1
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Palmioli A, Airoldi C. An NMR Toolkit to Probe Amyloid Oligomer Inhibition in Neurodegenerative Diseases: From Ligand Screening to Dissecting Binding Topology and Mechanisms of Action. Chempluschem 2024:e202400243. [PMID: 38712695 DOI: 10.1002/cplu.202400243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
The aggregation of amyloid peptides and proteins into toxic oligomers is a hallmark of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Machado-Joseph's disease, and transmissible spongiform encephalopathies. Inhibition of amyloid oligomers formation and interactions with biological counterparts, as well as the triggering of non-toxic amorphous aggregates, are strategies towards preventive interventions against these pathologies. NMR spectroscopy addresses the need for structural characterization of amyloid proteins and their aggregates, their binding to inhibitors, and rapid screening of compound libraries for ligand identification. Here we briefly discuss the solution experiments constituting the NMR spectroscopist's toolkit and provide examples of their application.
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Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
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2
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Martinez Pomier K, Ahmed R, Huang J, Melacini G. Inhibition of toxic metal-alpha synuclein interactions by human serum albumin. Chem Sci 2024; 15:3502-3515. [PMID: 38455030 PMCID: PMC10915811 DOI: 10.1039/d3sc06285f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/12/2024] [Indexed: 03/09/2024] Open
Abstract
Human serum albumin (HSA), the most abundant protein in plasma and cerebrospinal fluid, not only serves as a crucial carrier of various exogenous and endogenous ligands but also modulates the aggregation of amyloidogenic proteins, including alpha synuclein (αSyn), which is associated with Parkinson's disease and other α-synucleinopathies. HSA decreases αSyn toxicity through the direct binding to monomeric and oligomeric αSyn species. However, it is possible that HSA also sequesters metal ions that otherwise promote aggregation. Cu(ii) ions, for example, enhance αSyn fibrillization in vitro, while also leading to neurotoxicity by generating reactive oxygen species (ROS). However, it is currently unclear if and how HSA affects Cu(ii)-binding to αSyn. Using an integrated set of NMR experiments, we show that HSA is able to chelate Cu(ii) ions from αSyn more efficiently than standard chelators such as EDTA, revealing an unexpected cooperativity between the HSA metal-binding sites. Notably, fatty acid binding to HSA perturbs this cooperativity, thus interfering with the sequestration of Cu(ii) ions from αSyn. We also observed that glycation of HSA diminished Cu(ii)-binding affinity, while largely preserving the degree of cooperativity between the HSA metal-binding sites. Additionally, our results show that Cu(ii)-binding to HSA stabilizes the interactions of HSA with αSyn primarily at two different regions, i.e. the N-terminus, Tyr 39 and the majority of the C-terminus. Our study not only unveils the effect of fatty acid binding and age-related posttranslational modifications, such as glycation, on the neuroprotective mechanisms of HSA, but also highlights the potential of αSyn as a viable NMR-based sensor to investigate HSA-metal interactions.
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Affiliation(s)
| | - Rashik Ahmed
- Department of Chemistry and Chemical Biology, McMaster University ON L8S 4M1 Canada
| | - Jinfeng Huang
- Department of Chemistry and Chemical Biology, McMaster University ON L8S 4M1 Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University ON L8S 4M1 Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton ON L8S 4M1 Canada
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3
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Huang J, Ahmed R, Akimoto M, Martinez Pomier K, Melacini G. Early-Onset Parkinson Mutation Remodels Monomer-Fibril Interactions to Allosterically Amplify Synuclein's Amyloid Cascade. JACS AU 2023; 3:3485-3493. [PMID: 38155658 PMCID: PMC10751762 DOI: 10.1021/jacsau.3c00655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/30/2023]
Abstract
Alpha synuclein (αS) aggregates are the main component of Lewy bodies (LBs) associated with Parkinson's disease (PD). A longstanding question about αS and PD pertains to the autosomal dominant E46K αS mutant, which leads to the early onset of PD and LB dementias. The E46K mutation not only promotes αS aggregation but also stabilizes αS monomers in "closed" conformers, which are compact and aggregation-incompetent. Hence, the mechanism of action of the E46K mutation is currently unclear. Here, we show that αS monomers harboring the E46K mutation exhibit more extensive interactions with fibrils compared to those of WT. Such monomer-fibril interactions are sufficient to allosterically drive transitions of αS monomers from closed to open conformations, enabling αS aggregation. We also show that E46K promotes head-to-tail monomer-monomer interactions in early self-association events. This multipronged mechanism provides a new framework to explain how the E46K mutation and possibly other αS variants trigger early-onset PD.
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Affiliation(s)
- Jinfeng Huang
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Rashik Ahmed
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Madoka Akimoto
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Karla Martinez Pomier
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and
Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
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4
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Al-Harthi S, Kharchenko V, Mandal P, Gourdoupis S, Jaremko Ł. Zinc ions prevent α-synuclein aggregation by enhancing chaperone function of human serum albumin. Int J Biol Macromol 2022; 222:2878-2887. [DOI: 10.1016/j.ijbiomac.2022.10.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/24/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
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5
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Interactions of intrinsically disordered proteins with the unconventional chaperone human serum albumin: From mechanisms of amyloid inhibition to therapeutic opportunities. Biophys Chem 2022; 282:106743. [PMID: 35093643 DOI: 10.1016/j.bpc.2021.106743] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 12/29/2022]
Abstract
Human Serum Albumin (HSA), the most abundant protein in plasma, serves a diverse repertoire of biological functions including regulation of oncotic pressure and redox potential, transport of serum solutes, but also chaperoning of misfolded proteins. Here we review how HSA interacts with a wide spectrum of client proteins including intrinsically disordered proteins (IDPs) such as Aβ, the islet amyloid peptide (IAPP), alpha synuclein and stressed globular proteins such as insulin. The comparative analysis of the HSA chaperone - client interactions reveals that the amyloid-inhibitory function of HSA arises from at least four emerging mechanisms. Two mechanisms (the monomer stabilizer model and the monomer competitor model) involve the direct binding of HSA to either IDP monomers or oligomers, while other mechanisms (metal chelation and membrane protection) rely on the indirect modulation by HSA of other factors that drive IDP aggregation. While HSA is not the only extracellular chaperone, given its abundance, HSA is likely to account for a significant fraction of the chaperoning effects in plasma, thus opening new therapeutic opportunities in the context of the peripheral sink hypothesis.
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6
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Ahmed R, Huang J, Lifshitz R, Martinez Pomier K, Melacini G. Structural determinants of the interactions of catechins with Aβ oligomers and lipid membranes. J Biol Chem 2021; 298:101502. [PMID: 34929173 PMCID: PMC8800114 DOI: 10.1016/j.jbc.2021.101502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 02/08/2023] Open
Abstract
The aberrant self-assembly of intrinsically disordered proteins (IDPs) into soluble oligomers and their interactions with biological membranes underlie the pathogenesis of numerous neurodegenerative diseases, including Alzheimer's disease. Catechins have emerged as useful tools to reduce the toxicity of IDP oligomers by modulating their interactions with membranes. However, the structural determinants of catechin binding to IDP oligomers and membranes remain largely elusive. Here, we assemble a catechin library by combining several naturally occurring chemical modifications and, using a coupled NMR-statistical approach, we map at atomic resolution the interactions of such library with the Alzheimer's-associated amyloid-beta (Aβ) oligomers and model membranes. Our results reveal multiple catechin affinity drivers and show that the combination of affinity-reducing covalent changes may lead to unexpected net gains in affinity. Interestingly, we find that the positive cooperativity is more prevalent for Aβ oligomers than membrane binding, and that the determinants underlying catechin recognition by membranes are markedly different from those dissected for Aβ oligomers. Notably, we find that the unanticipated positive cooperativity arises from the critical regulatory role of the gallate catechin moiety, which recruits previously disengaged substituents into the binding interface and leads to an overall greater compaction of the receptor-bound conformation. Overall, the previously elusive structural attributes mapped here provide an unprecedented foundation to establish structure-activity relationships of catechins.
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Affiliation(s)
- Rashik Ahmed
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jinfeng Huang
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Romi Lifshitz
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Karla Martinez Pomier
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada,For correspondence: Giuseppe Melacini
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7
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Sharma S, Modi P, Sharma G, Deep S. Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition. Biophys Chem 2021; 278:106665. [PMID: 34419715 DOI: 10.1016/j.bpc.2021.106665] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
Protein aggregation phenomenon is closely related to the formation of amyloids which results in many neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. In order to prevent and treat these diseases, a clear understanding of the mechanism of misfolding and self-assembly of peptides and proteins is very crucial. The aggregation of a protein may involve various microscopic events. Multiple simulations utilizing the solutions of the master equation have given a better understanding of the kinetic profiles involved in the presence and absence of a particular microscopic event. This review focuses on understanding the contribution of these molecular events to protein aggregation based on the analysis of kinetic profiles of aggregation. We also discuss the effect of inhibitors, which target various species of aggregation pathways, on the kinetic profile of protein aggregation. At the end of this review, some strategies for the inhibition of aggregation that can be utilized by combining the chemical kinetics approach with thermodynamics are proposed.
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Affiliation(s)
- Shilpa Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Priya Modi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Gargi Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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8
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Andersen CB, Yoshimura Y, Nielsen J, Otzen DE, Mulder FAA. How epigallocatechin gallate binds and assembles oligomeric forms of human alpha-synuclein. J Biol Chem 2021; 296:100788. [PMID: 34019875 PMCID: PMC8191297 DOI: 10.1016/j.jbc.2021.100788] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 11/25/2022] Open
Abstract
The intrinsically disordered human protein α-synuclein (αSN) can self-associate into oligomers and amyloid fibrils. Several lines of evidence suggest that oligomeric αSN is cytotoxic, making it important to devise strategies to either prevent oligomer formation and/or inhibit the ensuing toxicity. (−)-epigallocatechin gallate (EGCG) has emerged as a molecular modulator of αSN self-assembly, as it reduces the flexibility of the C-terminal region of αSN in the oligomer and inhibits the oligomer's ability to perturb phospholipid membranes and induce cell death. However, a detailed structural and kinetic characterization of this interaction is still lacking. Here, we use liquid-state NMR spectroscopy to investigate how EGCG interacts with monomeric and oligomeric forms of αSN. We find that EGCG can bind to all parts of monomeric αSN but exhibits highest affinity for the N-terminal region. Monomeric αSN binds ∼54 molecules of EGCG in total during oligomerization. Furthermore, kinetic data suggest that EGCG dimerization is coupled with the αSN association reaction. In contrast, preformed oligomers only bind ∼7 EGCG molecules per protomer, in agreement with the more compact nature of the oligomer compared with the natively unfolded monomer. In previously conducted cell assays, as little as 0.36 EGCG per αSN reduce oligomer toxicity by 50%. Our study thus demonstrates that αSN cytotoxicity can be inhibited by small molecules at concentrations at least an order of magnitude below full binding capacity. We speculate this is due to cooperative binding of protein-stabilized EGCG dimers, which in turn implies synergy between protein association and EGCG dimerization.
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Affiliation(s)
- Camilla B Andersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | - Yuichi Yoshimura
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark; Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark; Department of Chemistry, Aarhus University, Aarhus C, Denmark.
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9
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Ahmed R, Melacini G. A biophysical toolset to probe the microscopic processes underlying protein aggregation and its inhibition by molecular chaperones. Biophys Chem 2021; 269:106508. [PMID: 33310607 DOI: 10.1016/j.bpc.2020.106508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 10/22/2022]
Abstract
Given the breadth and depth of the scientific contributions of Sir Christopher Dobson, with over 870 publications to date, it is inconceivable to convey in a single review the impact of his work and its legacy. This review therefore primarily focuses on his contributions to the development of strategies for preventing aberrant protein misfolding. The first section of this review highlights his seminal work on the elucidation of the microscopic nucleation processes underlying protein aggregation. Next, we discuss the specific inhibition of these steps by candidate drugs and biologics, with a particular emphasis on the role of molecular chaperones. In the final section, we review how protein aggregation principles can be exploited for the rational design of novel and more potent aggregation inhibitors. These milestones serve as excellent examples of the profound impact of Dobson's seminal work on fundamental science and its translation into drug discovery.
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Affiliation(s)
- Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4M1, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada.
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10
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Pagano K, Tomaselli S, Molinari H, Ragona L. Natural Compounds as Inhibitors of Aβ Peptide Aggregation: Chemical Requirements and Molecular Mechanisms. Front Neurosci 2020; 14:619667. [PMID: 33414705 PMCID: PMC7783407 DOI: 10.3389/fnins.2020.619667] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/04/2020] [Indexed: 12/29/2022] Open
Abstract
Alzheimer’s disease (AD) is one of the most common neurodegenerative disorders, with no cure and preventive therapy. Misfolding and extracellular aggregation of Amyloid-β (Aβ) peptides are recognized as the main cause of AD progression, leading to the formation of toxic Aβ oligomers and to the deposition of β-amyloid plaques in the brain, representing the hallmarks of AD. Given the urgent need to provide alternative therapies, natural products serve as vital resources for novel drugs. In recent years, several natural compounds with different chemical structures, such as polyphenols, alkaloids, terpenes, flavonoids, tannins, saponins and vitamins from plants have received attention for their role against the neurodegenerative pathological processes. However, only for a small subset of them experimental evidences are provided on their mechanism of action. This review focuses on those natural compounds shown to interfere with Aβ aggregation by direct interaction with Aβ peptide and whose inhibitory mechanism has been investigated by means of biophysical and structural biology experimental approaches. In few cases, the combination of approaches offering a macroscopic characterization of the oligomers, such as TEM, AFM, fluorescence, together with high-resolution methods could shed light on the complex mechanism of inhibition. In particular, solution NMR spectroscopy, through peptide-based and ligand-based observation, was successfully employed to investigate the interactions of the natural compounds with both soluble NMR-visible (monomer and low molecular weight oligomers) and NMR-invisible (high molecular weight oligomers and protofibrils) species. The molecular determinants of the interaction of promising natural compounds are here compared to infer the chemical requirements of the inhibitors and the common mechanisms of inhibition. Most of the data converge to indicate that the Aβ regions relevant to perturb the aggregation cascade and regulate the toxicity of the stabilized oligomers, are the N-term and β1 region. The ability of the natural aggregation inhibitors to cross the brain blood barrier, together with the tactics to improve their low bioavailability are discussed. The analysis of the data ensemble can provide a rationale for the selection of natural compounds as molecular scaffolds for the design of new therapeutic strategies against the progression of early and late stages of AD.
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Affiliation(s)
- Katiuscia Pagano
- NMR Laboratory, Istituto di Scienze e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche - CNR, Milan, Italy
| | - Simona Tomaselli
- NMR Laboratory, Istituto di Scienze e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche - CNR, Milan, Italy
| | - Henriette Molinari
- NMR Laboratory, Istituto di Scienze e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche - CNR, Milan, Italy
| | - Laura Ragona
- NMR Laboratory, Istituto di Scienze e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche - CNR, Milan, Italy
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11
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Park S, Yi Y, Lim MH. Reactivity of Flavonoids Containing a Catechol or Pyrogallol Moiety with Metal‐Free and Metal‐Associated Amyloid‐β. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Seongmin Park
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Yelim Yi
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
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12
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García-Viñuales S, Ahmed R, Sciacca MFM, Lanza V, Giuffrida ML, Zimbone S, Romanucci V, Zarrelli A, Bongiorno C, Spinella N, Galati C, Di Fabio G, Melacini G, Milardi D. Trehalose Conjugates of Silybin as Prodrugs for Targeting Toxic Aβ Aggregates. ACS Chem Neurosci 2020; 11:2566-2576. [PMID: 32687307 DOI: 10.1021/acschemneuro.0c00232] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Alzheimer's disease (AD) is linked to the abnormal accumulation of amyloid β peptide (Aβ) aggregates in the brain. Silybin B, a natural compound extracted from milk thistle (Silybum marianum), has been shown to significantly inhibit Aβ aggregation in vitro and to exert neuroprotective properties in vivo. However, further explorations of silybin B's clinical potential are currently limited by three main factors: (a) poor solubility, (b) instability in blood serum, and (c) only partial knowledge of silybin's mechanism of action. Here, we address these three limitations. We demonstrate that conjugation of a trehalose moiety to silybin significantly increases both water solubility and stability in blood serum without significantly compromising its antiaggregation properties. Furthermore, using a combination of biophysical techniques with different spatial resolution, that is, TEM, ThT fluorescence, CD, and NMR spectroscopy, we profile the interactions of the trehalose conjugate with both Aβ monomers and oligomers and evidence that silybin may shield the "toxic" surfaces formed by the N-terminal and central hydrophobic regions of Aβ. Finally, comparative analysis with silybin A, a less active diastereoisomer of silybin B, revealed how even subtle differences in chemical structure may entail different effects on amyloid inhibition. The resulting insight on the mechanism of action of silybins as aggregation inhibitors is anticipated to facilitate the future investigation of silybin's therapeutic potential.
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Affiliation(s)
- Sara García-Viñuales
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Sede Secondaria di Catania, Via Paolo Gaifami 18, 95126 Catania, Italy
| | - Rashik Ahmed
- Departments of Chemistry and Chemical Biology & Biochemistry and Biomedical Sciences, McMaster University, Hamilton ON L8S 4M1, Canada
| | - Michele F. M. Sciacca
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Sede Secondaria di Catania, Via Paolo Gaifami 18, 95126 Catania, Italy
| | - Valeria Lanza
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Sede Secondaria di Catania, Via Paolo Gaifami 18, 95126 Catania, Italy
| | - Maria Laura Giuffrida
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Sede Secondaria di Catania, Via Paolo Gaifami 18, 95126 Catania, Italy
| | - Stefania Zimbone
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Sede Secondaria di Catania, Via Paolo Gaifami 18, 95126 Catania, Italy
| | - Valeria Romanucci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, I-80126 Napoli, Italy
| | - Armando Zarrelli
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, I-80126 Napoli, Italy
| | - Corrado Bongiorno
- Institute for Microelectronics and Microsystems, National Research Council, Stradale Primosole 50, 95121 Catania, Italy
| | | | - Clelia Galati
- STMicroelectronics, Stradale Primosole 50, 95121 Catania, Italy
| | - Giovanni Di Fabio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, I-80126 Napoli, Italy
| | - Giuseppe Melacini
- Departments of Chemistry and Chemical Biology & Biochemistry and Biomedical Sciences, McMaster University, Hamilton ON L8S 4M1, Canada
| | - Danilo Milardi
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Sede Secondaria di Catania, Via Paolo Gaifami 18, 95126 Catania, Italy
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13
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Tavanti F, Pedone A, Menziani MC. Insights into the Effect of Curcumin and (-)-Epigallocatechin-3-Gallate on the Aggregation of Aβ(1-40) Monomers by Means of Molecular Dynamics. Int J Mol Sci 2020; 21:ijms21155462. [PMID: 32751722 PMCID: PMC7432714 DOI: 10.3390/ijms21155462] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 12/29/2022] Open
Abstract
In this study, we compared the effects of two well-known natural compounds on the early step of the fibrillation process of amyloid-β (1–40), responsible for the formation of plaques in the brains of patients affected by Alzheimer’s disease (AD). The use of extensive replica exchange simulations up to the µs scale allowed us to characterize the inhibition activity of (–)-epigallocatechin-3-gallate (EGCG) and curcumin (CUR) on unfolded amyloid fibrils. A reduced number of β-strands, characteristic of amyloid fibrils, and an increased distance between the amino acids that are responsible for the intra- and interprotein aggregations are observed. The central core region of the amyloid-β (Aβ(1–40)) fibril is found to have a high affinity to EGCG and CUR due to the presence of hydrophobic residues. Lastly, the free binding energy computed using the Poisson Boltzmann Surface Ares suggests that EGCG is more likely to bind to unfolded Aβ(1–40) fibrils and that this molecule can be a good candidate to develop new and more effective congeners to treat AD.
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Affiliation(s)
- Francesco Tavanti
- CNR–NANO Research Center S3, Via Campi 213/a, 41125 Modena, Italy
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (A.P.); (M.C.M.)
- Correspondence:
| | - Alfonso Pedone
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (A.P.); (M.C.M.)
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (A.P.); (M.C.M.)
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14
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Cox SJ, Lam B, Prasad A, Marietta HA, Stander NV, Joel JG, Sahoo BR, Guo F, Stoddard AK, Ivanova MI, Ramamoorthy A. High-Throughput Screening at the Membrane Interface Reveals Inhibitors of Amyloid-β. Biochemistry 2020; 59:2249-2258. [DOI: 10.1021/acs.biochem.0c00328] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah J. Cox
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brian Lam
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ajay Prasad
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hannah A. Marietta
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicholas V. Stander
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph G. Joel
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bikash R. Sahoo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fucheng Guo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andrea K. Stoddard
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Magdalena I. Ivanova
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Ahmed R, Huang J, Weber DK, Gopinath T, Veglia G, Akimoto M, Khondker A, Rheinstädter MC, Huynh V, Wylie RG, Bozelli JC, Epand RM, Melacini G. Molecular Mechanism for the Suppression of Alpha Synuclein Membrane Toxicity by an Unconventional Extracellular Chaperone. J Am Chem Soc 2020; 142:9686-9699. [DOI: 10.1021/jacs.0c01894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton ON L8S 4M1, Canada
| | - Jinfeng Huang
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ON L8S 4M1, Canada
| | - Daniel K. Weber
- Department of Biochemistry, Chemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Tata Gopinath
- Department of Biochemistry, Chemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Chemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Madoka Akimoto
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ON L8S 4M1, Canada
| | - Adree Khondker
- Department of Physics and Astronomy, McMaster University, Hamilton ON L8S 4M1, Canada
| | | | - Vincent Huynh
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ON L8S 4M1, Canada
| | - Ryan G. Wylie
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ON L8S 4M1, Canada
| | - José C. Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton ON L8S 4M1, Canada
| | - Richard M. Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton ON L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton ON L8S 4M1, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ON L8S 4M1, Canada
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16
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Sahoo BR, Cox SJ, Ramamoorthy A. High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease. Chem Commun (Camb) 2020; 56:4627-4639. [PMID: 32300761 PMCID: PMC7254607 DOI: 10.1039/d0cc01551b] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In Alzheimer's disease (AD), soluble oligomers of amyloid-β (Aβ) are emerging as a crucial entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna in establishing the structure to function relationship for Aβ oligomers prevents the development of an effective treatment for AD. While the transient and heterogeneous properties of Aβ oligomers impose many challenges for structural investigation, an effective use of a combination of NMR techniques has successfully identified and characterized them at atomic-resolution. Here, we review the successful utilization of solution and solid-state NMR techniques to probe the aggregation and structures of small and large oligomers of Aβ. Biophysical studies utilizing the commonly used solution and 19F based NMR experiments to identify the formation of small size early intermediates and to obtain their structures, and dock-lock mechanism of fiber growth at atomic-resolution are discussed. In addition, the use of proton-detected magic angle spinning (MAS) solid-state NMR experiments to obtain high-resolution insights into the aggregation pathways and structures of large oligomers and other aggregates is also presented. We expect these NMR based studies to be valuable for real-time monitoring of the depletion of monomers and the formation of toxic oligomers and high-order aggregates under a variety of conditions, and to solve the high-resolution structures of small and large size oligomers for most amyloid proteins, and therefore to develop inhibitors and drugs.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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17
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Munari F, D'Onofrio M, Assfalg M. Solution NMR insights into dynamic supramolecular assemblies of disordered amyloidogenic proteins. Arch Biochem Biophys 2020; 683:108304. [PMID: 32097611 DOI: 10.1016/j.abb.2020.108304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/29/2022]
Abstract
The extraordinary flexibility and structural heterogeneity of intrinsically disordered proteins (IDP) make them functionally versatile molecules. We have now begun to better understand their fundamental role in biology, however many aspects of their behaviour remain difficult to grasp experimentally. This is especially true for the intermolecular interactions which lead to the formation of transient or highly dynamic supramolecular self-assemblies, such as oligomers, aggregation intermediates and biomolecular condensates. Both the emerging functions and pathogenicity of these structures have stimulated great efforts to develop methodologies capable of providing useful insights. Significant progress in solution NMR spectroscopy has made this technique one of the most powerful to describe structural and dynamic features of IDPs within such assemblies at atomic resolution. Here, we review the most recent works that have illuminated key aspects of IDP assemblies and contributed significant advancements towards our understanding of the complex conformational landscape of prototypical disease-associated proteins. We also include a primer on some of the fundamental and innovative NMR methods being used in the discussed studies.
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Affiliation(s)
- Francesca Munari
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
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18
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Yu HJ, Zhao W, Xie M, Li X, Sun M, He J, Wang L, Yu L. Real-Time Monitoring of Self-Aggregation of β-Amyloid by a Fluorescent Probe Based on Ruthenium Complex. Anal Chem 2020; 92:2953-2960. [PMID: 31941275 DOI: 10.1021/acs.analchem.9b03566] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-accumulation of amyloid-β protein (Aβ) into insoluble fibrils is the major hallmark of Alzheimer's disease. Real-time monitoring of fibril growth is essential for clarifying the mechanism underlying aggregation and discovering therapeutic targets. A variety of approaches including NMR, electron microscopy (EM), atomic force microscopy (AFM), and total internal reflection fluorescence microscopy (TIRFM) have been explored to monitor the fibril growth or reveal morphology of Aβ aggregates. However, none of the methods allow real-time observation under physiological conditions while without any perturbations. Here, we present a fluorescent probe [Ru(phen)2(fipc)]2+ (Ru-fipc) (phen = 1,10-phenanthroline, fipc = 5-fluoro-N-(1,10-phenanthrolin-5-yl)-1H-indole-2-carboxamide) that can bind to all the Aβ forms, i.e., monomers, oligomers, and fibrils, while not perturbing aggregation. Using this probe in combination with laser confocal microscopy, the entire aggregation process could be clearly and exactly imaged at the single fibril level. The reliability of Ru-fipc was confirmed based on colocalization with thioflavin T (ThT). Importantly, Ru-fipc can be used to monitor the very early nucleation and oligomerization process, which is thought to be a critical step in the development of neurotoxicity while it cannot be visualized with ThT. To our knowledge, this is the first fluorescent probe developed for real-time monitoring of Aβ aggregation, especially for the very early assembly stage, in solution with minimal perturbation. This method is suitable for in vitro and in vivo studies. We believe this would provide a valuable complementary tool for the study of pathogenesis and discovery of therapeutic targets of neurodegenerative diseases.
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Affiliation(s)
- Hui-Juan Yu
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Wei Zhao
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Mengting Xie
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Xiaoqing Li
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Ming Sun
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Jun He
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Lu Wang
- Department of Nuclear Medicine and PET/CT-MRI Center, The First Affiliated Hospital of Jinan University and Institute of Molecular and Functional Imaging , Jinan University , 613 West Huangpu Avenue , Guangzhou 510630 PR China
| | - Lin Yu
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
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19
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Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
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Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
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20
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Sahoo BR, Bekier ME, Liu Z, Kocman V, Stoddard AK, Anantharamaiah GM, Nowick J, Fierke CA, Wang Y, Ramamoorthy A. Structural Interaction of Apolipoprotein A-I Mimetic Peptide with Amyloid-β Generates Toxic Hetero-oligomers. J Mol Biol 2019; 432:1020-1034. [PMID: 31866295 DOI: 10.1016/j.jmb.2019.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 01/21/2023]
Abstract
Apolipoproteins are involved in pathological conditions of Alzheimer's disease (AD), and it has been reported that truncated apolipoprotein fragments and β-amyloid (Aβ) peptides coexist as neurotoxic heteromers within the plaques. Therefore, it is important to investigate these complexes at the molecular level to better understand their properties and roles in the pathology of AD. Here, we present a mechanistic insight into such heteromerization using a structurally homologue apolipoprotein fragment of apoA-I (4F) complexed with Aβ(M1-42) and characterize their toxicity. The 4F peptide slows down the aggregation kinetics of Aβ(M1-42) by constraining its structural plasticity. NMR and CD experiments identified 4F-Aβ(M1-42) heteromers comprised of unstructured Aβ(M1-42) and helical 4F. A uniform two-fold reduction in 15N/1H NMR signal intensities of Aβ(M1-42) with no observable chemical shift perturbation indicated the formation of a large complex, which was further confirmed by diffusion NMR experiments. Microsecond-scale atomistic molecular dynamics simulations showed that 4F interaction with Aβ(M1-42) is electrostatically driven and induces unfolding of Aβ(M1-42). Neurotoxicity profiling of Aβ(M1-42) complexed with 4F confirms a significant reduction in cell viability and neurite growth. Thus, the molecular architecture of heteromerization between 4F and Aβ(M1-42) discovered in this study provides evidence toward our understanding of the role of apolipoproteins or their truncated fragments in exacerbating AD pathology.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Michael E Bekier
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - Zichen Liu
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Vojc Kocman
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Andrea K Stoddard
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - G M Anantharamaiah
- Department of Medicine, University of Alabama at Birmingham Medical Center, Birmingham, AL, 35294, USA
| | - James Nowick
- Department of Chemistry, University of California-Irvine, Irvine, CA, 92697-2025, USA
| | - Carol A Fierke
- Department of Chemistry, University of Texas A&M, College Station, TX, 77843-3255, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA.
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21
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Sarkar D, Chakraborty I, Condorelli M, Ghosh B, Mass T, Weingarth M, Mandal AK, La Rosa C, Subramanian V, Bhunia A. Self‐Assembly and Neurotoxicity of β‐Amyloid (21–40) Peptide Fragment: The Regulatory Role of GxxxG Motifs. ChemMedChem 2019; 15:293-301. [DOI: 10.1002/cmdc.201900620] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/19/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Dibakar Sarkar
- Department of Biophysics Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Ipsita Chakraborty
- Department of Biophysics Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | | | - Baijayanti Ghosh
- Division of Molecular Medicine Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Thorben Mass
- Department of Chemistry Utrecht University Padualaan 8 3584 Utrecht The Netherlands
| | - Markus Weingarth
- Department of Chemistry Utrecht University Padualaan 8 3584 Utrecht The Netherlands
| | - Atin K Mandal
- Division of Molecular Medicine Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
| | - Carmelo La Rosa
- Department of Chemical Sciences University of Catania 95125 Catania Italy
| | | | - Anirban Bhunia
- Department of Biophysics Bose Institute P-1/12 CIT Scheme VII (M) Kolkata 700054 India
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22
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Ahmed R, Akcan M, Khondker A, Rheinstädter MC, Bozelli JC, Epand RM, Huynh V, Wylie RG, Boulton S, Huang J, Verschoor CP, Melacini G. Atomic resolution map of the soluble amyloid beta assembly toxic surfaces. Chem Sci 2019; 10:6072-6082. [PMID: 31360412 PMCID: PMC6585597 DOI: 10.1039/c9sc01331h] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/19/2019] [Indexed: 12/11/2022] Open
Abstract
Atomic resolution map of the soluble amyloid beta assembly (Aβn) “toxic surfaces” that facilitate the early pathogenic events in Alzheimer's disease (AD).
Soluble amyloid beta assemblies (Aβn) are neurotoxic and play a central role in the early phases of the pathogenesis cascade leading to Alzheimer's disease. However, the current knowledge about the molecular determinants of Aβn toxicity is at best scant. Here, we comparatively analyze Aβn prepared in the absence or presence of a catechin library that modulates cellular toxicity. By combining solution NMR with dynamic light scattering, fluorescence spectroscopy, electron microscopy, wide-angle X-ray diffraction and cell viability assays, we identify a cluster of unique molecular signatures that distinguish toxic vs. nontoxic Aβ assemblies. These include the exposure of a hydrophobic surface spanning residues 17–28 and the concurrent shielding of the highly charged N-terminus. We show that the combination of these two dichotomous structural transitions promotes the colocalization and insertion of β-sheet rich Aβn into the membrane, compromising membrane integrity. These previously elusive toxic surfaces mapped here provide an unprecedented foundation to establish structure-toxicity relationships of Aβ assemblies.
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Affiliation(s)
- Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Michael Akcan
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Adree Khondker
- Department of Physics and Astronomy , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Maikel C Rheinstädter
- Department of Physics and Astronomy , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - José C Bozelli
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Vincent Huynh
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Ryan G Wylie
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Stephen Boulton
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada .
| | - Jinfeng Huang
- Department of Chemistry and Chemical Biology , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Chris P Verschoor
- Department of Health Research Methods, Evidence, and Impact (HEI) , McMaster University , Hamilton , ON L8S 4M1 , Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences , McMaster University , Hamilton , ON L8S 4M1 , Canada . .,Department of Chemistry and Chemical Biology , McMaster University , Hamilton , ON L8S 4M1 , Canada
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23
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Al-Harthi S, Lachowicz JI, Nowakowski ME, Jaremko M, Jaremko Ł. Towards the functional high-resolution coordination chemistry of blood plasma human serum albumin. J Inorg Biochem 2019; 198:110716. [PMID: 31153112 DOI: 10.1016/j.jinorgbio.2019.110716] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022]
Abstract
Human serum albumin (HSA) is a monomeric, globular, multi-carrier and the most abundant protein in the blood. HSA displays multiple ligand binding sites with extraordinary binding capacity for a wide range of ions and molecules. For decades, HSA's ability to bind to various ligands has led many scientists to study its physiological properties and protein structure; indeed, a better understanding of HSA-ligand interactions in human blood, at the atomic level, will likely foster the development of more potent, and overall more performant, diagnostic and therapeutic tools against serious human disorders such as diabetes, cardiovascular disorders, and cancer. Here, we present a concise overview of the current knowledge of HSA's structural characteristics, and its coordination chemistry with transition metal ions, within the scope and limitations of current techniques and biophysical methods to reach atomic resolution in solution and in blood serum. We also highlight the overwhelming need of a detailed atomistic understanding of HSA dynamic structures and interactions that are transient, weak, multi-site and multi-step, and allosterically affected by each other. Considering the fact that HSA is a current clinical tool for drug delivery systems and a potential contender as molecular cargo and nano-vehicle used in biophysical, clinical and industrial fields, we underline the emerging need for novel approaches to target the dynamic functional coordination chemistry of the human blood serum albumin in solution, at the atomic level.
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Affiliation(s)
- Samah Al-Harthi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), 23955-6900 Thuwal, Saudi Arabia
| | - Joanna Izabela Lachowicz
- Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Michal Eligiusz Nowakowski
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), 23955-6900 Thuwal, Saudi Arabia; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Mariusz Jaremko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), 23955-6900 Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), 23955-6900 Thuwal, Saudi Arabia.
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24
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Bellomo G, Bologna S, Cerofolini L, Paciotti S, Gatticchi L, Ravera E, Parnetti L, Fragai M, Luchinat C. Dissecting the Interactions between Human Serum Albumin and α-Synuclein: New Insights on the Factors Influencing α-Synuclein Aggregation in Biological Fluids. J Phys Chem B 2019; 123:4380-4386. [PMID: 31034772 DOI: 10.1021/acs.jpcb.9b02381] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
α-Synuclein (α-syn) is found to be naturally present in biofluids such as cerebrospinal fluid (CSF) and serum. Human serum albumin (HSA) is the most abundant protein found in these biofluids, which, beyond transporting hormones and drugs, also exerts a chaperone-like activity binding other proteins in blood and inhibiting their aggregation. Contrasting results are reported in the literature about the effects of albumin on α-syn aggregation. We characterized the binding region of HSA on α-syn by high-field solution NMR spectroscopy and the effect of HSA on α-syn aggregation by thioflavin-T (ThT) fluorescence under both low-ionic-strength and physiological conditions at the albumin concentration in serum and CSF. We found that HSA, at the concentration found in human serum, slows the aggregation of α-syn significantly. α-Syn interacts with HSA in an ionic strength- and pH-dependent manner. The binding is driven by hydrophobic interactions at the N-terminus under physiological experimental conditions and by electrostatic interactions at the C-terminus at low ionic strength. This work provides novel information about the proteostasis of α-syn in biofluids and supports the hypothesis of a chaperone-like behavior of HSA.
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Affiliation(s)
- Giovanni Bellomo
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Sara Bologna
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Silvia Paciotti
- Department of Experimental Medicine , University of Perugia , Piazzale Gambuli 1 , 06132 Perugia , Italy
| | - Leonardo Gatticchi
- Department of Experimental Medicine , University of Perugia , Piazzale Gambuli 1 , 06132 Perugia , Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Lucilla Parnetti
- Clinica Neurologica , Università degli Studi di Perugia , Piazzale Gambuli 1 , 06132 Perugia , Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
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25
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bioNMR-based identification of natural anti-Aβ compounds in Peucedanum ostruthium. Bioorg Chem 2019; 83:76-86. [DOI: 10.1016/j.bioorg.2018.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/07/2018] [Accepted: 10/09/2018] [Indexed: 01/20/2023]
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26
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Lee YH, Lin Y, Cox SJ, Kinoshita M, Sahoo BR, Ivanova M, Ramamoorthy A. Zinc boosts EGCG's hIAPP amyloid Inhibition both in solution and membrane. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:529-536. [PMID: 30468883 DOI: 10.1016/j.bbapap.2018.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/14/2018] [Accepted: 11/17/2018] [Indexed: 12/22/2022]
Abstract
Amyloid aggregation of human islet amyloid polypeptide (hIAPP) is linked to insulin-producing islet cell death in type II diabetes. Previous studies have shown that zinc (Zn(II)) and insulin, co-secreted with hIAPP, have an inhibition effect on hIAPP aggregation. Lipid membranes have also been shown to significantly influence the aggregation kinetics of hIAPP. An increasing number of studies report the importance of developing small molecule inhibitors to suppress the hIAPP's aggregation and subsequent toxicity. The ability of epigallocatechin-gallate (EGCG) to inhibit aggregation of a variety of amyloid peptide/proteins initiated numerous studies as well as the development of derivative compounds to potentially treat amyloid diseases. In this study, a combination of Thioflavin-T fluorescence kinetics, transmission electron microscopy, isothermal titration calorimetery, circular dicrosim and nucelar magnetic resonance experiments were used to demonstrate a significant enhancement in EGCG's efficiency when complexed with Zn(II). We demonstrate that the Zn-EGCG complex is able to significantly suppress hIAPP's amyloid aggregation both in presence and absence of lipid membrane. Circular dichroism experiments indicate the formation and stabilization of a helical structure of hIAPP in presence of the EGCG:Zn(II) complex. Our results also reveal the ability of EGCG or EGCG:Zn(II) to efficiently suppress hIAPP's cellular toxicity. We believe that the reported results could be useful to develop strategies to trap hIAPP intermediates for further biophysical and structural studies, and also to devise approaches to abolish amyloid aggregation and cellular toxicity.
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Affiliation(s)
- Young-Ho Lee
- Institute for Protein research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan; Protein Structure Research Group, Division of Bioconvergence Analysis, Korea Basic Science Institute, Chungcheongbuk-do 28119, South Korea
| | - Yuxi Lin
- Department of Chemistry, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, South Korea
| | - Sarah J Cox
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Misaki Kinoshita
- Institute for Protein research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Magdalena Ivanova
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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27
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Pagano K, Galante D, D'Arrigo C, Corsaro A, Nizzari M, Florio T, Molinari H, Tomaselli S, Ragona L. Effects of Prion Protein on Aβ42 and Pyroglutamate-Modified AβpΕ3-42 Oligomerization and Toxicity. Mol Neurobiol 2018; 56:1957-1971. [PMID: 29981054 DOI: 10.1007/s12035-018-1202-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/26/2018] [Indexed: 11/24/2022]
Abstract
Soluble Aβ oligomers are widely recognized as the toxic forms responsible for triggering AD, and Aβ receptors are hypothesized to represent the first step in a neuronal cascade leading to dementia. Cellular prion protein (PrP) has been reported as a high-affinity binder of Aβ oligomers. The interactions of PrP with both Aβ42 and the highly toxic N-truncated pyroglutamylated species (AβpE3-42) are here investigated, at a molecular level, by means of ThT fluorescence, NMR and TEM. We demonstrate that soluble PrP binds both Aβ42 and AβpE3-42, preferentially interacting with oligomeric species and delaying fibril formation. Residue level analysis of Aβ42 oligomerization process reveals, for the first time, that PrP is able to differently interact with the forming oligomers, depending on the aggregation state of the starting Aβ42 sample. A distinct behavior is observed for Aβ42 1-30 region and C-terminal residues, suggesting that PrP protects Aβ42 N-tail from entangling on the mature NMR-invisible fibril, consistent with the hypothesis that Aβ42 N-tail is the locus of interaction with PrP. PrP/AβpE3-42 interactions are here reported for the first time. All interaction data are validated and complemented by cellular tests performed on Wt and PrP-silenced neuronal cell lines, clearly showing PrP dependent Aβ oligomer cell internalization and toxicity. The ability of soluble PrP to compete with membrane-anchored PrP for binding to Aβ oligomers bears relevance for studies of druggable pathways.
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Affiliation(s)
- Katiuscia Pagano
- Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Milan, Italy
| | | | | | - Alessandro Corsaro
- Section of Pharmacology, Department of Internal Medicine, and Center of Excellence for Biomedical research (CEBR), University of Genoa, Genoa, Italy
| | - Mario Nizzari
- Section of Pharmacology, Department of Internal Medicine, and Center of Excellence for Biomedical research (CEBR), University of Genoa, Genoa, Italy
| | - Tullio Florio
- Section of Pharmacology, Department of Internal Medicine, and Center of Excellence for Biomedical research (CEBR), University of Genoa, Genoa, Italy
| | | | - Simona Tomaselli
- Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Milan, Italy.
| | - Laura Ragona
- Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Milan, Italy.
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28
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Computational Insight into the Effect of Natural Compounds on the Destabilization of Preformed Amyloid-β(1⁻40) Fibrils. Molecules 2018; 23:molecules23061320. [PMID: 29857500 PMCID: PMC6100107 DOI: 10.3390/molecules23061320] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/31/2022] Open
Abstract
One of the principal hallmarks of Alzheimer’s disease (AD) is related to the aggregation of amyloid-β fibrils in an insoluble form in the brain, also known as amyloidosis. Therefore, a prominent therapeutic strategy against AD consists of either blocking the amyloid aggregation and/or destroying the already formed aggregates. Natural products have shown significant therapeutic potential as amyloid inhibitors from in vitro studies as well as in vivo animal tests. In this study, the interaction of five natural biophenols (curcumin, dopamine, (-)-epigallocatechin-3-gallate, quercetin, and rosmarinic acid) with amyloid-β(1–40) fibrils has been studied through computational simulations. The results allowed the identification and characterization of the different binding modalities of each compounds and their consequences on fibril dynamics and aggregation. It emerges that the lateral aggregation of the fibrils is strongly influenced by the intercalation of the ligands, which modulates the double-layered structure stability.
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29
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Wójcik S, Birol M, Rhoades E, Miranker AD, Levine ZA. Targeting the Intrinsically Disordered Proteome Using Small-Molecule Ligands. Methods Enzymol 2018; 611:703-734. [DOI: 10.1016/bs.mie.2018.09.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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