-pyrrolidin-1-yl-N-[4-[4-(2-pyrrolidin-1-yl-acetylamino)-benzyl]-phenyl]-acetamide; DMSO, dimethyl sulfoxide; ScN2A, scrapie infected neuroblastoma cells; IC50, inhibitory concentration for 50% reduction; recMoPrP 23-231, recombinant full-length mouse prion protein residues 23-231; EDTA; PICUP, photo-induced cross-linking of unmodified protein; BSA, bovine serum albumin;; PMSF, phenylmethanesulfonyl fluoride.
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Affiliation(s)
| | - Li Ross
- Brain Research Centre, University of British Columbia, Vancouver, Canada
| | | | - Lun Zhang
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Trent C. Bjorndahl
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Neil Cashman
- Brain Research Centre, University of British Columbia, Vancouver, Canada
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
- Department of Computing Science, University of Alberta, Edmonton, Canada
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21
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Choi J, Kim HJ, Jin X, Lim H, Kim S, Roh IS, Kang HE, No KT, Sohn HJ. Application of the fragment molecular orbital method to discover novel natural products for prion disease. Sci Rep 2018; 8:13063. [PMID: 30166585 PMCID: PMC6117342 DOI: 10.1038/s41598-018-31080-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/07/2018] [Indexed: 01/16/2023] Open
Abstract
Conformational conversion of the normal cellular isoform of the prion protein PrPC into an infectious isoform PrPSc causes pathogenesis in prion diseases. To date, numerous antiprion compounds have been developed to block this conversion and to detect the molecular mechanisms of prion inhibition using several computational studies. Thus far, no suitable drug has been identified for clinical use. For these reasons, more accurate and predictive approaches to identify novel compounds with antiprion effects are required. Here, we have applied an in silico approach that integrates our previously described pharmacophore model and fragment molecular orbital (FMO) calculations, enabling the ab initio calculation of protein-ligand complexes. The FMO-based virtual screening suggested that two natural products with antiprion activity exhibited good binding interactions, with hotspot residues within the PrPC binding site, and effectively reduced PrPSc levels in a standard scrapie cell assay. Overall, the outcome of this study will be used as a promising strategy to discover antiprion compounds. Furthermore, the SAR-by-FMO approach can provide extremely powerful tools in quickly establishing virtual SAR to prioritise compounds for synthesis in further studies.
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Affiliation(s)
- Jiwon Choi
- Bioinformatics and Molecular Design Research Center (BMDRC), Yonsei University, Seoul, 03722, Korea
| | - Hyo-Jin Kim
- OIE Reference Laboratory for CWD, Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbukdo, 39660, Korea
| | - Xuemei Jin
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Hocheol Lim
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Songmi Kim
- Bioinformatics and Molecular Design Research Center (BMDRC), Yonsei University, Seoul, 03722, Korea
| | - In-Soon Roh
- OIE Reference Laboratory for CWD, Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbukdo, 39660, Korea
| | - Hae-Eun Kang
- OIE Reference Laboratory for CWD, Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbukdo, 39660, Korea
| | - Kyoung Tai No
- Bioinformatics and Molecular Design Research Center (BMDRC), Yonsei University, Seoul, 03722, Korea.
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea.
| | - Hyun-Joo Sohn
- OIE Reference Laboratory for CWD, Foreign Animal Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbukdo, 39660, Korea.
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22
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The engineered β-lactoglobulin with complementarity to the chlorpromazine chiral conformers. Int J Biol Macromol 2018; 114:85-96. [DOI: 10.1016/j.ijbiomac.2018.03.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/28/2018] [Accepted: 03/15/2018] [Indexed: 12/19/2022]
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23
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Baral PK, Swayampakula M, Aguzzi A, James MNG. Structural characterization of
POM
6 Fab and mouse prion protein complex identifies key regions for prions conformational conversion. FEBS J 2018; 285:1701-1714. [DOI: 10.1111/febs.14438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 02/02/2018] [Accepted: 03/16/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry Faculty of Medicine and Dentistry University of Alberta Edmonton Canada
| | - Mridula Swayampakula
- Department of Biochemistry Faculty of Medicine and Dentistry University of Alberta Edmonton Canada
| | - Adriano Aguzzi
- Institute of Neuropathology University of Zurich Switzerland
| | - Michael N. G. James
- Department of Biochemistry Faculty of Medicine and Dentistry University of Alberta Edmonton Canada
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24
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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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25
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Gilberg E, Gütschow M, Bajorath J. X-ray Structures of Target–Ligand Complexes Containing Compounds with Assay Interference Potential. J Med Chem 2018; 61:1276-1284. [DOI: 10.1021/acs.jmedchem.7b01780] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Erik Gilberg
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
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26
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Mukherjee M, Jana J, Chatterjee S. A Small Molecule Impedes Insulin Fibrillation: Another New Role of Phenothiazine Derivatives. ChemistryOpen 2018; 7:68-79. [PMID: 29318099 PMCID: PMC5754551 DOI: 10.1002/open.201700131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/24/2017] [Indexed: 11/16/2022] Open
Abstract
Protein misfolding is interrelated to several diseases, including neurodegenerative diseases and type II diabetes. Misfolded/unfolded proteins produce soluble oligomers that accumulate into "amyloid plaques". Inhibition of amyloid-plaque formation by those misfolded/unfolded proteins will lead to the invention of new therapeutic approaches for amyloid-related diseases. Herein, methylene blue (MB), a well-defined drug against multiple diseases and disorders, is used to impede insulin fibrillation. In this study, we perform an array of in vitro experiments to monitor the effects of MB on the fibrillation of bovine insulin. Our results confirm that MB distresses the kinetics of insulin fibrillation by interacting with insulin in its monomeric form. A thioflavin T assay indicates that insulin fibrillation is interrupted upon the addition of MB. The same results are confirmed by circular dichroism, dynamic light scattering (DLS), and size-exclusion chromatography (SEC). According to the DLS data, the insulin fibrils are 800 nm in diameter, and the addition of MB reduces the size of the fibrils, which remain 23 nm in size, and this indicates that no fibrillation of insulin occurs in the presence of MB. This data is also supported by SEC. Saturation transfer difference NMR spectroscopy and molecular dynamics simulations demonstrate the interactions between insulin and MB at the atomic level.
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Affiliation(s)
- Meghomukta Mukherjee
- Department of BiophysicsBose Institute, P 1/12 CIT, Scheme VII MKankurgachiKolkata700054India
| | - Jagannath Jana
- Department of BiophysicsBose Institute, P 1/12 CIT, Scheme VII MKankurgachiKolkata700054India
| | - Subhrangsu Chatterjee
- Department of BiophysicsBose Institute, P 1/12 CIT, Scheme VII MKankurgachiKolkata700054India
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Li L, Zhu Y, Zhou S, An X, Zhang Y, Bai Q, He YX, Liu H, Yao X. Experimental and Theoretical Insights into the Inhibition Mechanism of Prion Fibrillation by Resveratrol and its Derivatives. ACS Chem Neurosci 2017; 8:2698-2707. [PMID: 28817252 DOI: 10.1021/acschemneuro.7b00240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Resveratrol and its derivatives have been shown to display beneficial effects to neurodegenerative diseases. However, the molecular mechanism of resveratrol and its derivatives on prion conformational conversion is poorly understood. In this work, the interaction mechanism between prion and resveratrol as well as its derivatives was investigated using steady-state fluorescence quenching, Thioflavin T binding assay, Western blotting, and molecular dynamics simulation. Protein fluorescence quenching method and Thioflavin T assay revealed that resveratrol and its derivatives could interact with prion and interrupt prion fibril formation. Molecular dynamics simulation results indicated that resveratrol can stabilize the PrP127-147 peptide mainly through π-π stacking interactions between resveratrol and Tyr128. The hydrogen bonds interactions between resveratrol and the PrP127-147 peptide could further reduce the flexibility and the propensity to aggregate. The results of this study not only can provide useful information about the interaction mechanism between resveratrol and prion, but also can provide useful clues for further design of new inhibitors inhibiting prion aggregation.
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Affiliation(s)
- Lanlan Li
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Yongchang Zhu
- School
of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Shuangyan Zhou
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
- School
of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Xiaoli An
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Yan Zhang
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
- School
of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Qifeng Bai
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Yong-Xing He
- School
of Life Sciences, Lanzhou University, Lanzhou 730000, P. R. China
| | - Huanxiang Liu
- School
of Pharmacy, Lanzhou University, Lanzhou 730000, P. R. China
| | - Xiaojun Yao
- State
Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, P. R. China
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28
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Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods. J Comput Aided Mol Des 2017; 31:1053-1062. [PMID: 29159521 DOI: 10.1007/s10822-017-0086-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 11/15/2017] [Indexed: 11/27/2022]
Abstract
Conformational conversion of the normal cellular prion protein, PrPC, into the misfolded isoform, PrPSc, is considered to be a central event in the development of fatal neurodegenerative diseases. Stabilization of prion protein at the normal cellular form (PrPC) with small molecules is a rational and efficient strategy for treatment of prion related diseases. However, few compounds have been identified as potent prion inhibitors by binding to the normal conformation of prion. In this work, to rational screening of inhibitors capable of stabilizing cellular form of prion protein, multiple approaches combining docking-based virtual screening, steady-state fluorescence quenching, surface plasmon resonance and thioflavin T fluorescence assay were used to discover new compounds interrupting PrPC to PrPSc conversion. Compound 3253-0207 that can bind to PrPC with micromolar affinity and inhibit prion fibrillation was identified from small molecule databases. Molecular dynamics simulation indicated that compound 3253-0207 can bind to the hotspot residues in the binding pocket composed by β1, β2 and α2, which are significant structure moieties in conversion from PrPC to PrPSc.
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29
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Fernández-Borges N, Parra B, Vidal E, Eraña H, Sánchez-Martín MA, de Castro J, Elezgarai SR, Pumarola M, Mayoral T, Castilla J. Unraveling the key to the resistance of canids to prion diseases. PLoS Pathog 2017; 13:e1006716. [PMID: 29131852 PMCID: PMC5703577 DOI: 10.1371/journal.ppat.1006716] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/27/2017] [Accepted: 10/28/2017] [Indexed: 01/08/2023] Open
Abstract
One of the characteristics of prions is their ability to infect some species but not others and prion resistant species have been of special interest because of their potential in deciphering the determinants for susceptibility. Previously, we developed different in vitro and in vivo models to assess the susceptibility of species that were erroneously considered resistant to prion infection, such as members of the Leporidae and Equidae families. Here we undertake in vitro and in vivo approaches to understand the unresolved low prion susceptibility of canids. Studies based on the amino acid sequence of the canine prion protein (PrP), together with a structural analysis in silico, identified unique key amino acids whose characteristics could orchestrate its high resistance to prion disease. Cell- and brain-based PMCA studies were performed highlighting the relevance of the D163 amino acid in proneness to protein misfolding. This was also investigated by the generation of a novel transgenic mouse model carrying this substitution and these mice showed complete resistance to disease despite intracerebral challenge with three different mouse prion strains (RML, 22L and 301C) known to cause disease in wild-type mice. These findings suggest that dog D163 amino acid is primarily, if not totally, responsible for the prion resistance of canids. Detection of individuals or whole species resistant to any infectious disease is vital to understand the determinants of susceptibility and to develop appropriate therapeutic and preventative strategies. Canids have long been considered resistant to prion infection given the absence of clinical disease despite exposure to the causal agent. Through extensive analysis of the canine prion protein we have detected a key amino acid that might be responsible for their universal resistance to prion disease. Using in vitro and in vivo models we demonstrated that the presence of this residue confers resistance to prion infection when introduced to susceptible animals, opening the way to develop a new therapeutic approach against these, at present, untreatable disorders.
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Affiliation(s)
| | - Beatriz Parra
- Laboratorio Central de Veterinaria (LCV), Madrid, Spain
| | - Enric Vidal
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Hasier Eraña
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio, Bizkaia, Spain
| | - Manuel A. Sánchez-Martín
- Servicio de Transgénesis, Nucleus, Universidad de Salamanca, Salamanca, Spain
- IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
| | - Jorge de Castro
- Department of Infectology, Scripps Florida, Jupiter, Florida, United States of America
| | | | - Martí Pumarola
- Department of Animal Medicine and Surgery, Veterinary faculty, Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Tomás Mayoral
- Laboratorio Central de Veterinaria (LCV), Madrid, Spain
| | - Joaquín Castilla
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio, Bizkaia, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
- * E-mail:
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30
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Stincardini C, Massignan T, Biggi S, Elezgarai SR, Sangiovanni V, Vanni I, Pancher M, Adami V, Moreno J, Stravalaci M, Maietta G, Gobbi M, Negro A, Requena JR, Castilla J, Nonno R, Biasini E. An antipsychotic drug exerts anti-prion effects by altering the localization of the cellular prion protein. PLoS One 2017; 12:e0182589. [PMID: 28787011 PMCID: PMC5546605 DOI: 10.1371/journal.pone.0182589] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/20/2017] [Indexed: 02/01/2023] Open
Abstract
Prion diseases are neurodegenerative conditions characterized by the conformational conversion of the cellular prion protein (PrPC), an endogenous membrane glycoprotein of uncertain function, into PrPSc, a pathological isoform that replicates by imposing its abnormal folding onto PrPC molecules. A great deal of evidence supports the notion that PrPC plays at least two roles in prion diseases, by acting as a substrate for PrPSc replication, and as a mediator of its toxicity. This conclusion was recently supported by data suggesting that PrPC may transduce neurotoxic signals elicited by other disease-associated protein aggregates. Thus, PrPC may represent a convenient pharmacological target for prion diseases, and possibly other neurodegenerative conditions. Here, we sought to characterize the activity of chlorpromazine (CPZ), an antipsychotic previously shown to inhibit prion replication by directly binding to PrPC. By employing biochemical and biophysical techniques, we provide direct experimental evidence indicating that CPZ does not bind PrPC at biologically relevant concentrations. Instead, the compound exerts anti-prion effects by inducing the relocalization of PrPC from the plasma membrane. Consistent with these findings, CPZ also inhibits the cytotoxic effects delivered by a PrP mutant. Interestingly, we found that the different pharmacological effects of CPZ could be mimicked by two inhibitors of the GTPase activity of dynamins, a class of proteins involved in the scission of newly formed membrane vesicles, and recently reported as potential pharmacological targets of CPZ. Collectively, our results redefine the mechanism by which CPZ exerts anti-prion effects, and support a primary role for dynamins in the membrane recycling of PrPC, as well as in the propagation of infectious prions.
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Affiliation(s)
- Claudia Stincardini
- Dulbecco Telethon Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Tania Massignan
- Dulbecco Telethon Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Silvia Biggi
- Dulbecco Telethon Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Saioa R. Elezgarai
- Dulbecco Telethon Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Valeria Sangiovanni
- Dulbecco Telethon Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Ilaria Vanni
- Department of Food Safety and Veterinary Health, Istituto Superiore di Sanitá, Rome, Italy
| | - Michael Pancher
- HTS Core Facility, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Valentina Adami
- HTS Core Facility, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Jorge Moreno
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio
| | - Matteo Stravalaci
- Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Giulia Maietta
- Dulbecco Telethon Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Marco Gobbi
- Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Alessandro Negro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela, Santiago de Compostela, Spain
- Department of Medical Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Joaquín Castilla
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio
- IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Romolo Nonno
- Department of Food Safety and Veterinary Health, Istituto Superiore di Sanitá, Rome, Italy
| | - Emiliano Biasini
- Dulbecco Telethon Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
- * E-mail:
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31
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Exploring Anti-Prion Glyco-Based and Aromatic Scaffolds: A Chemical Strategy for the Quality of Life. Molecules 2017; 22:molecules22060864. [PMID: 28538692 PMCID: PMC6152669 DOI: 10.3390/molecules22060864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 01/08/2023] Open
Abstract
Prion diseases are fatal neurodegenerative disorders caused by protein misfolding and aggregation, affecting the brain progressively and consequently the quality of life. Alzheimer’s is also a protein misfolding disease, causing dementia in over 40 million people worldwide. There are no therapeutics able to cure these diseases. Cellular prion protein is a high-affinity binding partner of amyloid β (Aβ) oligomers, the most toxic species in Alzheimer’s pathology. These findings motivate the development of new chemicals for a better understanding of the events involved. Disease control is far from being reached by the presently known therapeutics. In this review we describe the synthesis and mode of action of molecular entities with intervention in prion diseases’ biological processes and, if known, their role in Alzheimer’s. A diversity of structures is covered, based on glycans, steroids and terpenes, heterocycles, polyphenols, most of them embodying aromatics and a structural complexity. These molecules may be regarded as chemical tools to foster the understanding of the complex mechanisms involved, and to encourage the scientific community towards further developments for the cure of these devastating diseases.
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32
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Romão MJ, Coelho C, Santos-Silva T, Foti A, Terao M, Garattini E, Leimkühler S. Structural basis for the role of mammalian aldehyde oxidases in the metabolism of drugs and xenobiotics. Curr Opin Chem Biol 2017; 37:39-47. [DOI: 10.1016/j.cbpa.2017.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
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33
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Abstract
Although an effective therapy for prion disease has not yet been established, many advances have been made toward understanding its pathogenesis, which has facilitated research into therapeutics for the disease. Several compounds, including flupirtine, quinacrine, pentosan polysulfate, and doxycycline, have recently been used on a trial basis for patients with prion disease. Concomitantly, several lead antiprion compounds, including compound B (compB), IND series, and anle138b, have been discovered. However, clinical trials are still far from yielding significantly beneficial results, and the findings of lead compound studies in animals have highlighted new challenges. These efforts have highlighted areas that need improvement or further exploration to achieve more effective therapies. In this work, we review recent advances in prion-related therapeutic research and discuss basic scientific issues to be resolved for meaningful medical intervention of prion disease.
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Choi H, Chang HJ, Lee M, Na S. Characterizing Structural Stability of Amyloid Motif Fibrils Mediated by Water Molecules. Chemphyschem 2017; 18:817-827. [PMID: 28160391 DOI: 10.1002/cphc.201601327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/12/2017] [Indexed: 11/12/2022]
Abstract
In biological systems, structural confinements of amyloid fibrils can be mediated by the role of water molecules. However, the underlying effect of the dynamic behavior of water molecules on structural stabilities of amyloid fibrils is still unclear. By performing molecular dynamics simulations, we investigate the dynamic features and the effect of interior water molecules on conformations and mechanical characteristics of various amyloid fibrils. We find that a specific mechanism induced by the dynamic properties of interior water molecules can affect diffusion of water molecules inside amyloid fibrils, inducing their different structural stabilities. The conformation of amyloid fibrils induced by interior water molecules show the fibrils' different mechanical features. We elucidate the role of confined and movable interior water molecules in structural stabilities of various amyloid fibrils. Our results offer insights not only in further understanding of mechanical features of amyloids as mediated by water molecules, but also in the fine-tuning of the functional abilities of amyloid fibrils for applications.
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Affiliation(s)
- Hyunsung Choi
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Hyun Joon Chang
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Myeongsang Lee
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
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Choi J, Govindaraj RG, Hyeon JW, Lee K, Ma S, Kim SY, Lee J, No KT. Structural insight into the antiprion compound inhibition mechanism of native prion folding over misfolding. Chem Biol Drug Des 2017; 89:907-917. [PMID: 27933736 DOI: 10.1111/cbdd.12916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 12/24/2022]
Abstract
Transition of a physiological folded prion (PrPC ) into a pathogenic misfolded prion (PrPSc ) causes lethal neurodegenerative disorders and prion diseases. Antiprion compounds have been developed to prevent this conversion; however, their mechanism of action remains unclear. Recently, we reported two antiprion compounds, BMD29 and BMD35, identified by in silico and in vitro screening. In this study, we used extensive explicit-solvent molecular dynamics simulations to investigate ligand-binding inhibition by antiprion compounds in prion folding over misfolding behavior at acidic pH. The two antiprion compounds and the previously reported GN8 compound resulted in a remarkably stabilized intermediate by binding to the hotspot region of PrPC , whereas free PrPC and the inactive compound BMD01 destabilized the structure of PrPC leading to the misfolded form. The results uncovered a secondary structural transition of free PrPC and transition suppression by the antiprion compounds. One of the major misfolding processes in PrPC , alternation of hydrophobic core residues, disruption of intramolecular interactions, and the increase in residue solvent exposure were significantly inhibited by both antiprion compounds. These findings provide insights into prion misfolding and inhibition by antiprion compounds.
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Affiliation(s)
- Jiwon Choi
- Bioinformatics and Molecular Design Research Center, Yonsei University, Seoul, Korea
| | - Rajiv Gandhi Govindaraj
- Bioinformatics and Molecular Design Research Center, Yonsei University, Seoul, Korea.,Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Jae Wook Hyeon
- Division of Zoonoses, Center for Immunology & Pathology, National Institute of Health, Korea Centers for Disease Control & Prevention, Seoul, Chungcheongbuk-do, Korea
| | - Kyungro Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - SongLing Ma
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Su Yeon Kim
- Division of Zoonoses, Center for Immunology & Pathology, National Institute of Health, Korea Centers for Disease Control & Prevention, Seoul, Chungcheongbuk-do, Korea
| | - Jeongmin Lee
- Division of Zoonoses, Center for Immunology & Pathology, National Institute of Health, Korea Centers for Disease Control & Prevention, Seoul, Chungcheongbuk-do, Korea
| | - Kyoung Tai No
- Bioinformatics and Molecular Design Research Center, Yonsei University, Seoul, Korea.,Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
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36
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Therapeutic Approaches to Prion Diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 150:433-453. [DOI: 10.1016/bs.pmbts.2017.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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37
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Kumar V, Sami N, Kashav T, Islam A, Ahmad F, Hassan MI. Protein aggregation and neurodegenerative diseases: From theory to therapy. Eur J Med Chem 2016; 124:1105-1120. [DOI: 10.1016/j.ejmech.2016.07.054] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/23/2022]
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38
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Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A. Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering. Biophys J 2016; 109:793-805. [PMID: 26287631 DOI: 10.1016/j.bpj.2015.06.065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/22/2015] [Accepted: 06/30/2015] [Indexed: 10/23/2022] Open
Abstract
Aberrant self-assembly, induced by structural misfolding of the prion proteins, leads to a number of neurodegenerative disorders. In particular, misfolding of the mostly α-helical cellular prion protein (PrP(C)) into a β-sheet-rich disease-causing isoform (PrP(Sc)) is the key molecular event in the formation of PrP(Sc) aggregates. The molecular mechanisms underlying the PrP(C)-to-PrP(Sc) conversion and subsequent aggregation remain to be elucidated. However, in persistently prion-infected cell-culture models, it was shown that treatment with monoclonal antibodies against defined regions of the prion protein (PrP) led to the clearing of PrP(Sc) in cultured cells. To gain more insight into this process, we characterized PrP-antibody complexes in solution using a fast protein liquid chromatography coupled with small-angle x-ray scattering (FPLC-SAXS) procedure. High-quality SAXS data were collected for full-length recombinant mouse PrP [denoted recPrP(23-230)] and N-terminally truncated recPrP(89-230), as well as their complexes with each of two Fab fragments (HuM-P and HuM-R1), which recognize N- and C-terminal epitopes of PrP, respectively. In-line measurements by fast protein liquid chromatography coupled with SAXS minimized data artifacts caused by a non-monodispersed sample, allowing structural analysis of PrP alone and in complex with Fab antibodies. The resulting structural models suggest two mechanisms for how these Fabs may prevent the conversion of PrP(C) into PrP(Sc).
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Affiliation(s)
- Lester Carter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California
| | - Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California
| | - Jan Stöhr
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California; Department of Neurology, University of California San Francisco, San Francisco, California
| | - Guillaume Poncet-Montange
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Hiro Tsuruta
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California; Department of Neurology, University of California San Francisco, San Francisco, California.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California.
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39
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Massignan T, Cimini S, Stincardini C, Cerovic M, Vanni I, Elezgarai SR, Moreno J, Stravalaci M, Negro A, Sangiovanni V, Restelli E, Riccardi G, Gobbi M, Castilla J, Borsello T, Nonno R, Biasini E. A cationic tetrapyrrole inhibits toxic activities of the cellular prion protein. Sci Rep 2016; 6:23180. [PMID: 26976106 PMCID: PMC4791597 DOI: 10.1038/srep23180] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/29/2016] [Indexed: 12/11/2022] Open
Abstract
Prion diseases are rare neurodegenerative conditions associated with the conformational conversion of the cellular prion protein (PrPC) into PrPSc, a self-replicating isoform (prion) that accumulates in the central nervous system of affected individuals. The structure of PrPSc is poorly defined, and likely to be heterogeneous, as suggested by the existence of different prion strains. The latter represents a relevant problem for therapy in prion diseases, as some potent anti-prion compounds have shown strain-specificity. Designing therapeutics that target PrPC may provide an opportunity to overcome these problems. PrPC ligands may theoretically inhibit the replication of multiple prion strains, by acting on the common substrate of any prion replication reaction. Here, we characterized the properties of a cationic tetrapyrrole [Fe(III)-TMPyP], which was previously shown to bind PrPC, and inhibit the replication of a mouse prion strain. We report that the compound is active against multiple prion strains in vitro and in cells. Interestingly, we also find that Fe(III)-TMPyP inhibits several PrPC-related toxic activities, including the channel-forming ability of a PrP mutant, and the PrPC-dependent synaptotoxicity of amyloid-β (Aβ) oligomers, which are associated with Alzheimer’s Disease. These results demonstrate that molecules binding to PrPC may produce a dual effect of blocking prion replication and inhibiting PrPC-mediated toxicity.
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Affiliation(s)
- Tania Massignan
- Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy.,Dulbecco Telethon Institute, Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Sara Cimini
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy
| | - Claudia Stincardini
- Dulbecco Telethon Institute, Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Milica Cerovic
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy
| | - Ilaria Vanni
- Department of Food Safety and Veterinary Health, Istituto Superiore di Sanitá, 00161 Rome, Italy
| | - Saioa R Elezgarai
- Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy.,Dulbecco Telethon Institute, Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Jorge Moreno
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio 48160, Bizkaia, Spain
| | - Matteo Stravalaci
- Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy
| | - Alessandro Negro
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy
| | - Valeria Sangiovanni
- Dulbecco Telethon Institute, Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Elena Restelli
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy
| | - Geraldina Riccardi
- Department of Food Safety and Veterinary Health, Istituto Superiore di Sanitá, 00161 Rome, Italy
| | - Marco Gobbi
- Department of Molecular Biochemistry and Pharmacology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy
| | - Joaquín Castilla
- CIC bioGUNE, Parque tecnológico de Bizkaia, Derio 48160, Bizkaia, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Bizkaia, Spain
| | - Tiziana Borsello
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy.,Department of Pharmacological and Biomolecular Sciences, Milan University, 20133 Milan Italy
| | - Romolo Nonno
- Department of Food Safety and Veterinary Health, Istituto Superiore di Sanitá, 00161 Rome, Italy
| | - Emiliano Biasini
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156 Milan, Italy.,Department of Food Safety and Veterinary Health, Istituto Superiore di Sanitá, 00161 Rome, Italy.,Dulbecco Telethon Institute, Laboratory of Prions and Amyloids, Centre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
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40
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Discovery of Novel Anti-prion Compounds Using In Silico and In Vitro Approaches. Sci Rep 2015; 5:14944. [PMID: 26449325 PMCID: PMC4598813 DOI: 10.1038/srep14944] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 09/02/2015] [Indexed: 12/01/2022] Open
Abstract
Prion diseases are associated with the conformational conversion of the physiological form of cellular prion protein (PrPC) to the pathogenic form, PrPSc. Compounds that inhibit this process by blocking conversion to the PrPSc could provide useful anti-prion therapies. However, no suitable drugs have been identified to date. To identify novel anti-prion compounds, we developed a combined structure- and ligand-based virtual screening system in silico. Virtual screening of a 700,000-compound database, followed by cluster analysis, identified 37 compounds with strong interactions with essential hotspot PrP residues identified in a previous study of PrPC interaction with a known anti-prion compound (GN8). These compounds were tested in vitro using a multimer detection system, cell-based assays, and surface plasmon resonance. Some compounds effectively reduced PrPSc levels and one of these compounds also showed a high binding affinity for PrPC. These results provide a promising starting point for the development of anti-prion compounds.
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41
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Iraci N, Stincardini C, Barreca ML, Biasini E. Decoding the function of the N-terminal tail of the cellular prion protein to inspire novel therapeutic avenues for neurodegenerative diseases. Virus Res 2015; 207:62-8. [DOI: 10.1016/j.virusres.2014.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/18/2014] [Accepted: 10/14/2014] [Indexed: 01/13/2023]
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42
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Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase. Nat Chem Biol 2015; 11:779-83. [DOI: 10.1038/nchembio.1895] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/13/2015] [Indexed: 12/20/2022]
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43
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Baral PK, Swayampakula M, Aguzzi A, James MNG. X-ray structural and molecular dynamical studies of the globular domains of cow, deer, elk and Syrian hamster prion proteins. J Struct Biol 2015; 192:37-47. [PMID: 26320075 DOI: 10.1016/j.jsb.2015.08.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 08/17/2015] [Accepted: 08/25/2015] [Indexed: 02/03/2023]
Abstract
Misfolded prion proteins are the cause of neurodegenerative diseases that affect many mammalian species, including humans. Transmission of the prion diseases poses a considerable public-health risk as a specific prion disease such as bovine spongiform encephalopathy can be transferred to humans and other mammalian species upon contaminant exposure. The underlying mechanism of prion propagation and the species barriers that control cross species transmission has been investigated quite extensively. So far a number of prion strains have been characterized and those have been intimately linked to species-specific infectivity and other pathophysiological manifestations. These strains are encoded by a protein-only agent, and have a high degree of sequence identity across mammalian species. The molecular events that lead to strain differentiation remain elusive. In order to contribute to the understanding of strain differentiation, we have determined the crystal structures of the globular, folded domains of four prion proteins (cow, deer, elk and Syrian hamster) bound to the POM1 antibody fragment Fab. Although the overall structural folds of the mammalian prion proteins remains extremely similar, there are several local structural variations observed in the misfolding-initiator motifs. In additional molecular dynamics simulation studies on these several prion proteins reveal differences in the local fluctuations and imply that these differences have possible roles in the unfolding of the globular domains. These local variations in the structured domains perpetuate diverse patterns of prion misfolding and possibly facilitate the strain selection and adaptation.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mridula Swayampakula
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Adriano Aguzzi
- Department of Pathology, Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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44
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Singh J, Udgaonkar JB. Molecular Mechanism of the Misfolding and Oligomerization of the Prion Protein: Current Understanding and Its Implications. Biochemistry 2015; 54:4431-42. [PMID: 26171558 DOI: 10.1021/acs.biochem.5b00605] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Prion diseases, also known as transmissible spongiform encephalopathies, make up a group of fatal neurodegenerative disorders linked with the misfolding and aggregation of the prion protein (PrP). Although it is not yet understood how the misfolding of PrP induces neurodegeneration, it is widely accepted that the formation of misfolded prion protein (termed PrP(Sc)) is both the triggering event in the disease and the main component of the infectious agent responsible for disease transmission. Despite the clear involvement of PrP(Sc) in prion diseases, the exact composition of PrP(Sc) is not yet well-known. Recent studies show that misfolded oligomers of PrP could, however, be responsible for neurotoxicity and/or infectivity in the prion diseases. Hence, understanding the molecular mechanism of formation of the misfolded oligomers of PrP is critical for developing an understanding about the prion diseases and for developing anti-prion therapeutics. This review discusses recent advances in understanding the molecular mechanism of misfolded oligomer formation by PrP and its implications for the development of anti-prion therapeutics.
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Affiliation(s)
- Jogender Singh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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45
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Yu L, Lee SJ, Yee VC. Crystal Structures of Polymorphic Prion Protein β1 Peptides Reveal Variable Steric Zipper Conformations. Biochemistry 2015; 54:3640-8. [PMID: 25978088 DOI: 10.1021/acs.biochem.5b00425] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The pathogenesis of prion diseases is associated with the conformational conversion of normal, predominantly α-helical prion protein (PrP(C)) into a pathogenic form that is enriched with β-sheets (PrP(Sc)). Several PrP(C) crystal structures have revealed β1-mediated intermolecular sheets, suggesting that the β1 strand may contribute to a possible initiation site for β-sheet-mediated PrP(Sc) propagation. This β1 strand contains the polymorphic residue 129 that influences disease susceptibility and phenotype. To investigate the effect of the residue 129 polymorphism on the conformation of amyloid-like continuous β-sheets formed by β1, crystal structures of β1 peptides containing each of the polymorphic residues were determined. To probe the conformational influence of the peptide construct design, four different lengths of β1 peptides were studied. From the 12 peptides studied, 11 yielded crystal structures ranging in resolution from 0.9 to 1.4 Å. This ensemble of β1 crystal structures reveals conformational differences that are influenced by both the nature of the polymorphic residue and the extent of the peptide construct, indicating that comprehensive studies in which peptide constructs vary are a more rigorous approach to surveying conformational possibilities.
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Affiliation(s)
- Lu Yu
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Seung-Joo Lee
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Vivien C Yee
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
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46
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Huang D, Caflisch A. Evolutionary Conserved Tyr169 Stabilizes the β2-α2 Loop of the Prion Protein. J Am Chem Soc 2015; 137:2948-57. [DOI: 10.1021/ja511568m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Danzhi Huang
- Department
of Biochemistry University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department
of Biochemistry University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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47
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Bolognesi ML, Legname G. Approaches for discovering anti-prion compounds: lessons learned and challenges ahead. Expert Opin Drug Discov 2015; 10:389-97. [PMID: 25682812 DOI: 10.1517/17460441.2015.1016498] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Recent years have witnessed major advances in our understanding of the molecular bases of prion diseases. These studies not only highlight the protein misfolding as a potential initiator of a neurodegenerative process, they also provide a foundation for considering whether such a process can be common to many neurodegenerative diseases, including Alzheimer's disease. This makes prion diseases a sort of prototype of neurodegenerative disease, endowed with some intrinsic positive features in terms of drug development. Thanks to the fact that disappearance of the scrapie protein can serve as a clear readout of drug efficiency, phenotypic approaches have high potential for prion disease drug discovery. AREAS COVERED In this review, the authors discuss phenotypic screening and how it lends itself to drug repositioning. Furthermore, they discuss the advantages of working with a molecule with proven safety, tolerability and drug-like properties in combination with a reliable phenotypic screening and how it could improve the success rate for prion drug development. They also provide examples of several interesting candidates that have been identified using this approach, including quinacrine, astemizole, guanabenz and doxycycline. EXPERT OPINION The availability of persistently scrapie-infected murine neuroblastoma cells has greatly helped to identify compounds that inhibit prion formation. However, a human neuronal model infected with the human isoform would ultimately serve as the ideal disease model toward the discovery of effective drugs.
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Affiliation(s)
- Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna , Via Belmeloro 6, 40126 Bologna , Italy
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48
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49
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Abstract
Prions cause neurodegenerative diseases for which no cure exists. Despite decades of research activities the function of the prion protein (PrP) in mammalians is not known. Moreover, little is known on the molecular mechanisms of the self-assembly of the PrP from its monomeric state (cellular PrP, PrP(C)) to the multimeric state. The latter state includes the toxic species (scrapie PrP, PrP(Sc)) knowledge of which would facilitate the development of drugs against prion diseases. Here we analyze the role of a tyrosine residue (Y169) which is strictly conserved in mammalian PrPs. Nuclear magnetic resonance (NMR) spectroscopy studies of many mammalian PrP(C) proteins have provided evidence of a conformational equilibrium between a 3(10)-helical turn and a type I β turn conformation in the β2-α2 loop (residues 165-175). In vitro cell-free experiments of the seeded conversion of PrP(C) indicate that non-aromatic residues at position 169 reduce the formation of proteinase K-resistant PrP. Recent molecular dynamics (MD) simulations of monomeric PrP and several single-point mutants show that Y169 stabilizes the 3(10)-helical turn conformation more than single-point mutants at position 169 or residues in contact with it. In the 3(10)-helical turn conformation the hydrophobic and aggregation-prone segment 169-YSNQNNF-175 is buried and thus not-available for self-assembly. From the combined analysis of simulation and experimental results it emerges that Y169 is an aggregation gatekeeper with a twofold role. Mutations related to 3 human prion diseases are interpreted on the basis of the gatekeeper role in the monomeric state. Another potential role of the Y169 side chain is the stabilization of the ordered aggregates, i.e., reduction of frangibility of filamentous protofibrils and fibrils, which is likely to reduce the generation of toxic species.
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Affiliation(s)
- Danzhi Huang
- Department of Biochemistry; University of Zurich; Zurich, Switzerland
- Correspondance to: Danzhi Huang; , Amedeo Caflisch;
| | - Amedeo Caflisch
- Department of Biochemistry; University of Zurich; Zurich, Switzerland
- Correspondance to: Danzhi Huang; , Amedeo Caflisch;
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50
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Berhanu WM, Hansmann UHE. Stability of amyloid oligomers. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:113-41. [PMID: 25443956 DOI: 10.1016/bs.apcsb.2014.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Molecular simulations are now commonly used to complement experimental techniques in investigating amyloids and their role in human diseases. In this chapter, we will summarize techniques and approaches often used in amyloid simulations and will present recent success stories. Our examples will be focused on lessons learned from molecular dynamics simulations in aqueous environments that start from preformed aggregates. These studies explore the limitations that arise from the choice of force field, the role of mutations in the growth of amyloid aggregates, segmental polymorphism, and the importance of cross-seeding. Furthermore, they give evidence for potential toxicity mechanisms. We finally discuss the role of molecular simulations in the search for aggregation inhibitors.
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Affiliation(s)
- Workalemahu M Berhanu
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, USA.
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