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Björk L, Klingstedt T, Nilsson KPR. Thiophene-Based Ligands: Design, Synthesis and Their Utilization for Optical Assignment of Polymorphic-Disease-Associated Protein Aggregates. Chembiochem 2023; 24:e202300044. [PMID: 36891883 PMCID: PMC10404026 DOI: 10.1002/cbic.202300044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 03/10/2023]
Abstract
The development of ligands for detecting protein aggregates is of great interest, as these aggregated proteinaceous species are the pathological hallmarks of several devastating diseases, including Alzheimer's disease. In this regard, thiophene-based ligands have emerged as powerful tools for fluorescent assessment of these pathological entities. The intrinsic conformationally sensitive photophysical properties of poly- and oligothiophenes have allowed optical assignment of disease-associated protein aggregates in tissue sections, as well as real-time in vivo imaging of protein deposits. Herein, we recount the chemical evolution of different generations of thiophene-based ligands, and exemplify their use for the optical distinction of polymorphic protein aggregates. Furthermore, the chemical determinants for achieving a superior fluorescent thiophene-based ligand, as well as the next generation of thiophene-based ligands targeting distinct aggregated species are described. Finally, the directions for future research into the chemical design of thiophene-based ligands that can aid in resolving the scientific challenges around protein aggregation diseases are discussed.
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Affiliation(s)
- Linnea Björk
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Therése Klingstedt
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - K Peter R Nilsson
- Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
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Hartmann J, Zacharias M. Analysis of amyloidogenic transthyretin mutations using continuum solvent free energy calculations. Proteins 2022; 90:2080-2090. [PMID: 35841533 DOI: 10.1002/prot.26399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/26/2022] [Accepted: 07/08/2022] [Indexed: 12/28/2022]
Abstract
Many proteins can undergo pathological conformational changes that result in the formation of amyloidogenic fibril structures. Various neurodegenerative diseases are associated with such pathological fibril formation of specific proteins. Transthyretin (TTR) is a tetrameric globular transport protein in the blood plasma that can dissociate, unfold, and form long and stable fibrils. Many TTR mutations are known that promote (TTR) amyloidosis and cause severe diseases. TTR amyloidosis has been studied extensively using biochemical methods and structures of various mutations in the globular form have been characterized. Recently, also the structure of a TTR fibril has been determined. In an effort to better understand why some mutations increase or decrease the tendency of amyloid formation, we have applied a combined molecular dynamics and continuum solvent approach to calculate the energetic influence of residue changes in the globular versus fibril form. For 29 out of 36 tested TTR single residue mutations, the approach correctly predicts the increased or decreased tendency for amyloidosis allowing us also to elucidate the origins of the tendency. We find that indeed the destabilization of the globular monomer or changes in dimer and tetramer stability due to mutation has a dominant influence on the amyloidogenic tendency. The continuum solvent model predicts a significantly more favorable mean energy per residue of the fibril form compared to the globular form. This effect is only slightly modulated by single-point mutations preserving the energetic preference for fibril formation upon protein unfolding. It explains why no correlation between experimental amyloidosis and calculated change in fibril stability was observed.
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Affiliation(s)
- Julian Hartmann
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Bavaria, Germany
| | - Martin Zacharias
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching, Bavaria, Germany
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Nakase T, Yamashita T, Matsuo Y, Nomura T, Sasada K, Masuda T, Misumi Y, Takamatsu K, Oda S, Furukawa Y, Obayashi K, Matsui H, Ando Y, Ueda M. Hereditary ATTR Amyloidosis with Cardiomyopathy Caused by the Novel Variant Transthyretin Y114S (p.Y134S). Intern Med 2019; 58:2695-2698. [PMID: 31178489 PMCID: PMC6794161 DOI: 10.2169/internalmedicine.2456-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the clinical features of a patient with hereditary transthyretin (ATTR) amyloidosis associated with a novel mutation (Y114S, p.Y134S). A 65-year-old Japanese man was admitted to our hospital after a 3-year history of progressive dyspnea on exertion. Five years previously, he presented dysesthesia in both hands caused by carpal tunnel syndrome. A genetic analysis revealed a base pair substitution of adenine to cytosine in the second codon of exon 4, residue 114, in the TTR gene (c.401A>C). The clinical characteristics were progressive cardiomyopathy with a poor vital prognosis, late onset, sporadic case, bilateral carpal tunnel syndrome, hypothyroidism, and small fiber neuropathy.
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Affiliation(s)
- Taku Nakase
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Taro Yamashita
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
- Amyloidosis Medical Practice Center, Kumamoto University Hospital, Japan
| | - Yoshimasa Matsuo
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Toshiya Nomura
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Keiko Sasada
- Department of Laboratory Medicine, Kumamoto University Hospital, Japan
| | - Teruaki Masuda
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Yohei Misumi
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Kotaro Takamatsu
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Seitaro Oda
- Department of Diagnostic Radiology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Yutaro Furukawa
- Department of Cardiology, Oita Japanese Red Cross Hospital, Japan
| | - Konen Obayashi
- Department of Morphological and Physiological Sciences, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Hirotaka Matsui
- Department of Laboratory Medicine, Kumamoto University Hospital, Japan
- Department of Molecular Laboratory Medicine, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Yukio Ando
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Japan
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Li G, Liu X, Huang S, Zeng Y, Yang G, Lu Z, Zhang Y, Ma X, Wang L, Huang X, Liu J. Efficient Generation of Pathogenic A-to-G Mutations in Human Tripronuclear Embryos via ABE-Mediated Base Editing. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 17:289-296. [PMID: 31279230 PMCID: PMC6611966 DOI: 10.1016/j.omtn.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022]
Abstract
Base editing systems show their power in modeling and correcting the pathogenic mutations of genetic diseases. Previous studies have already demonstrated the editing efficiency of BE3-mediated C-to-T conversion in human embryos. However, the precision and efficiency of a recently developed adenine base editor (ABE), which converts A-to-G editing in human embryos, remain to be addressed. Here we selected reported pathogenic mutations to characterize the ABE in human tripronuclear embryos. We found effective A-to-G editing occurred at the desirable sites using the ABE system. Furthermore, ABE-mediated A-to-G editing in the single blastomere of the edited embryos exhibited high product purity. By deep sequencing and whole-genome sequencing, A or T mutations didn’t increase significantly, and no off-target or insertion or deletion (indel) mutations were detected in these edited embryos, indicating the ABE-mediated base editing in human embryos is precise and controllable. For some sites, since a different editing pattern was obtained from the cells and the embryos targeted with the same single guide RNA (sgRNA), it suggests that ABE-mediated editing might have different specificity in vivo. Taken together, we efficiently generated pathogenic A-to-G mutations in human tripronuclear embryos via ABE-mediated base editing.
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Affiliation(s)
- Guanglei Li
- Department of Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Xinyi Liu
- Department of Gastroenterology, Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 510632, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Pudong New Area, Shanghai 201210, China
| | - Yanting Zeng
- Department of Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Guang Yang
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Pudong New Area, Shanghai 201210, China
| | - Zongyang Lu
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Pudong New Area, Shanghai 201210, China
| | - Yu Zhang
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Pudong New Area, Shanghai 201210, China
| | - Xu Ma
- National Research Institute for Family Planning, No. 12 Dahuishi Road, Beijing 100081, China
| | - Lisheng Wang
- Department of Gastroenterology, Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 510632, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Pudong New Area, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
| | - Jianqiao Liu
- Department of Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China.
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Fändrich M, Nyström S, Nilsson KPR, Böckmann A, LeVine H, Hammarström P. Amyloid fibril polymorphism: a challenge for molecular imaging and therapy. J Intern Med 2018; 283:218-237. [PMID: 29360284 PMCID: PMC5820168 DOI: 10.1111/joim.12732] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The accumulation of misfolded proteins (MPs), both unique and common, for different diseases is central for many chronic degenerative diseases. In certain patients, MP accumulation is systemic (e.g. TTR amyloid), and in others, this is localized to a specific cell type (e.g. Alzheimer's disease). In neurodegenerative diseases, NDs, it is noticeable that the accumulation of MP progressively spreads throughout the nervous system. Our main hypothesis of this article is that MPs are not only markers but also active carriers of pathogenicity. Here, we discuss studies from comprehensive molecular approaches aimed at understanding MP conformational variations (polymorphism) and their bearing on spreading of MPs, MP toxicity, as well as MP targeting in imaging and therapy. Neurodegenerative disease (ND) represents a major and growing societal challenge, with millions of people worldwide suffering from Alzheimer's or Parkinson's diseases alone. For all NDs, current treatment is palliative without addressing the primary cause and is not curative. Over recent years, particularly the shape-shifting properties of misfolded proteins and their spreading pathways have been intensively researched. The difficulty in addressing ND has prompted most major pharma companies to severely downsize their nervous system disorder research. Increased academic research is pivotal for filling this void and to translate basic research into tools for medical professionals. Recent discoveries of targeting drug design against MPs and improved model systems to study structure, pathology spreading and toxicity strongly encourage future studies along these lines to provide an opportunity for selective imaging, prognostic diagnosis and therapy.
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Affiliation(s)
- Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm, Germany
| | - Sofie Nyström
- Department of Physics, Chemistry and Biology, division of Chemistry, Linköping University, Linköping, Sweden
| | - K. Peter R. Nilsson
- Department of Physics, Chemistry and Biology, division of Chemistry, Linköping University, Linköping, Sweden
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Harry LeVine
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA; Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Per Hammarström
- Department of Physics, Chemistry and Biology, division of Chemistry, Linköping University, Linköping, Sweden
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