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Li JY, Zhou CM, Jin RL, Song JH, Yang KC, Li SL, Tan BH, Li YC. The detection methods currently available for protein aggregation in neurological diseases. J Chem Neuroanat 2024; 138:102420. [PMID: 38626816 DOI: 10.1016/j.jchemneu.2024.102420] [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: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024]
Abstract
Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.
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Affiliation(s)
- Jing-Yi Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Cheng-Mei Zhou
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Rui-Lin Jin
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Jia-Hui Song
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Ke-Chao Yang
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Shu-Lei Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Bai-Hong Tan
- Laboratory Teaching Center of Basic Medicine, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Yan-Chao Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China.
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2
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Karunarathne K, Kee TR, Jeon H, Cazzaro S, Gamage YI, Pan J, Woo JAA, Kang DE, Muschol M. Crystal Violet Selectively Detects Aβ Oligomers but Not Fibrils In Vitro and in Alzheimer's Disease Brain Tissue. Biomolecules 2024; 14:615. [PMID: 38927020 PMCID: PMC11201545 DOI: 10.3390/biom14060615] [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: 03/28/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 06/28/2024] Open
Abstract
Deposition of extracellular Amyloid Beta (Aβ) and intracellular tau fibrils in post-mortem brains remains the only way to conclusively confirm cases of Alzheimer's Disease (AD). Substantial evidence, though, implicates small globular oligomers instead of fibrils as relevant biomarkers of, and critical contributors to, the clinical symptoms of AD. Efforts to verify and utilize amyloid oligomers as AD biomarkers in vivo have been limited by the near-exclusive dependence on conformation-selective antibodies for oligomer detection. While antibodies have yielded critical evidence for the role of both Aβ and tau oligomers in AD, they are not suitable for imaging amyloid oligomers in vivo. Therefore, it would be desirable to identify a set of oligomer-selective small molecules for subsequent development into Positron Emission Tomography (PET) probes. Using a kinetics-based screening assay, we confirm that the triarylmethane dye Crystal Violet (CV) is oligomer-selective for Aβ42 oligomers (AβOs) grown under near-physiological solution conditions in vitro. In postmortem brains of an AD mouse model and human AD patients, we demonstrate that A11 antibody-positive oligomers but not Thioflavin S (ThioS)-positive fibrils colocalize with CV staining, confirming in vitro results. Therefore, our kinetic screen represents a robust approach for identifying new classes of small molecules as candidates for oligomer-selective dyes (OSDs). Such OSDs, in turn, provide promising starting points for the development of PET probes for pre-mortem imaging of oligomer deposits in humans.
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Affiliation(s)
| | - Teresa R. Kee
- Department of Molecular Medicine, USF Health, Morsani College of Medicine, Tampa, FL 33620, USA
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Hanna Jeon
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sara Cazzaro
- Department of Molecular Medicine, USF Health, Morsani College of Medicine, Tampa, FL 33620, USA
| | - Yasith I. Gamage
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Jung-A. A. Woo
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - David E. Kang
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
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3
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Metangle S, Ranjan N. Preferential Binding of a Red Emissive Julolidine Derivative to a Promoter G-Quadruplex. Chembiochem 2024; 25:e202300527. [PMID: 37926689 DOI: 10.1002/cbic.202300527] [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: 07/21/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
The therapeutic potential of G-quadruplexes has increased significantly with the growing understanding of their functional roles in pathogens apart from human diseases such as cancer. Here, we report the synthesis of three julolidine-based molecules and their binding to nucleic acids. Among the synthesized molecules, compound 1 exhibited red emissive fluorescence with a distinct preference for Pu22 G-quadruplex. The binding of compound 1 to Pu22 G-quadruplex, initially identified through a fluorescence-based screening, was further confirmed by UV-vis, fluorescence spectroscopy, and circular dichroism-based experiments. Thermal denaturation of compound 1 in the presence of Pu22 G-quadruplex revealed a concentration-dependent stabilization (~10.0 °C at 1 : 3 stoichiometry). Fluorescence-based experiments revealed 1 : 1 stoichiometry of the interaction and an association constant (Ka ) of 5.67×106 M-1 . CD experiments displayed that the parallel conformation of the G-quadruplex was retained on compound 1's binding and signs of higher order binding/complex formation were observed at high compound 1 to DNA ratio. Molecular docking studies revealed the dominance of stacking and van der Waals interactions in the molecular recognition which was aided by some close-distance interactions involving the quinolinium nitrogen atom.
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Affiliation(s)
- Sachin Metangle
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India
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Kumagai T, Kinoshita B, Hirashima S, Sugiyama H, Park S. Thiophene-Extended Fluorescent Nucleosides as Molecular Rotor-Type Fluorogenic Sensors for Biomolecular Interactions. ACS Sens 2023; 8:923-932. [PMID: 36740828 DOI: 10.1021/acssensors.2c02617] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescent molecular rotors are versatile tools for the investigation of biomolecular interactions and the monitoring of microenvironmental changes in biological systems. They can transform invisible information into a fluorescence signal as a straightforward response. Their utility is synergistically amplified when they are merged with biomolecules. Despite the tremendous significance and superior programmability of nucleic acids, there are very few reports on the development of molecular rotor-type isomorphic nucleosides. Here, we report the synthesis and characterization of a highly emissive molecular rotor-containing thymine nucleoside (ThexT) and its 2'-O-methyluridine analogue (2'-OMe-ThexU) as fluorogenic microenvironment-sensitive sensors that emit vivid fluorescence via an interaction with the target proteins. ThexT and 2'-OMe-ThexU may potentially serve as robust probes for a broad range of applications, such as fluorescence mapping, to monitor viscosity changes and specific protein-binding interactions in biological systems.
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Affiliation(s)
- Tomotaka Kumagai
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ban Kinoshita
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shingo Hirashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
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Pauly T, Zhang T, Sternke-Hoffmann R, Nagel-Steger L, Willbold D. Differentiation of subnucleus-sized oligomers and nucleation-competent assemblies of the Aβ peptide. Biophys J 2023; 122:269-278. [PMID: 36529991 PMCID: PMC9892607 DOI: 10.1016/j.bpj.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
A significant feature of Alzheimer's disease is the formation of amyloid deposits in the brain consisting mainly of misfolded derivatives of proteolytic cleavage products of the amyloid precursor protein amyloid-β (Aβ) peptide. While high-resolution structures already exist for both the monomer and the amyloid fibril of the Aβ peptide, the mechanism of amyloid formation itself still defies precise characterization. In this study, low and high molecular weight oligomers (LMWOs and HMWOs) were identified by sedimentation velocity analysis, and for the first time, the temporal evolution of oligomer size distributions was correlated with the kinetics of amyloid formation as determined by thioflavin T-binding studies. LMWOs of subnucleus size contain fewer than seven monomer units and exist alongside a heterogeneous group of HMWOs with 20-160 monomer units that represent potential centers of nucleus formation due to high local monomer concentrations. These HMWOs already have slightly increased β-strand content and appear structurally similar regardless of size, as shown by examination with a range of fluorescent dyes. Once fibril nuclei are formed, the monomer concentration begins to decrease, followed by a decrease in oligomer concentration, starting with LMWOs, which are the least stable species. The observed behavior classifies the two LMWOs as off pathway. In contrast, we consider HMWOs to be on-pathway, prefibrillar intermediates, representing structures in which nucleated conformational conversion is facilitated by high local concentrations. Aβ40 and Aβ42 M35ox take much longer to form nuclei and enter the growth phase than Aβ42 under identical reaction conditions, presumably because both the size and the concentration of HMWOs formed are much smaller.
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Affiliation(s)
- Thomas Pauly
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | | | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany.
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
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Figueira AJ, Saavedra J, Cardoso I, Gomes CM. S100B chaperone multimers suppress the formation of oligomers during Aβ42 aggregation. Front Neurosci 2023; 17:1162741. [PMID: 37025373 PMCID: PMC10070764 DOI: 10.3389/fnins.2023.1162741] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
Extracellular aggregation of the amyloid-β 1-42 (Aβ42) peptide is a major hallmark of Alzheimer's disease (AD), with recent data suggesting that Aβ intermediate oligomers (AβO) are more cytotoxic than mature amyloid fibrils. Understanding how chaperones harness such amyloid oligomers is critical toward establishing the mechanisms underlying regulation of proteostasis in the diseased brain. This includes S100B, an extracellular signaling Ca2+-binding protein which is increased in AD as a response to neuronal damage and whose holdase-type chaperone activity was recently unveiled. Driven by this evidence, we here investigate how different S100B chaperone multimers influence the formation of oligomers during Aβ42 fibrillation. Resorting to kinetic analysis coupled with simulation of AβO influx distributions, we establish that supra-stoichiometric ratios of dimeric S100B-Ca2+ drastically decrease Aβ42 oligomerization rate by 95% and AβO levels by 70% due to preferential inhibition of surface-catalyzed secondary nucleation, with a concomitant redirection of aggregation toward elongation. We also determined that sub-molar ratios of tetrameric apo-S100B decrease Aβ42 oligomerization influx down to 10%, while precluding both secondary nucleation and, more discreetly, fibril elongation. Coincidently, the mechanistic predictions comply with the independent screening of AβO using a combination of the thioflavin-T and X-34 fluorophores. Altogether, our findings illustrate that different S100B multimers act as complementary suppressors of Aβ42 oligomerization and aggregation, further underpinning their potential neuroprotective role in AD.
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Affiliation(s)
- António J. Figueira
- BioISI–Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Saavedra
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Isabel Cardoso
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC–Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Cláudio M. Gomes
- BioISI–Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- *Correspondence: Cláudio M. Gomes,
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7
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Mora AK, Murudkar S, Shivran N, Mula S, Chattopadhyay S, Nath S. Monitoring the formation of insulin oligomers using a NIR emitting glucose-conjugated BODIPY dye. Int J Biol Macromol 2020; 166:1121-1130. [PMID: 33159943 DOI: 10.1016/j.ijbiomac.2020.10.267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/17/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
Protein oligomers, which are formed due to the aggregation of protein molecules under physiological stress, are neurotoxic and responsible for several neurological diseases. Early detection of protein oligomers is essential for the timely intervention in the associated diseases. Although several probes have been developed for the detection of insoluble matured protein fibrils, fluorescent probes with emission in the near infrared (NIR) region for probing protein oligomers are very rare. In the present study we have designed and synthesized a glucose-conjugated BODIPY dye with emission in the NIR spectral range. Our detailed studies show that the new probe is not only capable of detecting matured fibrils but can also probe the formation of oligomers from the native protein. The new probe shows a large increase in its emission intensity upon association with oligomers and matured fibrils. Hence, the present probe has a great potential for the in vivo imaging of protein oligomers and matured fibrils. Detailed spectroscopic properties of the new probes in molecular solvents have been performed to understand its oligomers- and fibril- sensing mechanism.
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Affiliation(s)
- Aruna K Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sushant Murudkar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Neelam Shivran
- Bio-Organic Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Soumyaditya Mula
- Bio-Organic Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | | | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India.
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L. Almeida Z, M. M. Brito R. Structure and Aggregation Mechanisms in Amyloids. Molecules 2020; 25:molecules25051195. [PMID: 32155822 PMCID: PMC7179426 DOI: 10.3390/molecules25051195] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/27/2022] Open
Abstract
The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date. The identification and characterization of the molecular species critical for amyloid formation and disease development have been the focus of intense scrutiny. Methods such as X-ray and electron diffraction, solid-state nuclear magnetic resonance spectroscopy (ssNMR) and cryo-electron microscopy (cryo-EM) have been extensively used and they have contributed to shed a new light onto the structure of amyloid, revealing a multiplicity of polymorphic structures that generally fit the cross-β amyloid motif. The development of rational therapeutic approaches against these debilitating and increasingly frequent misfolding diseases requires a thorough understanding of the molecular mechanisms underlying the amyloid cascade. Here, we review the current knowledge on amyloid fibril formation for several proteins and peptides from a kinetic and thermodynamic point of view, the structure of the molecular species involved in the amyloidogenic process, and the origin of their cytotoxicity.
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Kirsch P, Hartman AM, Hirsch AKH, Empting M. Concepts and Core Principles of Fragment-Based Drug Design. Molecules 2019; 24:molecules24234309. [PMID: 31779114 PMCID: PMC6930586 DOI: 10.3390/molecules24234309] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/11/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
In this review, a general introduction to fragment-based drug design and the underlying concepts is given. General considerations and methodologies ranging from library selection/construction over biophysical screening and evaluation methods to in-depth hit qualification and subsequent optimization strategies are discussed. These principles can be generally applied to most classes of drug targets. The examples given for fragment growing, merging, and linking strategies at the end of the review are set in the fields of enzyme-inhibitor design and macromolecule–macromolecule interaction inhibition. Building upon the foundation of fragment-based drug discovery (FBDD) and its methodologies, we also highlight a few new trends in FBDD.
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Affiliation(s)
- Philine Kirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
| | - Alwin M. Hartman
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-988-062-031
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Katyal N, Deep S. A computational approach to get insights into multiple faces of additives in modulation of protein aggregation pathways. Phys Chem Chem Phys 2019; 21:24269-24285. [PMID: 31670327 DOI: 10.1039/c9cp03763b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enormous population worldwide is presently confronted with debilitating neurodegenerative diseases. The etiology of the disease is connected to protein aggregation and the events involved therein. Thus, a complete understanding of an inhibitor at different stages in the process is imperative for the formulation of a drug molecule. This review presents a detailed summary of the current status of different cosolvents. It further develops how the complex aggregation pathway can be simplified into three steps common to all proteins and the way computer simulations can be exploited to gain insights into the ways by which known inhibitors can affect all these stages. Computation of theoretical parameters in this regard and their correlation with experimental techniques is accentuated. In addition to providing an outline of the scope of different additives, this review showcases the way by which the problem of analyzing an effect of an additive can be addressed effectively via MD simulations.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, Delhi, India.
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11
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Lee D, Kim SM, Kim HY, Kim Y. Fluorescence Chemicals To Detect Insoluble and Soluble Amyloid-β Aggregates. ACS Chem Neurosci 2019; 10:2647-2657. [PMID: 31009195 DOI: 10.1021/acschemneuro.9b00199] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Misfolded amyloid-β (Aβ) is the key biomarker of Alzheimer's disease (AD), and discoveries of fluorescence chemicals visualizing such Aβ aggregates in the brain have made major contributions in postmortem and antemortem diagnosis of the disorder. Insoluble senile plaques of Aβ in brain tissues are commonly stained with thioflavin and congo red dyes and observed through microscopy, while those in living patient brains are detected via radioisotope-labeled fluorescence chemicals for positron emission tomography. Clinical evidence strongly supports the view that plaques are well-associated with the onset but not with the progression of AD. Plaques could accumulate while cognitive functions of at-risk individuals are still intact, and thus, another biomarker is needed to monitor neurodegeneration. Soluble Aβ oligomers are considered to have strong correlation with neuronal loss and brain atrophy as they are the most neurotoxic forms of misfolded Aβ. However, oligomer-targeting probes encounter several major difficulties in development. There is a significant structural distinction between two Aβ species-plaques are β-sheet-rich while oligomers are unordered-and it is still difficult to isolate and stabilize the oligomeric forms of Aβ. Due to these challenges, soluble oligomer-detecting imaging probes are relatively rare compared to the plaque-targeting chemical probes. This Review describes biochemical and optical characteristics of up-to-date fluorescence chemicals targeting insoluble plaques and soluble oligomers of Aβ. We also highlight the contributions of Aβ fluorescence chemicals to the clinical diagnosis of AD and technical challenges in searching for enhanced imaging probes.
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12
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Zhu W, Wang Y, Xie D, Cheng L, Wang P, Zeng Q, Li M, Zhao Y. In Situ Monitoring the Aggregation Dynamics of Amyloid-β Protein Aβ42 in Physiological Media via a Raman-Based Frequency Shift Method. ACS APPLIED BIO MATERIALS 2018; 1:814-824. [DOI: 10.1021/acsabm.8b00257] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wenfeng Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, China
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yibing Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Biomedical Nanotechnology Center, School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China
| | - Dan Xie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Linxiu Cheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Ping Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Biomedical Nanotechnology Center, School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China
| | - Qingdao Zeng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Min Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
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